Advances and trends in structures and dynamics; Proceedings of the Symposium, Washington, DC, October 22-25, 1984

NASA Technical Reports Server (NTRS)

Noor, A. K. (Editor); Hayduk, R. J. (Editor)

1985-01-01

Among the topics discussed are developments in structural engineering hardware and software, computation for fracture mechanics, trends in numerical analysis and parallel algorithms, mechanics of materials, advances in finite element methods, composite materials and structures, determinations of random motion and dynamic response, optimization theory, automotive tire modeling methods and contact problems, the damping and control of aircraft structures, and advanced structural applications. Specific topics covered include structural design expert systems, the evaluation of finite element system architectures, systolic arrays for finite element analyses, nonlinear finite element computations, hierarchical boundary elements, adaptive substructuring techniques in elastoplastic finite element analyses, automatic tracking of crack propagation, a theory of rate-dependent plasticity, the torsional stability of nonlinear eccentric structures, a computation method for fluid-structure interaction, the seismic analysis of three-dimensional soil-structure interaction, a stress analysis for a composite sandwich panel, toughness criterion identification for unidirectional composite laminates, the modeling of submerged cable dynamics, and damping synthesis for flexible spacecraft structures.

A computer lab exploring evolutionary aspects of chromatin structure and dynamics for an undergraduate chromatin course*.

PubMed

Eirín-López, José M

2013-01-01

The study of chromatin constitutes one of the most active research fields in life sciences, being subject to constant revisions that continuously redefine the state of the art in its knowledge. As every other rapidly changing field, chromatin biology requires clear and straightforward educational strategies able to efficiently translate such a vast body of knowledge to the classroom. With this aim, the present work describes a multidisciplinary computer lab designed to introduce undergraduate students to the dynamic nature of chromatin, within the context of the one semester course "Chromatin: Structure, Function and Evolution." This exercise is organized in three parts including (a) molecular evolutionary biology of histone families (using the H1 family as example), (b) histone structure and variation across different animal groups, and (c) effect of histone diversity on nucleosome structure and chromatin dynamics. By using freely available bioinformatic tools that can be run on common computers, the concept of chromatin dynamics is interactively illustrated from a comparative/evolutionary perspective. At the end of this computer lab, students are able to translate the bioinformatic information into a biochemical context in which the relevance of histone primary structure on chromatin dynamics is exposed. During the last 8 years this exercise has proven to be a powerful approach for teaching chromatin structure and dynamics, allowing students a higher degree of independence during the processes of learning and self-assessment. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Structural dynamics branch research and accomplishments

NASA Technical Reports Server (NTRS)

1990-01-01

Summaries are presented of fiscal year 1989 research highlights from the Structural Dynamics Branch at NASA Lewis Research Center. Highlights from the branch's major work areas include aeroelasticity, vibration control, dynamic systems, and computation structural methods. A listing of the fiscal year 1989 branch publications is given.

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

PubMed Central

Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth

2016-01-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts. PMID:27124275

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

PubMed

Maximova, Tatiana; Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth; Shehu, Amarda

2016-04-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.

Multidisciplinary Aerodynamic-Structural Shape Optimization Using Deformation (MASSOUD)

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2000-01-01

This paper presents a multidisciplinary shape parameterization approach. The approach consists of two basic concepts: (1) parameterizing the shape perturbations rather than the geometry itself and (2) performing the shape deformation by means of the soft object animation algorithms used in computer graphics. Because the formulation presented in this paper is independent of grid topology, we can treat computational fluid dynamics and finite element grids in the same manner. The proposed approach is simple, compact, and efficient. Also, the analytical sensitivity derivatives are easily computed for use in a gradient-based optimization. This algorithm is suitable for low-fidelity (e.g., linear aerodynamics and equivalent laminate plate structures) and high-fidelity (e.g., nonlinear computational fluid dynamics and detailed finite element modeling) analysis tools. This paper contains the implementation details of parameterizing for planform, twist, dihedral, thickness, camber, and free-form surface. Results are presented for a multidisciplinary application consisting of nonlinear computational fluid dynamics, detailed computational structural mechanics, and a simple performance module.

Multidisciplinary Aerodynamic-Structural Shape Optimization Using Deformation (MASSOUD)

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2000-01-01

This paper presents a multidisciplinary shape parameterization approach. The approach consists of two basic concepts: (1) parameterizing the shape perturbations rather than the geometry itself and (2) performing the shape deformation by means of the soft object animation algorithms used in computer graphics. Because the formulation presented in this paper is independent of grid topology, we can treat computational fluid dynamics and finite element grids in a similar manner. The proposed approach is simple, compact, and efficient. Also, the analytical sensitivity derivatives are easily computed for use in a gradient-based optimization. This algorithm is suitable for low-fidelity (e.g., linear aerodynamics and equivalent laminated plate structures) and high-fidelity (e.g., nonlinear computational fluid dynamics and detailed finite element modeling analysis tools. This paper contains the implementation details of parameterizing for planform, twist, dihedral, thickness, camber, and free-form surface. Results are presented for a multidisciplinary design optimization application consisting of nonlinear computational fluid dynamics, detailed computational structural mechanics, and a simple performance module.

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

Dynamic properties of epidemic spreading on finite size complex networks

NASA Astrophysics Data System (ADS)

Li, Ying; Liu, Yang; Shan, Xiu-Ming; Ren, Yong; Jiao, Jian; Qiu, Ben

2005-11-01

The Internet presents a complex topological structure, on which computer viruses can easily spread. By using theoretical analysis and computer simulation methods, the dynamic process of disease spreading on finite size networks with complex topological structure is investigated. On the finite size networks, the spreading process of SIS (susceptible-infected-susceptible) model is a finite Markov chain with an absorbing state. Two parameters, the survival probability and the conditional infecting probability, are introduced to describe the dynamic properties of disease spreading on finite size networks. Our results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks. Also, knowledge about the dynamic character of virus spreading is helpful for adopting immunity policy.

Virtual-pulse time integral methodology: A new explicit approach for computational dynamics - Theoretical developments for general nonlinear structural dynamics

NASA Technical Reports Server (NTRS)

Chen, Xiaoqin; Tamma, Kumar K.; Sha, Desong

1993-01-01

The present paper describes a new explicit virtual-pulse time integral methodology for nonlinear structural dynamics problems. The purpose of the paper is to provide the theoretical basis of the methodology and to demonstrate applicability of the proposed formulations to nonlinear dynamic structures. Different from the existing numerical methods such as direct time integrations or mode superposition techniques, the proposed methodology offers new perspectives and methodology of development, and possesses several unique and attractive computational characteristics. The methodology is tested and compared with the implicit Newmark method (trapezoidal rule) through a nonlinear softening and hardening spring dynamic models. The numerical results indicate that the proposed explicit virtual-pulse time integral methodology is an excellent alternative for solving general nonlinear dynamic problems.

A model of cerebellar computations for dynamical state estimation

NASA Technical Reports Server (NTRS)

Paulin, M. G.; Hoffman, L. F.; Assad, C.

2001-01-01

The cerebellum is a neural structure that is essential for agility in vertebrate movements. Its contribution to motor control appears to be due to a fundamental role in dynamical state estimation, which also underlies its role in various non-motor tasks. Single spikes in vestibular sensory neurons carry information about head state. We show how computations for optimal dynamical state estimation may be accomplished when signals are encoded in spikes. This provides a novel way to design dynamical state estimators, and a novel way to interpret the structure and function of the cerebellum.

Structural Dynamics Branch research and accomplishments for FY 1990

NASA Technical Reports Server (NTRS)

1991-01-01

Presented here is a collection of FY 1990 research highlights from the Structural Dynamics Branch at the NASA Lewis Research Center. Highlights are from the branch's major work areas: aeroelasticity, vibration control, dynamic systems, and computational structural methods. A listing is given of FY 1990 branch publications.

Understanding Angiography-Based Aneurysm Flow Fields through Comparison with Computational Fluid Dynamics.

PubMed

Cebral, J R; Mut, F; Chung, B J; Spelle, L; Moret, J; van Nijnatten, F; Ruijters, D

2017-06-01

Hemodynamics is thought to be an important factor for aneurysm progression and rupture. Our aim was to evaluate whether flow fields reconstructed from dynamic angiography data can be used to realistically represent the main flow structures in intracranial aneurysms. DSA-based flow reconstructions, obtained during interventional treatment, were compared qualitatively with flow fields obtained from patient-specific computational fluid dynamics models and quantitatively with projections of the computational fluid dynamics fields (by computing a directional similarity of the vector fields) in 15 cerebral aneurysms. The average similarity between the DSA and the projected computational fluid dynamics flow fields was 78% in the parent artery, while it was only 30% in the aneurysm region. Qualitatively, both the DSA and projected computational fluid dynamics flow fields captured the location of the inflow jet, the main vortex structure, the intrasaccular flow split, and the main rotation direction in approximately 60% of the cases. Several factors affect the reconstruction of 2D flow fields from dynamic angiography sequences. The most important factors are the 3-dimensionality of the intrasaccular flow patterns and inflow jets, the alignment of the main vortex structure with the line of sight, the overlapping of surrounding vessels, and possibly frame rate undersampling. Flow visualization with DSA from >1 projection is required for understanding of the 3D intrasaccular flow patterns. Although these DSA-based flow quantification techniques do not capture swirling or secondary flows in the parent artery, they still provide a good representation of the mean axial flow and the corresponding flow rate. © 2017 by American Journal of Neuroradiology.

| NREL

Science.gov Websites

of NREL's Computational Science Center, where he uses electronic structure calculations and other introductory chemistry and physical chemistry. Research Interests Electronic structure and dynamics in the quantum/classical molecular dynamics simulation|Coupling of molecular electronic structure to

Structural dynamics branch research and accomplishments to FY 1992

NASA Technical Reports Server (NTRS)

Lawrence, Charles

1992-01-01

This publication contains a collection of fiscal year 1992 research highlights from the Structural Dynamics Branch at NASA LeRC. Highlights from the branch's major work areas--Aeroelasticity, Vibration Control, Dynamic Systems, and Computational Structural Methods are included in the report as well as a listing of the fiscal year 1992 branch publications.

Parallel Three-Dimensional Computation of Fluid Dynamics and Fluid-Structure Interactions of Ram-Air Parachutes

NASA Technical Reports Server (NTRS)

Tezduyar, Tayfun E.

1998-01-01

This is a final report as far as our work at University of Minnesota is concerned. The report describes our research progress and accomplishments in development of high performance computing methods and tools for 3D finite element computation of aerodynamic characteristics and fluid-structure interactions (FSI) arising in airdrop systems, namely ram-air parachutes and round parachutes. This class of simulations involves complex geometries, flexible structural components, deforming fluid domains, and unsteady flow patterns. The key components of our simulation toolkit are a stabilized finite element flow solver, a nonlinear structural dynamics solver, an automatic mesh moving scheme, and an interface between the fluid and structural solvers; all of these have been developed within a parallel message-passing paradigm.

Modeling the Effect of Fluid-Structure Interaction on the Impact Dynamics of Pressurized Tank Cars

DOT National Transportation Integrated Search

2009-11-13

This paper presents a computational framework that : analyzes the effect of fluid-structure interaction (FSI) on the : impact dynamics of pressurized commodity tank cars using the : nonlinear dynamic finite element code ABAQUS/Explicit. : There exist...

Computational neuropharmacology: dynamical approaches in drug discovery.

PubMed

Aradi, Ildiko; Erdi, Péter

2006-05-01

Computational approaches that adopt dynamical models are widely accepted in basic and clinical neuroscience research as indispensable tools with which to understand normal and pathological neuronal mechanisms. Although computer-aided techniques have been used in pharmaceutical research (e.g. in structure- and ligand-based drug design), the power of dynamical models has not yet been exploited in drug discovery. We suggest that dynamical system theory and computational neuroscience--integrated with well-established, conventional molecular and electrophysiological methods--offer a broad perspective in drug discovery and in the search for novel targets and strategies for the treatment of neurological and psychiatric diseases.

Flexible Animation Computer Program

NASA Technical Reports Server (NTRS)

Stallcup, Scott S.

1990-01-01

FLEXAN (Flexible Animation), computer program animating structural dynamics on Evans and Sutherland PS300-series graphics workstation with VAX/VMS host computer. Typical application is animation of spacecraft undergoing structural stresses caused by thermal and vibrational effects. Displays distortions in shape of spacecraft. Program displays single natural mode of vibration, mode history, or any general deformation of flexible structure. Written in FORTRAN 77.

Structures and Dynamics Division research and technology plans, FY 1982

NASA Technical Reports Server (NTRS)

Bales, K. S.

1982-01-01

Computational devices to improve efficiency for structural calculations are assessed. The potential of large arrays of microprocessors operating in parallel for finite element analysis is defined, and the impact of specialized computer hardware on static, dynamic, thermal analysis in the optimization of structural analysis and design calculations is determined. General aviation aircraft crashworthiness and occupant survivability is also considered. Mechanics technology required for design coefficient, fault tolerant advanced composite aircraft components subject to combined loads, impact, postbuckling effects and local discontinuities are developed.

Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure-dynamics-function relationships in proteins.

PubMed

Hati, Sanchita; Bhattacharyya, Sudeep

2016-01-01

A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals. © 2016 The International Union of Biochemistry and Molecular Biology.

Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review

PubMed Central

Paquet, Eric; Viktor, Herna L.

2015-01-01

Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262

Computational and Experimental Investigations of the Molecular Scale Structure and Dynamics of Gologically Important Fluids and Mineral-Fluid Interfaces

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

Bowers, Geoffrey

United States Department of Energy grant DE-FG02-10ER16128, “Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces” (Geoffrey M. Bowers, P.I.) focused on developing a molecular-scale understanding of processes that occur in fluids and at solid-fluid interfaces using the combination of spectroscopic, microscopic, and diffraction studies with molecular dynamics computer modeling. The work is intimately tied to the twin proposal at Michigan State University (DOE DE-FG02-08ER15929; same title: R. James Kirkpatrick, P.I. and A. Ozgur Yazaydin, co-P.I.).

CSM parallel structural methods research

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.

1989-01-01

Parallel structural methods, research team activities, advanced architecture computers for parallel computational structural mechanics (CSM) research, the FLEX/32 multicomputer, a parallel structural analyses testbed, blade-stiffened aluminum panel with a circular cutout and the dynamic characteristics of a 60 meter, 54-bay, 3-longeron deployable truss beam are among the topics discussed.

The use of experimental structures to model protein dynamics.

PubMed

Katebi, Ataur R; Sankar, Kannan; Jia, Kejue; Jernigan, Robert L

2015-01-01

The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very high-for example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methods-Principal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to accomplish each step and show how to use these programs and tools. We also include computer programs to generate movies based on PCs and ENM modes and describe how to visualize them.

The Use of Experimental Structures to Model Protein Dynamics

PubMed Central

Katebi, Ataur R.; Sankar, Kannan; Jia, Kejue; Jernigan, Robert L.

2014-01-01

Summary The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very high – for example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methods – Principal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to accomplish each step and show how to use these programs and tools. We also include computer programs to generate movies based on PCs and ENM modes and describe how to visualize them. PMID:25330965

Multidisciplinary analysis of actively controlled large flexible spacecraft

NASA Technical Reports Server (NTRS)

Cooper, Paul A.; Young, John W.; Sutter, Thomas R.

1986-01-01

The control of Flexible Structures (COFS) program has supported the development of an analysis capability at the Langley Research Center called the Integrated Multidisciplinary Analysis Tool (IMAT) which provides an efficient data storage and transfer capability among commercial computer codes to aid in the dynamic analysis of actively controlled structures. IMAT is a system of computer programs which transfers Computer-Aided-Design (CAD) configurations, structural finite element models, material property and stress information, structural and rigid-body dynamic model information, and linear system matrices for control law formulation among various commercial applications programs through a common database. Although general in its formulation, IMAT was developed specifically to aid in the evaluation of the structures. A description of the IMAT system and results of an application of the system are given.

Cognitive Flexibility through Metastable Neural Dynamics Is Disrupted by Damage to the Structural Connectome.

PubMed

Hellyer, Peter J; Scott, Gregory; Shanahan, Murray; Sharp, David J; Leech, Robert

2015-06-17

Current theory proposes that healthy neural dynamics operate in a metastable regime, where brain regions interact to simultaneously maximize integration and segregation. Metastability may confer important behavioral properties, such as cognitive flexibility. It is increasingly recognized that neural dynamics are constrained by the underlying structural connections between brain regions. An important challenge is, therefore, to relate structural connectivity, neural dynamics, and behavior. Traumatic brain injury (TBI) is a pre-eminent structural disconnection disorder whereby traumatic axonal injury damages large-scale connectivity, producing characteristic cognitive impairments, including slowed information processing speed and reduced cognitive flexibility, that may be a result of disrupted metastable dynamics. Therefore, TBI provides an experimental and theoretical model to examine how metastable dynamics relate to structural connectivity and cognition. Here, we use complementary empirical and computational approaches to investigate how metastability arises from the healthy structural connectome and relates to cognitive performance. We found reduced metastability in large-scale neural dynamics after TBI, measured with resting-state functional MRI. This reduction in metastability was associated with damage to the connectome, measured using diffusion MRI. Furthermore, decreased metastability was associated with reduced cognitive flexibility and information processing. A computational model, defined by empirically derived connectivity data, demonstrates how behaviorally relevant changes in neural dynamics result from structural disconnection. Our findings suggest how metastable dynamics are important for normal brain function and contingent on the structure of the human connectome. Copyright © 2015 the authors 0270-6474/15/359050-14$15.00/0.

Structural Stability of Mathematical Models of National Economy

NASA Astrophysics Data System (ADS)

Ashimov, Abdykappar A.; Sultanov, Bahyt T.; Borovskiy, Yuriy V.; Adilov, Zheksenbek M.; Ashimov, Askar A.

2011-12-01

In the paper we test robustness of particular dynamic systems in a compact regions of a plane and a weak structural stability of one dynamic system of high order in a compact region of its phase space. The test was carried out based on the fundamental theory of dynamical systems on a plane and based on the conditions for weak structural stability of high order dynamic systems. A numerical algorithm for testing the weak structural stability of high order dynamic systems has been proposed. Based on this algorithm we assess the weak structural stability of one computable general equilibrium model.

Simulating Vibrations in a Complex Loaded Structure

NASA Technical Reports Server (NTRS)

Cao, Tim T.

2005-01-01

The Dynamic Response Computation (DIRECT) computer program simulates vibrations induced in a complex structure by applied dynamic loads. Developed to enable rapid analysis of launch- and landing- induced vibrations and stresses in a space shuttle, DIRECT also can be used to analyze dynamic responses of other structures - for example, the response of a building to an earthquake, or the response of an oil-drilling platform and attached tanks to large ocean waves. For a space-shuttle simulation, the required input to DIRECT includes mathematical models of the space shuttle and its payloads, and a set of forcing functions that simulates launch and landing loads. DIRECT can accommodate multiple levels of payload attachment and substructure as well as nonlinear dynamic responses of structural interfaces. DIRECT combines the shuttle and payload models into a single structural model, to which the forcing functions are then applied. The resulting equations of motion are reduced to an optimum set and decoupled into a unique format for simulating dynamics. During the simulation, maximum vibrations, loads, and stresses are monitored and recorded for subsequent analysis to identify structural deficiencies in the shuttle and/or payloads.

Fast normal mode computations of capsid dynamics inspired by resonance

NASA Astrophysics Data System (ADS)

Na, Hyuntae; Song, Guang

2018-07-01

Increasingly more and larger structural complexes are being determined experimentally. The sizes of these systems pose a formidable computational challenge to the study of their vibrational dynamics by normal mode analysis. To overcome this challenge, this work presents a novel resonance-inspired approach. Tests on large shell structures of protein capsids demonstrate that there is a strong resonance between the vibrations of a whole capsid and those of individual capsomeres. We then show how this resonance can be taken advantage of to significantly speed up normal mode computations.

Bimolecular dynamics by computer analysis

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

Eilbeck, J.C.; Lomdahl, P.S.; Scott, A.C.

1984-01-01

As numerical tools (computers and display equipment) become more powerful and the atomic structures of important biological molecules become known, the importance of detailed computation of nonequilibrium biomolecular dynamics increases. In this manuscript we report results from a well developed study of the hydrogen bonded polypeptide crystal acetanilide, a model protein. Directions for future research are suggested. 9 references, 6 figures.

NERVA dynamic analysis methodology, SPRVIB

NASA Technical Reports Server (NTRS)

Vronay, D. F.

1972-01-01

The general dynamic computer code called SPRVIB (Spring Vib) developed in support of the NERVA (nuclear engine for rocket vehicle application) program is described. Using normal mode techniques, the program computes kinematical responses of a structure caused by various combinations of harmonic and elliptic forcing functions or base excitations. Provision is made for a graphical type of force or base excitation input to the structure. A description of the required input format and a listing of the program are presented, along with several examples illustrating the use of the program. SPRVIB is written in FORTRAN 4 computer language for use on the CDC 6600 or the IBM 360/75 computers.

A Novel Shape Parameterization Approach

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

1999-01-01

This paper presents a novel parameterization approach for complex shapes suitable for a multidisciplinary design optimization application. The approach consists of two basic concepts: (1) parameterizing the shape perturbations rather than the geometry itself and (2) performing the shape deformation by means of the soft objects animation algorithms used in computer graphics. Because the formulation presented in this paper is independent of grid topology, we can treat computational fluid dynamics and finite element grids in a similar manner. The proposed approach is simple, compact, and efficient. Also, the analytical sensitivity derivatives are easily computed for use in a gradient-based optimization. This algorithm is suitable for low-fidelity (e.g., linear aerodynamics and equivalent laminated plate structures) and high-fidelity analysis tools (e.g., nonlinear computational fluid dynamics and detailed finite element modeling). This paper contains the implementation details of parameterizing for planform, twist, dihedral, thickness, and camber. The results are presented for a multidisciplinary design optimization application consisting of nonlinear computational fluid dynamics, detailed computational structural mechanics, performance, and a simple propulsion module.

Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype A Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design

DTIC Science & Technology

2009-11-01

dynamics of the complex predicted by multiple molecular dynamics simulations , and discuss further structural optimization to achieve better in vivo efficacy...complex with BoNTAe and the dynamics of the complex predicted by multiple molecular dynamics simulations (MMDSs). On the basis of the 3D model, we discuss...is unlimited whereas AHP exhibited 54% inhibition under the same conditions (Table 1). Computer Simulation Twenty different molecular dynamics

Composite mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1987-01-01

Recent research activities and accomplishments at Lewis Research Center on composite mechanics for engine structures are summarized. The activities focused mainly on developing procedures for the computational simulation of composite intrinsic and structural behavior. The computational simulation encompasses all aspects of composite mechanics, advanced three-dimensional finite-element methods, damage tolerance, composite structural and dynamic response, and structural tailoring and optimization.

Composite mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1989-01-01

Recent research activities and accomplishments at Lewis Research Center on composite mechanics for engine structures are summarized. The activities focused mainly on developing procedures for the computational simulation of composite intrinsic and structural behavior. The computational simulation encompasses all aspects of composite mechanics, advanced three-dimensional finite-element methods, damage tolerance, composite structural and dynamic response, and structural tailoring and optimization.

Mid-frequency Band Dynamics of Large Space Structures

NASA Technical Reports Server (NTRS)

Coppolino, Robert N.; Adams, Douglas S.

2004-01-01

High and low intensity dynamic environments experienced by a spacecraft during launch and on-orbit operations, respectively, induce structural loads and motions, which are difficult to reliably predict. Structural dynamics in low- and mid-frequency bands are sensitive to component interface uncertainty and non-linearity as evidenced in laboratory testing and flight operations. Analytical tools for prediction of linear system response are not necessarily adequate for reliable prediction of mid-frequency band dynamics and analysis of measured laboratory and flight data. A new MATLAB toolbox, designed to address the key challenges of mid-frequency band dynamics, is introduced in this paper. Finite-element models of major subassemblies are defined following rational frequency-wavelength guidelines. For computational efficiency, these subassemblies are described as linear, component mode models. The complete structural system model is composed of component mode subassemblies and linear or non-linear joint descriptions. Computation and display of structural dynamic responses are accomplished employing well-established, stable numerical methods, modern signal processing procedures and descriptive graphical tools. Parametric sensitivity and Monte-Carlo based system identification tools are used to reconcile models with experimental data and investigate the effects of uncertainties. Models and dynamic responses are exported for employment in applications, such as detailed structural integrity and mechanical-optical-control performance analyses.

GPU-accelerated computing for Lagrangian coherent structures of multi-body gravitational regimes

NASA Astrophysics Data System (ADS)

Lin, Mingpei; Xu, Ming; Fu, Xiaoyu

2017-04-01

Based on a well-established theoretical foundation, Lagrangian Coherent Structures (LCSs) have elicited widespread research on the intrinsic structures of dynamical systems in many fields, including the field of astrodynamics. Although the application of LCSs in dynamical problems seems straightforward theoretically, its associated computational cost is prohibitive. We propose a block decomposition algorithm developed on Compute Unified Device Architecture (CUDA) platform for the computation of the LCSs of multi-body gravitational regimes. In order to take advantage of GPU's outstanding computing properties, such as Shared Memory, Constant Memory, and Zero-Copy, the algorithm utilizes a block decomposition strategy to facilitate computation of finite-time Lyapunov exponent (FTLE) fields of arbitrary size and timespan. Simulation results demonstrate that this GPU-based algorithm can satisfy double-precision accuracy requirements and greatly decrease the time needed to calculate final results, increasing speed by approximately 13 times. Additionally, this algorithm can be generalized to various large-scale computing problems, such as particle filters, constellation design, and Monte-Carlo simulation.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

Dynamic response analysis of structure under time-variant interval process model

NASA Astrophysics Data System (ADS)

Xia, Baizhan; Qin, Yuan; Yu, Dejie; Jiang, Chao

2016-10-01

Due to the aggressiveness of the environmental factor, the variation of the dynamic load, the degeneration of the material property and the wear of the machine surface, parameters related with the structure are distinctly time-variant. Typical model for time-variant uncertainties is the random process model which is constructed on the basis of a large number of samples. In this work, we propose a time-variant interval process model which can be effectively used to deal with time-variant uncertainties with limit information. And then two methods are presented for the dynamic response analysis of the structure under the time-variant interval process model. The first one is the direct Monte Carlo method (DMCM) whose computational burden is relative high. The second one is the Monte Carlo method based on the Chebyshev polynomial expansion (MCM-CPE) whose computational efficiency is high. In MCM-CPE, the dynamic response of the structure is approximated by the Chebyshev polynomials which can be efficiently calculated, and then the variational range of the dynamic response is estimated according to the samples yielded by the Monte Carlo method. To solve the dependency phenomenon of the interval operation, the affine arithmetic is integrated into the Chebyshev polynomial expansion. The computational effectiveness and efficiency of MCM-CPE is verified by two numerical examples, including a spring-mass-damper system and a shell structure.

Joint nonlinearity effects in the design of a flexible truss structure control system

NASA Technical Reports Server (NTRS)

Mercadal, Mathieu

1986-01-01

Nonlinear effects are introduced in the dynamics of large space truss structures by the connecting joints which are designed with rather important tolerances to facilitate the assembly of the structures in space. The purpose was to develop means to investigate the nonlinear dynamics of the structures, particularly the limit cycles that might occur when active control is applied to the structures. An analytical method was sought and derived to predict the occurrence of limit cycles and to determine their stability. This method is mainly based on the quasi-linearization of every joint using describing functions. This approach was proven successful when simple dynamical systems were tested. Its applicability to larger systems depends on the amount of computations it requires, and estimates of the computational task tend to indicate that the number of individual sources of nonlinearity should be limited. Alternate analytical approaches, which do not account for every single nonlinearity, or the simulation of a simplified model of the dynamical system should, therefore, be investigated to determine a more effective way to predict limit cycles in large dynamical systems with an important number of distributed nonlinearities.

Nonlinear Computational Aeroelasticity: Formulations and Solution Algorithms

DTIC Science & Technology

2003-03-01

problem is proposed. Fluid-structure coupling algorithms are then discussed with some emphasis on distributed computing strategies. Numerical results...the structure and the exchange of structure motion to the fluid. The computational fluid dynamics code PFES is our finite element code for the numerical ...unstructured meshes). It was numerically demonstrated [1-3] that EBS can be less diffusive than SUPG [4-6] and the standard Finite Volume schemes

A Model Structure for the Heterodimer apoA-IMilano–apoA-II Supports Its Peculiar Susceptibility to Proteolysis

PubMed Central

Rocco, Alessandro Guerini; Mollica, Luca; Gianazza, Elisabetta; Calabresi, Laura; Franceschini, Guido; Sirtori, Cesare R.; Eberini, Ivano

2006-01-01

In this study, we propose a structure for the heterodimer between apolipoprotein A-IMilano and apolipoprotein A-II (apoA-IM–apoA-II) in a synthetic high-density lipoprotein (HDL) containing L-α-palmitoyloleoyl phosphatidylcholine. We applied bioinformatics/computational tools and procedures, such as molecular docking, molecular and essential dynamics, starting from published crystal structures for apolipoprotein A-I and apolipoprotein A-II. Structural and energetic analyses onto the simulated system showed that the molecular dynamics produced a stabilized synthetic HDL. The essential dynamic analysis showed a deviation from the starting belt structure. Our structural results were validated by limited proteolysis experiments on HDL from apoA-IM carriers in comparison with control HDL. The high sensitivity of apoA-IM–apoA-II to proteases was in agreement with the high root mean-square fluctuation values and the reduction in secondary structure content from molecular dynamics data. Circular dichroism on synthetic HDL containing apoA-IM–apoA-II was consistent with the α-helix content computed on the proposed model. PMID:16891368

Computational structures for robotic computations

NASA Technical Reports Server (NTRS)

Lee, C. S. G.; Chang, P. R.

1987-01-01

The computational problem of inverse kinematics and inverse dynamics of robot manipulators by taking advantage of parallelism and pipelining architectures is discussed. For the computation of inverse kinematic position solution, a maximum pipelined CORDIC architecture has been designed based on a functional decomposition of the closed-form joint equations. For the inverse dynamics computation, an efficient p-fold parallel algorithm to overcome the recurrence problem of the Newton-Euler equations of motion to achieve the time lower bound of O(log sub 2 n) has also been developed.

Computational structures technology and UVA Center for CST

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1992-01-01

Rapid advances in computer hardware have had a profound effect on various engineering and mechanics disciplines, including the materials, structures, and dynamics disciplines. A new technology, computational structures technology (CST), has recently emerged as an insightful blend between material modeling, structural and dynamic analysis and synthesis on the one hand, and other disciplines such as computer science, numerical analysis, and approximation theory, on the other hand. CST is an outgrowth of finite element methods developed over the last three decades. The focus of this presentation is on some aspects of CST which can impact future airframes and propulsion systems, as well as on the newly established University of Virginia (UVA) Center for CST. The background and goals for CST are described along with the motivations for developing CST, and a brief discussion is made on computational material modeling. We look at the future in terms of technical needs, computing environment, and research directions. The newly established UVA Center for CST is described. One of the research projects of the Center is described, and a brief summary of the presentation is given.

Supercomputer optimizations for stochastic optimal control applications

NASA Technical Reports Server (NTRS)

Chung, Siu-Leung; Hanson, Floyd B.; Xu, Huihuang

1991-01-01

Supercomputer optimizations for a computational method of solving stochastic, multibody, dynamic programming problems are presented. The computational method is valid for a general class of optimal control problems that are nonlinear, multibody dynamical systems, perturbed by general Markov noise in continuous time, i.e., nonsmooth Gaussian as well as jump Poisson random white noise. Optimization techniques for vector multiprocessors or vectorizing supercomputers include advanced data structures, loop restructuring, loop collapsing, blocking, and compiler directives. These advanced computing techniques and superconducting hardware help alleviate Bellman's curse of dimensionality in dynamic programming computations, by permitting the solution of large multibody problems. Possible applications include lumped flight dynamics models for uncertain environments, such as large scale and background random aerospace fluctuations.

Fluid-Structure Interaction in Composite Structures

DTIC Science & Technology

2014-03-01

polymer composite structures. Some previous experimental observations were confirmed using the results from the computer simulations , which also...computer simulations , which also enhanced understanding the effect of FSI on dynamic responses of composite structures. vi THIS PAGE INTENTIONALLY...forces) are applied. A great amount of research has been made using the FEM to study and simulate the cases when the structures are surrounded by

Advances in engineering science, volume 2

NASA Technical Reports Server (NTRS)

1976-01-01

Papers are presented dealing with structural dynamics; structural synthesis; and the nonlinear analysis of structures, structural members, and composite structures and materials. Applications of mathematics and computer science are included.

Cooperative storage of shared files in a parallel computing system with dynamic block size

DOEpatents

Bent, John M.; Faibish, Sorin; Grider, Gary

2015-11-10

Improved techniques are provided for parallel writing of data to a shared object in a parallel computing system. A method is provided for storing data generated by a plurality of parallel processes to a shared object in a parallel computing system. The method is performed by at least one of the processes and comprises: dynamically determining a block size for storing the data; exchanging a determined amount of the data with at least one additional process to achieve a block of the data having the dynamically determined block size; and writing the block of the data having the dynamically determined block size to a file system. The determined block size comprises, e.g., a total amount of the data to be stored divided by the number of parallel processes. The file system comprises, for example, a log structured virtual parallel file system, such as a Parallel Log-Structured File System (PLFS).

Computation of structural flexibility for bridge health monitoring using ambient modal data

DOT National Transportation Integrated Search

1996-01-01

The issues surrounding the use of ambient vibration modes for the location of structural damage via dynamically : measured flexibility are examined. Several methods for obtaining the required mass-normalized : dynamic mode shapes from ambient modal d...

Protocols for Molecular Dynamics Simulations of RNA Nanostructures.

PubMed

Kim, Taejin; Kasprzak, Wojciech K; Shapiro, Bruce A

2017-01-01

Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package. We also show examples of post-simulation analysis steps and briefly mention selected tools beyond the Amber package. Limitations of the methods, tools, and protocols are also discussed. Most of the examples are illustrated for a small RNA duplex (helix), but the protocols are applicable to any nucleic acid structure, subject only to the computational speed and memory limitations of the hardware available to the user.

Parallel aeroelastic computations for wing and wing-body configurations

NASA Technical Reports Server (NTRS)

Byun, Chansup

1994-01-01

The objective of this research is to develop computationally efficient methods for solving fluid-structural interaction problems by directly coupling finite difference Euler/Navier-Stokes equations for fluids and finite element dynamics equations for structures on parallel computers. This capability will significantly impact many aerospace projects of national importance such as Advanced Subsonic Civil Transport (ASCT), where the structural stability margin becomes very critical at the transonic region. This research effort will have direct impact on the High Performance Computing and Communication (HPCC) Program of NASA in the area of parallel computing.

Computational Aeroelastic Modeling of Airframes and TurboMachinery: Progress and Challenges

NASA Technical Reports Server (NTRS)

Bartels, R. E.; Sayma, A. I.

2006-01-01

Computational analyses such as computational fluid dynamics and computational structural dynamics have made major advances toward maturity as engineering tools. Computational aeroelasticity is the integration of these disciplines. As computational aeroelasticity matures it too finds an increasing role in the design and analysis of aerospace vehicles. This paper presents a survey of the current state of computational aeroelasticity with a discussion of recent research, success and continuing challenges in its progressive integration into multidisciplinary aerospace design. This paper approaches computational aeroelasticity from the perspective of the two main areas of application: airframe and turbomachinery design. An overview will be presented of the different prediction methods used for each field of application. Differing levels of nonlinear modeling will be discussed with insight into accuracy versus complexity and computational requirements. Subjects will include current advanced methods (linear and nonlinear), nonlinear flow models, use of order reduction techniques and future trends in incorporating structural nonlinearity. Examples in which computational aeroelasticity is currently being integrated into the design of airframes and turbomachinery will be presented.

A digital computer program for the dynamic interaction simulation of controls and structure (DISCOS), volume 1

NASA Technical Reports Server (NTRS)

Bodley, C. S.; Devers, A. D.; Park, A. C.; Frisch, H. P.

1978-01-01

A theoretical development and associated digital computer program system for the dynamic simulation and stability analysis of passive and actively controlled spacecraft are presented. The dynamic system (spacecraft) is modeled as an assembly of rigid and/or flexible bodies not necessarily in a topological tree configuration. The computer program system is used to investigate total system dynamic characteristics, including interaction effects between rigid and/or flexible bodies, control systems, and a wide range of environmental loadings. In addition, the program system is used for designing attitude control systems and for evaluating total dynamic system performance, including time domain response and frequency domain stability analyses.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

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

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Heat transfer, thermal stress analysis and the dynamic behaviour of high power RF structures. [MARC and SUPERFISH codes

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

McKeown, J.; Labrie, J.P.

1983-08-01

A general purpose finite element computer code called MARC is used to calculate the temperature distribution and dimensional changes in linear accelerator rf structures. Both steady state and transient behaviour are examined with the computer model. Combining results from MARC with the cavity evaluation computer code SUPERFISH, the static and dynamic behaviour of a structure under power is investigated. Structure cooling is studied to minimize loss in shunt impedance and frequency shifts during high power operation. Results are compared with an experimental test carried out on a cw 805 MHz on-axis coupled structure at an energy gradient of 1.8 MeV/m.more » The model has also been used to compare the performance of on-axis and coaxial structures and has guided the mechanical design of structures suitable for average gradients in excess of 2.0 MeV/m at 2.45 GHz.« less

Discovering Coherent Structures Using Local Causal States

NASA Astrophysics Data System (ADS)

Rupe, Adam; Crutchfield, James P.; Kashinath, Karthik; Prabhat, Mr.

2017-11-01

Coherent structures were introduced in the study of fluid dynamics and were initially defined as regions characterized by high levels of coherent vorticity, i.e. regions where instantaneously space and phase correlated vorticity are high. In a more general spatiotemporal setting, coherent structures can be seen as localized broken symmetries which persist in time. Building off the computational mechanics framework, which integrates tools from computation and information theory to capture pattern and structure in nonlinear dynamical systems, we introduce a theory of coherent structures, in the more general sense. Central to computational mechanics is the causal equivalence relation, and a local spatiotemporal generalization of it is used to construct the local causal states, which are utilized to uncover a system's spatiotemporal symmetries. Coherent structures are then identified as persistent, localized deviations from these symmetries. We illustrate how novel patterns and structures can be discovered in cellular automata and outline the path from them to laminar, transitional and turbulent flows. Funded by Intel through the Big Data Center at LBNL and the IPCC at UC Davis.

Coarse-Grained Lattice Model Simulations of Sequence-Structure Fitness of a Ribosome-Inactivating Protein

DTIC Science & Technology

2007-11-05

limits of what is considered practical when applying all-atom molecular - dynamics simulation methods. Lattice models provide computationally robust...of expectation values from the density of states. All-atom molecular - dynamics simulations provide the most rigorous sampling method to generate con... molecular - dynamics simulations of protein folding,6–9 reported studies of computing a heat capacity or other calorimetric observables have been limited to

Beam Dynamics Simulation Platform and Studies of Beam Breakup in Dielectric Wakefield Structures

NASA Astrophysics Data System (ADS)

Schoessow, P.; Kanareykin, A.; Jing, C.; Kustov, A.; Altmark, A.; Gai, W.

2010-11-01

A particle-Green's function beam dynamics code (BBU-3000) to study beam breakup effects is incorporated into a parallel computing framework based on the Boinc software environment, and supports both task farming on a heterogeneous cluster and local grid computing. User access to the platform is through a web browser.

Integrating aerodynamic surface modeling for computational fluid dynamics with computer aided structural analysis, design, and manufacturing

NASA Technical Reports Server (NTRS)

Thorp, Scott A.

1992-01-01

This presentation will discuss the development of a NASA Geometry Exchange Specification for transferring aerodynamic surface geometry between LeRC systems and grid generation software used for computational fluid dynamics research. The proposed specification is based on a subset of the Initial Graphics Exchange Specification (IGES). The presentation will include discussion of how the NASA-IGES standard will accommodate improved computer aided design inspection methods and reverse engineering techniques currently being developed. The presentation is in viewgraph format.

Algorithms and software for nonlinear structural dynamics

NASA Technical Reports Server (NTRS)

Belytschko, Ted; Gilbertsen, Noreen D.; Neal, Mark O.

1989-01-01

The objective of this research is to develop efficient methods for explicit time integration in nonlinear structural dynamics for computers which utilize both concurrency and vectorization. As a framework for these studies, the program WHAMS, which is described in Explicit Algorithms for the Nonlinear Dynamics of Shells (T. Belytschko, J. I. Lin, and C.-S. Tsay, Computer Methods in Applied Mechanics and Engineering, Vol. 42, 1984, pp 225 to 251), is used. There are two factors which make the development of efficient concurrent explicit time integration programs a challenge in a structural dynamics program: (1) the need for a variety of element types, which complicates the scheduling-allocation problem; and (2) the need for different time steps in different parts of the mesh, which is here called mixed delta t integration, so that a few stiff elements do not reduce the time steps throughout the mesh.

Conifer ovulate cones accumulate pollen principally by simple impaction.

PubMed

Cresswell, James E; Henning, Kevin; Pennel, Christophe; Lahoubi, Mohamed; Patrick, Michael A; Young, Phillipe G; Tabor, Gavin R

2007-11-13

In many pine species (Family Pinaceae), ovulate cones structurally resemble a turbine, which has been widely interpreted as an adaptation for improving pollination by producing complex aerodynamic effects. We tested the turbine interpretation by quantifying patterns of pollen accumulation on ovulate cones in a wind tunnel and by using simulation models based on computational fluid dynamics. We used computer-aided design and computed tomography to create computational fluid dynamics model cones. We studied three species: Pinus radiata, Pinus sylvestris, and Cedrus libani. Irrespective of the approach or species studied, we found no evidence that turbine-like aerodynamics made a significant contribution to pollen accumulation, which instead occurred primarily by simple impaction. Consequently, we suggest alternative adaptive interpretations for the structure of ovulate cones.

Conifer ovulate cones accumulate pollen principally by simple impaction

PubMed Central

Cresswell, James E.; Henning, Kevin; Pennel, Christophe; Lahoubi, Mohamed; Patrick, Michael A.; Young, Phillipe G.; Tabor, Gavin R.

2007-01-01

In many pine species (Family Pinaceae), ovulate cones structurally resemble a turbine, which has been widely interpreted as an adaptation for improving pollination by producing complex aerodynamic effects. We tested the turbine interpretation by quantifying patterns of pollen accumulation on ovulate cones in a wind tunnel and by using simulation models based on computational fluid dynamics. We used computer-aided design and computed tomography to create computational fluid dynamics model cones. We studied three species: Pinus radiata, Pinus sylvestris, and Cedrus libani. Irrespective of the approach or species studied, we found no evidence that turbine-like aerodynamics made a significant contribution to pollen accumulation, which instead occurred primarily by simple impaction. Consequently, we suggest alternative adaptive interpretations for the structure of ovulate cones. PMID:17986613

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery.

PubMed

Papaleo, Elena; Saladino, Giorgio; Lambrughi, Matteo; Lindorff-Larsen, Kresten; Gervasio, Francesco Luigi; Nussinov, Ruth

2016-06-08

Proteins are dynamic entities that undergo a plethora of conformational changes that may take place on a wide range of time scales. These changes can be as small as the rotation of one or a few side-chain dihedral angles or involve concerted motions in larger portions of the three-dimensional structure; both kinds of motions can be important for biological function and allostery. It is becoming increasingly evident that "connector regions" are important components of the dynamic personality of protein structures. These regions may be either disordered loops, i.e., poorly structured regions connecting secondary structural elements, or linkers that connect entire protein domains. Experimental and computational studies have, however, revealed that these regions are not mere connectors, and their role in allostery and conformational changes has been emerging in the last few decades. Here we provide a detailed overview of the structural properties and classification of loops and linkers, as well as a discussion of the main computational methods employed to investigate their function and dynamical properties. We also describe their importance for protein dynamics and allostery using as examples key proteins in cellular biology and human diseases such as kinases, ubiquitinating enzymes, and transcription factors.

Towards Dynamic Remote Data Auditing in Computational Clouds

PubMed Central

Khurram Khan, Muhammad; Anuar, Nor Badrul

2014-01-01

Cloud computing is a significant shift of computational paradigm where computing as a utility and storing data remotely have a great potential. Enterprise and businesses are now more interested in outsourcing their data to the cloud to lessen the burden of local data storage and maintenance. However, the outsourced data and the computation outcomes are not continuously trustworthy due to the lack of control and physical possession of the data owners. To better streamline this issue, researchers have now focused on designing remote data auditing (RDA) techniques. The majority of these techniques, however, are only applicable for static archive data and are not subject to audit the dynamically updated outsourced data. We propose an effectual RDA technique based on algebraic signature properties for cloud storage system and also present a new data structure capable of efficiently supporting dynamic data operations like append, insert, modify, and delete. Moreover, this data structure empowers our method to be applicable for large-scale data with minimum computation cost. The comparative analysis with the state-of-the-art RDA schemes shows that the proposed scheme is secure and highly efficient in terms of the computation and communication overhead on the auditor and server. PMID:25121114

Towards dynamic remote data auditing in computational clouds.

PubMed

Sookhak, Mehdi; Akhunzada, Adnan; Gani, Abdullah; Khurram Khan, Muhammad; Anuar, Nor Badrul

2014-01-01

Cloud computing is a significant shift of computational paradigm where computing as a utility and storing data remotely have a great potential. Enterprise and businesses are now more interested in outsourcing their data to the cloud to lessen the burden of local data storage and maintenance. However, the outsourced data and the computation outcomes are not continuously trustworthy due to the lack of control and physical possession of the data owners. To better streamline this issue, researchers have now focused on designing remote data auditing (RDA) techniques. The majority of these techniques, however, are only applicable for static archive data and are not subject to audit the dynamically updated outsourced data. We propose an effectual RDA technique based on algebraic signature properties for cloud storage system and also present a new data structure capable of efficiently supporting dynamic data operations like append, insert, modify, and delete. Moreover, this data structure empowers our method to be applicable for large-scale data with minimum computation cost. The comparative analysis with the state-of-the-art RDA schemes shows that the proposed scheme is secure and highly efficient in terms of the computation and communication overhead on the auditor and server.

FAST Simulation Tool Containing Methods for Predicting the Dynamic Response of Wind Turbines

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

Jonkman, Jason

2015-08-12

FAST is a simulation tool (computer software) for modeling tlie dynamic response of horizontal-axis wind turbines. FAST employs a combined modal and multibody structural-dynamics formulation in the time domain.

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

PubMed Central

Ding, Feng; Sharma, Shantanu; Chalasani, Poornima; Demidov, Vadim V.; Broude, Natalia E.; Dokholyan, Nikolay V.

2008-01-01

RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse RNA sequences. The majority of DMD-predicted 3D structures have <4 Å deviations from experimental structures. The secondary structures corresponding to the predicted 3D structures consist of 94% native base-pair interactions. Folding thermodynamics and kinetics of tRNAPhe, pseudoknots, and mRNA fragments in DMD simulations are in agreement with previous experimental findings. Folding of RNA molecules features transient, non-native conformations, suggesting non-hierarchical RNA folding. Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses. PMID:18456842

Computational strategies to address chromatin structure problems

NASA Astrophysics Data System (ADS)

Perišić, Ognjen; Schlick, Tamar

2016-06-01

While the genetic information is contained in double helical DNA, gene expression is a complex multilevel process that involves various functional units, from nucleosomes to fully formed chromatin fibers accompanied by a host of various chromatin binding enzymes. The chromatin fiber is a polymer composed of histone protein complexes upon which DNA wraps, like yarn upon many spools. The nature of chromatin structure has been an open question since the beginning of modern molecular biology. Many experiments have shown that the chromatin fiber is a highly dynamic entity with pronounced structural diversity that includes properties of idealized zig-zag and solenoid models, as well as other motifs. This diversity can produce a high packing ratio and thus inhibit access to a majority of the wound DNA. Despite much research, chromatin’s dynamic structure has not yet been fully described. Long stretches of chromatin fibers exhibit puzzling dynamic behavior that requires interpretation in the light of gene expression patterns in various tissue and organisms. The properties of chromatin fiber can be investigated with experimental techniques, like in vitro biochemistry, in vivo imagining, and high-throughput chromosome capture technology. Those techniques provide useful insights into the fiber’s structure and dynamics, but they are limited in resolution and scope, especially regarding compact fibers and chromosomes in the cellular milieu. Complementary but specialized modeling techniques are needed to handle large floppy polymers such as the chromatin fiber. In this review, we discuss current approaches in the chromatin structure field with an emphasis on modeling, such as molecular dynamics and coarse-grained computational approaches. Combinations of these computational techniques complement experiments and address many relevant biological problems, as we will illustrate with special focus on epigenetic modulation of chromatin structure.

Functional connectivity dynamically evolves on multiple time-scales over a static structural connectome: Models and mechanisms.

PubMed

Cabral, Joana; Kringelbach, Morten L; Deco, Gustavo

2017-10-15

Over the last decade, we have observed a revolution in brain structural and functional Connectomics. On one hand, we have an ever-more detailed characterization of the brain's white matter structural connectome. On the other, we have a repertoire of consistent functional networks that form and dissipate over time during rest. Despite the evident spatial similarities between structural and functional connectivity, understanding how different time-evolving functional networks spontaneously emerge from a single structural network requires analyzing the problem from the perspective of complex network dynamics and dynamical system's theory. In that direction, bottom-up computational models are useful tools to test theoretical scenarios and depict the mechanisms at the genesis of resting-state activity. Here, we provide an overview of the different mechanistic scenarios proposed over the last decade via computational models. Importantly, we highlight the need of incorporating additional model constraints considering the properties observed at finer temporal scales with MEG and the dynamical properties of FC in order to refresh the list of candidate scenarios. Copyright © 2017 Elsevier Inc. All rights reserved.

APINetworks: A general API for the treatment of complex networks in arbitrary computational environments

NASA Astrophysics Data System (ADS)

Niño, Alfonso; Muñoz-Caro, Camelia; Reyes, Sebastián

2015-11-01

The last decade witnessed a great development of the structural and dynamic study of complex systems described as a network of elements. Therefore, systems can be described as a set of, possibly, heterogeneous entities or agents (the network nodes) interacting in, possibly, different ways (defining the network edges). In this context, it is of practical interest to model and handle not only static and homogeneous networks but also dynamic, heterogeneous ones. Depending on the size and type of the problem, these networks may require different computational approaches involving sequential, parallel or distributed systems with or without the use of disk-based data structures. In this work, we develop an Application Programming Interface (APINetworks) for the modeling and treatment of general networks in arbitrary computational environments. To minimize dependency between components, we decouple the network structure from its function using different packages for grouping sets of related tasks. The structural package, the one in charge of building and handling the network structure, is the core element of the system. In this work, we focus in this API structural component. We apply an object-oriented approach that makes use of inheritance and polymorphism. In this way, we can model static and dynamic networks with heterogeneous elements in the nodes and heterogeneous interactions in the edges. In addition, this approach permits a unified treatment of different computational environments. Tests performed on a C++11 version of the structural package show that, on current standard computers, the system can handle, in main memory, directed and undirected linear networks formed by tens of millions of nodes and edges. Our results compare favorably to those of existing tools.

Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.

PubMed

Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R

2015-07-08

We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching.

Computing the binding affinity of Zn2+ in human carbonic anhydrase II on the basis of all-atom molecular dynamics simulations.

NASA Astrophysics Data System (ADS)

Wambo, Thierry; Rodriguez, Roberto

Human carbonic anhydrase II (hCAII) is a metalloenzyme with a Zinc cation at its binding site. The presence of the Zinc turns the protein into an efficient enzyme which catalyzes the reversible hydration of carbon dioxide into bicarbonate anion. Available X-ray structures of the apo-hCAII and holo-hCAII show no significant differences in the overall structure of these proteins. What difference, if any, is there between the structures of the hydrated apo-hCAII and holo? How can we use computer simulation to efficiently compute the binding affinity of Zinc to hCAII? We will present a scheme developed to compute the binding affinity of Zinc cation to hCAII on the basis of all-atom molecular dynamics simulation where Zinc is represented as a point charge and the CHARMM36 force field is used for running the dynamics of the system. Our computed binding affinity of the cation to hCAII is in good agreement with experiment, within the margin of error, while a look at the dynamics of the binding site suggests that in the absence of the Zinc, there is a re-organization of the nearby histidine residues which adopt a new distinct configuration. The authors are thankful for the NIH support through Grants GM084834 and GM060655. They also acknowledge the Texas Advanced Computing Center at the University of Texas at Austin for the supercomputing time. They thank Dr Liao Chen for his comments.

Computational design of an endo-1,4-[beta]-xylanase ligand binding site

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

Morin, Andrew; Kaufmann, Kristian W.; Fortenberry, Carie

2012-09-05

The field of computational protein design has experienced important recent success. However, the de novo computational design of high-affinity protein-ligand interfaces is still largely an open challenge. Using the Rosetta program, we attempted the in silico design of a high-affinity protein interface to a small peptide ligand. We chose the thermophilic endo-1,4-{beta}-xylanase from Nonomuraea flexuosa as the protein scaffold on which to perform our designs. Over the course of the study, 12 proteins derived from this scaffold were produced and assayed for binding to the target ligand. Unfortunately, none of the designed proteins displayed evidence of high-affinity binding. Structural characterizationmore » of four designed proteins revealed that although the predicted structure of the protein model was highly accurate, this structural accuracy did not translate into accurate prediction of binding affinity. Crystallographic analyses indicate that the lack of binding affinity is possibly due to unaccounted for protein dynamics in the 'thumb' region of our design scaffold intrinsic to the family 11 {beta}-xylanase fold. Further computational analysis revealed two specific, single amino acid substitutions responsible for an observed change in backbone conformation, and decreased dynamic stability of the catalytic cleft. These findings offer new insight into the dynamic and structural determinants of the {beta}-xylanase proteins.« less

Construction of Rational Maps on the Projective Line with Given Dynamical Structure

DTIC Science & Technology

2016-05-11

References 42 4 1. Introduction The is a paper in arithmetic dynamics, a relatively young field at the intersection of the older studies of number theory...computers became available. The exponentially increased computational power and access to larger data sets rocketed the field forward, allowing...theory and dy- 5 namical systems, have come together to create a new field : arithmetic dynamics. Relative to the study of mathematics as a whole

Analysis on pseudo excitation of random vibration for structure of time flight counter

NASA Astrophysics Data System (ADS)

Wu, Qiong; Li, Dapeng

2015-03-01

Traditional computing method is inefficient for getting key dynamical parameters of complicated structure. Pseudo Excitation Method(PEM) is an effective method for calculation of random vibration. Due to complicated and coupling random vibration in rocket or shuttle launching, the new staging white noise mathematical model is deduced according to the practical launch environment. This deduced model is applied for PEM to calculate the specific structure of Time of Flight Counter(ToFC). The responses of power spectral density and the relevant dynamic characteristic parameters of ToFC are obtained in terms of the flight acceptance test level. Considering stiffness of fixture structure, the random vibration experiments are conducted in three directions to compare with the revised PEM. The experimental results show the structure can bear the random vibration caused by launch without any damage and key dynamical parameters of ToFC are obtained. The revised PEM is similar with random vibration experiment in dynamical parameters and responses are proved by comparative results. The maximum error is within 9%. The reasons of errors are analyzed to improve reliability of calculation. This research provides an effective method for solutions of computing dynamical characteristic parameters of complicated structure in the process of rocket or shuttle launching.

The Advanced Software Development and Commercialization Project

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

Gallopoulos, E.; Canfield, T.R.; Minkoff, M.

1990-09-01

This is the first of a series of reports pertaining to progress in the Advanced Software Development and Commercialization Project, a joint collaborative effort between the Center for Supercomputing Research and Development of the University of Illinois and the Computing and Telecommunications Division of Argonne National Laboratory. The purpose of this work is to apply techniques of parallel computing that were pioneered by University of Illinois researchers to mature computational fluid dynamics (CFD) and structural dynamics (SD) computer codes developed at Argonne. The collaboration in this project will bring this unique combination of expertise to bear, for the first time,more » on industrially important problems. By so doing, it will expose the strengths and weaknesses of existing techniques for parallelizing programs and will identify those problems that need to be solved in order to enable wide spread production use of parallel computers. Secondly, the increased efficiency of the CFD and SD codes themselves will enable the simulation of larger, more accurate engineering models that involve fluid and structural dynamics. In order to realize the above two goals, we are considering two production codes that have been developed at ANL and are widely used by both industry and Universities. These are COMMIX and WHAMS-3D. The first is a computational fluid dynamics code that is used for both nuclear reactor design and safety and as a design tool for the casting industry. The second is a three-dimensional structural dynamics code used in nuclear reactor safety as well as crashworthiness studies. These codes are currently available for both sequential and vector computers only. Our main goal is to port and optimize these two codes on shared memory multiprocessors. In so doing, we shall establish a process that can be followed in optimizing other sequential or vector engineering codes for parallel processors.« less

Current capabilities for simulating the extreme distortion of thin structures subjected to severe impacts

NASA Technical Reports Server (NTRS)

Key, Samuel W.

1993-01-01

The explicit transient dynamics technology in use today for simulating the impact and subsequent transient dynamic response of a structure has its origins in the 'hydrocodes' dating back to the late 1940's. The growth in capability in explicit transient dynamics technology parallels the growth in speed and size of digital computers. Computer software for simulating the explicit transient dynamic response of a structure is characterized by algorithms that use a large number of small steps. In explicit transient dynamics software there is a significant emphasis on speed and simplicity. The finite element technology used to generate the spatial discretization of a structure is based on a compromise between completeness of the representation for the physical processes modelled and speed in execution. That is, since it is expected in every calculation that the deformation will be finite and the material will be strained beyond the elastic range, the geometry and the associated gradient operators must be reconstructed, as well as complex stress-strain models evaluated at every time step. As a result, finite elements derived for explicit transient dynamics software use the simplest and barest constructions possible for computational efficiency while retaining an essential representation of the physical behavior. The best example of this technology is the four-node bending quadrilateral derived by Belytschko, Lin and Tsay. Today, the speed, memory capacity and availability of computer hardware allows a number of the previously used algorithms to be 'improved.' That is, it is possible with today's computing hardware to modify many of the standard algorithms to improve their representation of the physical process at the expense of added complexity and computational effort. The purpose is to review a number of these algorithms and identify the improvements possible. In many instances, both the older, faster version of the algorithm and the improved and somewhat slower version of the algorithm are found implemented together in software. Specifically, the following seven algorithmic items are examined: the invariant time derivatives of stress used in material models expressed in rate form; incremental objectivity and strain used in the numerical integration of the material models; the use of one-point element integration versus mean quadrature; shell elements used to represent the behavior of thin structural components; beam elements based on stress-resultant plasticity versus cross-section integration; the fidelity of elastic-plastic material models in their representation of ductile metals; and the use of Courant subcycling to reduce computational effort.

Methods for simulation-based analysis of fluid-structure interaction.

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

Barone, Matthew Franklin; Payne, Jeffrey L.

2005-10-01

Methods for analysis of fluid-structure interaction using high fidelity simulations are critically reviewed. First, a literature review of modern numerical techniques for simulation of aeroelastic phenomena is presented. The review focuses on methods contained within the arbitrary Lagrangian-Eulerian (ALE) framework for coupling computational fluid dynamics codes to computational structural mechanics codes. The review treats mesh movement algorithms, the role of the geometric conservation law, time advancement schemes, wetted surface interface strategies, and some representative applications. The complexity and computational expense of coupled Navier-Stokes/structural dynamics simulations points to the need for reduced order modeling to facilitate parametric analysis. The proper orthogonalmore » decomposition (POD)/Galerkin projection approach for building a reduced order model (ROM) is presented, along with ideas for extension of the methodology to allow construction of ROMs based on data generated from ALE simulations.« less

Modelling and enhanced molecular dynamics to steer structure-based drug discovery.

PubMed

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

2014-05-01

The ever-increasing gap between the availabilities of the genome sequences and the crystal structures of proteins remains one of the significant challenges to the modern drug discovery efforts. The knowledge of structure-dynamics-functionalities of proteins is important in order to understand several key aspects of structure-based drug discovery, such as drug-protein interactions, drug binding and unbinding mechanisms and protein-protein interactions. This review presents a brief overview on the different state of the art computational approaches that are applied for protein structure modelling and molecular dynamics simulations of biological systems. We give an essence of how different enhanced sampling molecular dynamics approaches, together with regular molecular dynamics methods, assist in steering the structure based drug discovery processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Clustering molecular dynamics trajectories for optimizing docking experiments.

PubMed

De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C

2015-01-01

Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

Study of Geometric Porosity on Static Stability and Drag Using Computational Fluid Dynamics for Rigid Parachute Shapes

NASA Technical Reports Server (NTRS)

Greathouse, James S.; Schwing, Alan M.

2015-01-01

This paper explores use of computational fluid dynamics to study the e?ect of geometric porosity on static stability and drag for NASA's Multi-Purpose Crew Vehicle main parachute. Both of these aerodynamic characteristics are of interest to in parachute design, and computational methods promise designers the ability to perform detailed parametric studies and other design iterations with a level of control previously unobtainable using ground or flight testing. The approach presented here uses a canopy structural analysis code to define the inflated parachute shapes on which structured computational grids are generated. These grids are used by the computational fluid dynamics code OVERFLOW and are modeled as rigid, impermeable bodies for this analysis. Comparisons to Apollo drop test data is shown as preliminary validation of the technique. Results include several parametric sweeps through design variables in order to better understand the trade between static stability and drag. Finally, designs that maximize static stability with a minimal loss in drag are suggested for further study in subscale ground and flight testing.

Self-consistent Green's function embedding for advanced electronic structure methods based on a dynamical mean-field concept

NASA Astrophysics Data System (ADS)

Chibani, Wael; Ren, Xinguo; Scheffler, Matthias; Rinke, Patrick

2016-04-01

We present an embedding scheme for periodic systems that facilitates the treatment of the physically important part (here a unit cell or a supercell) with advanced electronic structure methods, that are computationally too expensive for periodic systems. The rest of the periodic system is treated with computationally less demanding approaches, e.g., Kohn-Sham density-functional theory, in a self-consistent manner. Our scheme is based on the concept of dynamical mean-field theory formulated in terms of Green's functions. Our real-space dynamical mean-field embedding scheme features two nested Dyson equations, one for the embedded cluster and another for the periodic surrounding. The total energy is computed from the resulting Green's functions. The performance of our scheme is demonstrated by treating the embedded region with hybrid functionals and many-body perturbation theory in the GW approach for simple bulk systems. The total energy and the density of states converge rapidly with respect to the computational parameters and approach their bulk limit with increasing cluster (i.e., computational supercell) size.

Protein folding, protein structure and the origin of life: Theoretical methods and solutions of dynamical problems

NASA Technical Reports Server (NTRS)

Weaver, D. L.

1982-01-01

Theoretical methods and solutions of the dynamics of protein folding, protein aggregation, protein structure, and the origin of life are discussed. The elements of a dynamic model representing the initial stages of protein folding are presented. The calculation and experimental determination of the model parameters are discussed. The use of computer simulation for modeling protein folding is considered.

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

Dynamic Programming for Structured Continuous Markov Decision Problems

NASA Technical Reports Server (NTRS)

Dearden, Richard; Meuleau, Nicholas; Washington, Richard; Feng, Zhengzhu

2004-01-01

We describe an approach for exploiting structure in Markov Decision Processes with continuous state variables. At each step of the dynamic programming, the state space is dynamically partitioned into regions where the value function is the same throughout the region. We first describe the algorithm for piecewise constant representations. We then extend it to piecewise linear representations, using techniques from POMDPs to represent and reason about linear surfaces efficiently. We show that for complex, structured problems, our approach exploits the natural structure so that optimal solutions can be computed efficiently.

Dynamic Deployment Simulations of Inflatable Space Structures

NASA Technical Reports Server (NTRS)

Wang, John T.

2005-01-01

The feasibility of using Control Volume (CV) method and the Arbitrary Lagrangian Eulerian (ALE) method in LSDYNA to simulate the dynamic deployment of inflatable space structures is investigated. The CV and ALE methods were used to predict the inflation deployments of three folded tube configurations. The CV method was found to be a simple and computationally efficient method that may be adequate for modeling slow inflation deployment sine the inertia of the inflation gas can be neglected. The ALE method was found to be very computationally intensive since it involves the solving of three conservative equations of fluid as well as dealing with complex fluid structure interactions.

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Flight Dynamics of Flexible Aircraft with Aeroelastic and Inertial Force Interactions

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T.; Tuzcu, Ilhan

2009-01-01

This paper presents an integrated flight dynamic modeling method for flexible aircraft that captures coupled physics effects due to inertial forces, aeroelasticity, and propulsive forces that are normally present in flight. The present approach formulates the coupled flight dynamics using a structural dynamic modeling method that describes the elasticity of a flexible, twisted, swept wing using an equivalent beam-rod model. The structural dynamic model allows for three types of wing elastic motion: flapwise bending, chordwise bending, and torsion. Inertial force coupling with the wing elasticity is formulated to account for aircraft acceleration. The structural deflections create an effective aeroelastic angle of attack that affects the rigid-body motion of flexible aircraft. The aeroelastic effect contributes to aerodynamic damping forces that can influence aerodynamic stability. For wing-mounted engines, wing flexibility can cause the propulsive forces and moments to couple with the wing elastic motion. The integrated flight dynamics for a flexible aircraft are formulated by including generalized coordinate variables associated with the aeroelastic-propulsive forces and moments in the standard state-space form for six degree-of-freedom flight dynamics. A computational structural model for a generic transport aircraft has been created. The eigenvalue analysis is performed to compute aeroelastic frequencies and aerodynamic damping. The results will be used to construct an integrated flight dynamic model of a flexible generic transport aircraft.

NASA LeRC/Akron University Graduate Cooperative Fellowship Program and Graduate Student Researchers Program

NASA Technical Reports Server (NTRS)

Fertis, D. G.; Simon, A. L.

1981-01-01

The requisite methodology to solve linear and nonlinear problems associated with the static and dynamic analysis of rotating machinery, their static and dynamic behavior, and the interaction between the rotating and nonrotating parts of an engine is developed. Linear and nonlinear structural engine problems are investigated by developing solution strategies and interactive computational methods whereby the man and computer can communicate directly in making analysis decisions. Representative examples include modifying structural models, changing material, parameters, selecting analysis options and coupling with interactive graphical display for pre- and postprocessing capability.

Detailed Multidimensional Simulations of the Structure and Dynamics of Flames

NASA Technical Reports Server (NTRS)

Patnaik, G.; Kailasanath, K.

1999-01-01

Numerical simulations in which the various physical and chemical processes can be independently controlled can significantly advance our understanding of the structure, stability, dynamics and extinction of flames. Therefore, our approach has been to use detailed time-dependent, multidimensional, multispecies numerical models to perform carefully designed computational experiments of flames on Earth and in microgravity environments. Some of these computational experiments are complementary to physical experiments performed under the Microgravity Program while others provide a fundamental understanding that cannot be obtained from physical experiments alone. In this report, we provide a brief summary of our recent research highlighting the contributions since the previous microgravity combustion workshop. There are a number of mechanisms that can cause flame instabilities and result in the formation of dynamic multidimensional structures. In the past, we have used numerical simulations to show that it is the thermo-diffusive instability rather than an instability due to preferential diffusion that is the dominant mechanism for the formation of cellular flames in lean hydrogen-air mixtures. Other studies have explored the role of gravity on flame dynamics and extinguishment, multi-step kinetics and radiative losses on flame instabilities in rich hydrogen-air flames, and heat losses on burner-stabilized flames in microgravity. The recent emphasis of our work has been on exploring flame-vortex interactions and further investigating the structure and dynamics of lean hydrogen-air flames in microgravity. These topics are briefly discussed after a brief discussion of our computational approach for solving these problems.

Transport in Dynamical Astronomy and Multibody Problems

NASA Astrophysics Data System (ADS)

Dellnitz, Michael; Junge, Oliver; Koon, Wang Sang; Lekien, Francois; Lo, Martin W.; Marsden, Jerrold E.; Padberg, Kathrin; Preis, Robert; Ross, Shane D.; Thiere, Bianca

We combine the techniques of almost invariant sets (using tree structured box elimination and graph partitioning algorithms) with invariant manifold and lobe dynamics techniques. The result is a new computational technique for computing key dynamical features, including almost invariant sets, resonance regions as well as transport rates and bottlenecks between regions in dynamical systems. This methodology can be applied to a variety of multibody problems, including those in molecular modeling, chemical reaction rates and dynamical astronomy. In this paper we focus on problems in dynamical astronomy to illustrate the power of the combination of these different numerical tools and their applicability. In particular, we compute transport rates between two resonance regions for the three-body system consisting of the Sun, Jupiter and a third body (such as an asteroid). These resonance regions are appropriate for certain comets and asteroids.

Modal Response of Trapezoidal Wing Structures Using Second Order Shape Sensitivities

NASA Technical Reports Server (NTRS)

Liu, Youhua; Kapania, Rakesh K.

2000-01-01

The modal response of wing structures is very important for assessing their dynamic response including dynamic aeroelastic instabilities. Moreover, in a recent study an efficient structural optimization approach was developed using structural modes to represent the static aeroelastic wing response (both displacement and stress). In this paper, the modal response of general trapezoidal wing structures is approximated using shape sensitivities up to the 2nd order. Also different approaches of computing the derivatives are investigated.

Methods for Computationally Efficient Structured CFD Simulations of Complex Turbomachinery Flows

NASA Technical Reports Server (NTRS)

Herrick, Gregory P.; Chen, Jen-Ping

2012-01-01

This research presents more efficient computational methods by which to perform multi-block structured Computational Fluid Dynamics (CFD) simulations of turbomachinery, thus facilitating higher-fidelity solutions of complicated geometries and their associated flows. This computational framework offers flexibility in allocating resources to balance process count and wall-clock computation time, while facilitating research interests of simulating axial compressor stall inception with more complete gridding of the flow passages and rotor tip clearance regions than is typically practiced with structured codes. The paradigm presented herein facilitates CFD simulation of previously impractical geometries and flows. These methods are validated and demonstrate improved computational efficiency when applied to complicated geometries and flows.

On some methods for improving time of reachability sets computation for the dynamic system control problem

NASA Astrophysics Data System (ADS)

Zimovets, Artem; Matviychuk, Alexander; Ushakov, Vladimir

2016-12-01

The paper presents two different approaches to reduce the time of computer calculation of reachability sets. First of these two approaches use different data structures for storing the reachability sets in the computer memory for calculation in single-threaded mode. Second approach is based on using parallel algorithms with reference to the data structures from the first approach. Within the framework of this paper parallel algorithm of approximate reachability set calculation on computer with SMP-architecture is proposed. The results of numerical modelling are presented in the form of tables which demonstrate high efficiency of parallel computing technology and also show how computing time depends on the used data structure.

Dynamic Docking Test System (DDTS) active table computer program NASA Advanced Docking System (NADS)

NASA Technical Reports Server (NTRS)

Gates, R. M.; Jantz, R. E.

1974-01-01

A computer program was developed to describe the three-dimensional motion of the Dynamic Docking Test System active table. The input consists of inertia and geometry data, actuator structural data, forcing function data, hydraulics data, servo electronics data, and integration control data. The output consists of table responses, actuator bending responses, and actuator responses.

Model structure identification for wastewater treatment simulation based on computational fluid dynamics.

PubMed

Alex, J; Kolisch, G; Krause, K

2002-01-01

The objective of this presented project is to use the results of an CFD simulation to automatically, systematically and reliably generate an appropriate model structure for simulation of the biological processes using CSTR activated sludge compartments. Models and dynamic simulation have become important tools for research but also increasingly for the design and optimisation of wastewater treatment plants. Besides the biological models several cases are reported about the application of computational fluid dynamics ICFD) to wastewater treatment plants. One aim of the presented method to derive model structures from CFD results is to exclude the influence of empirical structure selection to the result of dynamic simulations studies of WWTPs. The second application of the approach developed is the analysis of badly performing treatment plants where the suspicion arises that bad flow behaviour such as short cut flows is part of the problem. The method suggested requires as the first step the calculation of fluid dynamics of the biological treatment step at different loading situations by use of 3-dimensional CFD simulation. The result of this information is used to generate a suitable model structure for conventional dynamic simulation of the treatment plant by use of a number of CSTR modules with a pattern of exchange flows between the tanks automatically. The method is explained in detail and the application to the WWTP Wuppertal Buchenhofen is presented.

Frequency response function-based explicit framework for dynamic identification in human-structure systems

NASA Astrophysics Data System (ADS)

Wei, Xiaojun; Živanović, Stana

2018-05-01

The aim of this paper is to propose a novel theoretical framework for dynamic identification in a structure occupied by a single human. The framework enables the prediction of the dynamics of the human-structure system from the known properties of the individual system components, the identification of human body dynamics from the known dynamics of the empty structure and the human-structure system and the identification of the properties of the structure from the known dynamics of the human and the human-structure system. The novelty of the proposed framework is the provision of closed-form solutions in terms of frequency response functions obtained by curve fitting measured data. The advantages of the framework over existing methods are that there is neither need for nonlinear optimisation nor need for spatial/modal models of the empty structure and the human-structure system. In addition, the second-order perturbation method is employed to quantify the effect of uncertainties in human body dynamics on the dynamic identification of the empty structure and the human-structure system. The explicit formulation makes the method computationally efficient and straightforward to use. A series of numerical examples and experiments are provided to illustrate the working of the method.

Aeroelastic, CFD, and Dynamic Computation and Optimization for Buffet and Flutter Application

NASA Technical Reports Server (NTRS)

Kandil, Osama A.

1997-01-01

The work presented in this paper include: 'Coupled and Uncoupled Bending-Torsion Responses of Twin-Tail Buffet'; 'Fluid/Structure Twin Tail Buffet Response Over a Wide Range of Angles of Attack'; 'Resent Advances in Multidisciplinary Aeronautical Problems of Fluids/Structures/Dynamics Interaction'; and'Development of a Coupled Fluid/Structure Aeroelastic Solver with Applications to Vortex Breakdown induced Twin Tail Buffeting.

Symposium on Parallel Computational Methods for Large-scale Structural Analysis and Design, 2nd, Norfolk, VA, US

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O. (Editor); Housner, Jerrold M. (Editor)

1993-01-01

Computing speed is leaping forward by several orders of magnitude each decade. Engineers and scientists gathered at a NASA Langley symposium to discuss these exciting trends as they apply to parallel computational methods for large-scale structural analysis and design. Among the topics discussed were: large-scale static analysis; dynamic, transient, and thermal analysis; domain decomposition (substructuring); and nonlinear and numerical methods.

Dynamic regime marginal structural mean models for estimation of optimal dynamic treatment regimes, Part II: proofs of results.

PubMed

Orellana, Liliana; Rotnitzky, Andrea; Robins, James M

2010-03-03

In this companion article to "Dynamic Regime Marginal Structural Mean Models for Estimation of Optimal Dynamic Treatment Regimes, Part I: Main Content" [Orellana, Rotnitzky and Robins (2010), IJB, Vol. 6, Iss. 2, Art. 7] we present (i) proofs of the claims in that paper, (ii) a proposal for the computation of a confidence set for the optimal index when this lies in a finite set, and (iii) an example to aid the interpretation of the positivity assumption.

Coarse-grained modeling of RNA 3D structure.

PubMed

Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

2016-07-01

Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Aeroelastic, CFD, and Dynamics Computation and Optimization for Buffet and Flutter Applications

NASA Technical Reports Server (NTRS)

Kandil, Osama A.

1997-01-01

Accomplishments achieved during the reporting period are listed. These accomplishments included 6 papers published in various journals or presented at various conferences; 1 abstract submitted to a technical conference; production of 2 animated movies; and a proposal for use of the National Aerodynamic Simulation Facility at NASA Ames Research Center for further research. The published and presented papers and animated movies addressed the following topics: aeroelasticity, computational fluid dynamics, structural dynamics, wing and tail buffet, vortical flow interactions, and delta wings.

New Flutter Analysis Technique for Time-Domain Computational Aeroelasticity

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Lung, Shun-Fat

2017-01-01

A new time-domain approach for computing flutter speed is presented. Based on the time-history result of aeroelastic simulation, the unknown unsteady aerodynamics model is estimated using a system identification technique. The full aeroelastic model is generated via coupling the estimated unsteady aerodynamic model with the known linear structure model. The critical dynamic pressure is computed and used in the subsequent simulation until the convergence of the critical dynamic pressure is achieved. The proposed method is applied to a benchmark cantilevered rectangular wing.

Morphological communication: exploiting coupled dynamics in a complex mechanical structure to achieve locomotion

PubMed Central

Rieffel, John A.; Valero-Cuevas, Francisco J.; Lipson, Hod

2010-01-01

Traditional engineering approaches strive to avoid, or actively suppress, nonlinear dynamic coupling among components. Biological systems, in contrast, are often rife with these dynamics. Could there be, in some cases, a benefit to high degrees of dynamical coupling? Here we present a distributed robotic control scheme inspired by the biological phenomenon of tensegrity-based mechanotransduction. This emergence of morphology-as-information-conduit or ‘morphological communication’, enabled by time-sensitive spiking neural networks, presents a new paradigm for the decentralized control of large, coupled, modular systems. These results significantly bolster, both in magnitude and in form, the idea of morphological computation in robotic control. Furthermore, they lend further credence to ideas of embodied anatomical computation in biological systems, on scales ranging from cellular structures up to the tendinous networks of the human hand. PMID:19776146

For operation of the Computer Software Management and Information Center (COSMIC)

NASA Technical Reports Server (NTRS)

Carmon, J. L.

1983-01-01

Computer programs for degaussing, magnetic field calculation, low speed wing flap systems aerodynamics, structural panel analysis, dynamic stress/strain data acquisition, allocation and network scheduling, and digital filters are discussed.

Static and dynamic structural-sensitivity derivative calculations in the finite-element-based Engineering Analysis Language (EAL) system

NASA Technical Reports Server (NTRS)

Camarda, C. J.; Adelman, H. M.

1984-01-01

The implementation of static and dynamic structural-sensitivity derivative calculations in a general purpose, finite-element computer program denoted the Engineering Analysis Language (EAL) System is described. Derivatives are calculated with respect to structural parameters, specifically, member sectional properties including thicknesses, cross-sectional areas, and moments of inertia. Derivatives are obtained for displacements, stresses, vibration frequencies and mode shapes, and buckling loads and mode shapes. Three methods for calculating derivatives are implemented (analytical, semianalytical, and finite differences), and comparisons of computer time and accuracy are made. Results are presented for four examples: a swept wing, a box beam, a stiffened cylinder with a cutout, and a space radiometer-antenna truss.

Reduced-Order Models for the Aeroelastic Analysis of Ares Launch Vehicles

NASA Technical Reports Server (NTRS)

Silva, Walter A.; Vatsa, Veer N.; Biedron, Robert T.

2010-01-01

This document presents the development and application of unsteady aerodynamic, structural dynamic, and aeroelastic reduced-order models (ROMs) for the ascent aeroelastic analysis of the Ares I-X flight test and Ares I crew launch vehicles using the unstructured-grid, aeroelastic FUN3D computational fluid dynamics (CFD) code. The purpose of this work is to perform computationally-efficient aeroelastic response calculations that would be prohibitively expensive via computation of multiple full-order aeroelastic FUN3D solutions. These efficient aeroelastic ROM solutions provide valuable insight regarding the aeroelastic sensitivity of the vehicles to various parameters over a range of dynamic pressures.

Visualization of Dynamic Vortex Structures in Magnetic Films with Uniaxial Anisotropy (Micromagnetic Simulation)

NASA Astrophysics Data System (ADS)

Zverev, V. V.; Izmozherov, I. M.; Filippov, B. N.

2018-02-01

Three-dimensional computer simulation of dynamic processes in a moving domain boundary separating domains in a soft magnetic uniaxial film with planar anisotropy is performed by numerical solution of Landau-Lifshitz-Gilbert equations. The developed visualization methods are used to establish the connection between the motion of surface vortices and antivortices, singular (Bloch) points, and core lines of intrafilm vortex structures. A relation between the character of magnetization dynamics and the film thickness is found. The analytical models of spatial vortex structures for imitation of topological properties of the structures observed in micromagnetic simulation are constructed.

Control Law Design in a Computational Aeroelasticity Environment

NASA Technical Reports Server (NTRS)

Newsom, Jerry R.; Robertshaw, Harry H.; Kapania, Rakesh K.

2003-01-01

A methodology for designing active control laws in a computational aeroelasticity environment is given. The methodology involves employing a systems identification technique to develop an explicit state-space model for control law design from the output of a computational aeroelasticity code. The particular computational aeroelasticity code employed in this paper solves the transonic small disturbance aerodynamic equation using a time-accurate, finite-difference scheme. Linear structural dynamics equations are integrated simultaneously with the computational fluid dynamics equations to determine the time responses of the structure. These structural responses are employed as the input to a modern systems identification technique that determines the Markov parameters of an "equivalent linear system". The Eigensystem Realization Algorithm is then employed to develop an explicit state-space model of the equivalent linear system. The Linear Quadratic Guassian control law design technique is employed to design a control law. The computational aeroelasticity code is modified to accept control laws and perform closed-loop simulations. Flutter control of a rectangular wing model is chosen to demonstrate the methodology. Various cases are used to illustrate the usefulness of the methodology as the nonlinearity of the aeroelastic system is increased through increased angle-of-attack changes.

Computational procedures for evaluating the sensitivity derivatives of vibration frequencies and Eigenmodes of framed structures

NASA Technical Reports Server (NTRS)

Fetterman, Timothy L.; Noor, Ahmed K.

1987-01-01

Computational procedures are presented for evaluating the sensitivity derivatives of the vibration frequencies and eigenmodes of framed structures. Both a displacement and a mixed formulation are used. The two key elements of the computational procedure are: (a) Use of dynamic reduction techniques to substantially reduce the number of degrees of freedom; and (b) Application of iterative techniques to improve the accuracy of the derivatives of the eigenmodes. The two reduction techniques considered are the static condensation and a generalized dynamic reduction technique. Error norms are introduced to assess the accuracy of the eigenvalue and eigenvector derivatives obtained by the reduction techniques. The effectiveness of the methods presented is demonstrated by three numerical examples.

Application of a distributed network in computational fluid dynamic simulations

NASA Technical Reports Server (NTRS)

Deshpande, Manish; Feng, Jinzhang; Merkle, Charles L.; Deshpande, Ashish

1994-01-01

A general-purpose 3-D, incompressible Navier-Stokes algorithm is implemented on a network of concurrently operating workstations using parallel virtual machine (PVM) and compared with its performance on a CRAY Y-MP and on an Intel iPSC/860. The problem is relatively computationally intensive, and has a communication structure based primarily on nearest-neighbor communication, making it ideally suited to message passing. Such problems are frequently encountered in computational fluid dynamics (CDF), and their solution is increasingly in demand. The communication structure is explicitly coded in the implementation to fully exploit the regularity in message passing in order to produce a near-optimal solution. Results are presented for various grid sizes using up to eight processors.

Dynamic Identification for Control of Large Space Structures

NASA Technical Reports Server (NTRS)

Ibrahim, S. R.

1985-01-01

This is a compilation of reports by the one author on one subject. It consists of the following five journal articles: (1) A Parametric Study of the Ibrahim Time Domain Modal Identification Algorithm; (2) Large Modal Survey Testing Using the Ibrahim Time Domain Identification Technique; (3) Computation of Normal Modes from Identified Complex Modes; (4) Dynamic Modeling of Structural from Measured Complex Modes; and (5) Time Domain Quasi-Linear Identification of Nonlinear Dynamic Systems.

A Fluid Structure Interaction Strategy with Application to Low Reynolds Number Flapping Flight

DTIC Science & Technology

2010-01-01

using a predictor - corrector strategy. Dynamic fluid grid adaptation is implemented to reduce the number of grid points and computation costs...governing the dynamics of the ow and the structure are simultaneously advanced in time by using a predictor - corrector strategy. Dynamic uid grid...colleague Patrick Rabenold, the math-guy, who provided the seminal work on adaptive mesh refine- ment for incompressible flow using the Paramesh c

Conformational diversity and computational enzyme design

PubMed Central

Lassila, Jonathan K.

2010-01-01

The application of computational protein design methods to the design of enzyme active sites offers potential routes to new catalysts and new reaction specificities. Computational design methods have typically treated the protein backbone as a rigid structure for the sake of computational tractability. However, this fixed-backbone approximation introduces its own special challenges for enzyme design and it contrasts with an emerging picture of natural enzymes as dynamic ensembles with multiple conformations and motions throughout a reaction cycle. This review considers the impact of conformational variation and dynamics on computational enzyme design and it highlights new approaches to addressing protein conformational diversity in enzyme design including recent advances in multistate design, backbone flexibility, and computational library design. PMID:20829099

Method of performing computational aeroelastic analyses

NASA Technical Reports Server (NTRS)

Silva, Walter A. (Inventor)

2011-01-01

Computational aeroelastic analyses typically use a mathematical model for the structural modes of a flexible structure and a nonlinear aerodynamic model that can generate a plurality of unsteady aerodynamic responses based on the structural modes for conditions defining an aerodynamic condition of the flexible structure. In the present invention, a linear state-space model is generated using a single execution of the nonlinear aerodynamic model for all of the structural modes where a family of orthogonal functions is used as the inputs. Then, static and dynamic aeroelastic solutions are generated using computational interaction between the mathematical model and the linear state-space model for a plurality of periodic points in time.

Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

PubMed Central

De Paris, Renata; Quevedo, Christian V.; Ruiz, Duncan D.; Norberto de Souza, Osmar; Barros, Rodrigo C.

2015-01-01

Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand. PMID:25873944

Solution x-ray scattering and structure formation in protein dynamics

NASA Astrophysics Data System (ADS)

Nasedkin, Alexandr; Davidsson, Jan; Niemi, Antti J.; Peng, Xubiao

2017-12-01

We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analyzing experimental data in the case of Engrailed homeodomain protein as an example. We demonstrate how to interpret S/WAXS data qualitatively with a good precision and over an extended temperature range. We explain experimental observations in terms of protein phase structure, and we make predictions for future experiments and for how to analyze data at different ambient temperature values. We conclude that the approach we propose has the potential to become a highly accurate, computationally effective, and predictive tool for analyzing S/WAXS data. For this, we compare our results with those obtained previously in an all-atom molecular dynamics simulation.

Model selection and parameter estimation in structural dynamics using approximate Bayesian computation

NASA Astrophysics Data System (ADS)

Ben Abdessalem, Anis; Dervilis, Nikolaos; Wagg, David; Worden, Keith

2018-01-01

This paper will introduce the use of the approximate Bayesian computation (ABC) algorithm for model selection and parameter estimation in structural dynamics. ABC is a likelihood-free method typically used when the likelihood function is either intractable or cannot be approached in a closed form. To circumvent the evaluation of the likelihood function, simulation from a forward model is at the core of the ABC algorithm. The algorithm offers the possibility to use different metrics and summary statistics representative of the data to carry out Bayesian inference. The efficacy of the algorithm in structural dynamics is demonstrated through three different illustrative examples of nonlinear system identification: cubic and cubic-quintic models, the Bouc-Wen model and the Duffing oscillator. The obtained results suggest that ABC is a promising alternative to deal with model selection and parameter estimation issues, specifically for systems with complex behaviours.

Quantum Dynamics of Helium Clusters

DTIC Science & Technology

1993-03-01

the structure of both these and the HeN clusters in the body fixed frame by computing principal moments of inertia, thereby avoiding the...8217 of helium clusters, with the modification that we subtract 0.96 K from the computed values so that lor sufficiently large clusters we recover the...phonon spectrum of liquid He. To get a picture of these spectra one needs to compute the structure functions 51. Monte Carlo random walk simulations

Using Molecular Dynamics Simulations as an Aid in the Prediction of Domain Swapping of Computationally Designed Protein Variants.

PubMed

Mou, Yun; Huang, Po-Ssu; Thomas, Leonard M; Mayo, Stephen L

2015-08-14

In standard implementations of computational protein design, a positive-design approach is used to predict sequences that will be stable on a given backbone structure. Possible competing states are typically not considered, primarily because appropriate structural models are not available. One potential competing state, the domain-swapped dimer, is especially compelling because it is often nearly identical with its monomeric counterpart, differing by just a few mutations in a hinge region. Molecular dynamics (MD) simulations provide a computational method to sample different conformational states of a structure. Here, we tested whether MD simulations could be used as a post-design screening tool to identify sequence mutations leading to domain-swapped dimers. We hypothesized that a successful computationally designed sequence would have backbone structure and dynamics characteristics similar to that of the input structure and that, in contrast, domain-swapped dimers would exhibit increased backbone flexibility and/or altered structure in the hinge-loop region to accommodate the large conformational change required for domain swapping. While attempting to engineer a homodimer from a 51-amino-acid fragment of the monomeric protein engrailed homeodomain (ENH), we had instead generated a domain-swapped dimer (ENH_DsD). MD simulations on these proteins showed increased B-factors derived from MD simulation in the hinge loop of the ENH_DsD domain-swapped dimer relative to monomeric ENH. Two point mutants of ENH_DsD designed to recover the monomeric fold were then tested with an MD simulation protocol. The MD simulations suggested that one of these mutants would adopt the target monomeric structure, which was subsequently confirmed by X-ray crystallography. Copyright © 2015. Published by Elsevier Ltd.

Computational Methods for Structural Mechanics and Dynamics, part 1

NASA Technical Reports Server (NTRS)

Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)

1989-01-01

The structural analysis methods research has several goals. One goal is to develop analysis methods that are general. This goal of generality leads naturally to finite-element methods, but the research will also include other structural analysis methods. Another goal is that the methods be amenable to error analysis; that is, given a physical problem and a mathematical model of that problem, an analyst would like to know the probable error in predicting a given response quantity. The ultimate objective is to specify the error tolerances and to use automated logic to adjust the mathematical model or solution strategy to obtain that accuracy. A third goal is to develop structural analysis methods that can exploit parallel processing computers. The structural analysis methods research will focus initially on three types of problems: local/global nonlinear stress analysis, nonlinear transient dynamics, and tire modeling.

A computer-assisted study of pulse dynamics in anisotropic media

NASA Astrophysics Data System (ADS)

Krishnan, J.; Engelborghs, K.; Bär, M.; Lust, K.; Roose, D.; Kevrekidis, I. G.

2001-06-01

This study focuses on the computer-assisted stability analysis of travelling pulse-like structures in spatially periodic heterogeneous reaction-diffusion media. The physical motivation comes from pulse propagation in thin annular domains on a diffusionally anisotropic catalytic surface. The study was performed by computing the travelling pulse-like structures as limit cycles of the spatially discretized PDE, which in turn is performed in two ways: a Newton method based on a pseudospectral discretization of the PDE, and a Newton-Picard method based on a finite difference discretization. Details about the spectra of these modulated pulse-like structures are discussed, including how they may be compared with the spectra of pulses in homogeneous media. The effects of anisotropy on the dynamics of pulses and pulse pairs are studied. Beyond shifting the location of bifurcations present in homogeneous media, anisotropy can also introduce certain new instabilities.

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.; Nguyen, Duc T.; Baddourah, Majdi; Qin, Jiangning

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigensolution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization search analysis and domain decomposition. The source code for many of these algorithms is available.

Development of Multidisciplinary, Multifidelity Analysis, Integration, and Optimization of Aerospace Vehicles

DTIC Science & Technology

2010-02-27

investigated in more detail. The intermediate level of fidelity, though more expensive, is then used to refine the analysis , add geometric detail, and...design stage is used to further refine the analysis , narrowing the design to a handful of options. Figure 1. Integrated Hierarchical Framework. In...computational structural and computational fluid modeling. For the structural analysis tool we used McIntosh Structural Dynamics’ finite element code CNEVAL

Estimation of Unsteady Aerodynamic Models from Dynamic Wind Tunnel Data

NASA Technical Reports Server (NTRS)

Murphy, Patrick; Klein, Vladislav

2011-01-01

Demanding aerodynamic modelling requirements for military and civilian aircraft have motivated researchers to improve computational and experimental techniques and to pursue closer collaboration in these areas. Model identification and validation techniques are key components for this research. This paper presents mathematical model structures and identification techniques that have been used successfully to model more general aerodynamic behaviours in single-degree-of-freedom dynamic testing. Model parameters, characterizing aerodynamic properties, are estimated using linear and nonlinear regression methods in both time and frequency domains. Steps in identification including model structure determination, parameter estimation, and model validation, are addressed in this paper with examples using data from one-degree-of-freedom dynamic wind tunnel and water tunnel experiments. These techniques offer a methodology for expanding the utility of computational methods in application to flight dynamics, stability, and control problems. Since flight test is not always an option for early model validation, time history comparisons are commonly made between computational and experimental results and model adequacy is inferred by corroborating results. An extension is offered to this conventional approach where more general model parameter estimates and their standard errors are compared.

Absolute comparison of simulated and experimental protein-folding dynamics

NASA Astrophysics Data System (ADS)

Snow, Christopher D.; Nguyen, Houbi; Pande, Vijay S.; Gruebele, Martin

2002-11-01

Protein folding is difficult to simulate with classical molecular dynamics. Secondary structure motifs such as α-helices and β-hairpins can form in 0.1-10µs (ref. 1), whereas small proteins have been shown to fold completely in tens of microseconds. The longest folding simulation to date is a single 1-µs simulation of the villin headpiece; however, such single runs may miss many features of the folding process as it is a heterogeneous reaction involving an ensemble of transition states. Here, we have used a distributed computing implementation to produce tens of thousands of 5-20-ns trajectories (700µs) to simulate mutants of the designed mini-protein BBA5. The fast relaxation dynamics these predict were compared with the results of laser temperature-jump experiments. Our computational predictions are in excellent agreement with the experimentally determined mean folding times and equilibrium constants. The rapid folding of BBA5 is due to the swift formation of secondary structure. The convergence of experimentally and computationally accessible timescales will allow the comparison of absolute quantities characterizing in vitro and in silico (computed) protein folding.

Effect of Material Ion Exchanges on the Mechanical Stiffness Properties and Shear Deformation of Hydrated Cement Material Chemistry Structure C-S-H Jennite -- A Computational Modeling Study

NASA Astrophysics Data System (ADS)

Adebiyi, Babatunde Mattew

Material properties and performance are governed by material molecular chemistry structures and molecular level interactions. Methods to understand relationships between the material properties and performance and their correlation to the molecular level chemistry and morphology, and thus find ways of manipulating and adjusting matters at the atomistic level in order to improve material performance, are required. A computational material modeling methodology is investigated and demonstrated for a key cement hydrated component material chemistry structure of Calcium-Silicate-Hydrate (C-S-H) Jennite in this work. The effect of material ion exchanges on the mechanical stiffness properties and shear deformation behavior of hydrated cement material chemistry structure of Calcium Silicate Hydrate (C-S-H) Jennite was studied. Calcium ions were replaced with Magnesium ions in Jennite structure of the C-S-H gel. Different level of substitution of the ions was used. The traditional Jennite structure was obtained from the American Mineralogist Crystal Structure Database and super cells of the structures were created using a Molecular Dynamics Analyzer and Visualizer Material Studio. Molecular dynamics parameters used in the modeling analysis were determined by carrying out initial dynamic studies. 64 unit cell of C-S-H Jennite was used in material modeling analysis studies based on convergence results obtained from the elastic modulus and total energies. NVT forcite dynamics using COMPASS force field based on 200 ps dynamics time was used to determine mechanical modulus of the traditional C-S-H gel and the Magnesium ion modified structures. NVT Discover dynamics using COMPASS forcefield was used in the material modeling studies to investigate the influence of ionic exchange on the shear deformation of the associated material chemistry structures. A prior established quasi-static deformation method to emulate shear deformation of C-S-H material chemistry structure that is based on a triclinic crystal structure was used, by deforming the triclinic crystal structure at 0.2 degree per time step for 75 steps of deformation. It was observed that there is a decrease in the total energies of the systems as the percentage of magnesium ion increases in the C-S-H Jennite molecular structure systems. Investigation of effect of ion exchange on the elastic modulus shows that the elastic stiffness modulus tends to decrease as the amount of Mg in the systems increases, using either COMPASS or universal force field. On the other hand, shear moduli obtained after deforming the structures computed from the stress-strain curve obtained from material modeling increases as the amount of Mg increases in the system. The present investigations also showed that ultimate shear stress obtained from predicted shear stress---strain also increases with amount of Mg in the chemistry structure. Present study clearly demonstrates that computational material modeling following molecular dynamics analysis methodology is an effective way to predict and understand the effective material chemistry and additive changes on the stiffness and deformation characteristics in cementitious materials, and the results suggest that this method can be extended to other materials.

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

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC, year 2 quarter 1 progress report.

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

Lottes, S.A.; Bojanowski, C.; Shen, J.

2012-04-09

The computational fluid dynamics (CFD) and computational structural mechanics (CSM) focus areas at Argonne's Transportation Research and Analysis Computing Center (TRACC) initiated a project to support and compliment the experimental programs at the Turner-Fairbank Highway Research Center (TFHRC) with high performance computing based analysis capabilities in August 2010. The project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at TFHRC for a period of five years, beginning in October 2010. Themore » analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water effects on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to improve design allowing for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, CFD analysis of the operation of the wind tunnel in the TFHRC wind engineering laboratory. This quarterly report documents technical progress on the project tasks for the period of October through December 2011.« less

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC, year 2 quarter 2 progress report

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

Lottes, S.A.; Bojanowski, C.; Shen, J.

2012-06-28

The computational fluid dynamics (CFD) and computational structural mechanics (CSM) focus areas at Argonne's Transportation Research and Analysis Computing Center (TRACC) initiated a project to support and compliment the experimental programs at the Turner-Fairbank Highway Research Center (TFHRC) with high performance computing based analysis capabilities in August 2010. The project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at TFHRC for a period of five years, beginning in October 2010. Themore » analysis methods employ well benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water effects on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to improve design allowing for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, CFD analysis of the operation of the wind tunnel in the TFHRC wind engineering laboratory. This quarterly report documents technical progress on the project tasks for the period of January through March 2012.« less

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC, year 1 quarter 3 progress report.

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

Lottes, S.A.; Kulak, R.F.; Bojanowski, C.

2011-08-26

The computational fluid dynamics (CFD) and computational structural mechanics (CSM) focus areas at Argonne's Transportation Research and Analysis Computing Center (TRACC) initiated a project to support and compliment the experimental programs at the Turner-Fairbank Highway Research Center (TFHRC) with high performance computing based analysis capabilities in August 2010. The project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at TFHRC for a period of five years, beginning in October 2010. Themore » analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water loads on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to assess them for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, vehicle stability under high wind loading, and the use of electromagnetic shock absorbers to improve vehicle stability under high wind conditions. This quarterly report documents technical progress on the project tasks for the period of April through June 2011.« less

Current Progress of a Finite Element Computational Fluid Dynamics Prediction of Flutter for the AeroStructures Test Wing

NASA Technical Reports Server (NTRS)

Arena, Andrew S., Jr.

2002-01-01

This progress report focuses on the use of the STructural Analysis RoutineS suite program, SOLIDS, input for the AeroStructures Test Wing. The AeroStructures Test Wing project as a whole is described. The use of the SOLIDS code to find the mode shapes of a structure is discussed. The frequencies, and the structural dynamics to which they relate are examined. The results of the CFD predictions are compared to experimental data from a Ground Vibration Test.

Interactive computer graphics and its role in control system design of large space structures

NASA Technical Reports Server (NTRS)

Reddy, A. S. S. R.

1985-01-01

This paper attempts to show the relevance of interactive computer graphics in the design of control systems to maintain attitude and shape of large space structures to accomplish the required mission objectives. The typical phases of control system design, starting from the physical model such as modeling the dynamics, modal analysis, and control system design methodology are reviewed and the need of the interactive computer graphics is demonstrated. Typical constituent parts of large space structures such as free-free beams and free-free plates are used to demonstrate the complexity of the control system design and the effectiveness of the interactive computer graphics.

PDEMOD: Software for control/structures optimization

NASA Technical Reports Server (NTRS)

Taylor, Lawrence W., Jr.; Zimmerman, David

1991-01-01

Because of the possibility of adverse interaction between the control system and the structural dynamics of large, flexible spacecraft, great care must be taken to ensure stability and system performance. Because of the high cost of insertion of mass into low earth orbit, it is prudent to optimize the roles of structure and control systems simultaneously. Because of the difficulty and the computational burden in modeling and analyzing the control structure system dynamics, the total problem is often split and treated iteratively. It would aid design if the control structure system dynamics could be represented in a single system of equations. With the use of the software PDEMOD (Partial Differential Equation Model), it is now possible to optimize structure and control systems simultaneously. The distributed parameter modeling approach enables embedding the control system dynamics into the same equations for the structural dynamics model. By doing this, the current difficulties involved in model order reduction are avoided. The NASA Mini-MAST truss is used an an example for studying integrated control structure design.

Computational Methods for Nonlinear Dynamic Problems in Solid and Structural Mechanics: Progress in the Theory and Modeling of Friction and in the Control of Dynamical Systems with Frictional Forces

DTIC Science & Technology

1989-03-31

present several numerical studies designed to reveal the effect that some of the governing parameters have on the behavior of the system and, whenever...Friction and in the Control of Dynamical Systems with Frictional Forces FINAL TECHNICAL REPORT March 31, 1989 _ -- I -.7: .-.- - : AFOSR Contract F49620...SOLID AND STRUCTURAL MECHANICS: Progress in the Theory and Modeling of Friction and in the Control of Dynamical Systems with Frictional Forces I I * FINAL

Dynamic Regime Marginal Structural Mean Models for Estimation of Optimal Dynamic Treatment Regimes, Part II: Proofs of Results*

PubMed Central

Orellana, Liliana; Rotnitzky, Andrea; Robins, James M.

2010-01-01

In this companion article to “Dynamic Regime Marginal Structural Mean Models for Estimation of Optimal Dynamic Treatment Regimes, Part I: Main Content” [Orellana, Rotnitzky and Robins (2010), IJB, Vol. 6, Iss. 2, Art. 7] we present (i) proofs of the claims in that paper, (ii) a proposal for the computation of a confidence set for the optimal index when this lies in a finite set, and (iii) an example to aid the interpretation of the positivity assumption. PMID:20405047

Dynamic displacement measurement of large-scale structures based on the Lucas-Kanade template tracking algorithm

NASA Astrophysics Data System (ADS)

Guo, Jie; Zhu, Chang`an

2016-01-01

The development of optics and computer technologies enables the application of the vision-based technique that uses digital cameras to the displacement measurement of large-scale structures. Compared with traditional contact measurements, vision-based technique allows for remote measurement, has a non-intrusive characteristic, and does not necessitate mass introduction. In this study, a high-speed camera system is developed to complete the displacement measurement in real time. The system consists of a high-speed camera and a notebook computer. The high-speed camera can capture images at a speed of hundreds of frames per second. To process the captured images in computer, the Lucas-Kanade template tracking algorithm in the field of computer vision is introduced. Additionally, a modified inverse compositional algorithm is proposed to reduce the computing time of the original algorithm and improve the efficiency further. The modified algorithm can rapidly accomplish one displacement extraction within 1 ms without having to install any pre-designed target panel onto the structures in advance. The accuracy and the efficiency of the system in the remote measurement of dynamic displacement are demonstrated in the experiments on motion platform and sound barrier on suspension viaduct. Experimental results show that the proposed algorithm can extract accurate displacement signal and accomplish the vibration measurement of large-scale structures.

Thermal Protection System Cavity Heating for Simplified and Actual Geometries Using Computational Fluid Dynamics Simulations with Unstructured Grids

NASA Technical Reports Server (NTRS)

McCloud, Peter L.

2010-01-01

Thermal Protection System (TPS) Cavity Heating is predicted using Computational Fluid Dynamics (CFD) on unstructured grids for both simplified cavities and actual cavity geometries. Validation was performed using comparisons to wind tunnel experimental results and CFD predictions using structured grids. Full-scale predictions were made for simplified and actual geometry configurations on the Space Shuttle Orbiter in a mission support timeframe.

Good coupling for the multiscale patch scheme on systems with microscale heterogeneity

NASA Astrophysics Data System (ADS)

Bunder, J. E.; Roberts, A. J.; Kevrekidis, I. G.

2017-05-01

Computational simulation of microscale detailed systems is frequently only feasible over spatial domains much smaller than the macroscale of interest. The 'equation-free' methodology couples many small patches of microscale computations across space to empower efficient computational simulation over macroscale domains of interest. Motivated by molecular or agent simulations, we analyse the performance of various coupling schemes for patches when the microscale is inherently 'rough'. As a canonical problem in this universality class, we systematically analyse the case of heterogeneous diffusion on a lattice. Computer algebra explores how the dynamics of coupled patches predict the large scale emergent macroscale dynamics of the computational scheme. We determine good design for the coupling of patches by comparing the macroscale predictions from patch dynamics with the emergent macroscale on the entire domain, thus minimising the computational error of the multiscale modelling. The minimal error on the macroscale is obtained when the coupling utilises averaging regions which are between a third and a half of the patch. Moreover, when the symmetry of the inter-patch coupling matches that of the underlying microscale structure, patch dynamics predicts the desired macroscale dynamics to any specified order of error. The results confirm that the patch scheme is useful for macroscale computational simulation of a range of systems with microscale heterogeneity.

Dynamic analysis for shuttle design verification

NASA Technical Reports Server (NTRS)

Fralich, R. W.; Green, C. E.; Rheinfurth, M. H.

1972-01-01

Two approaches that are used for determining the modes and frequencies of space shuttle structures are discussed. The first method, direct numerical analysis, involves finite element mathematical modeling of the space shuttle structure in order to use computer programs for dynamic structural analysis. The second method utilizes modal-coupling techniques of experimental verification made by vibrating only spacecraft components and by deducing modes and frequencies of the complete vehicle from results obtained in the component tests.

User's Manual for Computer Program ROTOR. [to calculate tilt-rotor aircraft dynamic characteristics

NASA Technical Reports Server (NTRS)

Yasue, M.

1974-01-01

A detailed description of a computer program to calculate tilt-rotor aircraft dynamic characteristics is presented. This program consists of two parts: (1) the natural frequencies and corresponding mode shapes of the rotor blade and wing are developed from structural data (mass distribution and stiffness distribution); and (2) the frequency response (to gust and blade pitch control inputs) and eigenvalues of the tilt-rotor dynamic system, based on the natural frequencies and mode shapes, are derived. Sample problems are included to assist the user.

Dynamic Probabilistic Instability of Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

2009-01-01

A computationally effective method is described to evaluate the non-deterministic dynamic instability (probabilistic dynamic buckling) of thin composite shells. The method is a judicious combination of available computer codes for finite element, composite mechanics and probabilistic structural analysis. The solution method is incrementally updated Lagrangian. It is illustrated by applying it to thin composite cylindrical shell subjected to dynamic loads. Both deterministic and probabilistic buckling loads are evaluated to demonstrate the effectiveness of the method. A universal plot is obtained for the specific shell that can be used to approximate buckling loads for different load rates and different probability levels. Results from this plot show that the faster the rate, the higher the buckling load and the shorter the time. The lower the probability, the lower is the buckling load for a specific time. Probabilistic sensitivity results show that the ply thickness, the fiber volume ratio and the fiber longitudinal modulus, dynamic load and loading rate are the dominant uncertainties in that order.

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Nguyen, D. T.; Baddourah, M. A.; Qin, J.

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigen-solution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization algorithm and domain decomposition. The source code for many of these algorithms is available from NASA Langley.

Computing by physical interaction in neurons.

PubMed

Aur, Dorian; Jog, Mandar; Poznanski, Roman R

2011-12-01

The electrodynamics of action potentials represents the fundamental level where information is integrated and processed in neurons. The Hodgkin-Huxley model cannot explain the non-stereotyped spatial charge density dynamics that occur during action potential propagation. Revealed in experiments as spike directivity, the non-uniform charge density dynamics within neurons carry meaningful information and suggest that fragments of information regarding our memories are endogenously stored in structural patterns at a molecular level and are revealed only during spiking activity. The main conceptual idea is that under the influence of electric fields, efficient computation by interaction occurs between charge densities embedded within molecular structures and the transient developed flow of electrical charges. This process of computation underlying electrical interactions and molecular mechanisms at the subcellular level is dissimilar from spiking neuron models that are completely devoid of physical interactions. Computation by interaction describes a more powerful continuous model of computation than the one that consists of discrete steps as represented in Turing machines.

Investigation on the forced response of a radial turbine under aerodynamic excitations

NASA Astrophysics Data System (ADS)

Ma, Chaochen; Huang, Zhi; Qi, Mingxu

2016-04-01

Rotor blades in a radial turbine with nozzle guide vanes typically experience harmonic aerodynamic excitations due to the rotor stator interaction. Dynamic stresses induced by the harmonic excitations can result in high cycle fatigue (HCF) of the blades. A reliable prediction method for forced response issue is essential to avoid the HCF problem. In this work, the forced response mechanisms were investigated based on a fluid structure interaction (FSI) method. Aerodynamic excitations were obtained by three-dimensional unsteady computational fluid dynamics (CFD) simulation with phase shifted periodic boundary conditions. The first two harmonic pressures were determined as the primary components of the excitation and applied to finite element (FE) model to conduct the computational structural dynamics (CSD) simulation. The computed results from the harmonic forced response analysis show good agreement with the predictions of Singh's advanced frequency evaluation (SAFE) diagram. Moreover, the mode superposition method used in FE simulation offers an efficient way to provide quantitative assessments of mode response levels and resonant strength.

Computer program determines vibration in three-dimensional space of hydraulic lines excited by forced displacements

NASA Technical Reports Server (NTRS)

Dodge, W. G.

1968-01-01

Computer program determines the forced vibration in three dimensional space of a multiple degree of freedom beam type structural system. Provision is made for the longitudinal axis of the analytical model to change orientation at any point along its length. This program is used by industries in which structural design dynamic analyses are performed.

Ion-ion dynamic structure factor of warm dense mixtures

DOE PAGES

Gill, N. M.; Heinonen, R. A.; Starrett, C. E.; ...

2015-06-25

In this study, the ion-ion dynamic structure factor of warm dense matter is determined using the recently developed pseudoatom molecular dynamics method [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. The method uses density functional theory to determine ion-ion pair interaction potentials that have no free parameters. These potentials are used in classical molecular dynamics simulations. This constitutes a computationally efficient and realistic model of dense plasmas. Comparison with recently published simulations of the ion-ion dynamic structure factor and sound speed of warm dense aluminum finds good to reasonable agreement. Using this method, we make predictions of the ion-ionmore » dynamical structure factor and sound speed of a warm dense mixture—equimolar carbon-hydrogen. This material is commonly used as an ablator in inertial confinement fusion capsules, and our results are amenable to direct experimental measurement.« less

A NASTRAN-based computer program for structural dynamic analysis of Horizontal Axis Wind Turbines

NASA Technical Reports Server (NTRS)

Lobitz, Don W.

1995-01-01

This paper describes a computer program developed for structural dynamic analysis of horizontal axis wind turbines (HAWT's). It is based on the finite element method through its reliance on NASTRAN for the development of mass, stiffness, and damping matrices of the tower end rotor, which are treated in NASTRAN as separate structures. The tower is modeled in a stationary frame and the rotor in one rotating at a constant angular velocity. The two structures are subsequently joined together (external to NASTRAN) using a time-dependent transformation consistent with the hub configuration. Aerodynamic loads are computed with an established flow model based on strip theory. Aeroelastic effects are included by incorporating the local velocity and twisting deformation of the blade in the load computation. The turbulent nature of the wind, both in space and time, is modeled by adding in stochastic wind increments. The resulting equations of motion are solved in the time domain using the implicit Newmark-Beta integrator. Preliminary comparisons with data from the Boeing/NASA MOD2 HAWT indicate that the code is capable of accurately and efficiently predicting the response of HAWT's driven by turbulent winds.

Fluid Structure Interaction in a Turbine Blade

NASA Technical Reports Server (NTRS)

Gorla, Rama S. R.

2004-01-01

An unsteady, three dimensional Navier-Stokes solution in rotating frame formulation for turbomachinery applications is presented. Casting the governing equations in a rotating frame enabled the freezing of grid motion and resulted in substantial savings in computer time. The turbine blade was computationally simulated and probabilistically evaluated in view of several uncertainties in the aerodynamic, structural, material and thermal variables that govern the turbine blade. The interconnection between the computational fluid dynamics code and finite element structural analysis code was necessary to couple the thermal profiles with the structural design. The stresses and their variations were evaluated at critical points on the Turbine blade. Cumulative distribution functions and sensitivity factors were computed for stress responses due to aerodynamic, geometric, mechanical and thermal random variables.

Computing the Ediz eccentric connectivity index of discrete dynamic structures

NASA Astrophysics Data System (ADS)

Wu, Hualong; Kamran Siddiqui, Muhammad; Zhao, Bo; Gan, Jianhou; Gao, Wei

2017-06-01

From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.

Dynamic Load-Balancing for Distributed Heterogeneous Computing of Parallel CFD Problems

NASA Technical Reports Server (NTRS)

Ecer, A.; Chien, Y. P.; Boenisch, T.; Akay, H. U.

2000-01-01

The developed methodology is aimed at improving the efficiency of executing block-structured algorithms on parallel, distributed, heterogeneous computers. The basic approach of these algorithms is to divide the flow domain into many sub- domains called blocks, and solve the governing equations over these blocks. Dynamic load balancing problem is defined as the efficient distribution of the blocks among the available processors over a period of several hours of computations. In environments with computers of different architecture, operating systems, CPU speed, memory size, load, and network speed, balancing the loads and managing the communication between processors becomes crucial. Load balancing software tools for mutually dependent parallel processes have been created to efficiently utilize an advanced computation environment and algorithms. These tools are dynamic in nature because of the chances in the computer environment during execution time. More recently, these tools were extended to a second operating system: NT. In this paper, the problems associated with this application will be discussed. Also, the developed algorithms were combined with the load sharing capability of LSF to efficiently utilize workstation clusters for parallel computing. Finally, results will be presented on running a NASA based code ADPAC to demonstrate the developed tools for dynamic load balancing.

Computational predictions of the new Gallium nitride nanoporous structures

NASA Astrophysics Data System (ADS)

Lien, Le Thi Hong; Tuoc, Vu Ngoc; Duong, Do Thi; Thu Huyen, Nguyen

2018-05-01

Nanoporous structural prediction is emerging area of research because of their advantages for a wide range of materials science and technology applications in opto-electronics, environment, sensors, shape-selective and bio-catalysis, to name just a few. We propose a computationally and technically feasible approach for predicting Gallium nitride nanoporous structures with hollows at the nano scale. The designed porous structures are studied with computations using the density functional tight binding (DFTB) and conventional density functional theory methods, revealing a variety of promising mechanical and electronic properties, which can potentially find future realistic applications. Their stability is discussed by means of the free energy computed within the lattice-dynamics approach. Our calculations also indicate that all the reported hollow structures are wide band gap semiconductors in the same fashion with their parent’s bulk stable phase. The electronic band structures of these nanoporous structures are finally examined in detail.

Expansion and improvements of the FORMA system for response and load analysis. Volume 1: Programming manual

NASA Technical Reports Server (NTRS)

Wohlen, R. L.

1976-01-01

Techniques are presented for the solution of structural dynamic systems on an electronic digital computer using FORMA (FORTRAN Matrix Analysis). FORMA is a library of subroutines coded in FORTRAN 4 for the efficient solution of structural dynamics problems. These subroutines are in the form of building blocks that can be put together to solve a large variety of structural dynamics problems. The obvious advantage of the building block approach is that programming and checkout time are limited to that required for putting the blocks together in the proper order.

Structural dynamics division research and technology accomplishments for fiscal year 1990 and plans for fiscal year 1991

NASA Technical Reports Server (NTRS)

Wynne, Eleanor C.

1991-01-01

The research accomplishments of the Structural Dynamics Division for F.Y. 1991 are presented. The work is discussed in terms of highlights of accomplishments during the past year and plans for the current year as they relate to 5-year plans and the objectives of each technical area. Included is research on unsteady aerodynamics, helicopter rotors, computational fluid dynamics, oscillations of leading edge flaps of a delta wing, and aircraft wing loads.

Summary of research in applied mathematics, numerical analysis, and computer sciences

NASA Technical Reports Server (NTRS)

1986-01-01

The major categories of current ICASE research programs addressed include: numerical methods, with particular emphasis on the development and analysis of basic numerical algorithms; control and parameter identification problems, with emphasis on effective numerical methods; computational problems in engineering and physical sciences, particularly fluid dynamics, acoustics, and structural analysis; and computer systems and software, especially vector and parallel computers.

Computational challenges of structure-based approaches applied to HIV.

PubMed

Forli, Stefano; Olson, Arthur J

2015-01-01

Here, we review some of the opportunities and challenges that we face in computational modeling of HIV therapeutic targets and structural biology, both in terms of methodology development and structure-based drug design (SBDD). Computational methods have provided fundamental support to HIV research since the initial structural studies, helping to unravel details of HIV biology. Computational models have proved to be a powerful tool to analyze and understand the impact of mutations and to overcome their structural and functional influence in drug resistance. With the availability of structural data, in silico experiments have been instrumental in exploiting and improving interactions between drugs and viral targets, such as HIV protease, reverse transcriptase, and integrase. Issues such as viral target dynamics and mutational variability, as well as the role of water and estimates of binding free energy in characterizing ligand interactions, are areas of active computational research. Ever-increasing computational resources and theoretical and algorithmic advances have played a significant role in progress to date, and we envision a continually expanding role for computational methods in our understanding of HIV biology and SBDD in the future.

Cluster Morphology-Polymer Dynamics Correlations in Sulfonated Polystyrene Melts: Computational Study

DOE PAGES

Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S.

2016-04-11

Reaching exceptionally long times up to 500 ns in equilibrium and nonequilibrium molecular dynamics simulations studies, we have attained a fundamental molecular understanding of the correlation of ionomer clusters structure and multiscale dynamics, providing new insight into one critical, long-standing challenge in ionic polymer physics. The cluster structure in melts of sulfonated polystyrene with Na + and Mg 2+ counterions are resolved and correlated with the dynamics on multiple length and time scales extracted from measurements of the dynamic structure factor and shear rheology. We find that as the morphology of the ionic clusters changes from ladderlike for Na +more » to disordered structures for Mg 2+, the dynamic structure factor is affected on the length scale corresponding to the ionic clusters. Lastly, rheology studies show that the viscosity for Mg 2+ melts is higher than for Na + ones for all shear rates, which is well correlated with the larger ionic clusters’ size for the Mg 2+ melts.« less

IMAT (Integrated Multidisciplinary Analysis Tool) user's guide for the VAX/VMS computer

NASA Technical Reports Server (NTRS)

Meissner, Frances T. (Editor)

1988-01-01

The Integrated Multidisciplinary Analysis Tool (IMAT) is a computer software system for the VAX/VMS computer developed at the Langley Research Center. IMAT provides researchers and analysts with an efficient capability to analyze satellite control systems influenced by structural dynamics. Using a menu-driven executive system, IMAT leads the user through the program options. IMAT links a relational database manager to commercial and in-house structural and controls analysis codes. This paper describes the IMAT software system and how to use it.

Structural anomaly and dynamic heterogeneity in cycloether/water binary mixtures: Signatures from composition dependent dynamic fluorescence measurements and computer simulations

NASA Astrophysics Data System (ADS)

Indra, Sandipa; Guchhait, Biswajit; Biswas, Ranjit

2016-03-01

We have performed steady state UV-visible absorption and time-resolved fluorescence measurements and computer simulations to explore the cosolvent mole fraction induced changes in structural and dynamical properties of water/dioxane (Diox) and water/tetrahydrofuran (THF) binary mixtures. Diox is a quadrupolar solvent whereas THF is a dipolar one although both are cyclic molecules and represent cycloethers. The focus here is on whether these cycloethers can induce stiffening and transition of water H-bond network structure and, if they do, whether such structural modification differentiates the chemical nature (dipolar or quadrupolar) of the cosolvent molecules. Composition dependent measured fluorescence lifetimes and rotation times of a dissolved dipolar solute (Coumarin 153, C153) suggest cycloether mole-fraction (XTHF/Diox) induced structural transition for both of these aqueous binary mixtures in the 0.1 ≤ XTHF/Diox ≤ 0.2 regime with no specific dependence on the chemical nature. Interestingly, absorption measurements reveal stiffening of water H-bond structure in the presence of both the cycloethers at a nearly equal mole-fraction, XTHF/Diox ˜ 0.05. Measurements near the critical solution temperature or concentration indicate no role for the solution criticality on the anomalous structural changes. Evidences for cycloether aggregation at very dilute concentrations have been found. Simulated radial distribution functions reflect abrupt changes in respective peak heights at those mixture compositions around which fluorescence measurements revealed structural transition. Simulated water coordination numbers (for a dissolved C153) and number of H-bonds also exhibit minima around these cosolvent concentrations. In addition, several dynamic heterogeneity parameters have been simulated for both the mixtures to explore the effects of structural transition and chemical nature of cosolvent on heterogeneous dynamics of these systems. Simulated four-point dynamic susceptibility suggests formation of clusters inducing local heterogeneity in the solution structure.

Gravitational field calculations on a dynamic lattice by distributed computing.

NASA Astrophysics Data System (ADS)

Mähönen, P.; Punkka, V.

A new method of calculating numerically time evolution of a gravitational field in general relativity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.

Gravitation Field Calculations on a Dynamic Lattice by Distributed Computing

NASA Astrophysics Data System (ADS)

Mähönen, Petri; Punkka, Veikko

A new method of calculating numerically time evolution of a gravitational field in General Relatity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.

Nano-confined water in the interlayers of hydrocalumite: Reorientational dynamics probed by neutron spectroscopy and molecular dynamics computer simulations

NASA Astrophysics Data System (ADS)

Kalinichev, A. G.; Faraone, A.; Udovic, T.; Kolesnikov, A. I.; de Souza, N. R.; Reinholdt, M. X.; Kirkpatrick, R.

2008-12-01

Layered double hydroxides (LDHs, anionic clays) represent excellent model systems for detailed molecular- level studies of the structure, dynamics, and energetics of nano-confined water in mineral interlayers and nano-pores, because LDH interlayers can have a well-defined structures and contain H2O molecules and a wide variety of anions in structurally well-defined positions and coordinations. [Ca2Al(OH)6]Cl·2H2O, also known as hydrocalumite or Friedel's salt, has a well- ordered Ca,Al distribution in the hydroxide layer and a very high degree of H2O,Cl ordering in the interlayer. It is also one of the only LDH phase for which a single crystal structure refinement is available. Thus, it is currently the best model compound for understanding the structure and dynamical behavior of interlayer and surface species in other, less-ordered, LDHs. We investigated the structural and dynamic behavior of water in the interlayers of hydrocalumite using inelastic (INS) and quasielastic (QENS) neutron scattering and molecular dynamics computer simulations. The comperehensive neutron scattering studies were performed for one fully hydrated and one dehydrated sample of hydrocalumite using several complementary instruments (HFBS, DCS and FANS at NCNR; HRMECS and QENS at IPNS) at temperatures above and below the previously discovered order-disorder interlayer phase transition. Together the experimental and molecular modeling results capture the important details of the dynamics of nano-confined water and the effects of the orientational ordering of H2O molecules above and below the phase transition. They provide otherwise unobtainable experimental information about the transformation of H2O librational and diffusional modes across the order-disorder phase transition and significantly add to our current understanding of the structure and dynamics of water in LDH phases based on the earlier NMR, IR, X-ray, and calorimetric measurements. The approach can now be extended to probe the dynamics of nano-confined and interfacial water in more disordered phases (LDH, clays, cement, etc.), for which much less initial structural information is available.

CSM solutions of rotating blade dynamics using integrating matrices

NASA Technical Reports Server (NTRS)

Lakin, William D.

1992-01-01

The dynamic behavior of flexible rotating beams continues to receive considerable research attention as it constitutes a fundamental problem in applied mechanics. Further, beams comprise parts of many rotating structures of engineering significance. A topic of particular interest at the present time involves the development of techniques for obtaining the behavior in both space and time of a rotor acted upon by a simple airload loading. Most current work on problems of this type use solution techniques based on normal modes. It is certainly true that normal modes cannot be disregarded, as knowledge of natural blade frequencies is always important. However, the present work has considered a computational structural mechanics (CSM) approach to rotor blade dynamics problems in which the physical properties of the rotor blade provide input for a direct numerical solution of the relevant boundary-and-initial-value problem. Analysis of the dynamics of a given rotor system may require solution of the governing equations over a long time interval corresponding to many revolutions of the loaded flexible blade. For this reason, most of the common techniques in computational mechanics, which treat the space-time behavior concurrently, cannot be applied to the rotor dynamics problem without a large expenditure of computational resources. By contrast, the integrating matrix technique of computational mechanics has the ability to consistently incorporate boundary conditions and 'remove' dependence on a space variable. For problems involving both space and time, this feature of the integrating matrix approach thus can generate a 'splitting' which forms the basis of an efficient CSM method for numerical solution of rotor dynamics problems.

A computer vision-based approach for structural displacement measurement

NASA Astrophysics Data System (ADS)

Ji, Yunfeng

2010-04-01

Along with the incessant advancement in optics, electronics and computer technologies during the last three decades, commercial digital video cameras have experienced a remarkable evolution, and can now be employed to measure complex motions of objects with sufficient accuracy, which render great assistance to structural displacement measurement in civil engineering. This paper proposes a computer vision-based approach for dynamic measurement of structures. One digital camera is used to capture image sequences of planar targets mounted on vibrating structures. The mathematical relationship between image plane and real space is established based on computer vision theory. Then, the structural dynamic displacement at the target locations can be quantified using point reconstruction rules. Compared with other tradition displacement measurement methods using sensors, such as accelerometers, linear-variable-differential-transducers (LVDTs) and global position system (GPS), the proposed approach gives the main advantages of great flexibility, a non-contact working mode and ease of increasing measurement points. To validate, four tests of sinusoidal motion of a point, free vibration of a cantilever beam, wind tunnel test of a cross-section bridge model, and field test of bridge displacement measurement, are performed. Results show that the proposed approach can attain excellent accuracy compared with the analytical ones or the measurements using conventional transducers, and proves to deliver an innovative and low cost solution to structural displacement measurement.

Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.

PubMed

Ziada, Sonia; Braka, Abdennour; Diharce, Julien; Aci-Sèche, Samia; Bonnet, Pascal

2018-01-01

Nobel Laureate Richard P. Feynman stated: "[…] everything that living things do can be understood in terms of jiggling and wiggling of atoms […]." The importance of computer simulations of macromolecules, which use classical mechanics principles to describe atom behavior, is widely acknowledged and nowadays, they are applied in many fields such as material sciences and drug discovery. With the increase of computing power, molecular dynamics simulations can be applied to understand biological mechanisms at realistic timescales. In this chapter, we share our computational experience providing a global view of two of the widely used enhanced molecular dynamics methods to study protein structure and dynamics through the description of their characteristics, limits and we provide some examples of their applications in drug design. We also discuss the appropriate choice of software and hardware. In a detailed practical procedure, we describe how to set up, run, and analyze two main molecular dynamics methods, the umbrella sampling (US) and the accelerated molecular dynamics (aMD) methods.

Evol and ProDy for bridging protein sequence evolution and structural dynamics

PubMed Central

Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R.; Bahar, Ivet

2014-01-01

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. Availability and implementation: ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/. Contact: bahar@pitt.edu PMID:24849577

Accurate detection of hierarchical communities in complex networks based on nonlinear dynamical evolution

NASA Astrophysics Data System (ADS)

Zhuo, Zhao; Cai, Shi-Min; Tang, Ming; Lai, Ying-Cheng

2018-04-01

One of the most challenging problems in network science is to accurately detect communities at distinct hierarchical scales. Most existing methods are based on structural analysis and manipulation, which are NP-hard. We articulate an alternative, dynamical evolution-based approach to the problem. The basic principle is to computationally implement a nonlinear dynamical process on all nodes in the network with a general coupling scheme, creating a networked dynamical system. Under a proper system setting and with an adjustable control parameter, the community structure of the network would "come out" or emerge naturally from the dynamical evolution of the system. As the control parameter is systematically varied, the community hierarchies at different scales can be revealed. As a concrete example of this general principle, we exploit clustered synchronization as a dynamical mechanism through which the hierarchical community structure can be uncovered. In particular, for quite arbitrary choices of the nonlinear nodal dynamics and coupling scheme, decreasing the coupling parameter from the global synchronization regime, in which the dynamical states of all nodes are perfectly synchronized, can lead to a weaker type of synchronization organized as clusters. We demonstrate the existence of optimal choices of the coupling parameter for which the synchronization clusters encode accurate information about the hierarchical community structure of the network. We test and validate our method using a standard class of benchmark modular networks with two distinct hierarchies of communities and a number of empirical networks arising from the real world. Our method is computationally extremely efficient, eliminating completely the NP-hard difficulty associated with previous methods. The basic principle of exploiting dynamical evolution to uncover hidden community organizations at different scales represents a "game-change" type of approach to addressing the problem of community detection in complex networks.

Teaching Ionic Solvation Structure with a Monte Carlo Liquid Simulation Program

ERIC Educational Resources Information Center

Serrano, Agostinho; Santos, Flavia M. T.; Greca, Ileana M.

2004-01-01

The use of molecular dynamics and Monte Carlo methods has provided efficient means to stimulate the behavior of molecular liquids and solutions. A Monte Carlo simulation program is used to compute the structure of liquid water and of water as a solvent to Na(super +), Cl(super -), and Ar on a personal computer to show that it is easily feasible to…

NASA/DOD Control/Structures Interaction Technology, 1986

NASA Technical Reports Server (NTRS)

Wright, Robert L. (Compiler)

1986-01-01

Control/structures interactions, deployment dynamics and system performance of large flexible spacecraft are discussed. Spacecraft active controls, deployable truss structures, deployable antennas, solar power systems for space stations, pointing control systems for space station gimballed payloads, computer-aided design for large space structures, and passive damping for flexible structures are among the topics covered.

Shock-driven fluid-structure interaction for civil design

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

Wood, Stephen L; Deiterding, Ralf

The multiphysics fluid-structure interaction simulation of shock-loaded structures requires the dynamic coupling of a shock-capturing flow solver to a solid mechanics solver for large deformations. The Virtual Test Facility combines a Cartesian embedded boundary approach with dynamic mesh adaptation in a generic software framework of flow solvers using hydrodynamic finite volume upwind schemes that are coupled to various explicit finite element solid dynamics solvers (Deiterding et al., 2006). This paper gives a brief overview of the computational approach and presents first simulations that utilize the general purpose solid dynamics code DYNA3D for complex 3D structures of interest in civil engineering.more » Results from simulations of a reinforced column, highway bridge, multistory building, and nuclear reactor building are presented.« less

A structure adapted multipole method for electrostatic interactions in protein dynamics

NASA Astrophysics Data System (ADS)

Niedermeier, Christoph; Tavan, Paul

1994-07-01

We present an algorithm for rapid approximate evaluation of electrostatic interactions in molecular dynamics simulations of proteins. Traditional algorithms require computational work of the order O(N2) for a system of N particles. Truncation methods which try to avoid that effort entail untolerably large errors in forces, energies and other observables. Hierarchical multipole expansion algorithms, which can account for the electrostatics to numerical accuracy, scale with O(N log N) or even with O(N) if they become augmented by a sophisticated scheme for summing up forces. To further reduce the computational effort we propose an algorithm that also uses a hierarchical multipole scheme but considers only the first two multipole moments (i.e., charges and dipoles). Our strategy is based on the consideration that numerical accuracy may not be necessary to reproduce protein dynamics with sufficient correctness. As opposed to previous methods, our scheme for hierarchical decomposition is adjusted to structural and dynamical features of the particular protein considered rather than chosen rigidly as a cubic grid. As compared to truncation methods we manage to reduce errors in the computation of electrostatic forces by a factor of 10 with only marginal additional effort.

Proteins with Novel Structure, Function and Dynamics

NASA Technical Reports Server (NTRS)

Pohorille, Andrew

2014-01-01

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Analysis of coherent dynamical processes through computer vision

NASA Astrophysics Data System (ADS)

Hack, M. J. Philipp

2016-11-01

Visualizations of turbulent boundary layers show an abundance of characteristic arc-shaped structures whose apparent similarity suggests a common origin in a coherent dynamical process. While the structures have been likened to the hairpin vortices observed in the late stages of transitional flow, a consistent description of the underlying mechanism has remained elusive. Detailed studies are complicated by the chaotic nature of turbulence which modulates each manifestation of the process and which renders the isolation of individual structures a challenging task. The present study applies methods from the field of computer vision to capture the time evolution of turbulent flow features and explore the associated physical mechanisms. The algorithm uses morphological operations to condense the structure of the turbulent flow field into a graph described by nodes and links. The low-dimensional geometric information is stored in a database and allows the identification and analysis of equivalent dynamical processes across multiple scales. The framework is not limited to turbulent boundary layers and can also be applied to different types of flows as well as problems from other fields of science.

STARS: An integrated general-purpose finite element structural, aeroelastic, and aeroservoelastic analysis computer program

NASA Technical Reports Server (NTRS)

Gupta, Kajal K.

1991-01-01

The details of an integrated general-purpose finite element structural analysis computer program which is also capable of solving complex multidisciplinary problems is presented. Thus, the SOLIDS module of the program possesses an extensive finite element library suitable for modeling most practical problems and is capable of solving statics, vibration, buckling, and dynamic response problems of complex structures, including spinning ones. The aerodynamic module, AERO, enables computation of unsteady aerodynamic forces for both subsonic and supersonic flow for subsequent flutter and divergence analysis of the structure. The associated aeroservoelastic analysis module, ASE, effects aero-structural-control stability analysis yielding frequency responses as well as damping characteristics of the structure. The program is written in standard FORTRAN to run on a wide variety of computers. Extensive graphics, preprocessing, and postprocessing routines are also available pertaining to a number of terminals.

A tutorial on dynamical systems concepts applied to Lagrangian transport in oceanic flows defined as finite time data sets: Theoretical and computational issues

NASA Astrophysics Data System (ADS)

Mancho, Ana M.; Small, Des; Wiggins, Stephen

2006-12-01

In the past 15 years the framework and ideas from dynamical systems theory have been applied to a variety of transport and mixing problems in oceanic flows. The motivation for this approach comes directly from advances in observational capabilities in oceanography (e.g., drifter deployments, remote sensing capabilities, satellite imagery, etc.) which reveal space-time structures that are highly suggestive of the structures one visualizes in the global, geometrical study of dynamical systems theory. In this tutorial, we motivate this approach by showing the relationship between fluid transport in two-dimensional time-periodic incompressible flows and the geometrical structures that exist for two-dimensional area-preserving maps, such as hyperbolic periodic orbits, their stable and unstable manifolds and KAM (Kolmogorov-Arnold-Moser) tori. This serves to set the stage for the attempt to “transfer” this approach to more realistic flows modelling the ocean. However, in order to accomplish this several difficulties must be overcome. The first difficulty that confronts us that any attempt to carry out a dynamical systems approach to transport requires us to obtain the appropriate “dynamical system”, which is the velocity field describing the fluid flow. In general, adequate model velocity fields are obtained by numerical solution of appropriate partial differential equations describing the dynamical evolution of the velocity field. Numerical solution of the partial differential equations can only be done for a finite time interval, and since the ocean is generally not time-periodic, this leads to a new type of dynamical system: a finite-time, aperiodically time-dependent velocity field defined as a data set on a space-time grid. The global, geometrical analysis of transport in such dynamical systems requires both new concepts and new analytical and computational tools, as well as the necessity to discard some of the standard ideas and results from dynamical systems theory. The purpose of this tutorial is to describe these new concepts and analytical tools first using simple dynamical systems where quantities can be computed exactly. We then discuss their computational implications and implementation in the context of a model geophysical flow: a turbulent wind-driven double-gyre in the quasigeostrophic approximation.

Symmetry structure in discrete models of biochemical systems: natural subsystems and the weak control hierarchy in a new model of computation driven by interactions.

PubMed

Nehaniv, Chrystopher L; Rhodes, John; Egri-Nagy, Attila; Dini, Paolo; Morris, Eric Rothstein; Horváth, Gábor; Karimi, Fariba; Schreckling, Daniel; Schilstra, Maria J

2015-07-28

Interaction computing is inspired by the observation that cell metabolic/regulatory systems construct order dynamically, through constrained interactions between their components and based on a wide range of possible inputs and environmental conditions. The goals of this work are to (i) identify and understand mathematically the natural subsystems and hierarchical relations in natural systems enabling this and (ii) use the resulting insights to define a new model of computation based on interactions that is useful for both biology and computation. The dynamical characteristics of the cellular pathways studied in systems biology relate, mathematically, to the computational characteristics of automata derived from them, and their internal symmetry structures to computational power. Finite discrete automata models of biological systems such as the lac operon, the Krebs cycle and p53-mdm2 genetic regulation constructed from systems biology models have canonically associated algebraic structures (their transformation semigroups). These contain permutation groups (local substructures exhibiting symmetry) that correspond to 'pools of reversibility'. These natural subsystems are related to one another in a hierarchical manner by the notion of 'weak control'. We present natural subsystems arising from several biological examples and their weak control hierarchies in detail. Finite simple non-Abelian groups are found in biological examples and can be harnessed to realize finitary universal computation. This allows ensembles of cells to achieve any desired finitary computational transformation, depending on external inputs, via suitably constrained interactions. Based on this, interaction machines that grow and change their structure recursively are introduced and applied, providing a natural model of computation driven by interactions.

Randomized Dynamic Mode Decomposition

NASA Astrophysics Data System (ADS)

Erichson, N. Benjamin; Brunton, Steven L.; Kutz, J. Nathan

2017-11-01

The dynamic mode decomposition (DMD) is an equation-free, data-driven matrix decomposition that is capable of providing accurate reconstructions of spatio-temporal coherent structures arising in dynamical systems. We present randomized algorithms to compute the near-optimal low-rank dynamic mode decomposition for massive datasets. Randomized algorithms are simple, accurate and able to ease the computational challenges arising with `big data'. Moreover, randomized algorithms are amenable to modern parallel and distributed computing. The idea is to derive a smaller matrix from the high-dimensional input data matrix using randomness as a computational strategy. Then, the dynamic modes and eigenvalues are accurately learned from this smaller representation of the data, whereby the approximation quality can be controlled via oversampling and power iterations. Here, we present randomized DMD algorithms that are categorized by how many passes the algorithm takes through the data. Specifically, the single-pass randomized DMD does not require data to be stored for subsequent passes. Thus, it is possible to approximately decompose massive fluid flows (stored out of core memory, or not stored at all) using single-pass algorithms, which is infeasible with traditional DMD algorithms.

An Approach for Dynamic Grids

NASA Technical Reports Server (NTRS)

Slater, John W.; Liou, Meng-Sing; Hindman, Richard G.

1994-01-01

An approach is presented for the generation of two-dimensional, structured, dynamic grids. The grid motion may be due to the motion of the boundaries of the computational domain or to the adaptation of the grid to the transient, physical solution. A time-dependent grid is computed through the time integration of the grid speeds which are computed from a system of grid speed equations. The grid speed equations are derived from the time-differentiation of the grid equations so as to ensure that the dynamic grid maintains the desired qualities of the static grid. The grid equations are the Euler-Lagrange equations derived from a variational statement for the grid. The dynamic grid method is demonstrated for a model problem involving boundary motion, an inviscid flow in a converging-diverging nozzle during startup, and a viscous flow over a flat plate with an impinging shock wave. It is shown that the approach is more accurate for transient flows than an approach in which the grid speeds are computed using a finite difference with respect to time of the grid. However, the approach requires significantly more computational effort.

Dynamic and fluid-structure interaction simulations of bioprosthetic heart valves using parametric design with T-splines and Fung-type material models

NASA Astrophysics Data System (ADS)

Hsu, Ming-Chen; Kamensky, David; Xu, Fei; Kiendl, Josef; Wang, Chenglong; Wu, Michael C. H.; Mineroff, Joshua; Reali, Alessandro; Bazilevs, Yuri; Sacks, Michael S.

2015-06-01

This paper builds on a recently developed immersogeometric fluid-structure interaction (FSI) methodology for bioprosthetic heart valve (BHV) modeling and simulation. It enhances the proposed framework in the areas of geometry design and constitutive modeling. With these enhancements, BHV FSI simulations may be performed with greater levels of automation, robustness and physical realism. In addition, the paper presents a comparison between FSI analysis and standalone structural dynamics simulation driven by prescribed transvalvular pressure, the latter being a more common modeling choice for this class of problems. The FSI computation achieved better physiological realism in predicting the valve leaflet deformation than its standalone structural dynamics counterpart.

Interplay of stereoelectronic and enviromental effects in tuning the structural and magnetic properties of a prototypical spin probe: further insights from a first principle dynamical approach.

PubMed

Pavone, Michele; Cimino, Paola; De Angelis, Filippo; Barone, Vincenzo

2006-04-05

The nitrogen isotropic hyperfine coupling constant (hcc) and the g tensor of a prototypical spin probe (di-tert-butyl nitroxide, DTBN) in aqueous solution have been investigated by means of an integrated computational approach including Car-Parrinello molecular dynamics and quantum mechanical calculations involving a discrete-continuum embedding. The quantitative agreement between computed and experimental parameters fully validates our integrated approach. Decoupling of the structural, dynamical, and environmental contributions acting onto the spectral observables allows an unbiased judgment of the role played by different effects in determining the overall experimental observables and highlights the importance of finite-temperature vibrational averaging. Together with their intrinsic interest, our results pave the route toward more reliable interpretations of EPR parameters of complex systems of biological and technological relevance.

Vortex Filaments in Grids for Scalable, Fine Smoke Simulation.

PubMed

Meng, Zhang; Weixin, Si; Yinling, Qian; Hanqiu, Sun; Jing, Qin; Heng, Pheng-Ann

2015-01-01

Vortex modeling can produce attractive visual effects of dynamic fluids, which are widely applicable for dynamic media, computer games, special effects, and virtual reality systems. However, it is challenging to effectively simulate intensive and fine detailed fluids such as smoke with fast increasing vortex filaments and smoke particles. The authors propose a novel vortex filaments in grids scheme in which the uniform grids dynamically bridge the vortex filaments and smoke particles for scalable, fine smoke simulation with macroscopic vortex structures. Using the vortex model, their approach supports the trade-off between simulation speed and scale of details. After computing the whole velocity, external control can be easily exerted on the embedded grid to guide the vortex-based smoke motion. The experimental results demonstrate the efficiency of using the proposed scheme for a visually plausible smoke simulation with macroscopic vortex structures.

Structured Overlapping Grid Simulations of Contra-rotating Open Rotor Noise

NASA Technical Reports Server (NTRS)

Housman, Jeffrey A.; Kiris, Cetin C.

2015-01-01

Computational simulations using structured overlapping grids with the Launch Ascent and Vehicle Aerodynamics (LAVA) solver framework are presented for predicting tonal noise generated by a contra-rotating open rotor (CROR) propulsion system. A coupled Computational Fluid Dynamics (CFD) and Computational AeroAcoustics (CAA) numerical approach is applied. Three-dimensional time-accurate hybrid Reynolds Averaged Navier-Stokes/Large Eddy Simulation (RANS/LES) CFD simulations are performed in the inertial frame, including dynamic moving grids, using a higher-order accurate finite difference discretization on structured overlapping grids. A higher-order accurate free-stream preserving metric discretization with discrete enforcement of the Geometric Conservation Law (GCL) on moving curvilinear grids is used to create an accurate, efficient, and stable numerical scheme. The aeroacoustic analysis is based on a permeable surface Ffowcs Williams-Hawkings (FW-H) approach, evaluated in the frequency domain. A time-step sensitivity study was performed using only the forward row of blades to determine an adequate time-step. The numerical approach is validated against existing wind tunnel measurements.

Digital system for structural dynamics simulation

NASA Technical Reports Server (NTRS)

Krauter, A. I.; Lagace, L. J.; Wojnar, M. K.; Glor, C.

1982-01-01

State-of-the-art digital hardware and software for the simulation of complex structural dynamic interactions, such as those which occur in rotating structures (engine systems). System were incorporated in a designed to use an array of processors in which the computation for each physical subelement or functional subsystem would be assigned to a single specific processor in the simulator. These node processors are microprogrammed bit-slice microcomputers which function autonomously and can communicate with each other and a central control minicomputer over parallel digital lines. Inter-processor nearest neighbor communications busses pass the constants which represent physical constraints and boundary conditions. The node processors are connected to the six nearest neighbor node processors to simulate the actual physical interface of real substructures. Computer generated finite element mesh and force models can be developed with the aid of the central control minicomputer. The control computer also oversees the animation of a graphics display system, disk-based mass storage along with the individual processing elements.

Force fields and scoring functions for carbohydrate simulation.

PubMed

Xiong, Xiuming; Chen, Zhaoqiang; Cossins, Benjamin P; Xu, Zhijian; Shao, Qiang; Ding, Kai; Zhu, Weiliang; Shi, Jiye

2015-01-12

Carbohydrate dynamics plays a vital role in many biological processes, but we are not currently able to probe this with experimental approaches. The highly flexible nature of carbohydrate structures differs in many aspects from other biomolecules, posing significant challenges for studies employing computational simulation. Over past decades, computational study of carbohydrates has been focused on the development of structure prediction methods, force field optimization, molecular dynamics simulation, and scoring functions for carbohydrate-protein interactions. Advances in carbohydrate force fields and scoring functions can be largely attributed to enhanced computational algorithms, application of quantum mechanics, and the increasing number of experimental structures determined by X-ray and NMR techniques. The conformational analysis of carbohydrates is challengeable and has gone into intensive study in elucidating the anomeric, the exo-anomeric, and the gauche effects. Here, we review the issues associated with carbohydrate force fields and scoring functions, which will have a broad application in the field of carbohydrate-based drug design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Automating the parallel processing of fluid and structural dynamics calculations

NASA Technical Reports Server (NTRS)

Arpasi, Dale J.; Cole, Gary L.

1987-01-01

The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilities to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.

Kinetic Monte Carlo and cellular particle dynamics simulations of multicellular systems

NASA Astrophysics Data System (ADS)

Flenner, Elijah; Janosi, Lorant; Barz, Bogdan; Neagu, Adrian; Forgacs, Gabor; Kosztin, Ioan

2012-03-01

Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Here we formulate two computer simulation methods: (1) a kinetic Monte Carlo (KMC) and (2) a cellular particle dynamics (CPD) method, which are capable of describing and predicting the shape evolution in time of three-dimensional multicellular systems during their biomechanical relaxation. Our work is motivated by the need of developing quantitative methods for optimizing postprinting structure formation in bioprinting-assisted tissue engineering. The KMC and CPD model parameters are determined and calibrated by using an original computational-theoretical-experimental framework applied to the fusion of two spherical cell aggregates. The two methods are used to predict the (1) formation of a toroidal structure through fusion of spherical aggregates and (2) cell sorting within an aggregate formed by two types of cells with different adhesivities.

Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins

PubMed Central

Han, Kyou-Hoon; Dokholyan, Nikolay V.; Tompa, Péter; Kalmár, Lajos; Hegedűs, Tamás

2014-01-01

Intrinsically disordered proteins (IDPs) lack a stable tertiary structure, but their short binding regions termed Pre-Structured Motifs (PreSMo) can form transient secondary structure elements in solution. Although disordered proteins are crucial in many biological processes and designing strategies to modulate their function is highly important, both experimental and computational tools to describe their conformational ensembles and the initial steps of folding are sparse. Here we report that discrete molecular dynamics (DMD) simulations combined with replica exchange (RX) method efficiently samples the conformational space and detects regions populating α-helical conformational states in disordered protein regions. While the available computational methods predict secondary structural propensities in IDPs based on the observation of protein-protein interactions, our ab initio method rests on physical principles of protein folding and dynamics. We show that RX-DMD predicts α-PreSMos with high confidence confirmed by comparison to experimental NMR data. Moreover, the method also can dissect α-PreSMos in close vicinity to each other and indicate helix stability. Importantly, simulations with disordered regions forming helices in X-ray structures of complexes indicate that a preformed helix is frequently the binding element itself, while in other cases it may have a role in initiating the binding process. Our results indicate that RX-DMD provides a breakthrough in the structural and dynamical characterization of disordered proteins by generating the structural ensembles of IDPs even when experimental data are not available. PMID:24763499

Structure and Dynamics of Ionic Block Copolymer Melts: Computational Study

DOE PAGES

Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora; ...

2017-09-06

Structure and dynamics of melts of copolymers with an ABCBA topology, where C is an ionizable block, have been studied by fully atomistic molecular dynamics (MD) simulations. Introducing an ionizable block for functionality adds a significant element to the coupled set of interactions that determine the structure and dynamics of the macromolecule. The polymer consists of a randomly sulfonated polystyrene C block tethered to a flexible poly(ethylene-r-propylene) bridge B and end-capped with poly(tert-butylstyrene) A. The chemical structure and topology of these polymers constitute a model for incorporation of ionic blocks within a framework that provides tactility and mechanical stability. Heremore » in this paper we resolve the structure and dynamics of a structured polymer on the nanoscale constrained by ionic clusters. We find that the melts form intertwined networks of the A and C blocks independent of the degree of sulfonation of the C block with no long-range order. The cluster cohesiveness and morphology affect both macroscopic translational motion and segmental dynamics of all the blocks.« less

Structure and Dynamics of Ionic Block Copolymer Melts: Computational Study

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

Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora

Structure and dynamics of melts of copolymers with an ABCBA topology, where C is an ionizable block, have been studied by fully atomistic molecular dynamics (MD) simulations. Introducing an ionizable block for functionality adds a significant element to the coupled set of interactions that determine the structure and dynamics of the macromolecule. The polymer consists of a randomly sulfonated polystyrene C block tethered to a flexible poly(ethylene-r-propylene) bridge B and end-capped with poly(tert-butylstyrene) A. The chemical structure and topology of these polymers constitute a model for incorporation of ionic blocks within a framework that provides tactility and mechanical stability. Heremore » in this paper we resolve the structure and dynamics of a structured polymer on the nanoscale constrained by ionic clusters. We find that the melts form intertwined networks of the A and C blocks independent of the degree of sulfonation of the C block with no long-range order. The cluster cohesiveness and morphology affect both macroscopic translational motion and segmental dynamics of all the blocks.« less

Orbital Maneuvering Engine Feed System Coupled Stability Investigation, Computer User's Manual

NASA Technical Reports Server (NTRS)

Schuman, M. D.; Fertig, K. W.; Hunting, J. K.; Kahn, D. R.

1975-01-01

An operating manual for the feed system coupled stability model was given, in partial fulfillment of a program designed to develop, verify, and document a digital computer model that can be used to analyze and predict engine/feed system coupled instabilities in pressure-fed storable propellant propulsion systems over a frequency range of 10 to 1,000 Hz. The first section describes the analytical approach to modelling the feed system hydrodynamics, combustion dynamics, chamber dynamics, and overall engineering model structure, and presents the governing equations in each of the technical areas. This is followed by the program user's guide, which is a complete description of the structure and operation of the computerized model. Last, appendices provide an alphabetized FORTRAN symbol table, detailed program logic diagrams, computer code listings, and sample case input and output data listings.

Coupled Aerodynamic and Structural Sensitivity Analysis of a High-Speed Civil Transport

NASA Technical Reports Server (NTRS)

Mason, B. H.; Walsh, J. L.

2001-01-01

An objective of the High Performance Computing and Communication Program at the NASA Langley Research Center is to demonstrate multidisciplinary shape and sizing optimization of a complete aerospace vehicle configuration by using high-fidelity, finite-element structural analysis and computational fluid dynamics aerodynamic analysis. In a previous study, a multi-disciplinary analysis system for a high-speed civil transport was formulated to integrate a set of existing discipline analysis codes, some of them computationally intensive, This paper is an extension of the previous study, in which the sensitivity analysis for the coupled aerodynamic and structural analysis problem is formulated and implemented. Uncoupled stress sensitivities computed with a constant load vector in a commercial finite element analysis code are compared to coupled aeroelastic sensitivities computed by finite differences. The computational expense of these sensitivity calculation methods is discussed.

Crowd computing: using competitive dynamics to develop and refine highly predictive models.

PubMed

Bentzien, Jörg; Muegge, Ingo; Hamner, Ben; Thompson, David C

2013-05-01

A recent application of a crowd computing platform to develop highly predictive in silico models for use in the drug discovery process is described. The platform, Kaggle™, exploits a competitive dynamic that results in model optimization as the competition unfolds. Here, this dynamic is described in detail and compared with more-conventional modeling strategies. The complete and full structure of the underlying dataset is disclosed and some thoughts as to the broader utility of such 'gamification' approaches to the field of modeling are offered. Copyright © 2013 Elsevier Ltd. All rights reserved.

Liquid li structure and dynamics: A comparison between OFDFT and second nearest-neighbor embedded-atom method

DOE PAGES

Chen, Mohan; Vella, Joseph R.; Panagiotopoulos, Athanassios Z.; ...

2015-04-08

The structure and dynamics of liquid lithium are studied using two simulation methods: orbital-free (OF) first-principles molecular dynamics (MD), which employs OF density functional theory (DFT), and classical MD utilizing a second nearest-neighbor embedded-atom method potential. The properties we studied include the dynamic structure factor, the self-diffusion coefficient, the dispersion relation, the viscosity, and the bond angle distribution function. Our simulation results were compared to available experimental data when possible. Each method has distinct advantages and disadvantages. For example, OFDFT gives better agreement with experimental dynamic structure factors, yet is more computationally demanding than classical simulations. Classical simulations can accessmore » a broader temperature range and longer time scales. The combination of first-principles and classical simulations is a powerful tool for studying properties of liquid lithium.« less

Time, space, and disorder in the expanding proteome universe.

PubMed

Minde, David-Paul; Dunker, A Keith; Lilley, Kathryn S

2017-04-01

Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins' dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (i) alternative sequences, (ii) alternative conformations, (iii) alternative interactions with a range of biomolecules, (iv) cellular localizations, (v) alternative behaviors in different cell types. While these aspects have traditionally been explored one protein at a time, we highlight recently emerging global approaches that accelerate comprehensive insights into these facets of the dynamic nature of protein structure. Computational tools that integrate and expand on multiple orthogonal data types promise to enable the transition from a disjointed list of static snapshots to a structurally explicit understanding of the dynamics of cellular mechanisms. © 2017 The Authors. Proteomics Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aeronautical engineering. A continuing bibliography with indexes

NASA Technical Reports Server (NTRS)

1982-01-01

This bibliography lists 326 reports, articles, and other documents introduced into the NASA scientific and technical information system in January 1982. Topics on aeronautical engineering and aerodynamics such as flight control systems, avionics, computer programs, computational fluid dynamics and composite structures are covered.

Research Reports: 1988 NASA/ASEE Summer Faculty Fellowship Program

NASA Technical Reports Server (NTRS)

Freeman, L. Michael (Editor); Chappell, Charles R. (Editor); Cothran, Ernestine K. (Editor); Karr, Gerald R. (Editor)

1988-01-01

The basic objectives are to further the professional knowledge of qualified engineering and science faculty members; to stimulate an exchange of ideas between participants and NASA: to enrich and refresh the research and teaching activities of the participants' institutions; and to contribute to the research objectives of the NASA centers. Topics addressed include: cryogenics; thunderstorm simulation; computer techniques; computer assisted instruction; system analysis weather forecasting; rocket engine design; crystal growth; control systems design; turbine pumps for the Space Shuttle Main engine; electron mobility; heat transfer predictions; rotor dynamics; mathematical models; computational fluid dynamics; and structural analysis.

Ascent Aerodynamic Pressure Distributions on WB001

NASA Technical Reports Server (NTRS)

Vu, B.; Ruf, J.; Canabal, F.; Brunty, J.

1996-01-01

To support the reusable launch vehicle concept study, the aerodynamic data and surface pressure for WB001 were predicted using three computational fluid dynamic (CFD) codes at several flow conditions between code to code and code to aerodynamic database as well as available experimental data. A set of particular solutions have been selected and recommended for use in preliminary conceptual designs. These computational fluid dynamic (CFD) results have also been provided to the structure group for wing loading analysis.

A new physical model with multilayer architecture for facial expression animation using dynamic adaptive mesh.

PubMed

Zhang, Yu; Prakash, Edmond C; Sung, Eric

2004-01-01

This paper presents a new physically-based 3D facial model based on anatomical knowledge which provides high fidelity for facial expression animation while optimizing the computation. Our facial model has a multilayer biomechanical structure, incorporating a physically-based approximation to facial skin tissue, a set of anatomically-motivated facial muscle actuators, and underlying skull structure. In contrast to existing mass-spring-damper (MSD) facial models, our dynamic skin model uses the nonlinear springs to directly simulate the nonlinear visco-elastic behavior of soft tissue and a new kind of edge repulsion spring is developed to prevent collapse of the skin model. Different types of muscle models have been developed to simulate distribution of the muscle force applied on the skin due to muscle contraction. The presence of the skull advantageously constrain the skin movements, resulting in more accurate facial deformation and also guides the interactive placement of facial muscles. The governing dynamics are computed using a local semi-implicit ODE solver. In the dynamic simulation, an adaptive refinement automatically adapts the local resolution at which potential inaccuracies are detected depending on local deformation. The method, in effect, ensures the required speedup by concentrating computational time only where needed while ensuring realistic behavior within a predefined error threshold. This mechanism allows more pleasing animation results to be produced at a reduced computational cost.

Dynamic Load Predictions for Launchers Using Extra-Large Eddy Simulations X-Les

NASA Astrophysics Data System (ADS)

Maseland, J. E. J.; Soemarwoto, B. I.; Kok, J. C.

2005-02-01

Flow-induced unsteady loads can have a strong impact on performance and flight characteristics of aerospace vehicles and therefore play a crucial role in their design and operation. Complementary to costly flight tests and delicate wind-tunnel experiments, unsteady loads can be calculated using time-accurate Computational Fluid Dynamics. A capability to accurately predict the dynamic loads on aerospace structures at flight Reynolds numbers can be of great value for the design and analysis of aerospace vehicles. Advanced space launchers are subject to dynamic loads in the base region during the ascent to space. In particular the engine and nozzle experience aerodynamic pressure fluctuations resulting from massive flow separations. Understanding these phenomena is essential for performance enhancements for future launchers which operate a larger nozzle. A new hybrid RANS-LES turbulence modelling approach termed eXtra-Large Eddy Simulations (X-LES) holds the promise to capture the flow structures associated with massive separations and enables the prediction of the broad-band spectrum of dynamic loads. This type of method has become a focal point, reducing the cost of full LES, driven by the demand for their applicability in an industrial environment. The industrial feasibility of X-LES simulations is demonstrated by computing the unsteady aerodynamic loads on the main-engine nozzle of a generic space launcher configuration. The potential to calculate the dynamic loads is qualitatively assessed for transonic flow conditions in a comparison to wind-tunnel experiments. In terms of turn-around-times, X-LES computations are already feasible within the time-frames of the development process to support the structural design. Key words: massive separated flows; buffet loads; nozzle vibrations; space launchers; time-accurate CFD; composite RANS-LES formulation.

Data-driven sensor placement from coherent fluid structures

NASA Astrophysics Data System (ADS)

Manohar, Krithika; Kaiser, Eurika; Brunton, Bingni W.; Kutz, J. Nathan; Brunton, Steven L.

2017-11-01

Optimal sensor placement is a central challenge in the prediction, estimation and control of fluid flows. We reinterpret sensor placement as optimizing discrete samples of coherent fluid structures for full state reconstruction. This permits a drastic reduction in the number of sensors required for faithful reconstruction, since complex fluid interactions can often be described by a small number of coherent structures. Our work optimizes point sensors using the pivoted matrix QR factorization to sample coherent structures directly computed from flow data. We apply this sampling technique in conjunction with various data-driven modal identification methods, including the proper orthogonal decomposition (POD) and dynamic mode decomposition (DMD). In contrast to POD-based sensors, DMD demonstrably enables the optimization of sensors for prediction in systems exhibiting multiple scales of dynamics. Finally, reconstruction accuracy from pivot sensors is shown to be competitive with sensors obtained using traditional computationally prohibitive optimization methods.

Structure and dynamics of gas phase ions: Interplay between experiments and computations in IRMPD spectroscopy

NASA Astrophysics Data System (ADS)

Coletti, Cecilia; Corinti, Davide; Paciotti, Roberto; Re, Nazzareno; Crestoni, Maria Elisa; Fornarini, Simonetta

2017-11-01

The investigation of the molecular structure and dynamics of ions in gas phase is an item of increasing interest, due the role such species play in many areas of chemistry and physics, not to mention that they often represent elusive intermediates in more complex reaction mechanisms. Infrared Multiple Photon Dissociation spectroscopy is today one of the most advanced technique to this purpose, because of its high sensitivity to even small structure changes. The interpretation of IRMPD spectra strongly relies on high level quantum mechanical computations, so that a close interplay is needed for a detailed understanding of structure and kinetics properties which can be gathered from the many applications of this powerful technique. Recent advances in experiment and theory in this field are here illustrated, with emphasis on recent progresses for the elucidation of the mechanism of action of cisplatin, one of the most widely used anticancer drugs.

Sub-domain decomposition methods and computational controls for multibody dynamical systems. [of spacecraft structures

NASA Technical Reports Server (NTRS)

Menon, R. G.; Kurdila, A. J.

1992-01-01

This paper presents a concurrent methodology to simulate the dynamics of flexible multibody systems with a large number of degrees of freedom. A general class of open-loop structures is treated and a redundant coordinate formulation is adopted. A range space method is used in which the constraint forces are calculated using a preconditioned conjugate gradient method. By using a preconditioner motivated by the regular ordering of the directed graph of the structures, it is shown that the method is order N in the total number of coordinates of the system. The overall formulation has the advantage that it permits fine parallelization and does not rely on system topology to induce concurrency. It can be efficiently implemented on the present generation of parallel computers with a large number of processors. Validation of the method is presented via numerical simulations of space structures incorporating large number of flexible degrees of freedom.

Experimental and Computational Study of Sonic and Supersonic Jet Plumes

NASA Technical Reports Server (NTRS)

Venkatapathy, E.; Naughton, J. W.; Fletcher, D. G.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock-shear-layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

PubMed

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

Applying Parallel Adaptive Methods with GeoFEST/PYRAMID to Simulate Earth Surface Crustal Dynamics

NASA Technical Reports Server (NTRS)

Norton, Charles D.; Lyzenga, Greg; Parker, Jay; Glasscoe, Margaret; Donnellan, Andrea; Li, Peggy

2006-01-01

This viewgraph presentation reviews the use Adaptive Mesh Refinement (AMR) in simulating the Crustal Dynamics of Earth's Surface. AMR simultaneously improves solution quality, time to solution, and computer memory requirements when compared to generating/running on a globally fine mesh. The use of AMR in simulating the dynamics of the Earth's Surface is spurred by future proposed NASA missions, such as InSAR for Earth surface deformation and other measurements. These missions will require support for large-scale adaptive numerical methods using AMR to model observations. AMR was chosen because it has been successful in computation fluid dynamics for predictive simulation of complex flows around complex structures.

Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces

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

R. James Kirkpatrick; Andrey G. Kalinichev

2008-11-25

Research supported by this grant focuses on molecular scale understanding of central issues related to the structure and dynamics of geochemically important fluids, fluid-mineral interfaces, and confined fluids using computational modeling and experimental methods. Molecular scale knowledge about fluid structure and dynamics, how these are affected by mineral surfaces and molecular-scale (nano-) confinement, and how water molecules and dissolved species interact with surfaces is essential to understanding the fundamental chemistry of a wide range of low-temperature geochemical processes, including sorption and geochemical transport. Our principal efforts are devoted to continued development of relevant computational approaches, application of these approaches tomore » important geochemical questions, relevant NMR and other experimental studies, and application of computational modeling methods to understanding the experimental results. The combination of computational modeling and experimental approaches is proving highly effective in addressing otherwise intractable problems. In 2006-2007 we have significantly advanced in new, highly promising research directions along with completion of on-going projects and final publication of work completed in previous years. New computational directions are focusing on modeling proton exchange reactions in aqueous solutions using ab initio molecular dynamics (AIMD), metadynamics (MTD), and empirical valence bond (EVB) approaches. Proton exchange is critical to understanding the structure, dynamics, and reactivity at mineral-water interfaces and for oxy-ions in solution, but has traditionally been difficult to model with molecular dynamics (MD). Our ultimate objective is to develop this capability, because MD is much less computationally demanding than quantum-chemical approaches. We have also extended our previous MD simulations of metal binding to natural organic matter (NOM) to a much longer time scale (up to 10 ns) for significantly larger systems. These calculations have allowed us, for the first time, to study the effects of metal cations with different charges and charge density on the NOM aggregation in aqueous solutions. Other computational work has looked at the longer-time-scale dynamical behavior of aqueous species at mineral-water interfaces investigated simultaneously by NMR spectroscopy. Our experimental NMR studies have focused on understanding the structure and dynamics of water and dissolved species at mineral-water interfaces and in two-dimensional nano-confinement within clay interlayers. Combined NMR and MD study of H2O, Na+, and Cl- interactions with the surface of quartz has direct implications regarding interpretation of sum frequency vibrational spectroscopic experiments for this phase and will be an important reference for future studies. We also used NMR to examine the behavior of K+ and H2O in the interlayer and at the surfaces of the clay minerals hectorite and illite-rich illite-smectite. This the first time K+ dynamics has been characterized spectroscopically in geochemical systems. Preliminary experiments were also performed to evaluate the potential of 75As NMR as a probe of arsenic geochemical behavior. The 75As NMR study used advanced signal enhancement methods, introduced a new data acquisition approach to minimize the time investment in ultra-wide-line NMR experiments, and provides the first evidence of a strong relationship between the chemical shift and structural parameters for this experimentally challenging nucleus. We have also initiated a series of inelastic and quasi-elastic neutron scattering measurements of water dynamics in the interlayers of clays and layered double hydroxides. The objective of these experiments is to probe the correlations of water molecular motions in confined spaces over the scale of times and distances most directly comparable to our MD simulations and on a time scale different than that probed by NMR. This work is being done in collaboration with Drs. C.-K. Loong, N. de Souza, and A.I. Kolesnikov at the Intense Pulsed Neutron Source facility of the Argonne National Lab, and Dr. A. Faraone at the NIST Center for Neutron Research. A manuscript reporting the first results of these experiments, which are highly complimentary to our previous NMR, X-ray, and infra-red results for these phases, is currently in preparation. In total, in 2006-2007 our work has resulted in the publication of 14 peer-reviewed research papers. We also devoted considerable effort to making our work known to a wide range of researchers, as indicated by the 24 contributed abstracts and 14 invited presentations.« less

Smart algorithms and adaptive methods in computational fluid dynamics

NASA Astrophysics Data System (ADS)

Tinsley Oden, J.

1989-05-01

A review is presented of the use of smart algorithms which employ adaptive methods in processing large amounts of data in computational fluid dynamics (CFD). Smart algorithms use a rationally based set of criteria for automatic decision making in an attempt to produce optimal simulations of complex fluid dynamics problems. The information needed to make these decisions is not known beforehand and evolves in structure and form during the numerical solution of flow problems. Once the code makes a decision based on the available data, the structure of the data may change, and criteria may be reapplied in order to direct the analysis toward an acceptable end. Intelligent decisions are made by processing vast amounts of data that evolve unpredictably during the calculation. The basic components of adaptive methods and their application to complex problems of fluid dynamics are reviewed. The basic components of adaptive methods are: (1) data structures, that is what approaches are available for modifying data structures of an approximation so as to reduce errors; (2) error estimation, that is what techniques exist for estimating error evolution in a CFD calculation; and (3) solvers, what algorithms are available which can function in changing meshes. Numerical examples which demonstrate the viability of these approaches are presented.

Insights from molecular dynamics simulations for computational protein design.

PubMed

Childers, Matthew Carter; Daggett, Valerie

2017-02-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

Insights from molecular dynamics simulations for computational protein design

PubMed Central

Childers, Matthew Carter; Daggett, Valerie

2017-01-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

Dynamical structure factor of the J1-J2 Heisenberg model in one dimension: The variational Monte Carlo approach

NASA Astrophysics Data System (ADS)

Ferrari, Francesco; Parola, Alberto; Sorella, Sandro; Becca, Federico

2018-06-01

The dynamical spin structure factor is computed within a variational framework to study the one-dimensional J1-J2 Heisenberg model. Starting from Gutzwiller-projected fermionic wave functions, the low-energy spectrum is constructed from two-spinon excitations. The direct comparison with Lanczos calculations on small clusters demonstrates the excellent description of both gapless and gapped (dimerized) phases, including incommensurate structures for J2/J1>0.5 . Calculations on large clusters show how the intensity evolves when increasing the frustrating ratio and give an unprecedented accurate characterization of the dynamical properties of (nonintegrable) frustrated spin models.

Structural dynamics analysis

NASA Technical Reports Server (NTRS)

Housner, J. M.; Anderson, M.; Belvin, W.; Horner, G.

1985-01-01

Dynamic analysis of large space antenna systems must treat the deployment as well as vibration and control of the deployed antenna. Candidate computer programs for deployment dynamics, and issues and needs for future program developments are reviewed. Some results for mast and hoop deployment are also presented. Modeling of complex antenna geometry with conventional finite element methods and with repetitive exact elements is considered. Analytical comparisons with experimental results for a 15 meter hoop/column antenna revealed the importance of accurate structural properties including nonlinear joints. Slackening of cables in this antenna is also a consideration. The technology of designing actively damped structures through analytical optimization is discussed and results are presented.

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC year 1 quarter 4 progress report.

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

Lottes, S.A.; Kulak, R.F.; Bojanowski, C.

2011-12-09

The computational fluid dynamics (CFD) and computational structural mechanics (CSM) focus areas at Argonne's Transportation Research and Analysis Computing Center (TRACC) initiated a project to support and compliment the experimental programs at the Turner-Fairbank Highway Research Center (TFHRC) with high performance computing based analysis capabilities in August 2010. The project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at TFHRC for a period of five years, beginning in October 2010. Themore » analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water effects on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to assess them for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, CFD analysis of the operation of the wind tunnel in the TFCHR wind engineering laboratory, vehicle stability under high wind loading, and the use of electromagnetic shock absorbers to improve vehicle stability under high wind conditions. This quarterly report documents technical progress on the project tasks for the period of July through September 2011.« less

Static and Dynamic Model Update of an Inflatable/Rigidizable Torus Structure

NASA Technical Reports Server (NTRS)

Horta, Lucas G.; Reaves, mercedes C.

2006-01-01

The present work addresses the development of an experimental and computational procedure for validating finite element models. A torus structure, part of an inflatable/rigidizable Hexapod, is used to demonstrate the approach. Because of fabrication, materials, and geometric uncertainties, a statistical approach combined with optimization is used to modify key model parameters. Static test results are used to update stiffness parameters and dynamic test results are used to update the mass distribution. Updated parameters are computed using gradient and non-gradient based optimization algorithms. Results show significant improvements in model predictions after parameters are updated. Lessons learned in the areas of test procedures, modeling approaches, and uncertainties quantification are presented.

Orbital maneuvering engine feed system coupled stability investigation

NASA Technical Reports Server (NTRS)

Kahn, D. R.; Schuman, M. D.; Hunting, J. K.; Fertig, K. W.

1975-01-01

A digital computer model used to analyze and predict engine feed system coupled instabilities over a frequency range of 10 to 1000 Hz was developed and verified. The analytical approach to modeling the feed system hydrodynamics, combustion dynamics, chamber dynamics, and overall engineering model structure is described and the governing equations in each of the technical areas are presented. This is followed by a description of the generalized computer model, including formulation of the discrete subprograms and their integration into an overall engineering model structure. The operation and capabilities of the engineering model were verified by comparing the model's theoretical predictions with experimental data from an OMS-type engine with a known feed system/engine chugging history.

Rotor Airloads Prediction Using Unstructured Meshes and Loose CFD/CSD Coupling

NASA Technical Reports Server (NTRS)

Biedron, Robert T.; Lee-Rausch, Elizabeth M.

2008-01-01

The FUN3D unsteady Reynolds-averaged Navier-Stokes solver for unstructured grids has been modified to allow prediction of trimmed rotorcraft airloads. The trim of the rotorcraft and the aeroelastic deformation of the rotor blades are accounted for via loose coupling with the CAMRAD II rotorcraft computational structural dynamics code. The set of codes is used to analyze the HART-II Baseline, Minimum Noise and Minimum Vibration test conditions. The loose coupling approach is found to be stable and convergent for the cases considered. Comparison of the resulting airloads and structural deformations with experimentally measured data is presented. The effect of grid resolution and temporal accuracy is examined. Rotorcraft airloads prediction presents a very substantial challenge for Computational Fluid Dynamics (CFD). Not only must the unsteady nature of the flow be accurately modeled, but since most rotorcraft blades are not structurally stiff, an accurate simulation must account for the blade structural dynamics. In addition, trim of the rotorcraft to desired thrust and moment targets depends on both aerodynamic loads and structural deformation, and vice versa. Further, interaction of the fuselage with the rotor flow field can be important, so that relative motion between the blades and the fuselage must be accommodated. Thus a complete simulation requires coupled aerodynamics, structures and trim, with the ability to model geometrically complex configurations. NASA has recently initiated a Subsonic Rotary Wing (SRW) Project under the overall Fundamental Aeronautics Program. Within the context of SRW are efforts aimed at furthering the state of the art of high-fidelity rotorcraft flow simulations, using both structured and unstructured meshes. Structured-mesh solvers have an advantage in computation speed, but even though remarkably complex configurations may be accommodated using the overset grid approach, generation of complex structured-mesh systems can require months to set up. As a result, many rotorcraft simulations using structured-grid CFD neglect the fuselage. On the other hand, unstructured-mesh solvers are easily able to handle complex geometries, but suffer from slower execution speed. However, advances in both computer hardware and CFD algorithms have made previously state-of-the-art computations routine for unstructured-mesh solvers, so that rotorcraft simulations using unstructured grids are now viable. The aim of the present work is to develop a first principles rotorcraft simulation tool based on an unstructured CFD solver.

Refinement of the experimental dynamic structure factor for liquid para-hydrogen and ortho-deuterium using semi-classical quantum simulation.

PubMed

Smith, Kyle K G; Poulsen, Jens Aage; Cunsolo, A; Rossky, Peter J

2014-01-21

The dynamic structure factor of liquid para-hydrogen and ortho-deuterium in corresponding thermodynamic states (T = 20.0 K, n = 21.24 nm(-3)) and (T = 23.0 K, n = 24.61 nm(-3)), respectively, has been computed by both the Feynman-Kleinert linearized path-integral (FK-LPI) and Ring-Polymer Molecular Dynamics (RPMD) methods and compared with Inelastic X Ray Scattering spectra. The combined use of computational and experimental methods enabled us to reduce experimental uncertainties in the determination of the true sample spectrum. Furthermore, the refined experimental spectrum of para-hydrogen and ortho-deuterium is consistently reproduced by both FK-LPI and RPMD results at momentum transfers lower than 12.8 nm(-1). At larger momentum transfers the FK-LPI results agree with experiment much better for ortho-deuterium than for para-hydrogen. More specifically we found that for k ∼ 20.0 nm(-1) para-hydrogen provides a test case for improved approximations to quantum dynamics.

Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models

NASA Astrophysics Data System (ADS)

Dodani, Sheel C.; Kiss, Gert; Cahn, Jackson K. B.; Su, Ye; Pande, Vijay S.; Arnold, Frances H.

2016-05-01

The dynamic motions of protein structural elements, particularly flexible loops, are intimately linked with diverse aspects of enzyme catalysis. Engineering of these loop regions can alter protein stability, substrate binding and even dramatically impact enzyme function. When these flexible regions are unresolvable structurally, computational reconstruction in combination with large-scale molecular dynamics simulations can be used to guide the engineering strategy. Here we present a collaborative approach that consists of both experiment and computation and led to the discovery of a single mutation in the F/G loop of the nitrating cytochrome P450 TxtE that simultaneously controls loop dynamics and completely shifts the enzyme's regioselectivity from the C4 to the C5 position of L-tryptophan. Furthermore, we find that this loop mutation is naturally present in a subset of homologous nitrating P450s and confirm that these uncharacterized enzymes exclusively produce 5-nitro-L-tryptophan, a previously unknown biosynthetic intermediate.

Exploring the Influence of Dynamic Disorder on Excitons in Solid Pentacene

NASA Astrophysics Data System (ADS)

Wang, Zhiping; Sharifzadeh, Sahar; Doak, Peter; Lu, Zhenfei; Neaton, Jeffrey

2014-03-01

A complete understanding of the spectroscopic and charge transport properties of organic semiconductors requires knowledge of the role of thermal fluctuations and dynamic disorder. We present a first-principles theoretical study aimed at understanding the degree to which dynamic disorder at room temperature results in energy level broadening and excited-state localization within bulk crystalline pentacene. Ab initio molecular dynamics simulations are well-equilibrated for 7-9 ps and tens of thousands of structural snapshots, taken at 0.5 fs intervals, provide input for many-body perturbation theory within the GW approximation and Bethe-Salpeter equation (BSE) approach. The GW-corrected density of states, including thousands of snapshots, indicates that thermal fluctuations significantly broaden the valence and conduction states by >0.2 eV. Additionally, we investigate the nature and energy of the lowest energy singlet and triplet excitons, computed for a set of uncorrelated and energetically preferred structures. This work supported by DOE; computational resources provided by NERSC.

Theoretical and software considerations for nonlinear dynamic analysis

NASA Technical Reports Server (NTRS)

Schmidt, R. J.; Dodds, R. H., Jr.

1983-01-01

In the finite element method for structural analysis, it is generally necessary to discretize the structural model into a very large number of elements to accurately evaluate displacements, strains, and stresses. As the complexity of the model increases, the number of degrees of freedom can easily exceed the capacity of present-day software system. Improvements of structural analysis software including more efficient use of existing hardware and improved structural modeling techniques are discussed. One modeling technique that is used successfully in static linear and nonlinear analysis is multilevel substructuring. This research extends the use of multilevel substructure modeling to include dynamic analysis and defines the requirements for a general purpose software system capable of efficient nonlinear dynamic analysis. The multilevel substructuring technique is presented, the analytical formulations and computational procedures for dynamic analysis and nonlinear mechanics are reviewed, and an approach to the design and implementation of a general purpose structural software system is presented.

Global Dynamics of Proteins: Bridging Between Structure and Function

PubMed Central

Bahar, Ivet; Lezon, Timothy R.; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold. PMID:20192781

Global dynamics of proteins: bridging between structure and function.

PubMed

Bahar, Ivet; Lezon, Timothy R; Yang, Lee-Wei; Eyal, Eran

2010-01-01

Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold.

Influence of the rotor-stator interaction on the dynamic stresses of Francis runners

NASA Astrophysics Data System (ADS)

Guillaume, R.; Deniau, J. L.; Scolaro, D.; Colombet, C.

2012-11-01

Thanks to advances in computing capabilities and Computational Fluid Dynamics (CFD) techniques, it is now possible to calculate realistic unsteady pressure fields in Francis turbines. This paper will explain methods to calculate the structural loads and the dynamic behaviour in order to optimize the turbine design and maximize its reliability and lifetime. Depending on the operating conditions of a Francis turbine, different hydraulic phenomena may impact the mechanical behaviour of the structure. According to their nature, these highly variable phenomena should be treated differently and specifically in order to estimate the potential risks arising on submerged structures, in particular the runner. The operating condition studied thereafter is the point at maximum power with the maximum head. Under this condition, the runner is excited by only one dynamic phenomenon named the Rotor-Stator Interaction (RSI). The origin of the phenomenon is located on the radial gap of the turbine and is the source of pressure fluctuations. A fluid-structure analysis is performed to observe the influence of that dynamic pressure field on the runner behaviour. The first part of the paper deals with the unsteady fluid computation. The RSI phenomenon is totally unsteady so the fluid simulation must take into account the entire machine and its rotation movement, in order to obtain a dynamic pressure field. In the second part of the paper, a method suitable for the RSI study is developed. It is known that the fluctuating pressure in this gap can be described as a sum of spatial components. By evaluating these components in the CFD results and on the scale model, it is possible to assess the relevance of the numerical results on the whole runner. After this step, the numerical pressure field can be used as the dynamic load of the structure. The final part of the paper presentsthe mechanical finite element calculations. A modal analysis of the runner in water and a harmonic analysis of its dynamic behaviour using the CFD results are carried out. These calculations will show that the RSI on the medium head Francis runner does not create damage on the runner even if the natural frequencies are closed to the wicket gates passing frequency. The numerical results are reinforced by experimental observations done on runner prototypes showing that the wicket gates passing frequency does not have significant influence on low and medium head Francis runner behaviour.

Taking the plunge: chemical reaction dynamics in liquids.

PubMed

Orr-Ewing, Andrew J

2017-12-11

The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.

Computational Models of Relational Processes in Cognitive Development

ERIC Educational Resources Information Center

Halford, Graeme S.; Andrews, Glenda; Wilson, William H.; Phillips, Steven

2012-01-01

Acquisition of relational knowledge is a core process in cognitive development. Relational knowledge is dynamic and flexible, entails structure-consistent mappings between representations, has properties of compositionality and systematicity, and depends on binding in working memory. We review three types of computational models relevant to…

Nature as a network of morphological infocomputational processes for cognitive agents

NASA Astrophysics Data System (ADS)

Dodig-Crnkovic, Gordana

2017-01-01

This paper presents a view of nature as a network of infocomputational agents organized in a dynamical hierarchy of levels. It provides a framework for unification of currently disparate understandings of natural, formal, technical, behavioral and social phenomena based on information as a structure, differences in one system that cause the differences in another system, and computation as its dynamics, i.e. physical process of morphological change in the informational structure. We address some of the frequent misunderstandings regarding the natural/morphological computational models and their relationships to physical systems, especially cognitive systems such as living beings. Natural morphological infocomputation as a conceptual framework necessitates generalization of models of computation beyond the traditional Turing machine model presenting symbol manipulation, and requires agent-based concurrent resource-sensitive models of computation in order to be able to cover the whole range of phenomena from physics to cognition. The central role of agency, particularly material vs. cognitive agency is highlighted.

Real-time path planning in dynamic virtual environments using multiagent navigation graphs.

PubMed

Sud, Avneesh; Andersen, Erik; Curtis, Sean; Lin, Ming C; Manocha, Dinesh

2008-01-01

We present a novel approach for efficient path planning and navigation of multiple virtual agents in complex dynamic scenes. We introduce a new data structure, Multi-agent Navigation Graph (MaNG), which is constructed using first- and second-order Voronoi diagrams. The MaNG is used to perform route planning and proximity computations for each agent in real time. Moreover, we use the path information and proximity relationships for local dynamics computation of each agent by extending a social force model [Helbing05]. We compute the MaNG using graphics hardware and present culling techniques to accelerate the computation. We also address undersampling issues and present techniques to improve the accuracy of our algorithm. Our algorithm is used for real-time multi-agent planning in pursuit-evasion, terrain exploration and crowd simulation scenarios consisting of hundreds of moving agents, each with a distinct goal.

Anticipatory Neurofuzzy Control

NASA Technical Reports Server (NTRS)

Mccullough, Claire L.

1994-01-01

Technique of feedback control, called "anticipatory neurofuzzy control," developed for use in controlling flexible structures and other dynamic systems for which mathematical models of dynamics poorly known or unknown. Superior ability to act during operation to compensate for, and adapt to, errors in mathematical model of dynamics, changes in dynamics, and noise. Also offers advantage of reduced computing time. Hybrid of two older fuzzy-logic control techniques: standard fuzzy control and predictive fuzzy control.

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.

Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time

PubMed Central

van den Bedem, Henry; Fraser, James S.

2015-01-01

Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836

Emergence of a snake-like structure in mobile distributed agents: an exploratory agent-based modeling approach.

PubMed

Niazi, Muaz A

2014-01-01

The body structure of snakes is composed of numerous natural components thereby making it resilient, flexible, adaptive, and dynamic. In contrast, current computer animations as well as physical implementations of snake-like autonomous structures are typically designed to use either a single or a relatively smaller number of components. As a result, not only these artificial structures are constrained by the dimensions of the constituent components but often also require relatively more computationally intensive algorithms to model and animate. Still, these animations often lack life-like resilience and adaptation. This paper presents a solution to the problem of modeling snake-like structures by proposing an agent-based, self-organizing algorithm resulting in an emergent and surprisingly resilient dynamic structure involving a minimal of interagent communication. Extensive simulation experiments demonstrate the effectiveness as well as resilience of the proposed approach. The ideas originating from the proposed algorithm can not only be used for developing self-organizing animations but can also have practical applications such as in the form of complex, autonomous, evolvable robots with self-organizing, mobile components with minimal individual computational capabilities. The work also demonstrates the utility of exploratory agent-based modeling (EABM) in the engineering of artificial life-like complex adaptive systems.

Emergence of a Snake-Like Structure in Mobile Distributed Agents: An Exploratory Agent-Based Modeling Approach

PubMed Central

Niazi, Muaz A.

2014-01-01

The body structure of snakes is composed of numerous natural components thereby making it resilient, flexible, adaptive, and dynamic. In contrast, current computer animations as well as physical implementations of snake-like autonomous structures are typically designed to use either a single or a relatively smaller number of components. As a result, not only these artificial structures are constrained by the dimensions of the constituent components but often also require relatively more computationally intensive algorithms to model and animate. Still, these animations often lack life-like resilience and adaptation. This paper presents a solution to the problem of modeling snake-like structures by proposing an agent-based, self-organizing algorithm resulting in an emergent and surprisingly resilient dynamic structure involving a minimal of interagent communication. Extensive simulation experiments demonstrate the effectiveness as well as resilience of the proposed approach. The ideas originating from the proposed algorithm can not only be used for developing self-organizing animations but can also have practical applications such as in the form of complex, autonomous, evolvable robots with self-organizing, mobile components with minimal individual computational capabilities. The work also demonstrates the utility of exploratory agent-based modeling (EABM) in the engineering of artificial life-like complex adaptive systems. PMID:24701135

Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm.

PubMed

Maximova, Tatiana; Plaku, Erion; Shehu, Amarda

2016-07-07

Proteins are macromolecules in perpetual motion, switching between structural states to modulate their function. A detailed characterization of the precise yet complex relationship between protein structure, dynamics, and function requires elucidating transitions between functionally-relevant states. Doing so challenges both wet and dry laboratories, as protein dynamics involves disparate temporal scales. In this paper we present a novel, sampling-based algorithm to compute transition paths. The algorithm exploits two main ideas. First, it leverages known structures to initialize its search and define a reduced conformation space for rapid sampling. This is key to address the insufficient sampling issue suffered by sampling-based algorithms. Second, the algorithm embeds samples in a nearest-neighbor graph where transition paths can be efficiently computed via queries. The algorithm adapts the probabilistic roadmap framework that is popular in robot motion planning. In addition to efficiently computing lowest-cost paths between any given structures, the algorithm allows investigating hypotheses regarding the order of experimentally-known structures in a transition event. This novel contribution is likely to open up new venues of research. Detailed analysis is presented on multiple-basin proteins of relevance to human disease. Multiscaling and the AMBER ff14SB force field are used to obtain energetically-credible paths at atomistic detail.

New computing systems and their impact on structural analysis and design

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1989-01-01

A review is given of the recent advances in computer technology that are likely to impact structural analysis and design. The computational needs for future structures technology are described. The characteristics of new and projected computing systems are summarized. Advances in programming environments, numerical algorithms, and computational strategies for new computing systems are reviewed, and a novel partitioning strategy is outlined for maximizing the degree of parallelism. The strategy is designed for computers with a shared memory and a small number of powerful processors (or a small number of clusters of medium-range processors). It is based on approximating the response of the structure by a combination of symmetric and antisymmetric response vectors, each obtained using a fraction of the degrees of freedom of the original finite element model. The strategy was implemented on the CRAY X-MP/4 and the Alliant FX/8 computers. For nonlinear dynamic problems on the CRAY X-MP with four CPUs, it resulted in an order of magnitude reduction in total analysis time, compared with the direct analysis on a single-CPU CRAY X-MP machine.

Research in applied mathematics, numerical analysis, and computer science

NASA Technical Reports Server (NTRS)

1984-01-01

Research conducted at the Institute for Computer Applications in Science and Engineering (ICASE) in applied mathematics, numerical analysis, and computer science is summarized and abstracts of published reports are presented. The major categories of the ICASE research program are: (1) numerical methods, with particular emphasis on the development and analysis of basic numerical algorithms; (2) control and parameter identification; (3) computational problems in engineering and the physical sciences, particularly fluid dynamics, acoustics, and structural analysis; and (4) computer systems and software, especially vector and parallel computers.

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

Water Ordering Controls the Dynamic Equilibrium of Micelle-Fiber Formation in Self-Assembly of Peptide Amphiphiles

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

Deshmukh, Sanket; Solomon, Lee A.; Kamath, Ganesh

Understanding the role of water in governing the kinetics of the self-assembly processes of amphiphilic peptides has still remained elusive. Here, using a multi-stage atomistic-coarse-grained approach, complemented by circular dichroism/infra-red spectroscopy and dynamic light scattering experiments, we highlight the dual nature of water in dictating the mechanism and dynamics of self-assembly of peptide amphiphiles (PAs). Our computational study shows that (i) Water cage formation and breakage near the hydrophobic groups controls the fusion dynamics and aggregation of PAs in the micellar stage, and (ii) Enhanced structural ordering of vicinal water near the hydrophilic amino acids shifts the equilibrium towards themore » fiber phase and stimulates structure and order in the PAs when they assemble into a hexagonal nanofiber architecture. Finally, spectroscopy and microscopy studies authenticate our computational observation that water ordering near the PAs increases with increase in time. The measured infra-red O-H bond stretch frequency reminiscent of ice-like suggests that the solvated water becomes increasingly solid-like with increased structural order in the assembled peptide network – thus shedding light on the role of water in a self-assembly process.« less

Water Ordering Controls the Dynamic Equilibrium of Micelle-Fiber Formation in Self-Assembly of Peptide Amphiphiles

DOE PAGES

Deshmukh, Sanket; Solomon, Lee A.; Kamath, Ganesh; ...

2016-08-24

Understanding the role of water in governing the kinetics of the self-assembly processes of amphiphilic peptides has still remained elusive. Here, using a multi-stage atomistic-coarse-grained approach, complemented by circular dichroism/infra-red spectroscopy and dynamic light scattering experiments, we highlight the dual nature of water in dictating the mechanism and dynamics of self-assembly of peptide amphiphiles (PAs). Our computational study shows that (i) Water cage formation and breakage near the hydrophobic groups controls the fusion dynamics and aggregation of PAs in the micellar stage, and (ii) Enhanced structural ordering of vicinal water near the hydrophilic amino acids shifts the equilibrium towards themore » fiber phase and stimulates structure and order in the PAs when they assemble into a hexagonal nanofiber architecture. Finally, spectroscopy and microscopy studies authenticate our computational observation that water ordering near the PAs increases with increase in time. The measured infra-red O-H bond stretch frequency reminiscent of ice-like suggests that the solvated water becomes increasingly solid-like with increased structural order in the assembled peptide network – thus shedding light on the role of water in a self-assembly process.« less

Prospects and expectations for unstructured methods

NASA Technical Reports Server (NTRS)

Baker, Timothy J.

1995-01-01

The last decade has witnessed a vigorous and sustained research effort on unstructured methods for computational fluid dynamics. Unstructured mesh generators and flow solvers have evolved to the point where they are now in use for design purposes throughout the aerospace industry. In this paper we survey the various mesh types, structured as well as unstructured, and examine their relative strengths and weaknesses. We argue that unstructured methodology does offer the best prospect for the next generation of computational fluid dynamics algorithms.

Computer studies of multiple-quantum spin dynamics

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

Murdoch, J.B.

The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment.

Computational prediction of hinge axes in proteins

PubMed Central

2014-01-01

Background A protein's function is determined by the wide range of motions exhibited by its 3D structure. However, current experimental techniques are not able to reliably provide the level of detail required for elucidating the exact mechanisms of protein motion essential for effective drug screening and design. Computational tools are instrumental in the study of the underlying structure-function relationship. We focus on a special type of proteins called "hinge proteins" which exhibit a motion that can be interpreted as a rotation of one domain relative to another. Results This work proposes a computational approach that uses the geometric structure of a single conformation to predict the feasible motions of the protein and is founded in recent work from rigidity theory, an area of mathematics that studies flexibility properties of general structures. Given a single conformational state, our analysis predicts a relative axis of motion between two specified domains. We analyze a dataset of 19 structures known to exhibit this hinge-like behavior. For 15, the predicted axis is consistent with a motion to a second, known conformation. We present a detailed case study for three proteins whose dynamics have been well-studied in the literature: calmodulin, the LAO binding protein and the Bence-Jones protein. Conclusions Our results show that incorporating rigidity-theoretic analyses can lead to effective computational methods for understanding hinge motions in macromolecules. This initial investigation is the first step towards a new tool for probing the structure-dynamics relationship in proteins. PMID:25080829

Mechanical properties of multifunctional structure with viscoelastic components based on FVE model

NASA Astrophysics Data System (ADS)

Hao, Dong; Zhang, Lin; Yu, Jing; Mao, Daiyong

2018-02-01

Based on the models of Lion and Kardelky (2004) and Hofer and Lion (2009), a finite viscoelastic (FVE) constitutive model, considering the predeformation-, frequency- and amplitude-dependent properties, has been proposed in our earlier paper [1]. FVE model is applied to investigating the dynamic characteristics of the multifunctional structure with the viscoelastic components. Combing FVE model with the finite element theory, the dynamic model of the multifunctional structure could be obtained. Additionally, the parametric identification and the experimental verification are also given via the frequency-sweep tests. The results show that the computational data agree well with the experimental data. FVE model has made a success of expressing the dynamic characteristics of the viscoelastic materials utilized in the multifunctional structure. The multifunctional structure technology has been verified by in-orbit experiments.

CEAS/AIAA/ICASE/NASA Langley International Forum on Aeroelasticity and Structural Dynamics 1999. Pt. 2

NASA Technical Reports Server (NTRS)

Whitlow, Jr., Woodrow (Editor); Todd, Emily N. (Editor)

1999-01-01

The proceedings of a workshop sponsored by the Confederation of European Aerospace Societies (CEAS), the American Institute of Aeronautics and Astronautics (AIAA), the National Aeronautics and Space Administration (NASA), Washington, D.C., and the Institute for Computer Applications in Science and Engineering (ICASE), Hampton, Virginia, and held in Williamsburg, Virginia June 22-25, 1999 represent a collection of the latest advances in aeroelasticity and structural dynamics from the world community. Research in the areas of unsteady aerodynamics and aeroelasticity, structural modeling and optimization, active control and adaptive structures, landing dynamics, certification and qualification, and validation testing are highlighted in the collection of papers. The wide range of results will lead to advances in the prediction and control of the structural response of aircraft and spacecraft.

Close-packed structure dynamics with finite-range interaction: computational mechanics with individual layer interaction.

PubMed

Rodriguez-Horta, Edwin; Estevez-Rams, Ernesto; Lora-Serrano, Raimundo; Neder, Reinhard

2017-09-01

This is the second contribution in a series of papers dealing with dynamical models in equilibrium theories of polytypism. A Hamiltonian introduced by Ahmad & Khan [Phys. Status Solidi B (2000), 218, 425-430] avoids the unphysical assignment of interaction terms to fictitious entities given by spins in the Hägg coding of the stacking arrangement. In this paper an analysis of polytype generation and disorder in close-packed structures is made for such a Hamiltonian. Results are compared with a previous analysis using the Ising model. Computational mechanics is the framework under which the analysis is performed. The competing effects of disorder and structure, as given by entropy density and excess entropy, respectively, are discussed. It is argued that the Ahmad & Khan model is simpler and predicts a larger set of polytypes than previous treatments.

Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses

DOE PAGES

Du, Jincheng; Rimsza, Jessica

2017-09-01

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Survey of NASA research on crash dynamics

NASA Technical Reports Server (NTRS)

Thomson, R. G.; Carden, H. D.; Hayduk, R. J.

1984-01-01

Ten years of structural crash dynamics research activities conducted on general aviation aircraft by the National Aeronautics and Space Administration (NASA) are described. Thirty-two full-scale crash tests were performed at Langley Research Center, and pertinent data on airframe and seat behavior were obtained. Concurrent with the experimental program, analytical methods were developed to help predict structural behavior during impact. The effects of flight parameters at impact on cabin deceleration pulses at the seat/occupant interface, experimental and analytical correlation of data on load-limiting subfloor and seat configurations, airplane section test results for computer modeling validation, and data from emergency-locator-transmitter (ELT) investigations to determine probable cause of false alarms and nonactivations are assessed. Computer programs which provide designers with analytical methods for predicting accelerations, velocities, and displacements of collapsing structures are also discussed.

The dynamic micro computed tomography at SSRF

NASA Astrophysics Data System (ADS)

Chen, R.; Xu, L.; Du, G.; Deng, B.; Xie, H.; Xiao, T.

2018-05-01

Synchrotron radiation micro-computed tomography (SR-μCT) is a critical technique for quantitative characterizing the 3D internal structure of samples, recently the dynamic SR-μCT has been attracting vast attention since it can evaluate the three-dimensional structure evolution of a sample. A dynamic μCT method, which is based on monochromatic beam, was developed at the X-ray Imaging and Biomedical Application Beamline at Shanghai Synchrotron Radiation Facility, by combining the compressed sensing based CT reconstruction algorithm and hardware upgrade. The monochromatic beam based method can achieve quantitative information, and lower dose than the white beam base method in which the lower energy beam is absorbed by the sample rather than contribute to the final imaging signal. The developed method is successfully used to investigate the compression of the air sac during respiration in a bell cricket, providing new knowledge for further research on the insect respiratory system.

NASTRAN computer system level 12.1

NASA Technical Reports Server (NTRS)

Butler, T. G.

1971-01-01

Program uses finite element displacement method for solving linear response of large, three-dimensional structures subject to static, dynamic, thermal, and random loadings. Program adapts to computers of different manufacture, permits up-dating and extention, allows interchange of output and input information between users, and is extensively documented.

Dynamic and fluid–structure interaction simulations of bioprosthetic heart valves using parametric design with T-splines and Fung-type material models

PubMed Central

Kamensky, David; Xu, Fei; Kiendl, Josef; Wang, Chenglong; Wu, Michael C. H.; Mineroff, Joshua; Reali, Alessandro; Bazilevs, Yuri; Sacks, Michael S.

2015-01-01

This paper builds on a recently developed immersogeometric fluid–structure interaction (FSI) methodology for bioprosthetic heart valve (BHV) modeling and simulation. It enhances the proposed framework in the areas of geometry design and constitutive modeling. With these enhancements, BHV FSI simulations may be performed with greater levels of automation, robustness and physical realism. In addition, the paper presents a comparison between FSI analysis and standalone structural dynamics simulation driven by prescribed transvalvular pressure, the latter being a more common modeling choice for this class of problems. The FSI computation achieved better physiological realism in predicting the valve leaflet deformation than its standalone structural dynamics counterpart. PMID:26392645

HART-II Acoustic Predictions using a Coupled CFD/CSD Method

NASA Technical Reports Server (NTRS)

Boyd, D. Douglas, Jr.

2009-01-01

This paper documents results to date from the Rotorcraft Acoustic Characterization and Mitigation activity under the NASA Subsonic Rotary Wing Project. The primary goal of this activity is to develop a NASA rotorcraft impulsive noise prediction capability which uses first principles fluid dynamics and structural dynamics. During this effort, elastic blade motion and co-processing capabilities have been included in a recent version of the computational fluid dynamics code (CFD). The CFD code is loosely coupled to computational structural dynamics (CSD) code using new interface codes. The CFD/CSD coupled solution is then used to compute impulsive noise on a plane under the rotor using the Ffowcs Williams-Hawkings solver. This code system is then applied to a range of cases from the Higher Harmonic Aeroacoustic Rotor Test II (HART-II) experiment. For all cases presented, the full experimental configuration (i.e., rotor and wind tunnel sting mount) are used in the coupled CFD/CSD solutions. Results show good correlation between measured and predicted loading and loading time derivative at the only measured radial station. A contributing factor for a typically seen loading mean-value offset between measured data and predictions data is examined. Impulsive noise predictions on the measured microphone plane under the rotor compare favorably with measured mid-frequency noise for all cases. Flow visualization of the BL and MN cases shows that vortex structures generated in the prediction method are consist with measurements. Future application of the prediction method is discussed.

Partitioning strategy for efficient nonlinear finite element dynamic analysis on multiprocessor computers

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Peters, Jeanne M.

1989-01-01

A computational procedure is presented for the nonlinear dynamic analysis of unsymmetric structures on vector multiprocessor systems. The procedure is based on a novel hierarchical partitioning strategy in which the response of the unsymmetric and antisymmetric response vectors (modes), each obtained by using only a fraction of the degrees of freedom of the original finite element model. The three key elements of the procedure which result in high degree of concurrency throughout the solution process are: (1) mixed (or primitive variable) formulation with independent shape functions for the different fields; (2) operator splitting or restructuring of the discrete equations at each time step to delineate the symmetric and antisymmetric vectors constituting the response; and (3) two level iterative process for generating the response of the structure. An assessment is made of the effectiveness of the procedure on the CRAY X-MP/4 computers.

Characterization of Unsteady Flow Structures Near Landing-Edge Slat. Part 2; 2D Computations

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi; Choudhari, Meelan M.; Jenkins, Luther N.

2004-01-01

In our previous computational studies of a generic high-lift configuration, quasi-laminar (as opposed to fully turbulent) treatment of the slat cove region proved to be an effective approach for capturing the unsteady dynamics of the cove flow field. Combined with acoustic propagation via Ffowes Williams and Hawkings formulation, the quasi-laminar simulations captured some important features of the slat cove noise measured with microphone array techniques. However. a direct assessment of the computed cove flow field was not feasible due to the unavailability of off-surface flow measurements. To remedy this shortcoming, we have undertaken a combined experiment and computational study aimed at characterizing the flow structures and fluid mechanical processes within the slat cove region. Part I of this paper outlines the experimental aspects of this investigation focused on the 30P30N high-lift configuration; the present paper describes the accompanying computational results including a comparison between computation and experiment at various angles of attack. Even through predictions of the time-averaged flow field agree well with the measured data, the study indicates the need for further refinement of the zonal turbulence approach in order to capture the full dynamics of the cove's fluctuating flow field.

Probabilistic structural mechanics research for parallel processing computers

NASA Technical Reports Server (NTRS)

Sues, Robert H.; Chen, Heh-Chyun; Twisdale, Lawrence A.; Martin, William R.

1991-01-01

Aerospace structures and spacecraft are a complex assemblage of structural components that are subjected to a variety of complex, cyclic, and transient loading conditions. Significant modeling uncertainties are present in these structures, in addition to the inherent randomness of material properties and loads. To properly account for these uncertainties in evaluating and assessing the reliability of these components and structures, probabilistic structural mechanics (PSM) procedures must be used. Much research has focused on basic theory development and the development of approximate analytic solution methods in random vibrations and structural reliability. Practical application of PSM methods was hampered by their computationally intense nature. Solution of PSM problems requires repeated analyses of structures that are often large, and exhibit nonlinear and/or dynamic response behavior. These methods are all inherently parallel and ideally suited to implementation on parallel processing computers. New hardware architectures and innovative control software and solution methodologies are needed to make solution of large scale PSM problems practical.

Aeroelasticity of wing and wing-body configurations on parallel computers

NASA Technical Reports Server (NTRS)

Byun, Chansup

1995-01-01

The objective of this research is to develop computationally efficient methods for solving aeroelasticity problems on parallel computers. Both uncoupled and coupled methods are studied in this research. For the uncoupled approach, the conventional U-g method is used to determine the flutter boundary. The generalized aerodynamic forces required are obtained by the pulse transfer-function analysis method. For the coupled approach, the fluid-structure interaction is obtained by directly coupling finite difference Euler/Navier-Stokes equations for fluids and finite element dynamics equations for structures. This capability will significantly impact many aerospace projects of national importance such as Advanced Subsonic Civil Transport (ASCT), where the structural stability margin becomes very critical at the transonic region. This research effort will have direct impact on the High Performance Computing and Communication (HPCC) Program of NASA in the area of parallel computing.

Improved Helicopter Rotor Performance Prediction through Loose and Tight CFD/CSD Coupling

NASA Astrophysics Data System (ADS)

Ickes, Jacob C.

Helicopters and other Vertical Take-Off or Landing (VTOL) vehicles exhibit an interesting combination of structural dynamic and aerodynamic phenomena which together drive the rotor performance. The combination of factors involved make simulating the rotor a challenging and multidisciplinary effort, and one which is still an active area of interest in the industry because of the money and time it could save during design. Modern tools allow the prediction of rotorcraft physics from first principles. Analysis of the rotor system with this level of accuracy provides the understanding necessary to improve its performance. There has historically been a divide between the comprehensive codes which perform aeroelastic rotor simulations using simplified aerodynamic models, and the very computationally intensive Navier-Stokes Computational Fluid Dynamics (CFD) solvers. As computer resources become more available, efforts have been made to replace the simplified aerodynamics of the comprehensive codes with the more accurate results from a CFD code. The objective of this work is to perform aeroelastic rotorcraft analysis using first-principles simulations for both fluids and structural predictions using tools available at the University of Toledo. Two separate codes are coupled together in both loose coupling (data exchange on a periodic interval) and tight coupling (data exchange each time step) schemes. To allow the coupling to be carried out in a reliable and efficient way, a Fluid-Structure Interaction code was developed which automatically performs primary functions of loose and tight coupling procedures. Flow phenomena such as transonics, dynamic stall, locally reversed flow on a blade, and Blade-Vortex Interaction (BVI) were simulated in this work. Results of the analysis show aerodynamic load improvement due to the inclusion of the CFD-based airloads in the structural dynamics analysis of the Computational Structural Dynamics (CSD) code. Improvements came in the form of improved peak/trough magnitude prediction, better phase prediction of these locations, and a predicted signal with a frequency content more like the flight test data than the CSD code acting alone. Additionally, a tight coupling analysis was performed as a demonstration of the capability and unique aspects of such an analysis. This work shows that away from the center of the flight envelope, the aerodynamic modeling of the CSD code can be replaced with a more accurate set of predictions from a CFD code with an improvement in the aerodynamic results. The better predictions come at substantially increased computational costs between 1,000 and 10,000 processor-hours.

Sonic and Supersonic Jet Plumes

NASA Technical Reports Server (NTRS)

Venkatapathy, E.; Naughton, J. W.; Flethcher, D. G.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock- shear- layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

Computational analysis of nonlinearities within dynamics of cable-based driving systems

NASA Astrophysics Data System (ADS)

Anghelache, G. D.; Nastac, S.

2017-08-01

This paper deals with computational nonlinear dynamics of mechanical systems containing some flexural parts within the actuating scheme, and, especially, the situations of the cable-based driving systems were treated. It was supposed both functional nonlinearities and the real characteristic of the power supply, in order to obtain a realistically computer simulation model being able to provide very feasible results regarding the system dynamics. It was taken into account the transitory and stable regimes during a regular exploitation cycle. The authors present a particular case of a lift system, supposed to be representatively for the objective of this study. The simulations were made based on the values of the essential parameters acquired from the experimental tests and/or the regular practice in the field. The results analysis and the final discussions reveal the correlated dynamic aspects within the mechanical parts, the driving system, and the power supply, whole of these supplying potential sources of particular resonances, within some transitory phases of the working cycle, and which can affect structural and functional dynamics. In addition, it was underlines the influences of computational hypotheses on the both quantitative and qualitative behaviour of the system. Obviously, the most significant consequence of this theoretical and computational research consist by developing an unitary and feasible model, useful to dignify the nonlinear dynamic effects into the systems with cable-based driving scheme, and hereby to help an optimization of the exploitation regime including a dynamics control measures.

Variation of the subsidence parameters, effective thermal conductivity, and mantle dynamics

NASA Astrophysics Data System (ADS)

Adam, C.; King, S. D.; Vidal, V.; Rabinowicz, M.; Jalobeanu, A.; Yoshida, M.

2015-09-01

The subsidence of young seafloor is generally considered to be a passive phenomenon related to the conductive cooling of the lithosphere after its creation at mid-oceanic ridges. Recent alternative theories suggest that the mantle dynamics plays an important role in the structure and depth of the oceanic lithosphere. However, the link between mantle dynamics and seafloor subsidence has still to be quantitatively assessed. Here we provide a statistical study of the subsidence parameters (subsidence rate and ridge depth) for all the oceans. These parameters are retrieved through two independent methods, the positive outliers method, a classical method used in signal processing, and through the MiFil method. From the subsidence rate, we compute the effective thermal conductivity, keff, which ranges between 1 and 7 W m-1 K-1. We also model the mantle flow pattern from the S40RTS tomography model. The density anomalies derived from S40RTS are used to compute the instantaneous flow in a global 3D spherical geometry. We show that departures from the keff = 3 Wm-1K-1 standard value are systematically related to mantle processes and not to lithospheric structure. Regions characterized by keff > 3 Wm-1K-1 are associated with mantle uplifts (mantle plumes or other local anomalies). Regions characterized by keff < 3 Wm-1K-1 are related to large-scale mantle downwellings such as the Australia-Antarctic Discordance (AAD) or the return flow from the South Pacific Superswell to the East Pacific Rise. This demonstrates that mantle dynamics plays a major role in the shaping of the oceanic seafloor. In particular, the parameters generally considered to quantify the lithosphere structure, such as the thermal conductivity, are not only representative of this structure but also incorporate signals from the mantle convection occurring beneath the lithosphere. The dynamic topography computed from the S40RTS tomography model reproduces the subsidence pattern observed in the bathymetry. Overall we find a good correlation between the subsidence parameters derived from the bathymetry and the dynamic topography. This demonstrates that these parameters are strongly dependent on mantle dynamics.

Dynamic isoperimetry and the geometry of Lagrangian coherent structures

NASA Astrophysics Data System (ADS)

Froyland, Gary

2015-10-01

The study of transport and mixing processes in dynamical systems is particularly important for the analysis of mathematical models of physical systems. We propose a novel, direct geometric method to identify subsets of phase space that remain strongly coherent over a finite time duration. This new method is based on a dynamic extension of classical (static) isoperimetric problems; the latter are concerned with identifying submanifolds with the smallest boundary size relative to their volume. The present work introduces dynamic isoperimetric problems; the study of sets with small boundary size relative to volume as they are evolved by a general dynamical system. We formulate and prove dynamic versions of the fundamental (static) isoperimetric (in)equalities; a dynamic Federer-Fleming theorem and a dynamic Cheeger inequality. We introduce a new dynamic Laplace operator and describe a computational method to identify coherent sets based on eigenfunctions of the dynamic Laplacian. Our results include formal mathematical statements concerning geometric properties of finite-time coherent sets, whose boundaries can be regarded as Lagrangian coherent structures. The computational advantages of our new approach are a well-separated spectrum for the dynamic Laplacian, and flexibility in appropriate numerical approximation methods. Finally, we demonstrate that the dynamic Laplace operator can be realised as a zero-diffusion limit of a newly advanced probabilistic transfer operator method [9] for finding coherent sets, which is based on small diffusion. Thus, the present approach sits naturally alongside the probabilistic approach [9], and adds a formal geometric interpretation.

Fluid-dynamics modelling of the human left ventricle with dynamic mesh for normal and myocardial infarction: preliminary study.

PubMed

Khalafvand, S S; Ng, E Y K; Zhong, L; Hung, T K

2012-08-01

Pulsating blood flow patterns in the left ventricular (LV) were computed for three normal subjects and three patients after myocardial infarction (MI). Cardiac magnetic resonance (MR) images were obtained, segmented and transformed into 25 frames of LV for a computational fluid dynamics (CFD) study. Multi-block structure meshes were generated for 25 frames and 75 intermediate grids. The complete LV cycle was modelled by using ANSYS-CFX 12. The flow patterns and pressure drops in the LV chamber of this study provided some useful information on intra-LV flow patterns with heart diseases. Copyright © 2012 Elsevier Ltd. All rights reserved.

An Assessment of the State-of-the-art in Multidisciplinary Aeromechanical Analyses

NASA Technical Reports Server (NTRS)

Datta, Anubhav; Johnson, Wayne

2008-01-01

This paper presents a survey of the current state-of-the-art in multidisciplinary aeromechanical analyses which integrate advanced Computational Structural Dynamics (CSD) and Computational Fluid Dynamics (CFD) methods. The application areas to be surveyed include fixed wing aircraft, turbomachinery, and rotary wing aircraft. The objective of the authors in the present paper, together with a companion paper on requirements, is to lay out a path for a High Performance Computing (HPC) based next generation comprehensive rotorcraft analysis. From this survey of the key technologies in other application areas it is possible to identify the critical technology gaps that stem from unique rotorcraft requirements.

NASA Lewis Research Center/university graduate research program on engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1985-01-01

NASA Lewis Research Center established a graduate research program in support of the Engine Structures Research activities. This graduate research program focuses mainly on structural and dynamics analyses, computational mechanics, mechanics of composites and structural optimization. The broad objectives of the program, the specific program, the participating universities and the program status are briefly described.

NASA Lewis Research Center/University Graduate Research Program on Engine Structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1985-01-01

NASA Lewis Research Center established a graduate research program in support of the Engine Structures Research activities. This graduate research program focuses mainly on structural and dynamics analyses, computational mechanics, mechanics of composites and structural optimization. The broad objectives of the program, the specific program, the participating universities and the program status are briefly described.

Excited state dynamics of thiophene and bithiophene: new insights into theoretically challenging systems.

PubMed

Prlj, Antonio; Curchod, Basile F E; Corminboeuf, Clémence

2015-06-14

The computational elucidation and proper description of the ultrafast deactivation mechanisms of simple organic electronic units, such as thiophene and its oligomers, is as challenging as it is contentious. A comprehensive excited state dynamics analysis of these systems utilizing reliable electronic structure approaches is currently lacking, with earlier pictures of the photochemistry of these systems being conceived based upon high-level static computations or lower level dynamic trajectories. Here a detailed surface hopping molecular dynamics of thiophene and bithiophene using the algebraic diagrammatic construction to second order (ADC(2)) method is presented. Our findings illustrate that ring puckering plays an important role in thiophene photochemistry and that the photostability increases when going upon dimerization into bithiophene.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

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

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE PAGES

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

2015-06-26

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Rating of Dynamic Coefficient for Simple Beam Bridge Design on High-Speed Railways

NASA Astrophysics Data System (ADS)

Diachenko, Leonid; Benin, Andrey; Smirnov, Vladimir; Diachenko, Anastasia

2018-06-01

The aim of the work is to improve the methodology for the dynamic computation of simple beam spans during the impact of high-speed trains. Mathematical simulation utilizing numerical and analytical methods of structural mechanics is used in the research. The article analyses parameters of the effect of high-speed trains on simple beam spanning bridge structures and suggests a technique of determining of the dynamic index to the live load. Reliability of the proposed methodology is confirmed by results of numerical simulation of high-speed train passage over spans with different speeds. The proposed algorithm of dynamic computation is based on a connection between maximum acceleration of the span in the resonance mode of vibrations and the main factors of stress-strain state. The methodology allows determining maximum and also minimum values of the main efforts in the construction that makes possible to perform endurance tests. It is noted that dynamic additions for the components of the stress-strain state (bending moments, transverse force and vertical deflections) are different. This condition determines the necessity for differentiated approach to evaluation of dynamic coefficients performing design verification of I and II groups of limiting state. The practical importance: the methodology of determining the dynamic coefficients allows making dynamic calculation and determining the main efforts in split beam spans without numerical simulation and direct dynamic analysis that significantly reduces the labour costs for design.

Analysis of passive damping in thick composite structures

NASA Technical Reports Server (NTRS)

Saravanos, D. A.

1993-01-01

Computational mechanics for the prediction of damping and other dynamic characteristics in composite structures of general thicknesses and laminations are presented. Discrete layer damping mechanics that account for the representation of interlaminar shear effects in the material are summarized. Finite element based structural mechanics for the analysis of damping are described, and a specialty finite element is developed. Applications illustrate the quality of the discrete layer damping mechanics in predicting the damped dynamic characteristics of composite structures with thicker sections and/or laminate configurations that induce interlaminar shear. The results also illustrate and quantify the significance of interlaminar shear damping in such composite structures.

Structural Mechanics and Dynamics Branch

NASA Technical Reports Server (NTRS)

Stefko, George

2003-01-01

The 2002 annual report of the Structural Mechanics and Dynamics Branch reflects the majority of the work performed by the branch staff during the 2002 calendar year. Its purpose is to give a brief review of the branch s technical accomplishments. The Structural Mechanics and Dynamics Branch develops innovative computational tools, benchmark experimental data, and solutions to long-term barrier problems in the areas of propulsion aeroelasticity, active and passive damping, engine vibration control, rotor dynamics, magnetic suspension, structural mechanics, probabilistics, smart structures, engine system dynamics, and engine containment. Furthermore, the branch is developing a compact, nonpolluting, bearingless electric machine with electric power supplied by fuel cells for future "more electric" aircraft. An ultra-high-power-density machine that can generate projected power densities of 50 hp/lb or more, in comparison to conventional electric machines, which generate usually 0.2 hp/lb, is under development for application to electric drives for propulsive fans or propellers. In the future, propulsion and power systems will need to be lighter, to operate at higher temperatures, and to be more reliable in order to achieve higher performance and economic viability. The Structural Mechanics and Dynamics Branch is working to achieve these complex, challenging goals.

Program of Research in Structures and Dynamics

NASA Technical Reports Server (NTRS)

1988-01-01

The Structures and Dynamics Program was first initiated in 1972 with the following two major objectives: to provide a basic understanding and working knowledge of some key areas pertinent to structures, solid mechanics, and dynamics technology including computer aided design; and to provide a comprehensive educational and research program at the NASA Langley Research Center leading to advanced degrees in the structures and dynamics areas. During the operation of the program the research work was done in support of the activities of both the Structures and Dynamics Division and the Loads and Aeroelasticity Division. During the period of 1972 to 1986 the Program provided support for two full-time faculty members, one part-time faculty member, three postdoctoral fellows, one research engineer, eight programmers, and 28 graduate research assistants. The faculty and staff of the program have published 144 papers and reports, and made 70 presentations at national and international meetings, describing their research findings. In addition, they organized and helped in the organization of 10 workshops and national symposia in the structures and dynamics areas. The graduate research assistants and the students enrolled in the program have written 20 masters theses and 2 doctoral dissertations. The overall progress is summarized.

Finite element dynamic analysis on CDC STAR-100 computer

NASA Technical Reports Server (NTRS)

Noor, A. K.; Lambiotte, J. J., Jr.

1978-01-01

Computational algorithms are presented for the finite element dynamic analysis of structures on the CDC STAR-100 computer. The spatial behavior is described using higher-order finite elements. The temporal behavior is approximated by using either the central difference explicit scheme or Newmark's implicit scheme. In each case the analysis is broken up into a number of basic macro-operations. Discussion is focused on the organization of the computation and the mode of storage of different arrays to take advantage of the STAR pipeline capability. The potential of the proposed algorithms is discussed and CPU times are given for performing the different macro-operations for a shell modeled by higher order composite shallow shell elements having 80 degrees of freedom.

A Framework for the Specification of the Semantics and the Dynamics of Instructional Applications

ERIC Educational Resources Information Center

Buendia-Garcia, Felix; Diaz, Paloma

2003-01-01

An instructional application consists of a set of resources and activities to implement interacting, interrelated, and structured experiences oriented towards achieving specific educational objectives. The development of computer-based instructional applications has to follow a well defined process, so models for computer-based instructional…

Conformational dynamics of proanthocyanidins: physical and computational approaches

Treesearch

Fred L. Tobiason; Richard W. Hemingway; T. Hatano

1998-01-01

The interaction of plant polyphenols with proteins accounts for a good part of their commercial (e.g., leather manufacture) and biological (e.g., antimicrobial activity) significance. The interplay between observations of physical data such as crystal structure, NMR analyses, and time-resolved fluorescence with results of computational chemistry approaches has been...

Semiannual report, 1 April - 30 September 1991

NASA Technical Reports Server (NTRS)

1991-01-01

The major categories of the current Institute for Computer Applications in Science and Engineering (ICASE) research program are: (1) numerical methods, with particular emphasis on the development and analysis of basic numerical algorithms; (2) control and parameter identification problems, with emphasis on effective numerical methods; (3) computational problems in engineering and the physical sciences, particularly fluid dynamics, acoustics, and structural analysis; and (4) computer systems and software for parallel computers. Research in these areas is discussed.

Student leadership in small group science inquiry

NASA Astrophysics Data System (ADS)

Oliveira, Alandeom W.; Boz, Umit; Broadwell, George A.; Sadler, Troy D.

2014-09-01

Background: Science educators have sought to structure collaborative inquiry learning through the assignment of static group roles. This structural approach to student grouping oversimplifies the complexities of peer collaboration and overlooks the highly dynamic nature of group activity. Purpose: This study addresses this issue of oversimplification of group dynamics by examining the social leadership structures that emerge in small student groups during science inquiry. Sample: Two small student groups investigating the burning of a candle under a jar participated in this study. Design and method: We used a mixed-method research approach that combined computational discourse analysis (computational quantification of social aspects of small group discussions) with microethnography (qualitative, in-depth examination of group discussions). Results: While in one group social leadership was decentralized (i.e., students shared control over topics and tasks), the second group was dominated by a male student (centralized social leadership). Further, decentralized social leadership was found to be paralleled by higher levels of student cognitive engagement. Conclusions: It is argued that computational discourse analysis can provide science educators with a powerful means of developing pedagogical models of collaborative science learning that take into account the emergent nature of group structures and highly fluid nature of student collaboration.

Cloud computing method for dynamically scaling a process across physical machine boundaries

DOEpatents

Gillen, Robert E.; Patton, Robert M.; Potok, Thomas E.; Rojas, Carlos C.

2014-09-02

A cloud computing platform includes first device having a graph or tree structure with a node which receives data. The data is processed by the node or communicated to a child node for processing. A first node in the graph or tree structure determines the reconfiguration of a portion of the graph or tree structure on a second device. The reconfiguration may include moving a second node and some or all of its descendant nodes. The second and descendant nodes may be copied to the second device.

Optimal dynamic remapping of parallel computations

NASA Technical Reports Server (NTRS)

Nicol, David M.; Reynolds, Paul F., Jr.

1987-01-01

A large class of computations are characterized by a sequence of phases, with phase changes occurring unpredictably. The decision problem was considered regarding the remapping of workload to processors in a parallel computation when the utility of remapping and the future behavior of the workload is uncertain, and phases exhibit stable execution requirements during a given phase, but requirements may change radically between phases. For these problems a workload assignment generated for one phase may hinder performance during the next phase. This problem is treated formally for a probabilistic model of computation with at most two phases. The fundamental problem of balancing the expected remapping performance gain against the delay cost was addressed. Stochastic dynamic programming is used to show that the remapping decision policy minimizing the expected running time of the computation has an extremely simple structure. Because the gain may not be predictable, the performance of a heuristic policy that does not require estimnation of the gain is examined. The heuristic method's feasibility is demonstrated by its use on an adaptive fluid dynamics code on a multiprocessor. The results suggest that except in extreme cases, the remapping decision problem is essentially that of dynamically determining whether gain can be achieved by remapping after a phase change. The results also suggest that this heuristic is applicable to computations with more than two phases.

Study-simulation of space station dynamics

NASA Technical Reports Server (NTRS)

Gaitens, M. J.

1971-01-01

Matrix algebra translator and executor /MATE/ takes equations describing structural control system environmental interaction problem for flexible spacecraft components and loads them into self programming computer.

Interfacial gauge methods for incompressible fluid dynamics

PubMed Central

Saye, Robert

2016-01-01

Designing numerical methods for incompressible fluid flow involving moving interfaces, for example, in the computational modeling of bubble dynamics, swimming organisms, or surface waves, presents challenges due to the coupling of interfacial forces with incompressibility constraints. A class of methods, denoted interfacial gauge methods, is introduced for computing solutions to the corresponding incompressible Navier-Stokes equations. These methods use a type of “gauge freedom” to reduce the numerical coupling between fluid velocity, pressure, and interface position, allowing high-order accurate numerical methods to be developed more easily. Making use of an implicit mesh discontinuous Galerkin framework, developed in tandem with this work, high-order results are demonstrated, including surface tension dynamics in which fluid velocity, pressure, and interface geometry are computed with fourth-order spatial accuracy in the maximum norm. Applications are demonstrated with two-phase fluid flow displaying fine-scaled capillary wave dynamics, rigid body fluid-structure interaction, and a fluid-jet free surface flow problem exhibiting vortex shedding induced by a type of Plateau-Rayleigh instability. The developed methods can be generalized to other types of interfacial flow and facilitate precise computation of complex fluid interface phenomena. PMID:27386567

Surface Modeling, Grid Generation, and Related Issues in Computational Fluid Dynamic (CFD) Solutions

NASA Technical Reports Server (NTRS)

Choo, Yung K. (Compiler)

1995-01-01

The NASA Steering Committee for Surface Modeling and Grid Generation (SMAGG) sponsored a workshop on surface modeling, grid generation, and related issues in Computational Fluid Dynamics (CFD) solutions at Lewis Research Center, Cleveland, Ohio, May 9-11, 1995. The workshop provided a forum to identify industry needs, strengths, and weaknesses of the five grid technologies (patched structured, overset structured, Cartesian, unstructured, and hybrid), and to exchange thoughts about where each technology will be in 2 to 5 years. The workshop also provided opportunities for engineers and scientists to present new methods, approaches, and applications in SMAGG for CFD. This Conference Publication (CP) consists of papers on industry overview, NASA overview, five grid technologies, new methods/ approaches/applications, and software systems.

Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers.

PubMed

Kanchi, Subbarao; Suresh, Gorle; Priyakumar, U Deva; Ayappa, K G; Maiti, Prabal K

2015-10-15

A new class of dendrimers, the poly(propyl ether imine) (PETIM) dendrimer, has been shown to be a novel hyperbranched polymer having potential applications as a drug delivery vehicle. Structure and dynamics of the amine terminated PETIM dendrimer and their changes with respect to the dendrimer generation are poorly understood. Since most drugs are hydrophobic in nature, the extent of hydrophobicity of the dendrimer core is related to its drug encapsulation and retention efficacy. In this study, we carry out fully atomistic molecular dynamics (MD) simulations to characterize the structure of PETIM (G2-G6) dendrimers in salt solution as a function of dendrimer generation at different protonation levels. Structural properties such as radius of gyration (Rg), radial density distribution, aspect ratio, and asphericity are calculated. In order to assess the hydrophilicity of the dendrimer, we compute the number of bound water molecules in the interior of dendrimer as well as the number of dendrimer-water hydrogen bonds. We conclude that PETIM dendrimers have relatively greater hydrophobicity and flexibility when compared with their extensively investigated PAMAM counterparts. Hence PETIM dendrimers are expected to have stronger interactions with lipid membranes as well as improved drug encapsulation and retention properties when compared with PAMAM dendrimers. We compute the root-mean-square fluctuation of dendrimers as well as their entropy to quantify the flexibility of the dendrimer. Finally we note that structural and solvation properties computed using force field parameters derived based on the CHARMM general purpose force field were in good quantitative agreement with those obtained using the generalized Amber force field (GAFF).

Comparison between a typical and a simplified model for blast load-induced structural response

NASA Astrophysics Data System (ADS)

Abd-Elhamed, A.; Mahmoud, S.

2017-02-01

As explosive blasts continue to cause severe damage as well as victims in both civil and military environments. There is a bad need for understanding the behavior of structural elements to such extremely short duration dynamic loads where it is of great concern nowadays. Due to the complexity of the typical blast pressure profile model and in order to reduce the modelling and computational efforts, the simplified triangle model for blast loads profile is used to analyze structural response. This simplified model considers only the positive phase and ignores the suction phase which characterizes the typical one in simulating blast loads. The closed from solution for the equation of motion under blast load as a forcing term modelled either typical or simplified models has been derived. The considered herein two approaches have been compared using the obtained results from simulation response analysis of a building structure under an applied blast load. The computed error in simulating response using the simplified model with respect to the typical one has been computed. In general, both simplified and typical models can perform the dynamic blast-load induced response of building structures. However, the simplified one shows a remarkably different response behavior as compared to the typical one despite its simplicity and the use of only positive phase for simulating the explosive loads. The prediction of the dynamic system responses using the simplified model is not satisfactory due to the obtained larger errors as compared to the system responses obtained using the typical one.

Redundant Asynchronous Microprocessor System

NASA Technical Reports Server (NTRS)

Meyer, G.; Johnston, J. O.; Dunn, W. R.

1985-01-01

Fault-tolerant computer structure called RAMPS (for redundant asynchronous microprocessor system) has simplicity of static redundancy but offers intermittent-fault handling ability of complex, dynamically redundant systems. New structure useful wherever several microprocessors are employed for control - in aircraft, industrial processes, robotics, and automatic machining, for example.

Formal Specification of Information Systems Requirements.

ERIC Educational Resources Information Center

Kampfner, Roberto R.

1985-01-01

Presents a formal model for specification of logical requirements of computer-based information systems that incorporates structural and dynamic aspects based on two separate models: the Logical Information Processing Structure and the Logical Information Processing Network. The model's role in systems development is discussed. (MBR)

A Model Comparison for Characterizing Protein Motions from Structure

NASA Astrophysics Data System (ADS)

David, Charles; Jacobs, Donald

2011-10-01

A comparative study is made using three computational models that characterize native state dynamics starting from known protein structures taken from four distinct SCOP classifications. A geometrical simulation is performed, and the results are compared to the elastic network model and molecular dynamics. The essential dynamics is quantified by a direct analysis of a mode subspace constructed from ANM and a principal component analysis on both the FRODA and MD trajectories using root mean square inner product and principal angles. Relative subspace sizes and overlaps are visualized using the projection of displacement vectors on the model modes. Additionally, a mode subspace is constructed from PCA on an exemplar set of X-ray crystal structures in order to determine similarly with respect to the generated ensembles. Quantitative analysis reveals there is significant overlap across the three model subspaces and the model independent subspace. These results indicate that structure is the key determinant for native state dynamics.

Dynamics starting at a conical intersection: Application to the photochemistry of pyrrole

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

Sellner, Bernhard; Barbatti, Mario; Lischka, Hans

The photochemical ring opening process in pyrrole has been investigated by performing classical on-the-fly dynamics using the multiconfiguration self-consistent field method for the computation of energies and energy gradients. As starting point for the dynamics the conical intersection corresponding to the ring-puckered ring-opened structure, determined previously [Barbatti et al., J. Chem. Phys. 125, 164323 (2006)], has been chosen. Two sets of initial conditions for the nuclear velocities were constructed: (i) nuclear velocities in the branching (g,h) plane of the conical intersection and (ii) statistical distribution for all atoms. Both sets of initial conditions show very similar results. Reactive trajectories aremore » only found in a very limited sector in the (g,h) plane and reaction products are very similar. Within the simulation time of 1 ps, ring opening of pyrrole to the biradical NH=CH-CH-CH=CH chain followed by ring closure to a substituted cyclopropene structure (NH=CH-C{sub 3}H{sub 3}) is observed. The computed structural data correlate well with the experimentally observed dissociation products.« less

Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes

PubMed Central

Schramm, Vern L.

2017-01-01

Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein’s dynamic architecture is linked to transition-state structure. Fast dynamic motions in catalytic sites are linked to transition-state generation. Enzymatic transition states have lifetimes of femtoseconds, the lifetime of bond vibrations. Binding isotope effects (BIEs) reveal relative reactant and transition-state analog binding distortion for comparison with actual transition states. PMID:21675920

Adaptive modeling, identification, and control of dynamic structural systems. I. Theory

USGS Publications Warehouse

Safak, Erdal

1989-01-01

A concise review of the theory of adaptive modeling, identification, and control of dynamic structural systems based on discrete-time recordings is presented. Adaptive methods have four major advantages over the classical methods: (1) Removal of the noise from the signal is done over the whole frequency band; (2) time-varying characteristics of systems can be tracked; (3) systems with unknown characteristics can be controlled; and (4) a small segment of the data is needed during the computations. Included in the paper are the discrete-time representation of single-input single-output (SISO) systems, models for SISO systems with noise, the concept of stochastic approximation, recursive prediction error method (RPEM) for system identification, and the adaptive control. Guidelines for model selection and model validation and the computational aspects of the method are also discussed in the paper. The present paper is the first of two companion papers. The theory given in the paper is limited to that which is necessary to follow the examples for applications in structural dynamics presented in the second paper.

Teachers' Organization of Participation Structures for Teaching Science with Computer Technology

NASA Astrophysics Data System (ADS)

Subramaniam, Karthigeyan

2016-08-01

This paper describes a qualitative study that investigated the nature of the participation structures and how the participation structures were organized by four science teachers when they constructed and communicated science content in their classrooms with computer technology. Participation structures focus on the activity structures and processes in social settings like classrooms thereby providing glimpses into the complex dynamics of teacher-students interactions, configurations, and conventions during collective meaning making and knowledge creation. Data included observations, interviews, and focus group interviews. Analysis revealed that the dominant participation structure evident within participants' instruction with computer technology was ( Teacher) initiation-( Student and Teacher) response sequences-( Teacher) evaluate participation structure. Three key events characterized the how participants organized this participation structure in their classrooms: setting the stage for interactive instruction, the joint activity, and maintaining accountability. Implications include the following: (1) teacher educators need to tap into the knowledge base that underscores science teachers' learning to teach philosophies when computer technology is used in instruction. (2) Teacher educators need to emphasize the essential idea that learning and cognition is not situated within the computer technology but within the pedagogical practices, specifically the participation structures. (3) The pedagogical practices developed with the integration or with the use of computer technology underscored by the teachers' own knowledge of classroom contexts and curriculum needs to be the focus for how students learn science content with computer technology instead of just focusing on how computer technology solely supports students learning of science content.

A transient FETI methodology for large-scale parallel implicit computations in structural mechanics

NASA Technical Reports Server (NTRS)

Farhat, Charbel; Crivelli, Luis; Roux, Francois-Xavier

1992-01-01

Explicit codes are often used to simulate the nonlinear dynamics of large-scale structural systems, even for low frequency response, because the storage and CPU requirements entailed by the repeated factorizations traditionally found in implicit codes rapidly overwhelm the available computing resources. With the advent of parallel processing, this trend is accelerating because explicit schemes are also easier to parallelize than implicit ones. However, the time step restriction imposed by the Courant stability condition on all explicit schemes cannot yet -- and perhaps will never -- be offset by the speed of parallel hardware. Therefore, it is essential to develop efficient and robust alternatives to direct methods that are also amenable to massively parallel processing because implicit codes using unconditionally stable time-integration algorithms are computationally more efficient when simulating low-frequency dynamics. Here we present a domain decomposition method for implicit schemes that requires significantly less storage than factorization algorithms, that is several times faster than other popular direct and iterative methods, that can be easily implemented on both shared and local memory parallel processors, and that is both computationally and communication-wise efficient. The proposed transient domain decomposition method is an extension of the method of Finite Element Tearing and Interconnecting (FETI) developed by Farhat and Roux for the solution of static problems. Serial and parallel performance results on the CRAY Y-MP/8 and the iPSC-860/128 systems are reported and analyzed for realistic structural dynamics problems. These results establish the superiority of the FETI method over both the serial/parallel conjugate gradient algorithm with diagonal scaling and the serial/parallel direct method, and contrast the computational power of the iPSC-860/128 parallel processor with that of the CRAY Y-MP/8 system.

Evol and ProDy for bridging protein sequence evolution and structural dynamics.

PubMed

Bakan, Ahmet; Dutta, Anindita; Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R; Bahar, Ivet

2014-09-15

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Modulation of phase transition of thermosensitive liposomes with leucine zipper-structured lipopeptides.

PubMed

Xu, Xiejun; Xiao, Xingqing; Wang, Yiming; Xu, Shouhong; Liu, Honglai

2018-06-13

Targeted therapy for cancer requires thermosensitive components in drug carriers for controlled drug release against viral cells. The conformational transition characteristic of leucine zipper-structured lipopeptides is utilized in our lab to modulate the phase transition temperature of liposomes, thus achieving temperature-responsive control. In this study, we computationally examined the conformational transition behaviors of leucine zipper-structured lipopeptides that were modified at the N-terminus by distinct functional groups. The conformational transition temperatures of these lipopeptides were determined by structural analysis of the implicit-solvent replica exchange molecular dynamics simulation trajectories using the dihedral angle principal component analysis and the dictionary of protein secondary structure method. Our calculations revealed that the computed transition temperatures of the lipopeptides are in good agreement with the experimental measurements. The effect of hydrogen bonds on the conformational stability of the lipopeptide dimers was examined in conventional explicit-solvent molecular dynamics simulations. A quantitative correlation of the degree of structural dissociation of the dimers and their binding strength is well described by an exponential fit of the binding free energies to the conformation transition temperatures of the lipopeptides.

Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide

NASA Astrophysics Data System (ADS)

Singh, Krishna P.; Baweja, Lokesh; Wolkenhauer, Olaf; Rahman, Qamar; Gupta, Shailendra K.

2018-03-01

Graphene-based nanomaterials (GBNMs) are widely used in various industrial and biomedical applications. GBNMs of different compositions, size and shapes are being introduced without thorough toxicity evaluation due to the unavailability of regulatory guidelines. Computational toxicity prediction methods are used by regulatory bodies to quickly assess health hazards caused by newer materials. Due to increasing demand of GBNMs in various size and functional groups in industrial and consumer based applications, rapid and reliable computational toxicity assessment methods are urgently needed. In the present work, we investigate the impact of graphene and graphene oxide nanomaterials on the structural conformations of small hepcidin peptide and compare the materials for their structural and conformational changes. Our molecular dynamics simulation studies revealed conformational changes in hepcidin due to its interaction with GBMNs, which results in a loss of its functional properties. Our results indicate that hepcidin peptide undergo severe structural deformations when superimposed on the graphene sheet in comparison to graphene oxide sheet. These observations suggest that graphene is more toxic than a graphene oxide nanosheet of similar area. Overall, this study indicates that computational methods based on structural deformation, using molecular dynamics (MD) simulations, can be used for the early evaluation of toxicity potential of novel nanomaterials.

WEBnm@ v2.0: Web server and services for comparing protein flexibility.

PubMed

Tiwari, Sandhya P; Fuglebakk, Edvin; Hollup, Siv M; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn H; Tekle, Kidane M; Reuter, Nathalie

2014-12-30

Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

Electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state

NASA Astrophysics Data System (ADS)

Petrov, Yu V.; Inogamov, N. A.; Mokshin, A. V.; Galimzyanov, B. N.

2018-01-01

The electrical resistivity and thermal conductivity of liquid aluminum in the two-temperature state is calculated by using the relaxation time approach and structural factor of ions obtained by molecular dynamics simulation. Resistivity witin the Ziman-Evans approach is also considered to be higher than in the approach with previously calculated conductivity via the relaxation time. Calculations based on the construction of the ion structural factor through the classical molecular dynamics and kinetic equation for electrons are more economical in terms of computing resources and give results close to the Kubo-Greenwood with the quantum molecular dynamics calculations.

A Nonlinear Dynamic Model and Free Vibration Analysis of Deployable Mesh Reflectors

NASA Technical Reports Server (NTRS)

Shi, H.; Yang, B.; Thomson, M.; Fang, H.

2011-01-01

This paper presents a dynamic model of deployable mesh reflectors, in which geometric and material nonlinearities of such a space structure are fully described. Then, by linearization around an equilibrium configuration of the reflector structure, a linearized model is obtained. With this linearized model, the natural frequencies and mode shapes of a reflector can be computed. The nonlinear dynamic model of deployable mesh reflectors is verified by using commercial finite element software in numerical simulation. As shall be seen, the proposed nonlinear model is useful for shape (surface) control of deployable mesh reflectors under thermal loads.

LATDYN - PROGRAM FOR SIMULATION OF LARGE ANGLE TRANSIENT DYNAMICS OF FLEXIBLE AND RIGID STRUCTURES

NASA Technical Reports Server (NTRS)

Housner, J. M.

1994-01-01

LATDYN is a computer code for modeling the Large Angle Transient DYNamics of flexible articulating structures and mechanisms involving joints about which members rotate through large angles. LATDYN extends and brings together some of the aspects of Finite Element Structural Analysis, Multi-Body Dynamics, and Control System Analysis; three disciplines that have been historically separate. It combines significant portions of their distinct capabilities into one single analysis tool. The finite element formulation for flexible bodies in LATDYN extends the conventional finite element formulation by using a convected coordinate system for constructing the equation of motion. LATDYN's formulation allows for large displacements and rotations of finite elements subject to the restriction that deformations within each are small. Also, the finite element approach implemented in LATDYN provides a convergent path for checking solutions simply by increasing mesh density. For rigid bodies and joints LATDYN borrows extensively from methodology used in multi-body dynamics where rigid bodies may be defined and connected together through joints (hinges, ball, universal, sliders, etc.). Joints may be modeled either by constraints or by adding joint degrees of freedom. To eliminate error brought about by the separation of structural analysis and control analysis, LATDYN provides symbolic capabilities for modeling control systems which are integrated with the structural dynamic analysis itself. Its command language contains syntactical structures which perform symbolic operations which are also interfaced directly with the finite element structural model, bypassing the modal approximation. Thus, when the dynamic equations representing the structural model are integrated, the equations representing the control system are integrated along with them as a coupled system. This procedure also has the side benefit of enabling a dramatic simplification of the user interface for modeling control systems. Three FORTRAN computer programs, the LATDYN Program, the Preprocessor, and the Postprocessor, make up the collective LATDYN System. The Preprocessor translates user commands into a form which can be used while the LATDYN program provides the computational core. The Postprocessor allows the user to interactively plot and manage a database of LATDYN transient analysis results. It also includes special facilities for modeling control systems and for programming changes to the model which take place during analysis sequence. The documentation includes a Demonstration Problem Manual for the evaluation and verification of results and a Postprocessor guide. Because the program should be viewed as a byproduct of research on technology development, LATDYN's scope is limited. It does not have a wide library of finite elements, and 3-D Graphics are not available. Nevertheless, it does have a measure of "user friendliness". The LATDYN program was developed over a period of several years and was implemented on a CDC NOS/VE & Convex Unix computer. It is written in FORTRAN 77 and has a virtual memory requirement of 1.46 MB. The program was validated on a DEC MICROVAX operating under VMS 5.2.

Thermodynamics of RNA structures by Wang–Landau sampling

PubMed Central

Lou, Feng; Clote, Peter

2010-01-01

Motivation: Thermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures. Results: A non-Boltzmannian Monte Carlo algorithm was designed by Wang and Landau to estimate the density of states for complex systems, such as the Ising model, that exhibit a phase transition. In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. Our method is shown to be much faster than existent software, such as RNAsubopt. From density of states, we compute the partition function over all secondary structures and over all pseudoknot-free hybridizations. The advantage of the WL method is that by adding a function to evaluate the free energy of arbitary pseudoknotted structures and of arbitrary hybridizations, we can estimate thermodynamic parameters for situations known to be NP-complete. This extension to pseudoknots will be made in the sequel to this article; in contrast, the current article describes the WL algorithm applied to pseudoknot-free secondary structures and hybridizations. Availability: The WL RNA hybridization web server is under construction at http://bioinformatics.bc.edu/clotelab/. Contact: clote@bc.edu PMID:20529917

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

Structural dynamics of shroudless, hollow fan blades with composite in-lays

NASA Technical Reports Server (NTRS)

Aiello, R. A.; Hirschbein, M. S.; Chamis, C. C.

1982-01-01

Structural and dynamic analyses are presented for a shroudless, hollow titanium fan blade proposed for future use in aircraft turbine engines. The blade was modeled and analyzed using the composite blade structural analysis computer program (COBSTRAN); an integrated program consisting of mesh generators, composite mechanics codes, NASTRAN, and pre- and post-processors. Vibration and impact analyses are presented. The vibration analysis was conducted with COBSTRAN. Results show the effect of the centrifugal force field on frequencies, twist, and blade camber. Bird impact analysis was performed with the multi-mode blade impact computer program. This program uses the geometric model and modal analysis from the COBSTRAN vibration analysis to determine the gross impact response of the fan blades to bird strikes. The structural performance of this blade is also compared to a blade of similar design but with composite in-lays on the outer surface. Results show that the composite in-lays can be selected (designed) to substantially modify the mechanical performance of the shroudless, hollow fan blade.

Preserving Lagrangian Structure in Nonlinear Model Reduction with Application to Structural Dynamics

DOE PAGES

Carlberg, Kevin; Tuminaro, Ray; Boggs, Paul

2015-03-11

Our work proposes a model-reduction methodology that preserves Lagrangian structure and achieves computational efficiency in the presence of high-order nonlinearities and arbitrary parameter dependence. As such, the resulting reduced-order model retains key properties such as energy conservation and symplectic time-evolution maps. We focus on parameterized simple mechanical systems subjected to Rayleigh damping and external forces, and consider an application to nonlinear structural dynamics. To preserve structure, the method first approximates the system's “Lagrangian ingredients''---the Riemannian metric, the potential-energy function, the dissipation function, and the external force---and subsequently derives reduced-order equations of motion by applying the (forced) Euler--Lagrange equation with thesemore » quantities. Moreover, from the algebraic perspective, key contributions include two efficient techniques for approximating parameterized reduced matrices while preserving symmetry and positive definiteness: matrix gappy proper orthogonal decomposition and reduced-basis sparsification. Our results for a parameterized truss-structure problem demonstrate the practical importance of preserving Lagrangian structure and illustrate the proposed method's merits: it reduces computation time while maintaining high accuracy and stability, in contrast to existing nonlinear model-reduction techniques that do not preserve structure.« less

Preserving Lagrangian Structure in Nonlinear Model Reduction with Application to Structural Dynamics

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

Carlberg, Kevin; Tuminaro, Ray; Boggs, Paul

Our work proposes a model-reduction methodology that preserves Lagrangian structure and achieves computational efficiency in the presence of high-order nonlinearities and arbitrary parameter dependence. As such, the resulting reduced-order model retains key properties such as energy conservation and symplectic time-evolution maps. We focus on parameterized simple mechanical systems subjected to Rayleigh damping and external forces, and consider an application to nonlinear structural dynamics. To preserve structure, the method first approximates the system's “Lagrangian ingredients''---the Riemannian metric, the potential-energy function, the dissipation function, and the external force---and subsequently derives reduced-order equations of motion by applying the (forced) Euler--Lagrange equation with thesemore » quantities. Moreover, from the algebraic perspective, key contributions include two efficient techniques for approximating parameterized reduced matrices while preserving symmetry and positive definiteness: matrix gappy proper orthogonal decomposition and reduced-basis sparsification. Our results for a parameterized truss-structure problem demonstrate the practical importance of preserving Lagrangian structure and illustrate the proposed method's merits: it reduces computation time while maintaining high accuracy and stability, in contrast to existing nonlinear model-reduction techniques that do not preserve structure.« less

Computational modeling of RNA 3D structures, with the aid of experimental restraints

PubMed Central

Magnus, Marcin; Matelska, Dorota; Łach, Grzegorz; Chojnowski, Grzegorz; Boniecki, Michal J; Purta, Elzbieta; Dawson, Wayne; Dunin-Horkawicz, Stanislaw; Bujnicki, Janusz M

2014-01-01

In addition to mRNAs whose primary function is transmission of genetic information from DNA to proteins, numerous other classes of RNA molecules exist, which are involved in a variety of functions, such as catalyzing biochemical reactions or performing regulatory roles. In analogy to proteins, the function of RNAs depends on their structure and dynamics, which are largely determined by the ribonucleotide sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that simulate either the physical process of RNA structure formation (“Greek science” approach) or utilize information derived from known structures of other RNA molecules (“Babylonian science” approach). All computational methods suffer from various limitations that make them generally unreliable for structure prediction of long RNA sequences. However, in many cases, the limitations of computational and experimental methods can be overcome by combining these two complementary approaches with each other. In this work, we review computational approaches for RNA structure prediction, with emphasis on implementations (particular programs) that can utilize restraints derived from experimental analyses. We also list experimental approaches, whose results can be relatively easily used by computational methods. Finally, we describe case studies where computational and experimental analyses were successfully combined to determine RNA structures that would remain out of reach for each of these approaches applied separately. PMID:24785264

Probabilistic Structural Analysis Theory Development

NASA Technical Reports Server (NTRS)

Burnside, O. H.

1985-01-01

The objective of the Probabilistic Structural Analysis Methods (PSAM) project is to develop analysis techniques and computer programs for predicting the probabilistic response of critical structural components for current and future space propulsion systems. This technology will play a central role in establishing system performance and durability. The first year's technical activity is concentrating on probabilistic finite element formulation strategy and code development. Work is also in progress to survey critical materials and space shuttle mian engine components. The probabilistic finite element computer program NESSUS (Numerical Evaluation of Stochastic Structures Under Stress) is being developed. The final probabilistic code will have, in the general case, the capability of performing nonlinear dynamic of stochastic structures. It is the goal of the approximate methods effort to increase problem solving efficiency relative to finite element methods by using energy methods to generate trial solutions which satisfy the structural boundary conditions. These approximate methods will be less computer intensive relative to the finite element approach.

Simultaneous Aerodynamic and Structural Design Optimization (SASDO) for a 3-D Wing

NASA Technical Reports Server (NTRS)

Gumbert, Clyde R.; Hou, Gene J.-W.; Newman, Perry A.

2001-01-01

The formulation and implementation of an optimization method called Simultaneous Aerodynamic and Structural Design Optimization (SASDO) is shown as an extension of the Simultaneous Aerodynamic Analysis and Design Optimization (SAADO) method. It is extended by the inclusion of structure element sizing parameters as design variables and Finite Element Method (FEM) analysis responses as constraints. The method aims to reduce the computational expense. incurred in performing shape and sizing optimization using state-of-the-art Computational Fluid Dynamics (CFD) flow analysis, FEM structural analysis and sensitivity analysis tools. SASDO is applied to a simple. isolated, 3-D wing in inviscid flow. Results show that the method finds the saine local optimum as a conventional optimization method with some reduction in the computational cost and without significant modifications; to the analysis tools.

Chemical calculations on Cray computers

NASA Technical Reports Server (NTRS)

Taylor, Peter R.; Bauschlicher, Charles W., Jr.; Schwenke, David W.

1989-01-01

The influence of recent developments in supercomputing on computational chemistry is discussed with particular reference to Cray computers and their pipelined vector/limited parallel architectures. After reviewing Cray hardware and software the performance of different elementary program structures are examined, and effective methods for improving program performance are outlined. The computational strategies appropriate for obtaining optimum performance in applications to quantum chemistry and dynamics are discussed. Finally, some discussion is given of new developments and future hardware and software improvements.

Nonlinear dynamic simulation of single- and multi-spool core engines

NASA Technical Reports Server (NTRS)

Schobeiri, T.; Lippke, C.; Abouelkheir, M.

1993-01-01

In this paper a new computational method for accurate simulation of the nonlinear dynamic behavior of single- and multi-spool core engines, turbofan engines, and power generation gas turbine engines is presented. In order to perform the simulation, a modularly structured computer code has been developed which includes individual mathematical modules representing various engine components. The generic structure of the code enables the dynamic simulation of arbitrary engine configurations ranging from single-spool thrust generation to multi-spool thrust/power generation engines under adverse dynamic operating conditions. For precise simulation of turbine and compressor components, row-by-row calculation procedures were implemented that account for the specific turbine and compressor cascade and blade geometry and characteristics. The dynamic behavior of the subject engine is calculated by solving a number of systems of partial differential equations, which describe the unsteady behavior of the individual components. In order to ensure the capability, accuracy, robustness, and reliability of the code, comprehensive critical performance assessment and validation tests were performed. As representatives, three different transient cases with single- and multi-spool thrust and power generation engines were simulated. The transient cases range from operating with a prescribed fuel schedule, to extreme load changes, to generator and turbine shut down.

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10).

PubMed

Park, HaJeung; González, Àlex L; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R; Fang, Pengfei; Guo, Min; Disney, Matthew D

2015-06-23

Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide (5')UCU(3')/(3')UCU(5') internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA.

Crystallographic and Computational Analyses of AUUCU Repeating RNA That Causes Spinocerebellar Ataxia Type 10 (SCA10)

PubMed Central

Park, HaJeung; González, Àlex L.; Yildirim, Ilyas; Tran, Tuan; Lohman, Jeremy R.; Fang, Pengfei; Guo, Min; Disney, Matthew D.

2016-01-01

Spinocerebellar ataxia type 10 (SCA10) is caused by a pentanucleotide repeat expansion of r(AUUCU) within intron 9 of the ATXN10 pre-mRNA. The RNA causes disease by a gain-of-function mechanism in which it inactivates proteins involved in RNA biogenesis. Spectroscopic studies showed that r(AUUCU) repeats form a hairpin structure; however, there were no high-resolution structural models prior to this work. Herein, we report the first crystal structure of model r(AUUCU) repeats refined to 2.8 Å and analysis of the structure via molecular dynamics simulations. The r(AUUCU) tracts adopt an overall A-form geometry in which 3 × 3 nucleotide 5′UCU3′/3′UCU5′ internal loops are closed by AU pairs. Helical parameters of the refined structure as well as the corresponding electron density map on the crystallographic model reflect dynamic features of the internal loop. The computational analyses captured dynamic motion of the loop closing pairs, which can form single-stranded conformations with relatively low energies. Overall, the results presented here suggest the possibility for r(AUUCU) repeats to form metastable A-from structures, which can rearrange into single-stranded conformations and attract proteins such as heterogeneous nuclear ribonucleoprotein K (hnRNP K). The information presented here may aid in the rational design of therapeutics targeting this RNA. PMID:26039897

Impact Damage and Strain Rate Effects for Toughened Epoxy Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Minnetyan, Levon

2006-01-01

Structural integrity of composite systems under dynamic impact loading is investigated herein. The GENOA virtual testing software environment is used to implement the effects of dynamic loading on fracture progression and damage tolerance. Combinations of graphite and glass fibers with a toughened epoxy matrix are investigated. The effect of a ceramic coating for the absorption of impact energy is also included. Impact and post impact simulations include verification and prediction of (1) Load and Impact Energy, (2) Impact Damage Size, (3) Maximum Impact Peak Load, (4) Residual Strength, (5) Maximum Displacement, (6) Contribution of Failure Modes to Failure Mechanisms, (7) Prediction of Impact Load Versus Time, and (8) Damage, and Fracture Pattern. A computer model is utilized for the assessment of structural response, progressive fracture, and defect/damage tolerance characteristics. Results show the damage progression sequence and the changes in the structural response characteristics due to dynamic impact. The fundamental premise of computational simulation is that the complete evaluation of composite fracture requires an assessment of ply and subply level damage/fracture processes as the structure is subjected to loads. Simulation results for the graphite/epoxy composite were compared with the impact and tension failure test data, correlation and verification was obtained that included: (1) impact energy, (2) damage size, (3) maximum impact peak load, (4) residual strength, (5) maximum displacement, and (6) failure mechanisms of the composite structure.

NASA Aeronautics: Research and Technology Program Highlights

NASA Technical Reports Server (NTRS)

1990-01-01

This report contains numerous color illustrations to describe the NASA programs in aeronautics. The basic ideas involved are explained in brief paragraphs. The seven chapters deal with Subsonic aircraft, High-speed transport, High-performance military aircraft, Hypersonic/Transatmospheric vehicles, Critical disciplines, National facilities and Organizations & installations. Some individual aircraft discussed are : the SR-71 aircraft, aerospace planes, the high-speed civil transport (HSCT), the X-29 forward-swept wing research aircraft, and the X-31 aircraft. Critical disciplines discussed are numerical aerodynamic simulation, computational fluid dynamics, computational structural dynamics and new experimental testing techniques.

High spatial resolution three-dimensional mapping of vegetation spectral dynamics using computer vision

Treesearch

Jonathan P. Dandois; Erle C. Ellis

2013-01-01

High spatial resolution three-dimensional (3D) measurements of vegetation by remote sensing are advancing ecological research and environmental management. However, substantial economic and logistical costs limit this application, especially for observing phenological dynamics in ecosystem structure and spectral traits. Here we demonstrate a new aerial remote sensing...

Geometric modeling of subcellular structures, organelles, and multiprotein complexes

PubMed Central

Feng, Xin; Xia, Kelin; Tong, Yiying; Wei, Guo-Wei

2013-01-01

SUMMARY Recently, the structure, function, stability, and dynamics of subcellular structures, organelles, and multi-protein complexes have emerged as a leading interest in structural biology. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics. This paper introduces a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation of biomolecular complexes. Particular emphasis is given to the modeling of cryo-electron microscopy data. Lagrangian-triangle meshes are employed for the surface presentation. On the basis of this representation, algorithms are developed for surface area and surface-enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to multiple choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical models are designed to test the computational accuracy and convergence of proposed algorithms. Finally, we select a set of six cryo-electron microscopy data representing typical subcellular complexes to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. This paper offers a comprehensive protocol for the geometric modeling of subcellular structures, organelles, and multiprotein complexes. PMID:23212797

Refinement of the experimental dynamic structure factor for liquid para-hydrogen and ortho-deuterium using semi-classical quantum simulation

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

Smith, Kyle K. G., E-mail: kylesmith@utexas.edu; Rossky, Peter J., E-mail: peter.rossky@austin.utexas.edu; Poulsen, Jens Aage, E-mail: jens72@chem.gu.se

The dynamic structure factor of liquid para-hydrogen and ortho-deuterium in corresponding thermodynamic states (T = 20.0 K, n = 21.24 nm{sup −3}) and (T = 23.0 K, n = 24.61 nm{sup −3}), respectively, has been computed by both the Feynman-Kleinert linearized path-integral (FK-LPI) and Ring-Polymer Molecular Dynamics (RPMD) methods and compared with Inelastic X Ray Scattering spectra. The combined use of computational and experimental methods enabled us to reduce experimental uncertainties in the determination of the true sample spectrum. Furthermore, the refined experimental spectrum of para-hydrogen and ortho-deuterium is consistently reproduced by both FK-LPI and RPMD results at momentum transfers lower than 12.8 nm{sup −1}.more » At larger momentum transfers the FK-LPI results agree with experiment much better for ortho-deuterium than for para-hydrogen. More specifically we found that for k ∼ 20.0 nm{sup −1} para-hydrogen provides a test case for improved approximations to quantum dynamics.« less

Ab initio molecular dynamics simulation of LiBr association in water

NASA Astrophysics Data System (ADS)

Izvekov, Sergei; Philpott, Michael R.

2000-12-01

A computationally economical scheme which unifies the density functional description of an ionic solute and the classical description of a solvent was developed. The density functional part of the scheme comprises Car-Parrinello and related formalisms. The substantial saving in the computer time is achieved by performing the ab initio molecular dynamics of the solute electronic structure in a relatively small basis set constructed from lowest energy Kohn-Sham orbitals calculated for a single anion in vacuum, instead of using plane wave basis. The methodology permits simulation of an ionic solution for longer time scales while keeping accuracy in the prediction of the solute electronic structure. As an example the association of the Li+-Br- ion-pair system in water is studied. The results of the combined molecular dynamics simulation are compared with that obtained from the classical simulation with ion-ion interaction described by the pair potential of Born-Huggins-Mayer type. The comparison reveals an important role played by the polarization of the Br- ion in the dynamics of ion pair association.

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.

Improved dynamic analysis method using load-dependent Ritz vectors

NASA Technical Reports Server (NTRS)

Escobedo-Torres, J.; Ricles, J. M.

1993-01-01

The dynamic analysis of large space structures is important in order to predict their behavior under operating conditions. Computer models of large space structures are characterized by having a large number of degrees of freedom, and the computational effort required to carry out the analysis is very large. Conventional methods of solution utilize a subset of the eigenvectors of the system, but for systems with many degrees of freedom, the solution of the eigenproblem is in many cases the most costly phase of the analysis. For this reason, alternate solution methods need to be considered. It is important that the method chosen for the analysis be efficient and that accurate results be obtainable. It is important that the method chosen for the analysis be efficient and that accurate results be obtainable. The load dependent Ritz vector method is presented as an alternative to the classical normal mode methods for obtaining dynamic responses of large space structures. A simplified model of a space station is used to compare results. Results show that the load dependent Ritz vector method predicts the dynamic response better than the classical normal mode method. Even though this alternate method is very promising, further studies are necessary to fully understand its attributes and limitations.

Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations.

PubMed

Uehara, Shota; Tanaka, Shigenori

2017-04-24

Protein flexibility is a major hurdle in current structure-based virtual screening (VS). In spite of the recent advances in high-performance computing, protein-ligand docking methods still demand tremendous computational cost to take into account the full degree of protein flexibility. In this context, ensemble docking has proven its utility and efficiency for VS studies, but it still needs a rational and efficient method to select and/or generate multiple protein conformations. Molecular dynamics (MD) simulations are useful to produce distinct protein conformations without abundant experimental structures. In this study, we present a novel strategy that makes use of cosolvent-based molecular dynamics (CMD) simulations for ensemble docking. By mixing small organic molecules into a solvent, CMD can stimulate dynamic protein motions and induce partial conformational changes of binding pocket residues appropriate for the binding of diverse ligands. The present method has been applied to six diverse target proteins and assessed by VS experiments using many actives and decoys of DEKOIS 2.0. The simulation results have revealed that the CMD is beneficial for ensemble docking. Utilizing cosolvent simulation allows the generation of druggable protein conformations, improving the VS performance compared with the use of a single experimental structure or ensemble docking by standard MD with pure water as the solvent.

Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters

PubMed Central

Singharoy, Abhishek; Sereda, Yuriy

2012-01-01

Macromolecular assemblies often display a hierarchical organization of macromolecules or their sub-assemblies. To model this, we have formulated a space warping method that enables capturing overall macromolecular structure and dynamics via a set of coarse-grained order parameters (OPs). This article is the first of two describing the construction and computational implementation of an additional class of OPs that has built into them the hierarchical architecture of macromolecular assemblies. To accomplish this, first, the system is divided into subsystems, each of which is described via a representative set of OPs. Then, a global set of variables is constructed from these subsystem-centered OPs to capture overall system organization. Dynamical properties of the resulting OPs are compared to those of our previous nonhierarchical ones, and implied conceptual and computational advantages are discussed for a 100ns, 2 million atom solvated Human Papillomavirus-like particle simulation. In the second article, the hierarchical OPs are shown to enable a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Langevin equations of stochastic OP dynamics. The latter is demonstrated via a force-field based simulation algorithm that probes key structural transition pathways, simultaneously accounting for all-atom details and overall structure. PMID:22661911

Computational simulation of acoustic fatigue for hot composite structures

NASA Technical Reports Server (NTRS)

Singhal, Surendra N.; Murthy, Pappu L. N.; Chamis, Christos C.; Nagpal, Vinod K.; Sutjahjo, Edhi

1991-01-01

Predictive methods/computer codes for the computational simulation of acoustic fatigue resistance of hot composite structures subjected to acoustic excitation emanating from an adjacent vibrating component are discussed. Select codes developed over the past two decades at the NASA Lewis Research Center are used. The codes include computation of acoustic noise generated from a vibrating component, degradation in material properties of a composite laminate at use temperature, dynamic response of acoustically excited hot multilayered composite structure, degradation in the first ply strength of the excited structure due to acoustic loading, and acoustic fatigue resistance of the excited structure, including the propulsion environment. Effects of the laminate lay-up and environment on the acoustic fatigue life are evaluated. The results show that, by keeping the angled plies on the outer surface of the laminate, a substantial increase in the acoustic fatigue life is obtained. The effect of environment (temperature and moisture) is to relieve the residual stresses leading to an increase in the acoustic fatigue life of the excited panel.

Dynamically Reconfigurable Approach to Multidisciplinary Problems

NASA Technical Reports Server (NTRS)

Alexandrov, Natalie M.; Lewis, Robert Michael

2003-01-01

The complexity and autonomy of the constituent disciplines and the diversity of the disciplinary data formats make the task of integrating simulations into a multidisciplinary design optimization problem extremely time-consuming and difficult. We propose a dynamically reconfigurable approach to MDO problem formulation wherein an appropriate implementation of the disciplinary information results in basic computational components that can be combined into different MDO problem formulations and solution algorithms, including hybrid strategies, with relative ease. The ability to re-use the computational components is due to the special structure of the MDO problem. We believe that this structure can and should be used to formulate and solve optimization problems in the multidisciplinary context. The present work identifies the basic computational components in several MDO problem formulations and examines the dynamically reconfigurable approach in the context of a popular class of optimization methods. We show that if the disciplinary sensitivity information is implemented in a modular fashion, the transfer of sensitivity information among the formulations under study is straightforward. This enables not only experimentation with a variety of problem formations in a research environment, but also the flexible use of formulations in a production design environment.

Atomic-scale Modeling of the Structure and Dynamics of Dislocations in Complex Alloys at High Temperatures

NASA Technical Reports Server (NTRS)

Daw, Murray S.; Mills, Michael J.

2003-01-01

We report on the progress made during the first year of the project. Most of the progress at this point has been on the theoretical and computational side. Here are the highlights: (1) A new code, tailored for high-end desktop computing, now combines modern Accelerated Dynamics (AD) with the well-tested Embedded Atom Method (EAM); (2) The new Accelerated Dynamics allows the study of relatively slow, thermally-activated processes, such as diffusion, which are much too slow for traditional Molecular Dynamics; (3) We have benchmarked the new AD code on a rather simple and well-known process: vacancy diffusion in copper; and (4) We have begun application of the AD code to the diffusion of vacancies in ordered intermetallics.

Computer simulation of the coffee leaf miner using sexual Penna aging model

NASA Astrophysics Data System (ADS)

de Oliveira, A. C. S.; Martins, S. G. F.; Zacarias, M. S.

2008-01-01

Forecast models based on climatic conditions are of great interest in Integrated Pest Management (IPM) programs. The success of these models depends, among other factors, on the knowledge of the temperature effect on the pests’ population dynamics. In this direction, a computer simulation was made for the population dynamics of the coffee leaf miner, L. coffeella, at different temperatures, considering experimental data relative to the pest. The age structure was inserted into the dynamics through sexual Penna Model. The results obtained, such as life expectancy, growth rate and annual generations’ number, in agreement to those in laboratory and field conditions, show that the simulation can be used as a forecast model for controlling L. coffeella.

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

PubMed Central

2017-01-01

The effects of crowding in biological environments on biomolecular structure, dynamics, and function remain not well understood. Computer simulations of atomistic models of concentrated peptide and protein systems at different levels of complexity are beginning to provide new insights. Crowding, weak interactions with other macromolecules and metabolites, and altered solvent properties within cellular environments appear to remodel the energy landscape of peptides and proteins in significant ways including the possibility of native state destabilization. Crowding is also seen to affect dynamic properties, both conformational dynamics and diffusional properties of macromolecules. Recent simulations that address these questions are reviewed here and discussed in the context of relevant experiments. PMID:28666087

Kentucky geotechnical database.

DOT National Transportation Integrated Search

2005-03-01

Development of a comprehensive dynamic, geotechnical database is described. Computer software selected to program the client/server application in windows environment, components and structure of the geotechnical database, and primary factors cons...

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

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

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu; Yang, Mo

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heatmore » transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.« less

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

NASA Astrophysics Data System (ADS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

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

Wang, Jianping, E-mail: jwang@iccas.ac.cn; Yang, Fan; Zhao, Juan

In this work, the structural dynamics of N-ethylpropionamide (NEPA), a model molecule of β-peptides, in four typical solvents (DMSO, CH{sub 3}CN, CHCl{sub 3}, and CCl{sub 4}), were examined using the N—H stretching vibration (or the amide-A mode) as a structural probe. Steady-state and transient infrared spectroscopic methods in combination with quantum chemical computations and molecular dynamics simulations were used. It was found that in these solvents, NEPA exists in different aggregation forms, including monomer, dimer, and oligomers. Hydrogen-bonding interaction and local-solvent environment both affect the amide-A absorption profile and its vibrational relaxation dynamics and also affect the structural dynamics ofmore » NEPA. In particular, a correlation between the red-shifted frequency for the NEPA monomer from nonpolar to polar solvent and the vibrational excitation relaxation rate of the N—H stretching mode was observed.« less

A Worst-Case Approach for On-Line Flutter Prediction

NASA Technical Reports Server (NTRS)

Lind, Rick C.; Brenner, Martin J.

1998-01-01

Worst-case flutter margins may be computed for a linear model with respect to a set of uncertainty operators using the structured singular value. This paper considers an on-line implementation to compute these robust margins in a flight test program. Uncertainty descriptions are updated at test points to account for unmodeled time-varying dynamics of the airplane by ensuring the robust model is not invalidated by measured flight data. Robust margins computed with respect to this uncertainty remain conservative to the changing dynamics throughout the flight. A simulation clearly demonstrates this method can improve the efficiency of flight testing by accurately predicting the flutter margin to improve safety while reducing the necessary flight time.

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions

PubMed Central

Bryan, Allen W; O’Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2012-01-01

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively ‘stitches’ strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer’s amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Proteins 2012. © 2011 Wiley Periodicals, Inc. PMID:22095906

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions.

PubMed

Bryan, Allen W; O'Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2012-02-01

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively 'stitches' strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer's amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Copyright © 2011 Wiley Periodicals, Inc.

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

PubMed Central

Brodie, Nicholas I.; Popov, Konstantin I.; Petrotchenko, Evgeniy V.; Dokholyan, Nikolay V.; Borchers, Christoph H.

2017-01-01

We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein—models for α helix–rich and β sheet–rich proteins, respectively—and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures. PMID:28695211

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.

PubMed

Brodie, Nicholas I; Popov, Konstantin I; Petrotchenko, Evgeniy V; Dokholyan, Nikolay V; Borchers, Christoph H

2017-07-01

We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein-models for α helix-rich and β sheet-rich proteins, respectively-and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures.

Software Design Strategies for Multidisciplinary Computational Fluid Dynamics

DTIC Science & Technology

2012-07-01

on the left-hand-side of Figure 3. The resulting unstructured grid system does a good job of representing the flowfield locally around the solid... Laboratory [16–19]. It uses Cartesian block structured grids, which lead to a substantially more efficient computational execution compared to the...including blade sectional lift and pitching moment. These Helios-computed airloads show good agreement with the experimental data. Many of the

Computer architecture evaluation for structural dynamics computations: Project summary

NASA Technical Reports Server (NTRS)

Standley, Hilda M.

1989-01-01

The intent of the proposed effort is the examination of the impact of the elements of parallel architectures on the performance realized in a parallel computation. To this end, three major projects are developed: a language for the expression of high level parallelism, a statistical technique for the synthesis of multicomputer interconnection networks based upon performance prediction, and a queueing model for the analysis of shared memory hierarchies.

2D Automatic body-fitted structured mesh generation using advancing extraction method

USDA-ARS?s Scientific Manuscript database

This paper presents an automatic mesh generation algorithm for body-fitted structured meshes in Computational Fluids Dynamics (CFD) analysis using the Advancing Extraction Method (AEM). The method is applicable to two-dimensional domains with complex geometries, which have the hierarchical tree-like...

2D automatic body-fitted structured mesh generation using advancing extraction method

USDA-ARS?s Scientific Manuscript database

This paper presents an automatic mesh generation algorithm for body-fitted structured meshes in Computational Fluids Dynamics (CFD) analysis using the Advancing Extraction Method (AEM). The method is applicable to two-dimensional domains with complex geometries, which have the hierarchical tree-like...

SPAR improved structure/fluid dynamic analysis capability

NASA Technical Reports Server (NTRS)

Oden, J. T.; Pearson, M. L.

1983-01-01

The capability of analyzing a coupled dynamic system of flowing fluid and elastic structure was added to the SPAR computer code. A method, developed and adopted for use in SPAR utilizes the existing assumed stress hybrid plan element in SPAR. An operational mode was incorporated in SPAR which provides the capability for analyzing the flaw of a two dimensional, incompressible, viscous fluid within rigid boundaries. Equations were developed to provide for the eventual analysis of the interaction of such fluids with an elastic solid.

Dynamic analysis using superelements for a large helicopter model

NASA Technical Reports Server (NTRS)

Patel, M. P.; Shah, L. C.

1978-01-01

Using superelements (substructures), modal and frequency response analysis was performed for a large model of the Advanced Attack Helicopter developed for the U.S. Army. Whiffletree concept was employed so that the residual structure along with the various superelements could be represented as beam-like structures for economical and accurate dynamic analysis. A very large DMAP alter to the rigid format was developed so that the modal analysis, the frequency response, and the strain energy in each component could be computed in the same run.

Structural-Vibration-Response Data Analysis

NASA Technical Reports Server (NTRS)

Smith, W. R.; Hechenlaible, R. N.; Perez, R. C.

1983-01-01

Computer program developed as structural-vibration-response data analysis tool for use in dynamic testing of Space Shuttle. Program provides fast and efficient time-domain least-squares curve-fitting procedure for reducing transient response data to obtain structural model frequencies and dampings from free-decay records. Procedure simultaneously identifies frequencies, damping values, and participation factors for noisy multiple-response records.

Transient analysis techniques in performing impact and crash dynamic studies

NASA Technical Reports Server (NTRS)

Pifko, A. B.; Winter, R.

1989-01-01

Because of the emphasis being placed on crashworthiness as a design requirement, increasing demands are being made by various organizations to analyze a wide range of complex structures that must perform safely when subjected to severe impact loads, such as those generated in a crash event. The ultimate goal of crashworthiness design and analysis is to produce vehicles with the ability to reduce the dynamic forces experienced by the occupants to specified levels, while maintaining a survivable envelope around them during a specified crash event. DYCAST is a nonlinear structural dynamic finite element computer code that started from the plans systems of a finite element program for static nonlinear structural analysis. The essential features of DYCAST are outlined.

Proceedings of the NASTRAN (Tradename) Users’ Colloquium (18th) Held in Portland, Oregon on 23-27 April 1990

DTIC Science & Technology

1990-04-01

Maxwell (Texas A&M University-) 4. ACCURACY OF THE QUAD& THICK SHELL ELEMENT ’........... .. 3.0 by William R. Case, Tiffany D. Bowles, Al ia K. Croft and...Computer Literacy: Mainframe Monsters and Pacman. Symposium on Advances and Trends in Structures and Dynamics, Washington, D.C., October 1984. 4. Woodward...No. 1, 1985. 5. Wilson, E.L., and M. Holt: CAL-80-Computer Assisted Learning of Structural Engineering. Symposium on Advances and Trends in

Volumetric visualization of 3D data

NASA Technical Reports Server (NTRS)

Russell, Gregory; Miles, Richard

1989-01-01

In recent years, there has been a rapid growth in the ability to obtain detailed data on large complex structures in three dimensions. This development occurred first in the medical field, with CAT (computer aided tomography) scans and now magnetic resonance imaging, and in seismological exploration. With the advances in supercomputing and computational fluid dynamics, and in experimental techniques in fluid dynamics, there is now the ability to produce similar large data fields representing 3D structures and phenomena in these disciplines. These developments have produced a situation in which currently there is access to data which is too complex to be understood using the tools available for data reduction and presentation. Researchers in these areas are becoming limited by their ability to visualize and comprehend the 3D systems they are measuring and simulating.

Molecular Structure and Free Energy Landscape for Electron Transport in the Deca-Heme Cytochrome MtrF

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

Breuer, Marian; Zarzycki, Piotr P.; Shi, Liang

2012-12-01

The free energy profile for electron flow through the bacterial deca-heme cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help validate the method and results, because differences in the profiles can be related to differences in the charged amino acids local to specific heme groups. First estimates of reorganization free energies λ yield a range consistent with expectations for partially solvent exposed cofactors, and reveal an activation energy range surmountable for electron flow. Future work will aim at increasing the accuracy of λ with polarizable force fieldmore » dynamics and quantum chemical energy gap calculations, as well as quantum chemical computation of electronic coupling matrix elements.« less

Dynamic condensation of non-classically damped structures using the method of Maclaurin expansion of the frequency response function in Laplace domain

NASA Astrophysics Data System (ADS)

Esmaeilzad, Armin; Khanlari, Karen

2018-07-01

As the number of degrees of freedom (DOFs) in structural dynamic problems becomes larger, the analyzing complexity and CPU usage of computers increase drastically. Condensation (or reduction) method is an efficient technique to reduce the size of the full model or the dimension of the structural matrices by eliminating the unimportant DOFs. After the first presentation of condensation method by Guyan in 1965 for undamped structures, which ignores the dynamic effects of the mass term, various forms of dynamic condensation methods were presented to overcome this issue. Moreover, researchers have tried to expand the dynamic condensation method to non-classically damped structures. Dynamic reduction of such systems is far more complicated than undamped systems. The proposed non-iterative method in this paper is introduced as 'Maclaurin Expansion of the frequency response function in Laplace Domain' (MELD) applied for dynamic reduction of non-classically damped structures. The present approach is implemented in four numerical examples of 2D bending-shear-axial frames with various numbers of stories and spans and also a floating raft isolation system. The results of natural frequencies and dynamic responses of models are compared with each other before and after the dynamic reduction. It is shown that the result accuracy has acceptable convergence in both cases. In addition, it is indicated that the result of the proposed method is more accurate than the results of some other existing condensation methods.

Dynamics of Oxidation of Aluminum Nanoclusters using Variable Charge Molecular-Dynamics Simulations on Parallel Computers

NASA Astrophysics Data System (ADS)

Campbell, Timothy; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya; Ogata, Shuji; Rodgers, Stephen

1999-06-01

Oxidation of aluminum nanoclusters is investigated with a parallel molecular-dynamics approach based on dynamic charge transfer among atoms. Structural and dynamic correlations reveal that significant charge transfer gives rise to large negative pressure in the oxide which dominates the positive pressure due to steric forces. As a result, aluminum moves outward and oxygen moves towards the interior of the cluster with the aluminum diffusivity 60% higher than that of oxygen. A stable 40 Å thick amorphous oxide is formed; this is in excellent agreement with experiments.

Multiscale Modeling of Grain Boundaries in ZrB2: Structure, Energetics, and Thermal Resistance

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Squire, Thomas H.; Bauschlicher, Charles W., Jr.

2012-01-01

A combination of ab initio, atomistic and finite element methods (FEM) were used to investigate the structures, energetics and lattice thermal conductance of grain boundaries for the ultra high temperature ceramic ZrB2. Atomic models of idealized boundaries were relaxed using density functional theory. Information about bonding across the interfaces was determined from the electron localization function. The Kapitza conductance of larger scale versions of the boundary models were computed using non-equilibrium molecular dynamics. The interfacial thermal parameters together with single crystal thermal conductivities were used as parameters in microstructural computations. FEM meshes were constructed on top of microstructural images. From these computations, the effective thermal conductivity of the polycrystalline structure was determined.

A Nonlinear Modal Aeroelastic Solver for FUN3D

NASA Technical Reports Server (NTRS)

Goldman, Benjamin D.; Bartels, Robert E.; Biedron, Robert T.; Scott, Robert C.

2016-01-01

A nonlinear structural solver has been implemented internally within the NASA FUN3D computational fluid dynamics code, allowing for some new aeroelastic capabilities. Using a modal representation of the structure, a set of differential or differential-algebraic equations are derived for general thin structures with geometric nonlinearities. ODEPACK and LAPACK routines are linked with FUN3D, and the nonlinear equations are solved at each CFD time step. The existing predictor-corrector method is retained, whereby the structural solution is updated after mesh deformation. The nonlinear solver is validated using a test case for a flexible aeroshell at transonic, supersonic, and hypersonic flow conditions. Agreement with linear theory is seen for the static aeroelastic solutions at relatively low dynamic pressures, but structural nonlinearities limit deformation amplitudes at high dynamic pressures. No flutter was found at any of the tested trajectory points, though LCO may be possible in the transonic regime.

Experimental validation of docking and capture using space robotics testbeds

NASA Technical Reports Server (NTRS)

Spofford, John; Schmitz, Eric; Hoff, William

1991-01-01

This presentation describes the application of robotic and computer vision systems to validate docking and capture operations for space cargo transfer vehicles. Three applications are discussed: (1) air bearing systems in two dimensions that yield high quality free-flying, flexible, and contact dynamics; (2) validation of docking mechanisms with misalignment and target dynamics; and (3) computer vision technology for target location and real-time tracking. All the testbeds are supported by a network of engineering workstations for dynamic and controls analyses. Dynamic simulation of multibody rigid and elastic systems are performed with the TREETOPS code. MATRIXx/System-Build and PRO-MATLAB/Simulab are the tools for control design and analysis using classical and modern techniques such as H-infinity and LQG/LTR. SANDY is a general design tool to optimize numerically a multivariable robust compensator with a user-defined structure. Mathematica and Macsyma are used to derive symbolically dynamic and kinematic equations.

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface

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

Lisal, Martin; Department of Physics, Faculty of Science, J. E. Purkinje University, 400 96 Usti n. Lab.; Izak, Pavel

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf{sub 2}N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 {mu}mol/m{sup 2} at 300 K. For [bmim][Tf{sub 2}N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are {+-}0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and itsmore » value decreases with increase of the n-hexane surface density. The [bmim][Tf{sub 2}N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.« less

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface.

PubMed

Lísal, Martin; Izák, Pavel

2013-07-07

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf2N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 μmol/m(2) at 300 K. For [bmim][Tf2N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are ±0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf2N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

Adaptations in Electronic Structure Calculations in Heterogeneous Environments

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

Talamudupula, Sai

Modern quantum chemistry deals with electronic structure calculations of unprecedented complexity and accuracy. They demand full power of high-performance computing and must be in tune with the given architecture for superior e ciency. To make such applications resourceaware, it is desirable to enable their static and dynamic adaptations using some external software (middleware), which may monitor both system availability and application needs, rather than mix science with system-related calls inside the application. The present work investigates scienti c application interlinking with middleware based on the example of the computational chemistry package GAMESS and middleware NICAN. The existing synchronous model ismore » limited by the possible delays due to the middleware processing time under the sustainable runtime system conditions. Proposed asynchronous and hybrid models aim at overcoming this limitation. When linked with NICAN, the fragment molecular orbital (FMO) method is capable of adapting statically and dynamically its fragment scheduling policy based on the computing platform conditions. Signi cant execution time and throughput gains have been obtained due to such static adaptations when the compute nodes have very di erent core counts. Dynamic adaptations are based on the main memory availability at run time. NICAN prompts FMO to postpone scheduling certain fragments, if there is not enough memory for their immediate execution. Hence, FMO may be able to complete the calculations whereas without such adaptations it aborts.« less

Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems.

PubMed

Williams, Richard A; Timmis, Jon; Qwarnstrom, Eva E

2016-01-01

Computational modelling and simulation is increasingly being used to complement traditional wet-lab techniques when investigating the mechanistic behaviours of complex biological systems. In order to ensure computational models are fit for purpose, it is essential that the abstracted view of biology captured in the computational model, is clearly and unambiguously defined within a conceptual model of the biological domain (a domain model), that acts to accurately represent the biological system and to document the functional requirements for the resultant computational model. We present a domain model of the IL-1 stimulated NF-κB signalling pathway, which unambiguously defines the spatial, temporal and stochastic requirements for our future computational model. Through the development of this model, we observe that, in isolation, UML is not sufficient for the purpose of creating a domain model, and that a number of descriptive and multivariate statistical techniques provide complementary perspectives, in particular when modelling the heterogeneity of dynamics at the single-cell level. We believe this approach of using UML to define the structure and interactions within a complex system, along with statistics to define the stochastic and dynamic nature of complex systems, is crucial for ensuring that conceptual models of complex dynamical biosystems, which are developed using UML, are fit for purpose, and unambiguously define the functional requirements for the resultant computational model.

Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems

PubMed Central

Timmis, Jon; Qwarnstrom, Eva E.

2016-01-01

Computational modelling and simulation is increasingly being used to complement traditional wet-lab techniques when investigating the mechanistic behaviours of complex biological systems. In order to ensure computational models are fit for purpose, it is essential that the abstracted view of biology captured in the computational model, is clearly and unambiguously defined within a conceptual model of the biological domain (a domain model), that acts to accurately represent the biological system and to document the functional requirements for the resultant computational model. We present a domain model of the IL-1 stimulated NF-κB signalling pathway, which unambiguously defines the spatial, temporal and stochastic requirements for our future computational model. Through the development of this model, we observe that, in isolation, UML is not sufficient for the purpose of creating a domain model, and that a number of descriptive and multivariate statistical techniques provide complementary perspectives, in particular when modelling the heterogeneity of dynamics at the single-cell level. We believe this approach of using UML to define the structure and interactions within a complex system, along with statistics to define the stochastic and dynamic nature of complex systems, is crucial for ensuring that conceptual models of complex dynamical biosystems, which are developed using UML, are fit for purpose, and unambiguously define the functional requirements for the resultant computational model. PMID:27571414

Software package for modeling spin-orbit motion in storage rings

NASA Astrophysics Data System (ADS)

Zyuzin, D. V.

2015-12-01

A software package providing a graphical user interface for computer experiments on the motion of charged particle beams in accelerators, as well as analysis of obtained data, is presented. The software package was tested in the framework of the international project on electric dipole moment measurement JEDI (Jülich Electric Dipole moment Investigations). The specific features of particle spin motion imply the requirement to use a cyclic accelerator (storage ring) consisting of electrostatic elements, which makes it possible to preserve horizontal polarization for a long time. Computer experiments study the dynamics of 106-109 particles in a beam during 109 turns in an accelerator (about 1012-1015 integration steps for the equations of motion). For designing an optimal accelerator structure, a large number of computer experiments on polarized beam dynamics are required. The numerical core of the package is COSY Infinity, a program for modeling spin-orbit dynamics.

The method of parallel-hierarchical transformation for rapid recognition of dynamic images using GPGPU technology

NASA Astrophysics Data System (ADS)

Timchenko, Leonid; Yarovyi, Andrii; Kokriatskaya, Nataliya; Nakonechna, Svitlana; Abramenko, Ludmila; Ławicki, Tomasz; Popiel, Piotr; Yesmakhanova, Laura

2016-09-01

The paper presents a method of parallel-hierarchical transformations for rapid recognition of dynamic images using GPU technology. Direct parallel-hierarchical transformations based on cluster CPU-and GPU-oriented hardware platform. Mathematic models of training of the parallel hierarchical (PH) network for the transformation are developed, as well as a training method of the PH network for recognition of dynamic images. This research is most topical for problems on organizing high-performance computations of super large arrays of information designed to implement multi-stage sensing and processing as well as compaction and recognition of data in the informational structures and computer devices. This method has such advantages as high performance through the use of recent advances in parallelization, possibility to work with images of ultra dimension, ease of scaling in case of changing the number of nodes in the cluster, auto scan of local network to detect compute nodes.

Perform - A performance optimizing computer program for dynamic systems subject to transient loadings

NASA Technical Reports Server (NTRS)

Pilkey, W. D.; Wang, B. P.; Yoo, Y.; Clark, B.

1973-01-01

A description and applications of a computer capability for determining the ultimate optimal behavior of a dynamically loaded structural-mechanical system are presented. This capability provides characteristics of the theoretically best, or limiting, design concept according to response criteria dictated by design requirements. Equations of motion of the system in first or second order form include incompletely specified elements whose characteristics are determined in the optimization of one or more performance indices subject to the response criteria in the form of constraints. The system is subject to deterministic transient inputs, and the computer capability is designed to operate with a large linear programming on-the-shelf software package which performs the desired optimization. The report contains user-oriented program documentation in engineering, problem-oriented form. Applications cover a wide variety of dynamics problems including those associated with such diverse configurations as a missile-silo system, impacting freight cars, and an aircraft ride control system.

Accelerating Time Integration for the Shallow Water Equations on the Sphere Using GPUs

DOE PAGES

Archibald, R.; Evans, K. J.; Salinger, A.

2015-06-01

The push towards larger and larger computational platforms has made it possible for climate simulations to resolve climate dynamics across multiple spatial and temporal scales. This direction in climate simulation has created a strong need to develop scalable timestepping methods capable of accelerating throughput on high performance computing. This study details the recent advances in the implementation of implicit time stepping of the spectral element dynamical core within the United States Department of Energy (DOE) Accelerated Climate Model for Energy (ACME) on graphical processing units (GPU) based machines. We demonstrate how solvers in the Trilinos project are interfaced with ACMEmore » and GPU kernels to increase computational speed of the residual calculations in the implicit time stepping method for the atmosphere dynamics. We demonstrate the optimization gains and data structure reorganization that facilitates the performance improvements.« less

Wind Farm Flow Modeling using an Input-Output Reduced-Order Model

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

Annoni, Jennifer; Gebraad, Pieter; Seiler, Peter

Wind turbines in a wind farm operate individually to maximize their own power regardless of the impact of aerodynamic interactions on neighboring turbines. There is the potential to increase power and reduce overall structural loads by properly coordinating turbines. To perform control design and analysis, a model needs to be of low computational cost, but retains the necessary dynamics seen in high-fidelity models. The objective of this work is to obtain a reduced-order model that represents the full-order flow computed using a high-fidelity model. A variety of methods, including proper orthogonal decomposition and dynamic mode decomposition, can be used tomore » extract the dominant flow structures and obtain a reduced-order model. In this paper, we combine proper orthogonal decomposition with a system identification technique to produce an input-output reduced-order model. This technique is used to construct a reduced-order model of the flow within a two-turbine array computed using a large-eddy simulation.« less

Molecular modeling of biomolecules by paramagnetic NMR and computational hybrid methods.

PubMed

Pilla, Kala Bharath; Gaalswyk, Kari; MacCallum, Justin L

2017-11-01

The 3D atomic structures of biomolecules and their complexes are key to our understanding of biomolecular function, recognition, and mechanism. However, it is often difficult to obtain structures, particularly for systems that are complex, dynamic, disordered, or exist in environments like cell membranes. In such cases sparse data from a variety of paramagnetic NMR experiments offers one possible source of structural information. These restraints can be incorporated in computer modeling algorithms that can accurately translate the sparse experimental data into full 3D atomic structures. In this review, we discuss various types of paramagnetic NMR/computational hybrid modeling techniques that can be applied to successful modeling of not only the atomic structure of proteins but also their interacting partners. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI

NASA Astrophysics Data System (ADS)

Alba, Josephine; Marcaida, Maria Jose; Prieto, Jesus; Montoya, Guillermo; Molina, Rafael; D'Abramo, Marco

2017-12-01

I-DmoI, from the hyperthermophilic archaeon Desulfurococcus mobilis, belongs to the LAGLIDADG homing endonuclease protein family. Its members are highly specific enzymes capable of recognizing long DNA target sequences, thus providing potential tools for genome manipulation. Working towards this particular application, many efforts have been made to generate mesophilic variants of I-DmoI that function at lower temperatures than the wild-type. Here, we report a structural and computational analysis of two I-DmoI mesophilic mutants. Despite very limited structural variations between the crystal structures of these variants and the wild-type, a different dynamical behaviour near the cleavage sites is observed. In particular, both the dynamics of the water molecules and the protein perturbation effect on the cleavage site correlate well with the changes observed in the experimental enzymatic activity.

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome.

PubMed

Šponer, Jiří; Banáš, Pavel; Jurečka, Petr; Zgarbová, Marie; Kührová, Petra; Havrila, Marek; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, Michal

2014-05-15

We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.

Bipartite graphs as models of population structures in evolutionary multiplayer games.

PubMed

Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, "games on graphs" study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner's dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner's dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

Comparing Classical Water Models Using Molecular Dynamics to Find Bulk Properties

ERIC Educational Resources Information Center

Kinnaman, Laura J.; Roller, Rachel M.; Miller, Carrie S.

2018-01-01

A computational chemistry exercise for the undergraduate physical chemistry laboratory is described. In this exercise, students use the molecular dynamics package Amber to generate trajectories of bulk liquid water for 4 different water models (TIP3P, OPC, SPC/E, and TIP4Pew). Students then process the trajectory to calculate structural (radial…

Earth and ocean modeling

NASA Technical Reports Server (NTRS)

Knezovich, F. M.

1976-01-01

A modular structured system of computer programs is presented utilizing earth and ocean dynamical data keyed to finitely defined parameters. The model is an assemblage of mathematical algorithms with an inherent capability of maturation with progressive improvements in observational data frequencies, accuracies and scopes. The Eom in its present state is a first-order approach to a geophysical model of the earth's dynamics.

Characterization, Modeling, and Failure Analysis of Composite Structure Materials under Static and Dynamic Loading

NASA Astrophysics Data System (ADS)

Werner, Brian Thomas

Composite structures have long been used in many industries where it is advantageous to reduce weight while maintaining high stiffness and strength. Composites can now be found in an ever broadening range of applications: sporting equipment, automobiles, marine and aerospace structures, and energy production. These structures are typically sandwich panels composed of fiber reinforced polymer composite (FRPC) facesheets which provide the stiffness and the strength and a low density polymeric foam core that adds bending rigidity with little additional weight. The expanding use of composite structures exposes them to high energy, high velocity dynamic loadings which produce multi-axial dynamic states of stress. This circumstance can present quite a challenge to designers, as composite structures are highly anisotropic and display properties that are sensitive to loading rates. Computer codes are continually in development to assist designers in the creation of safe, efficient structures. While the design of an optimal composite structure is more complex, engineers can take advantage of the effect of enhanced energy dissipation displayed by a composite when loaded at high strain rates. In order to build and verify effective computer codes, the underlying assumptions must be verified by laboratory experiments. Many of these codes look to use a micromechanical approach to determine the response of the structure. For this, the material properties of the constituent materials must be verified, three-dimensional constitutive laws must be developed, and failure of these materials must be investigated under static and dynamic loading conditions. In this study, simple models are sought not only to ease their implementation into such codes, but to allow for efficient characterization of new materials that may be developed. Characterization of composite materials and sandwich structures is a costly, time intensive process. A constituent based design approach evaluates potential combinations of materials in a much faster and more efficient manner.

Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design.

PubMed

Ludwiczak, Jan; Jarmula, Adam; Dunin-Horkawicz, Stanislaw

2018-07-01

Computational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensembles and showed that such a combined approach generates 20-30% more diverse sequences than currently available methods with only a slight increase in computation time. Importantly, the increase in diversity is achieved without a loss in the quality of the designed sequences assessed by their resemblance to natural sequences. We demonstrate that the MD-based procedure is also applicable to de novo design tasks started from backbone structures without any sequence information. In addition, we implemented a protocol that can be used to assess the stability of designed models and to select the best candidates for experimental validation. In sum our results demonstrate that the MD ensemble-based flexible backbone design can be a viable method for protein design, especially for tasks that require a large pool of diverse sequences. Copyright © 2018 Elsevier Inc. All rights reserved.

Interfacial gauge methods for incompressible fluid dynamics

DOE PAGES

Saye, R.

2016-06-10

Designing numerical methods for incompressible fluid flow involving moving interfaces, for example, in the computational modeling of bubble dynamics, swimming organisms, or surface waves, presents challenges due to the coupling of interfacial forces with incompressibility constraints. A class of methods, denoted interfacial gauge methods, is introduced for computing solutions to the corresponding incompressible Navier-Stokes equations. These methods use a type of "gauge freedom" to reduce the numerical coupling between fluid velocity, pressure, and interface position, allowing high-order accurate numerical methods to be developed more easily. Making use of an implicit mesh discontinuous Galerkin framework, developed in tandem with this work,more » high-order results are demonstrated, including surface tension dynamics in which fluid velocity, pressure, and interface geometry are computed with fourth-order spatial accuracy in the maximum norm. Applications are demonstrated with two-phase fluid flow displaying fine-scaled capillary wave dynamics, rigid body fluid-structure interaction, and a fluid-jet free surface flow problem exhibiting vortex shedding induced by a type of Plateau-Rayleigh instability. The developed methods can be generalized to other types of interfacial flow and facilitate precise computation of complex fluid interface phenomena.« less

Cumulutive reports and publications through December 31, 1984

NASA Technical Reports Server (NTRS)

1985-01-01

A complete list of the Institute for Computer Applications in Science and Engineering (ICASE) Reports are given. Since ICASE Reports are intended to be preprints of articles that will appear in journals or conference proceedings, the published reference is included when it is available. Topics include numerical methods, parameter identification, fluid dynamics, acoustics, structural analysis, and computers.

Grid Generation for Multidisciplinary Design and Optimization of an Aerospace Vehicle: Issues and Challenges

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2000-01-01

The purpose of this paper is to discuss grid generation issues and to challenge the grid generation community to develop tools suitable for automated multidisciplinary analysis and design optimization of aerospace vehicles. Special attention is given to the grid generation issues of computational fluid dynamics and computational structural mechanics disciplines.

A Branch-and-Bound Algorithm for Fitting Anti-Robinson Structures to Symmetric Dissimilarity Matrices.

ERIC Educational Resources Information Center

Brusco, Michael J.

2002-01-01

Developed a branch-and-bound algorithm that can be used to seriate a symmetric dissimilarity matrix by identifying a reordering of rows and columns of the matrix optimizing an anti-Robinson criterion. Computational results suggest that with respect to computational efficiency, the approach is generally competitive with dynamic programming. (SLD)

Graph Theoretic Foundations of Multibody Dynamics Part I: Structural Properties

PubMed Central

Jain, Abhinandan

2011-01-01

This is the first part of two papers that use concepts from graph theory to obtain a deeper understanding of the mathematical foundations of multibody dynamics. The key contribution is the development of a unifying framework that shows that key analytical results and computational algorithms in multibody dynamics are a direct consequence of structural properties and require minimal assumptions about the specific nature of the underlying multibody system. This first part focuses on identifying the abstract graph theoretic structural properties of spatial operator techniques in multibody dynamics. The second part paper exploits these structural properties to develop a broad spectrum of analytical results and computational algorithms. Towards this, we begin with the notion of graph adjacency matrices and generalize it to define block-weighted adjacency (BWA) matrices and their 1-resolvents. Previously developed spatial operators are shown to be special cases of such BWA matrices and their 1-resolvents. These properties are shown to hold broadly for serial and tree topology multibody systems. Specializations of the BWA and 1-resolvent matrices are referred to as spatial kernel operators (SKO) and spatial propagation operators (SPO). These operators and their special properties provide the foundation for the analytical and algorithmic techniques developed in the companion paper. We also use the graph theory concepts to study the topology induced sparsity structure of these operators and the system mass matrix. Similarity transformations of these operators are also studied. While the detailed development is done for the case of rigid-link multibody systems, the extension of these techniques to a broader class of systems (e.g. deformable links) are illustrated. PMID:22102790

Vibration-based health monitoring and model refinement of civil engineering structures

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

Farrar, C.R.; Doebling, S.W.

1997-10-01

Damage or fault detection, as determined by changes in the dynamic properties of structures, is a subject that has received considerable attention in the technical literature beginning approximately 30 years ago. The basic idea is that changes in the structure`s properties, primarily stiffness, will alter the dynamic properties of the structure such as resonant frequencies and mode shapes, and properties derived from these quantities such as modal-based flexibility. Recently, this technology has been investigated for applications to health monitoring of large civil engineering structures. This presentation will discuss such a study undertaken by engineers from New Mexico Sate University, Sandiamore » National Laboratory and Los Alamos National Laboratory. Experimental modal analyses were performed in an undamaged interstate highway bridge and immediately after four successively more severe damage cases were inflicted in the main girder of the structure. Results of these tests provide insight into the abilities of modal-based damage ID methods to identify damage and the current limitations of this technology. Closely related topics that will be discussed are the use of modal properties to validate computer models of the structure, the use of these computer models in the damage detection process, and the general lack of experimental investigation of large civil engineering structures.« less

Resting-state functional connectivity emerges from structurally and dynamically shaped slow linear fluctuations.

PubMed

Deco, Gustavo; Ponce-Alvarez, Adrián; Mantini, Dante; Romani, Gian Luca; Hagmann, Patric; Corbetta, Maurizio

2013-07-03

Brain fluctuations at rest are not random but are structured in spatial patterns of correlated activity across different brain areas. The question of how resting-state functional connectivity (FC) emerges from the brain's anatomical connections has motivated several experimental and computational studies to understand structure-function relationships. However, the mechanistic origin of resting state is obscured by large-scale models' complexity, and a close structure-function relation is still an open problem. Thus, a realistic but simple enough description of relevant brain dynamics is needed. Here, we derived a dynamic mean field model that consistently summarizes the realistic dynamics of a detailed spiking and conductance-based synaptic large-scale network, in which connectivity is constrained by diffusion imaging data from human subjects. The dynamic mean field approximates the ensemble dynamics, whose temporal evolution is dominated by the longest time scale of the system. With this reduction, we demonstrated that FC emerges as structured linear fluctuations around a stable low firing activity state close to destabilization. Moreover, the model can be further and crucially simplified into a set of motion equations for statistical moments, providing a direct analytical link between anatomical structure, neural network dynamics, and FC. Our study suggests that FC arises from noise propagation and dynamical slowing down of fluctuations in an anatomically constrained dynamical system. Altogether, the reduction from spiking models to statistical moments presented here provides a new framework to explicitly understand the building up of FC through neuronal dynamics underpinned by anatomical connections and to drive hypotheses in task-evoked studies and for clinical applications.

Molecular Dynamics Simulation of WSK-3, a Computationally Designed, Water-Soluble Variant of the Integral Membrane Protein KcsA

PubMed Central

Bronson, Jonathan; Lee, One-Sun; Saven, Jeffery G.

2006-01-01

Poor solubility and low expression levels often make membrane proteins difficult to study. An alternative to the use of detergents to solubilize these aggregation-prone proteins is the partial redesign of the sequence so as to confer water solubility. Recently, computationally assisted membrane protein solubilization (CAMPS) has been reported, where exposed hydrophobic residues on a protein's surface are computationally redesigned. Herein, the structure and fluctuations of a designed, water-soluble variant of KcsA (WSK-3) were studied using molecular dynamics simulations. The root mean square deviation of the protein from its starting structure, where the backbone coordinates are those of KcsA, was 1.8 Å. The structure of salt bridges involved in structural specificity and solubility were examined. The preferred configuration of ions and water in the selectivity filter of WSK-3 was consistent with the reported preferences for KcsA. The structure of the selectivity filter was maintained, which is consistent with WSK-3 having an affinity for agitoxin2 comparable to that of wild-type KcsA. In contrast to KcsA, the central cavity's side chains were observed to reorient, allowing water diffusion through the side of the cavity wall. These simulations provide an atomistic analysis of the CAMPS strategy and its implications for further investigations of membrane proteins. PMID:16299086

A dynamic structural model of expanded RNA CAG repeats: A refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations

PubMed Central

Yildirim, Ilyas; Park, Hajeung; Disney, Matthew D.; Schatz, George C.

2013-01-01

One class of functionally important RNA is repeating transcripts that cause disease through various mechanisms. For example, expanded r(CAG) repeats can cause Huntington’s and other disease through translation of toxic proteins. Herein, crystal structure of r[5ʹUUGGGC(CAG)3GUCC]2, a model of CAG expanded transcripts, refined to 1.65 Å resolution is disclosed that show both anti-anti and syn-anti orientations for 1×1 nucleotide AA internal loops. Molecular dynamics (MD) simulations using Amber force field in explicit solvent were run for over 500 ns on model systems r(5ʹGCGCAGCGC)2 (MS1) and r(5ʹCCGCAGCGG)2 (MS2). In these MD simulations, both anti-anti and syn-anti AA base pairs appear to be stable. While anti-anti AA base pairs were dynamic and sampled multiple anti-anti conformations, no syn-anti↔anti-anti transformations were observed. Umbrella sampling simulations were run on MS2, and a 2D free energy surface was created to extract transformation pathways. In addition, over 800 ns explicit solvent MD simulation was run on r[5ʹGGGC(CAG)3GUCC]2, which closely represents the refined crystal structure. One of the terminal AA base pairs (syn-anti conformation), transformed to anti-anti conformation. The pathway followed in this transformation was the one predicted by umbrella sampling simulations. Further analysis showed a binding pocket near AA base pairs in syn-anti conformations. Computational results combined with the refined crystal structure show that global minimum conformation of 1×1 nucleotide AA internal loops in r(CAG) repeats is anti-anti but can adopt syn-anti depending on the environment. These results are important to understand RNA dynamic-function relationships and develop small molecules that target RNA dynamic ensembles. PMID:23441937

Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.

PubMed Central

Guenot, J.; Kollman, P. A.

1992-01-01

Although aqueous simulations with periodic boundary conditions more accurately describe protein dynamics than in vacuo simulations, these are computationally intensive for most proteins. Trp repressor dynamic simulations with a small water shell surrounding the starting model yield protein trajectories that are markedly improved over gas phase, yet computationally efficient. Explicit water in molecular dynamics simulations maintains surface exposure of protein hydrophilic atoms and burial of hydrophobic atoms by opposing the otherwise asymmetric protein-protein forces. This properly orients protein surface side chains, reduces protein fluctuations, and lowers the overall root mean square deviation from the crystal structure. For simulations with crystallographic waters only, a linear or sigmoidal distance-dependent dielectric yields a much better trajectory than does a constant dielectric model. As more water is added to the starting model, the differences between using distance-dependent and constant dielectric models becomes smaller, although the linear distance-dependent dielectric yields an average structure closer to the crystal structure than does a constant dielectric model. Multiplicative constants greater than one, for the linear distance-dependent dielectric simulations, produced trajectories that are progressively worse in describing trp repressor dynamics. Simulations of bovine pancreatic trypsin were used to ensure that the trp repressor results were not protein dependent and to explore the effect of the nonbonded cutoff on the distance-dependent and constant dielectric simulation models. The nonbonded cutoff markedly affected the constant but not distance-dependent dielectric bovine pancreatic trypsin inhibitor simulations. As with trp repressor, the distance-dependent dielectric model with a shell of water surrounding the protein produced a trajectory in better agreement with the crystal structure than a constant dielectric model, and the physical properties of the trajectory average structure, both with and without a nonbonded cutoff, were comparable. PMID:1304396

Structural Loads Analysis for Wave Energy Converters

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

van Rij, Jennifer A; Yu, Yi-Hsiang; Guo, Yi

2017-06-03

This study explores and verifies the generalized body-modes method for evaluating the structural loads on a wave energy converter (WEC). Historically, WEC design methodologies have focused primarily on accurately evaluating hydrodynamic loads, while methodologies for evaluating structural loads have yet to be fully considered and incorporated into the WEC design process. As wave energy technologies continue to advance, however, it has become increasingly evident that an accurate evaluation of the structural loads will enable an optimized structural design, as well as the potential utilization of composites and flexible materials, and hence reduce WEC costs. Although there are many computational fluidmore » dynamics, structural analyses and fluid-structure-interaction (FSI) codes available, the application of these codes is typically too computationally intensive to be practical in the early stages of the WEC design process. The generalized body-modes method, however, is a reduced order, linearized, frequency-domain FSI approach, performed in conjunction with the linear hydrodynamic analysis, with computation times that could realistically be incorporated into the WEC design process.« less

Reduced-Order Aerothermoelastic Analysis of Hypersonic Vehicle Structures

NASA Astrophysics Data System (ADS)

Falkiewicz, Nathan J.

Design and simulation of hypersonic vehicles require consideration of a variety of disciplines due to the highly coupled nature of the flight regime. In order to capture all of the potential effects on vehicle dynamics, one must consider the aerodynamics, aerodynamic heating, heat transfer, and structural dynamics as well as the interactions between these disciplines. The problem is further complicated by the large computational expense involved in capturing all of these effects and their interactions in a full-order sense. While high-fidelity modeling techniques exist for each of these disciplines, the use of such techniques is computationally infeasible in a vehicle design and control system simulation setting for such a highly coupled problem. Early in the design stage, many iterations of analyses may need to be carried out as the vehicle design matures, thus requiring quick analysis turnaround time. Additionally, the number of states used in the analyses must be small enough to allow for efficient control simulation and design. As a result, alternatives to full-order models must be considered. This dissertation presents a fully coupled, reduced-order aerothermoelastic framework for the modeling and analysis of hypersonic vehicle structures. The reduced-order transient thermal solution is a modal solution based on the proper orthogonal decomposition. The reduced-order structural dynamic model is based on projection of the equations of motion onto a Ritz modal subspace that is identified a priori. The reduced-order models are assembled into a time-domain aerothermoelastic simulation framework which uses a partitioned time-marching scheme to account for the disparate time scales of the associated physics. The aerothermoelastic modeling framework is outlined and the formulations associated with the unsteady aerodynamics, aerodynamic heating, transient thermal, and structural dynamics are outlined. Results demonstrate the accuracy of the reduced-order transient thermal and structural dynamic models under variation in boundary conditions and flight conditions. The framework is applied to representative hypersonic vehicle control surface structures and a variety of studies are conducted to assess the impact of aerothermoelastic effects on hypersonic vehicle dynamics. The results presented in this dissertation demonstrate the ability of the proposed framework to perform efficient aerothermoelastic analysis.

Coarse-Grained Descriptions of Dynamics for Networks with Both Intrinsic and Structural Heterogeneities

PubMed Central

Bertalan, Tom; Wu, Yan; Laing, Carlo; Gear, C. William; Kevrekidis, Ioannis G.

2017-01-01

Finding accurate reduced descriptions for large, complex, dynamically evolving networks is a crucial enabler to their simulation, analysis, and ultimately design. Here, we propose and illustrate a systematic and powerful approach to obtaining good collective coarse-grained observables—variables successfully summarizing the detailed state of such networks. Finding such variables can naturally lead to successful reduced dynamic models for the networks. The main premise enabling our approach is the assumption that the behavior of a node in the network depends (after a short initial transient) on the node identity: a set of descriptors that quantify the node properties, whether intrinsic (e.g., parameters in the node evolution equations) or structural (imparted to the node by its connectivity in the particular network structure). The approach creates a natural link with modeling and “computational enabling technology” developed in the context of Uncertainty Quantification. In our case, however, we will not focus on ensembles of different realizations of a problem, each with parameters randomly selected from a distribution. We will instead study many coupled heterogeneous units, each characterized by randomly assigned (heterogeneous) parameter value(s). One could then coin the term Heterogeneity Quantification for this approach, which we illustrate through a model dynamic network consisting of coupled oscillators with one intrinsic heterogeneity (oscillator individual frequency) and one structural heterogeneity (oscillator degree in the undirected network). The computational implementation of the approach, its shortcomings and possible extensions are also discussed. PMID:28659781

Digging deeper on "deep" learning: A computational ecology approach.

PubMed

Buscema, Massimo; Sacco, Pier Luigi

2017-01-01

We propose an alternative approach to "deep" learning that is based on computational ecologies of structurally diverse artificial neural networks, and on dynamic associative memory responses to stimuli. Rather than focusing on massive computation of many different examples of a single situation, we opt for model-based learning and adaptive flexibility. Cross-fertilization of learning processes across multiple domains is the fundamental feature of human intelligence that must inform "new" artificial intelligence.

Use of CAD Geometry in MDO

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

1996-01-01

The purpose of this paper is to discuss the use of Computer-Aided Design (CAD) geometry in a Multi-Disciplinary Design Optimization (MDO) environment. Two techniques are presented to facilitate the use of CAD geometry by different disciplines, such as Computational Fluid Dynamics (CFD) and Computational Structural Mechanics (CSM). One method is to transfer the load from a CFD grid to a CSM grid. The second method is to update the CAD geometry for CSM deflection.

Aeroelastic Deflection of NURBS Geometry

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

1998-01-01

The purpose of this paper is to present an algorithm for using NonUniform Rational B-Spline (NURBS) representation in an aeroelastic loop. The algorithm is based on creating a least-squares NURBS surface representing the aeroelastic defection. The resulting NURBS surfaces are used to update either the original Computer- Aided Design (CAD) model, Computational Structural Mechanics (CSM) grid or the Computational Fluid Dynamics (CFD) grid. Results are presented for a generic High-Speed Civil Transport (HSCT).

The structure of aqueous sodium hydroxide solutions: a combined solution x-ray diffraction and simulation study.

PubMed

Megyes, Tünde; Bálint, Szabolcs; Grósz, Tamás; Radnai, Tamás; Bakó, Imre; Sipos, Pál

2008-01-28

To determine the structure of aqueous sodium hydroxide solutions, results obtained from x-ray diffraction and computer simulation (molecular dynamics and Car-Parrinello) have been compared. The capabilities and limitations of the methods in describing the solution structure are discussed. For the solutions studied, diffraction methods were found to perform very well in describing the hydration spheres of the sodium ion and yield structural information on the anion's hydration structure. Classical molecular dynamics simulations were not able to correctly describe the bulk structure of these solutions. However, Car-Parrinello simulation proved to be a suitable tool in the detailed interpretation of the hydration sphere of ions and bulk structure of solutions. The results of Car-Parrinello simulations were compared with the findings of diffraction experiments.

Identification of dynamic load for prosthetic structures.

PubMed

Zhang, Dequan; Han, Xu; Zhang, Zhongpu; Liu, Jie; Jiang, Chao; Yoda, Nobuhiro; Meng, Xianghua; Li, Qing

2017-12-01

Dynamic load exists in numerous biomechanical systems, and its identification signifies a critical issue for characterizing dynamic behaviors and studying biomechanical consequence of the systems. This study aims to identify dynamic load in the dental prosthetic structures, namely, 3-unit implant-supported fixed partial denture (I-FPD) and teeth-supported fixed partial denture. The 3-dimensional finite element models were constructed through specific patient's computerized tomography images. A forward algorithm and regularization technique were developed for identifying dynamic load. To verify the effectiveness of the identification method proposed, the I-FPD and teeth-supported fixed partial denture structures were investigated to determine the dynamic loads. For validating the results of inverse identification, an experimental force-measuring system was developed by using a 3-dimensional piezoelectric transducer to measure the dynamic load in the I-FPD structure in vivo. The computationally identified loads were presented with different noise levels to determine their influence on the identification accuracy. The errors between the measured load and identified counterpart were calculated for evaluating the practical applicability of the proposed procedure in biomechanical engineering. This study is expected to serve as a demonstrative role in identifying dynamic loading in biomedical systems, where a direct in vivo measurement may be rather demanding in some areas of interest clinically. Copyright © 2017 John Wiley & Sons, Ltd.

The Structure and Properties of Silica Glass Nanostructures using Novel Computational Systems

NASA Astrophysics Data System (ADS)

Doblack, Benjamin N.

The structure and properties of silica glass nanostructures are examined using computational methods in this work. Standard synthesis methods of silica and its associated material properties are first discussed in brief. A review of prior experiments on this amorphous material is also presented. Background and methodology for the simulation of mechanical tests on amorphous bulk silica and nanostructures are later presented. A new computational system for the accurate and fast simulation of silica glass is also presented, using an appropriate interatomic potential for this material within the open-source molecular dynamics computer program LAMMPS. This alternative computational method uses modern graphics processors, Nvidia CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model select materials, this enhancement allows the addition of accelerated molecular dynamics simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal of this project is to investigate the structure and size dependent mechanical properties of silica glass nanohelical structures under tensile MD conditions using the innovative computational system. Specifically, silica nanoribbons and nanosprings are evaluated which revealed unique size dependent elastic moduli when compared to the bulk material. For the nanoribbons, the tensile behavior differed widely between the models simulated, with distinct characteristic extended elastic regions. In the case of the nanosprings simulated, more clear trends are observed. In particular, larger nanospring wire cross-sectional radii (r) lead to larger Young's moduli, while larger helical diameters (2R) resulted in smaller Young's moduli. Structural transformations and theoretical models are also analyzed to identify possible factors which might affect the mechanical response of silica nanostructures under tension. The work presented outlines an innovative simulation methodology, and discusses how results can be validated against prior experimental and simulation findings. The ultimate goal is to develop new computational methods for the study of nanostructures which will make the field of materials science more accessible, cost effective and efficient.

Infinite possibilities: Computational structures technology

NASA Astrophysics Data System (ADS)

Beam, Sherilee F.

1994-12-01

Computational Fluid Dynamics (or CFD) methods are very familiar to the research community. Even the general public has had some exposure to CFD images, primarily through the news media. However, very little attention has been paid to CST--Computational Structures Technology. Yet, no important design can be completed without it. During the first half of this century, researchers only dreamed of designing and building structures on a computer. Today their dreams have become practical realities as computational methods are used in all phases of design, fabrication and testing of engineering systems. Increasingly complex structures can now be built in even shorter periods of time. Over the past four decades, computer technology has been developing, and early finite element methods have grown from small in-house programs to numerous commercial software programs. When coupled with advanced computing systems, they help engineers make dramatic leaps in designing and testing concepts. The goals of CST include: predicting how a structure will behave under actual operating conditions; designing and complementing other experiments conducted on a structure; investigating microstructural damage or chaotic, unpredictable behavior; helping material developers in improving material systems; and being a useful tool in design systems optimization and sensitivity techniques. Applying CST to a structure problem requires five steps: (1) observe the specific problem; (2) develop a computational model for numerical simulation; (3) develop and assemble software and hardware for running the codes; (4) post-process and interpret the results; and (5) use the model to analyze and design the actual structure. Researchers in both industry and academia continue to make significant contributions to advance this technology with improvements in software, collaborative computing environments and supercomputing systems. As these environments and systems evolve, computational structures technology will evolve. By using CST in the design and operation of future structures systems, engineers will have a better understanding of how a system responds and lasts, more cost-effective methods of designing and testing models, and improved productivity. For informational and educational purposes, a videotape is being produced using both static and dynamic images from research institutions, software and hardware companies, private individuals, and historical photographs and drawings. The extensive number of CST resources indicates its widespread use. Applications run the gamut from simpler university-simulated problems to those requiring solutions on supercomputers. In some cases, an image or an animation will be mapped onto the actual structure to show the relevance of the computer model to the structure.

Infinite possibilities: Computational structures technology

NASA Technical Reports Server (NTRS)

Beam, Sherilee F.

1994-01-01

Computational Fluid Dynamics (or CFD) methods are very familiar to the research community. Even the general public has had some exposure to CFD images, primarily through the news media. However, very little attention has been paid to CST--Computational Structures Technology. Yet, no important design can be completed without it. During the first half of this century, researchers only dreamed of designing and building structures on a computer. Today their dreams have become practical realities as computational methods are used in all phases of design, fabrication and testing of engineering systems. Increasingly complex structures can now be built in even shorter periods of time. Over the past four decades, computer technology has been developing, and early finite element methods have grown from small in-house programs to numerous commercial software programs. When coupled with advanced computing systems, they help engineers make dramatic leaps in designing and testing concepts. The goals of CST include: predicting how a structure will behave under actual operating conditions; designing and complementing other experiments conducted on a structure; investigating microstructural damage or chaotic, unpredictable behavior; helping material developers in improving material systems; and being a useful tool in design systems optimization and sensitivity techniques. Applying CST to a structure problem requires five steps: (1) observe the specific problem; (2) develop a computational model for numerical simulation; (3) develop and assemble software and hardware for running the codes; (4) post-process and interpret the results; and (5) use the model to analyze and design the actual structure. Researchers in both industry and academia continue to make significant contributions to advance this technology with improvements in software, collaborative computing environments and supercomputing systems. As these environments and systems evolve, computational structures technology will evolve. By using CST in the design and operation of future structures systems, engineers will have a better understanding of how a system responds and lasts, more cost-effective methods of designing and testing models, and improved productivity. For informational and educational purposes, a videotape is being produced using both static and dynamic images from research institutions, software and hardware companies, private individuals, and historical photographs and drawings. The extensive number of CST resources indicates its widespread use. Applications run the gamut from simpler university-simulated problems to those requiring solutions on supercomputers. In some cases, an image or an animation will be mapped onto the actual structure to show the relevance of the computer model to the structure. Transferring the digital files to videotape presents a number of problems related to maintaining the quality of the original image, while still producing a broadcast quality videotape. Since researchers normally do not create a computer image using traditional composition theories or video production requirements, often the image loses some of its original digital quality and impact when transferred to videotape. Although many CST images are currently available, those that are edited into the final project must meet two important criteria: they must complement the narration, and they must be broadcast quality when recorded on videotape.

Structure and Dynamics Ionic Block co-Polymer Melts: Computational Study

NASA Astrophysics Data System (ADS)

Aryal, Dipak; Perahia, Dvora; Grest, Gary S.

Tethering ionomer blocks into co-polymers enables engineering of polymeric systems designed to encompass transport while controlling structure. Here the structure and dynamics of symmetric pentablock copolymers melts are probed by fully atomistic molecular dynamics simulations. The center block consists of randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55 tethered to a hydrogenated polyisoprene (PI), end caped with poly(t-butyl styrene). We find that melts with f = 0.15 and 0.30 consist of isolated ionic clusters whereas melts with f = 0.55 exhibit a long-range percolating ionic network. Similar to polystyrene sulfonate, a small number of ionic clusters slow the mobility of the center of mass of the co-polymer, however, formation of the ionic clusters is slower and they are often intertwined with PI segments. Surprisingly, the segmental dynamics of the other blocks are also affected. NSF DMR-1611136; NERSC; Palmetto Cluster Clemson University; Kraton Polymers US, LLC.

Protein flexibility in the light of structural alphabets

PubMed Central

Craveur, Pierrick; Joseph, Agnel P.; Esque, Jeremy; Narwani, Tarun J.; Noël, Floriane; Shinada, Nicolas; Goguet, Matthieu; Leonard, Sylvain; Poulain, Pierre; Bertrand, Olivier; Faure, Guilhem; Rebehmed, Joseph; Ghozlane, Amine; Swapna, Lakshmipuram S.; Bhaskara, Ramachandra M.; Barnoud, Jonathan; Téletchéa, Stéphane; Jallu, Vincent; Cerny, Jiri; Schneider, Bohdan; Etchebest, Catherine; Srinivasan, Narayanaswamy; Gelly, Jean-Christophe; de Brevern, Alexandre G.

2015-01-01

Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases. PMID:26075209

Analysis of the structure and dynamics of human serum albumin.

PubMed

Guizado, T R Cuya

2014-10-01

Human serum albumin (HSA) is a biologically relevant protein that binds a variety of drugs and other small molecules. No less than 50 structures are deposited in the RCSB Protein Data Bank (PDB). Based on these structures, we first performed a clustering analysis. Despite the diversity of ligands, only two well defined conformations are detected, with a deviation of 0.46 nm between the average structures of the two clusters, while deviations within each cluster are smaller than 0.08 nm. Those two conformations are representative of the apoprotein and the HSA-myristate complex already identified in previous literature. Considering the structures within each cluster as a representative sample of the dynamical states of the corresponding conformation, we scrutinize the structural and dynamical differences between both conformations. Analysis of the fluctuations within each cluster set reveals that domain II is the most rigid one and better matches both structures. Then, taking this domain as reference, we show that the structural difference between both conformations can be expressed in terms of twist and hinge motions of domains I and III, respectively. We also characterize the dynamical difference between conformations by computing correlations and principal components for each set of dynamical states. The two conformations display different collective motions. The results are compared with those obtained from the trajectories of short molecular dynamics simulations, giving consistent outcomes. Let us remark that, beyond the relevance of the results for the structural and dynamical characterization of HAS conformations, the present methodology could be extended to other proteins in the PDB archive.

Exploring the Role of Receptor Flexibility in Structure-Based Drug Discovery

PubMed Central

Feixas, Ferran; Lindert, Steffen; Sinko, William; McCammon, J. Andrew

2015-01-01

The proper understanding of biomolecular recognition mechanisms that take place in a drug target is of paramount importance to improve the efficiency of drug discovery and development. The intrinsic dynamic character of proteins has a strong influence on biomolecular recognition mechanisms and models such as conformational selection have been widely used to account for this dynamic association process. However, conformational changes occurring in the receptor prior and upon association with other molecules are diverse and not obvious to predict when only a few structures of the receptor are available. In view of the prominent role of protein flexibility in ligand binding and its implications for drug discovery, it is of great interest to identify receptor conformations that play a major role in biomolecular recognition before starting rational drug design efforts. In this review, we discuss a number of recent advances in computer-aided drug discovery techniques that have been proposed to incorporate receptor flexibility into structure-based drug design. The allowance for receptor flexibility provided by computational techniques such as molecular dynamics simulations or enhanced sampling techniques helps to improve the accuracy of methods used to estimate binding affinities and, thus, such methods can contribute to the discovery of novel drug leads. PMID:24332165

Random graph models for dynamic networks

NASA Astrophysics Data System (ADS)

Zhang, Xiao; Moore, Cristopher; Newman, Mark E. J.

2017-10-01

Recent theoretical work on the modeling of network structure has focused primarily on networks that are static and unchanging, but many real-world networks change their structure over time. There exist natural generalizations to the dynamic case of many static network models, including the classic random graph, the configuration model, and the stochastic block model, where one assumes that the appearance and disappearance of edges are governed by continuous-time Markov processes with rate parameters that can depend on properties of the nodes. Here we give an introduction to this class of models, showing for instance how one can compute their equilibrium properties. We also demonstrate their use in data analysis and statistical inference, giving efficient algorithms for fitting them to observed network data using the method of maximum likelihood. This allows us, for example, to estimate the time constants of network evolution or infer community structure from temporal network data using cues embedded both in the probabilities over time that node pairs are connected by edges and in the characteristic dynamics of edge appearance and disappearance. We illustrate these methods with a selection of applications, both to computer-generated test networks and real-world examples.

Artificial proteins as allosteric modulators of PDZ3 and SH3 in two-domain constructs: A computational characterization of novel chimeric proteins.

PubMed

Kirubakaran, Palani; Pfeiferová, Lucie; Boušová, Kristýna; Bednarova, Lucie; Obšilová, Veronika; Vondrášek, Jiří

2016-10-01

Artificial multidomain proteins with enhanced structural and functional properties can be utilized in a broad spectrum of applications. The design of chimeric fusion proteins utilizing protein domains or one-domain miniproteins as building blocks is an important advancement for the creation of new biomolecules for biotechnology and medical applications. However, computational studies to describe in detail the dynamics and geometry properties of two-domain constructs made from structurally and functionally different proteins are lacking. Here, we tested an in silico design strategy using all-atom explicit solvent molecular dynamics simulations. The well-characterized PDZ3 and SH3 domains of human zonula occludens (ZO-1) (3TSZ), along with 5 artificial domains and 2 types of molecular linkers, were selected to construct chimeric two-domain molecules. The influence of the artificial domains on the structure and dynamics of the PDZ3 and SH3 domains was determined using a range of analyses. We conclude that the artificial domains can function as allosteric modulators of the PDZ3 and SH3 domains. Proteins 2016; 84:1358-1374. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The middeck 0-gravity dynamics experiment

NASA Technical Reports Server (NTRS)

Crawley, Edward F.; Vanschoor, Marthinus C.; Bokhour, Edward B.

1993-01-01

The Middeck 0-Gravity Dynamics Experiment (MODE), flown onboard the Shuttle STS-48 Mission, consists of three major elements: the Experiment Support Module, a dynamics test bed providing computer experiment control, analog signal conditioning, power conditioning, an operator interface consisting of a keypad and display, experiment electrical and thermal control, and archival data storage: the Fluid Test Article assembly, used to investigate the dynamics of fluid-structure interaction in 0-gravity; and the Structural Test Article for investigating the open-loop dynamics of structures in 0-gravity. Deployable, erectable, and rotary modules were assembled to form three one- and two-dimensional structures, in which variations in bracing wire and rotary joint preload could be introduced. Change in linear modal parameters as well as the change in nonlinear nature of the response is examined. Trends in modal parameters are presented as a function of force amplitude, joint preload, and ambient gravity. An experimental study of the lateral slosh behavior of contained fluids is also presented. A comparison of the measured earth and space results identifies and highlights the effects of gravity on the linear and nonlinear slosh behavior of these fluids.

GPS in pioneering dynamic monitoring of long-period structures

USGS Publications Warehouse

Celebi, M.; Sanli, A.

2002-01-01

Global Positioning System (GPS) technology with 10-20-Hz sampling rates allows scientifically justified dynamic measurements of relative displacements of long-period structures. The displacement response of a simulated tall building in real time and permanent deployment of GPS units at the roof of a building are described. To the authors' best knowledge, this is the first permanent deployment of GPS units (in the world) for continuous dynamic monitoring of a tall building. Data recorded from the building during a windy day is analyzed to determine the structural characteristics. When recorded during extreme motions caused by earthquakes and strong winds, such measurements can be used to compute average drift ratios and changes in dynamic characteristics, and therefore can be used by engineers and building owners or managers to assess the structural integrity and performance by establishing pre-established thresholds. Such information can be used to secure public safety and/or take steps to improve the performance of the building.

Comparison of Hydrodynamic Load Predictions Between Engineering Models and Computational Fluid Dynamics for the OC4-DeepCwind Semi-Submersible: Preprint

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

Benitz, M. A.; Schmidt, D. P.; Lackner, M. A.

Hydrodynamic loads on the platforms of floating offshore wind turbines are often predicted with computer-aided engineering tools that employ Morison's equation and/or potential-flow theory. This work compares results from one such tool, FAST, NREL's wind turbine computer-aided engineering tool, and the computational fluid dynamics package, OpenFOAM, for the OC4-DeepCwind semi-submersible analyzed in the International Energy Agency Wind Task 30 project. Load predictions from HydroDyn, the offshore hydrodynamics module of FAST, are compared with high-fidelity results from OpenFOAM. HydroDyn uses a combination of Morison's equations and potential flow to predict the hydrodynamic forces on the structure. The implications of the assumptionsmore » in HydroDyn are evaluated based on this code-to-code comparison.« less

A novel approach to multiple sequence alignment using hadoop data grids.

PubMed

Sudha Sadasivam, G; Baktavatchalam, G

2010-01-01

Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences.

Architectural Improvements and New Processing Tools for the Open XAL Online Model

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

Allen, Christopher K; Pelaia II, Tom; Freed, Jonathan M

The online model is the component of Open XAL providing accelerator modeling, simulation, and dynamic synchronization to live hardware. Significant architectural changes and feature additions have been recently made in two separate areas: 1) the managing and processing of simulation data, and 2) the modeling of RF cavities. Simulation data and data processing have been completely decoupled. A single class manages all simulation data while standard tools were developed for processing the simulation results. RF accelerating cavities are now modeled as composite structures where parameter and dynamics computations are distributed. The beam and hardware models both maintain their relative phasemore » information, which allows for dynamic phase slip and elapsed time computation.« less

Crashworthy airframe design concepts: Fabrication and testing

NASA Technical Reports Server (NTRS)

Cronkhite, J. D.; Berry, V. L.

1982-01-01

Crashworthy floor concepts applicable to general aviation aircraft metal airframe structures were investigated. Initially several energy absorbing lower fuselage structure concepts were evaluated. Full scale floor sections representative of a twin engine, general aviation airplane lower fuselage structure were designed and fabricated. The floors featured an upper high strength platform with an energy absorbing, crushable structure underneath. Eighteen floors were fabricated that incorporated five different crushable subfloor concepts. The floors were then evaluated through static and dynamic testing. Computer programs NASTRAN and KRASH were used for the static and dynamic analysis of the floor section designs. Two twin engine airplane fuselages were modified to incorporate the most promising crashworthy floor sections for test evaluation.

A Benchmark Problem for Development of Autonomous Structural Modal Identification

NASA Technical Reports Server (NTRS)

Pappa, Richard S.; Woodard, Stanley E.; Juang, Jer-Nan

1996-01-01

This paper summarizes modal identification results obtained using an autonomous version of the Eigensystem Realization Algorithm on a dynamically complex, laboratory structure. The benchmark problem uses 48 of 768 free-decay responses measured in a complete modal survey test. The true modal parameters of the structure are well known from two previous, independent investigations. Without user involvement, the autonomous data analysis identified 24 to 33 structural modes with good to excellent accuracy in 62 seconds of CPU time (on a DEC Alpha 4000 computer). The modal identification technique described in the paper is the baseline algorithm for NASA's Autonomous Dynamics Determination (ADD) experiment scheduled to fly on International Space Station assembly flights in 1997-1999.

Computation of the Fluid and Optical Fields About the Stratospheric Observatory for Infrared Astronomy (SOFIA) and the Coupling of Fluids, Dynamics, and Control Laws on Parallel Computers

NASA Technical Reports Server (NTRS)

Atwood, Christopher A.

1993-01-01

The June 1992 to May 1993 grant NCC-2-677 provided for the continued demonstration of Computational Fluid Dynamics (CFD) as applied to the Stratospheric Observatory for Infrared Astronomy (SOFIA). While earlier grant years allowed validation of CFD through comparison against experiments, this year a new design proposal was evaluated. The new configuration would place the cavity aft of the wing, as opposed to the earlier baseline which was located immediately aft of the cockpit. This aft cavity placement allows for simplified structural and aircraft modification requirements, thus lowering the program cost of this national astronomy resource. Three appendices concerning this subject are presented.

Dynamic Analyses Including Joints Of Truss Structures

NASA Technical Reports Server (NTRS)

Belvin, W. Keith

1991-01-01

Method for mathematically modeling joints to assess influences of joints on dynamic response of truss structures developed in study. Only structures with low-frequency oscillations considered; only Coulomb friction and viscous damping included in analysis. Focus of effort to obtain finite-element mathematical models of joints exhibiting load-vs.-deflection behavior similar to measured load-vs.-deflection behavior of real joints. Experiments performed to determine stiffness and damping nonlinearities typical of joint hardware. Algorithm for computing coefficients of analytical joint models based on test data developed to enable study of linear and nonlinear effects of joints on global structural response. Besides intended application to large space structures, applications in nonaerospace community include ground-based antennas and earthquake-resistant steel-framed buildings.

The NASTRAN theoretical manual

NASA Technical Reports Server (NTRS)

1981-01-01

Designed to accommodate additions and modifications, this commentary on NASTRAN describes the problem solving capabilities of the program in a narrative fashion and presents developments of the analytical and numerical procedures that underlie the program. Seventeen major sections and numerous subsections cover; the organizational aspects of the program, utility matrix routines, static structural analysis, heat transfer, dynamic structural analysis, computer graphics, special structural modeling techniques, error analysis, interaction between structures and fluids, and aeroelastic analysis.

Dynamics of propagation of premature impulses in structurally remodeled infarcted myocardium: a computational analysis

PubMed Central

Cabo, Candido

2014-01-01

Initiation of cardiac arrhythmias typically follows one or more premature impulses either occurring spontaneously or applied externally. In this study, we characterize the dynamics of propagation of single (S2) and double premature impulses (S3), and the mechanisms of block of premature impulses at structural heterogeneities caused by remodeling of gap junctional conductance (Gj) in infarcted myocardium. Using a sub-cellular computer model of infarcted tissue, we found that |INa,max|, prematurity (coupling interval with the previous impulse), and conduction velocity (CV) of premature impulses change dynamically as they propagate away from the site of initiation. There are fundamental differences between the dynamics of propagation of S2 and S3 premature impulses: for S2 impulses |INa,max| recovers fast, prematurity decreases and CV increases as propagation proceeds; for S3 impulses low values of |INa,max| persist, prematurity could increase, and CV could decrease as impulses propagate away from the site of initiation. As a consequence it is more likely that S3 impulses block at sites of structural heterogeneities causing source/sink mismatch than S2 impulses block. Whether premature impulses block at Gj heterogeneities or not is also determined by the values of Gj (and the space constant λ) in the regions proximal and distal to the heterogeneity: when λ in the direction of propagation increases >40%, premature impulses could block. The maximum slope of CV restitution curves for S2 impulses is larger than for S3 impulses. In conclusion: (1) The dynamics of propagation of premature impulses make more likely that S3 impulses block at sites of structural heterogeneities than S2 impulses block; (2) Structural heterogeneities causing an increase in λ (or CV) of >40% could result in block of premature impulses; (3) A decrease in the maximum slope of CV restitution curves of propagating premature impulses is indicative of an increased potential for block at structural heterogeneities. PMID:25566085

Dynamics of propagation of premature impulses in structurally remodeled infarcted myocardium: a computational analysis.

PubMed

Cabo, Candido

2014-01-01

Initiation of cardiac arrhythmias typically follows one or more premature impulses either occurring spontaneously or applied externally. In this study, we characterize the dynamics of propagation of single (S2) and double premature impulses (S3), and the mechanisms of block of premature impulses at structural heterogeneities caused by remodeling of gap junctional conductance (Gj) in infarcted myocardium. Using a sub-cellular computer model of infarcted tissue, we found that |INa,max|, prematurity (coupling interval with the previous impulse), and conduction velocity (CV) of premature impulses change dynamically as they propagate away from the site of initiation. There are fundamental differences between the dynamics of propagation of S2 and S3 premature impulses: for S2 impulses |INa,max| recovers fast, prematurity decreases and CV increases as propagation proceeds; for S3 impulses low values of |INa,max| persist, prematurity could increase, and CV could decrease as impulses propagate away from the site of initiation. As a consequence it is more likely that S3 impulses block at sites of structural heterogeneities causing source/sink mismatch than S2 impulses block. Whether premature impulses block at Gj heterogeneities or not is also determined by the values of Gj (and the space constant λ) in the regions proximal and distal to the heterogeneity: when λ in the direction of propagation increases >40%, premature impulses could block. The maximum slope of CV restitution curves for S2 impulses is larger than for S3 impulses. (1) The dynamics of propagation of premature impulses make more likely that S3 impulses block at sites of structural heterogeneities than S2 impulses block; (2) Structural heterogeneities causing an increase in λ (or CV) of >40% could result in block of premature impulses; (3) A decrease in the maximum slope of CV restitution curves of propagating premature impulses is indicative of an increased potential for block at structural heterogeneities.

Homology Modeling of Dopamine D2 and D3 Receptors: Molecular Dynamics Refinement and Docking Evaluation

PubMed Central

Platania, Chiara Bianca Maria; Salomone, Salvatore; Leggio, Gian Marco; Drago, Filippo; Bucolo, Claudio

2012-01-01

Dopamine (DA) receptors, a class of G-protein coupled receptors (GPCRs), have been targeted for drug development for the treatment of neurological, psychiatric and ocular disorders. The lack of structural information about GPCRs and their ligand complexes has prompted the development of homology models of these proteins aimed at structure-based drug design. Crystal structure of human dopamine D3 (hD3) receptor has been recently solved. Based on the hD3 receptor crystal structure we generated dopamine D2 and D3 receptor models and refined them with molecular dynamics (MD) protocol. Refined structures, obtained from the MD simulations in membrane environment, were subsequently used in molecular docking studies in order to investigate potential sites of interaction. The structure of hD3 and hD2L receptors was differentiated by means of MD simulations and D3 selective ligands were discriminated, in terms of binding energy, by docking calculation. Robust correlation of computed and experimental Ki was obtained for hD3 and hD2L receptor ligands. In conclusion, the present computational approach seems suitable to build and refine structure models of homologous dopamine receptors that may be of value for structure-based drug discovery of selective dopaminergic ligands. PMID:22970199

Initial dynamic load estimates during configuration design

NASA Technical Reports Server (NTRS)

Schiff, Daniel

1987-01-01

This analysis includes the structural response to shock and vibration and evaluates the maximum deflections and material stresses and the potential for the occurrence of elastic instability, fatigue and fracture. The required computations are often performed by means of finite element analysis (FEA) computer programs in which the structure is simulated by a finite element model which may contain thousands of elements. The formulation of a finite element model can be time consuming, and substantial additional modeling effort may be necessary if the structure requires significant changes after initial analysis. Rapid methods for obtaining rough estimates of the structural response to shock and vibration are presented for the purpose of providing guidance during the initial mechanical design configuration stage.

CABS-flex: Server for fast simulation of protein structure fluctuations.

PubMed

Jamroz, Michal; Kolinski, Andrzej; Kmiecik, Sebastian

2013-07-01

The CABS-flex server (http://biocomp.chem.uw.edu.pl/CABSflex) implements CABS-model-based protocol for the fast simulations of near-native dynamics of globular proteins. In this application, the CABS model was shown to be a computationally efficient alternative to all-atom molecular dynamics--a classical simulation approach. The simulation method has been validated on a large set of molecular dynamics simulation data. Using a single input (user-provided file in PDB format), the CABS-flex server outputs an ensemble of protein models (in all-atom PDB format) reflecting the flexibility of the input structure, together with the accompanying analysis (residue mean-square-fluctuation profile and others). The ensemble of predicted models can be used in structure-based studies of protein functions and interactions.

Self-Organization of Spatio-Temporal Hierarchy via Learning of Dynamic Visual Image Patterns on Action Sequences

PubMed Central

Jung, Minju; Hwang, Jungsik; Tani, Jun

2015-01-01

It is well known that the visual cortex efficiently processes high-dimensional spatial information by using a hierarchical structure. Recently, computational models that were inspired by the spatial hierarchy of the visual cortex have shown remarkable performance in image recognition. Up to now, however, most biological and computational modeling studies have mainly focused on the spatial domain and do not discuss temporal domain processing of the visual cortex. Several studies on the visual cortex and other brain areas associated with motor control support that the brain also uses its hierarchical structure as a processing mechanism for temporal information. Based on the success of previous computational models using spatial hierarchy and temporal hierarchy observed in the brain, the current report introduces a novel neural network model for the recognition of dynamic visual image patterns based solely on the learning of exemplars. This model is characterized by the application of both spatial and temporal constraints on local neural activities, resulting in the self-organization of a spatio-temporal hierarchy necessary for the recognition of complex dynamic visual image patterns. The evaluation with the Weizmann dataset in recognition of a set of prototypical human movement patterns showed that the proposed model is significantly robust in recognizing dynamically occluded visual patterns compared to other baseline models. Furthermore, an evaluation test for the recognition of concatenated sequences of those prototypical movement patterns indicated that the model is endowed with a remarkable capability for the contextual recognition of long-range dynamic visual image patterns. PMID:26147887

Self-Organization of Spatio-Temporal Hierarchy via Learning of Dynamic Visual Image Patterns on Action Sequences.

PubMed

Jung, Minju; Hwang, Jungsik; Tani, Jun

2015-01-01

It is well known that the visual cortex efficiently processes high-dimensional spatial information by using a hierarchical structure. Recently, computational models that were inspired by the spatial hierarchy of the visual cortex have shown remarkable performance in image recognition. Up to now, however, most biological and computational modeling studies have mainly focused on the spatial domain and do not discuss temporal domain processing of the visual cortex. Several studies on the visual cortex and other brain areas associated with motor control support that the brain also uses its hierarchical structure as a processing mechanism for temporal information. Based on the success of previous computational models using spatial hierarchy and temporal hierarchy observed in the brain, the current report introduces a novel neural network model for the recognition of dynamic visual image patterns based solely on the learning of exemplars. This model is characterized by the application of both spatial and temporal constraints on local neural activities, resulting in the self-organization of a spatio-temporal hierarchy necessary for the recognition of complex dynamic visual image patterns. The evaluation with the Weizmann dataset in recognition of a set of prototypical human movement patterns showed that the proposed model is significantly robust in recognizing dynamically occluded visual patterns compared to other baseline models. Furthermore, an evaluation test for the recognition of concatenated sequences of those prototypical movement patterns indicated that the model is endowed with a remarkable capability for the contextual recognition of long-range dynamic visual image patterns.

Nickel-aluminum alloy clusters -- structural and dynamical properties

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

Jellinek, J.; Krissinel, E.B.

1997-08-01

Structural and dynamical properties of mixed Ni{sub n}Al{sub m} alloy clusters mimicked by a many-body potential are studied computationally for all the possible compositions n and m such that n + m = 13. It is shown that the manifold of the usually very large number of the different possible structural forms can be systematized by introducing classes of structures corresponding to the same concentration of the components, geometry and type of the central atom. General definitions of mixing energy and mixing coefficient are introduced, and it is shown that the energy ordering of the structural forms within each classmore » is governed by the mixing coefficient. The peculiarities of the solid-to-liquid-like transition are described as a function of the concentration of the two types of atoms. These peculiarities are correlated with and explained in terms of the energy spectra of the structural forms. Class-dependent features of the dynamics are described and analyzed.« less

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

PubMed

Cossio, Pilar; Laio, Alessandro; Pietrucci, Fabio

2011-06-14

An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are different. By analyzing microseconds-long all-atom molecular dynamics simulations of a polypeptide, we find that a distance based on backbone dihedral angles performs very well in distinguishing structures that are kinetically correlated from those that are not, while the widely used C(α) root mean square distance performs more poorly. The root mean square difference between contact matrices turns out instead to be the metric providing the highest clustering coefficient, namely, according to this similarity measure, the neighbors of a structure are also, on average, neighbors among themselves. We also propose a combined distance measure which, for the system considered here, performs well both for distinguishing structures which are distant in time and for giving a consistent cluster analysis. This journal is © the Owner Societies 2011

Structures and properties of materials recovered from high shock pressures

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

Nellis, W.J.

1994-03-01

Shock compression produces high dynamic pressures, densities, temperatures, and their quench rates. Because of these extreme conditions, shock compression produces materials with novel crystal structures, microstructures, and physical properties. Using a 6.5-m-long two-stage gun, we perform experiments with specimens up to 10 mm in diameter and 0.001--1 mm thick. For example, oriented disks of melt-textured superconducting YBa{sub 2}Cu{sub 3}O{sub 7} were shocked to 7 GPa without macroscopic fracture. Lattice defects are deposited in the crystal, which improve magnetic hysteresis at {approximately}1 kOe. A computer code has been developed to simulate shock compaction of 100 powder particles. Computations will be comparedmore » with experiments with 15--20 {mu}m Cu powders. The method is applicable to other powders and dynamic conditions.« less

An Assessment of CFD/CSD Prediction State-of-the-Art by Using the HART II International Workshop Data

NASA Technical Reports Server (NTRS)

Smith, Marilyn J.; Lim, Joon W.; vanderWall, Berend G.; Baeder, James D.; Biedron, Robert T.; Boyd, D. Douglas, Jr.; Jayaraman, Buvana; Jung, Sung N.; Min, Byung-Young

2012-01-01

Over the past decade, there have been significant advancements in the accuracy of rotor aeroelastic simulations with the application of computational fluid dynamics methods coupled with computational structural dynamics codes (CFD/CSD). The HART II International Workshop database, which includes descent operating conditions with strong blade-vortex interactions (BVI), provides a unique opportunity to assess the ability of CFD/CSD to capture these physics. In addition to a baseline case with BVI, two additional cases with 3/rev higher harmonic blade root pitch control (HHC) are available for comparison. The collaboration during the workshop permits assessment of structured, unstructured, and hybrid overset CFD/CSD methods from across the globe on the dynamics, aerodynamics, and wake structure. Evaluation of the plethora of CFD/CSD methods indicate that the most important numerical variables associated with most accurately capturing BVI are a two-equation or detached eddy simulation (DES)-based turbulence model and a sufficiently small time step. An appropriate trade-off between grid fidelity and spatial accuracy schemes also appears to be pertinent for capturing BVI on the advancing rotor disk. Overall, the CFD/CSD methods generally fall within the same accuracy; cost-effective hybrid Navier-Stokes/Lagrangian wake methods provide accuracies within 50% the full CFD/CSD methods for most parameters of interest, except for those highly influenced by torsion. The importance of modeling the fuselage is observed, and other computational requirements are discussed.

Sensitivity Analysis of Multidisciplinary Rotorcraft Simulations

NASA Technical Reports Server (NTRS)

Wang, Li; Diskin, Boris; Biedron, Robert T.; Nielsen, Eric J.; Bauchau, Olivier A.

2017-01-01

A multidisciplinary sensitivity analysis of rotorcraft simulations involving tightly coupled high-fidelity computational fluid dynamics and comprehensive analysis solvers is presented and evaluated. An unstructured sensitivity-enabled Navier-Stokes solver, FUN3D, and a nonlinear flexible multibody dynamics solver, DYMORE, are coupled to predict the aerodynamic loads and structural responses of helicopter rotor blades. A discretely-consistent adjoint-based sensitivity analysis available in FUN3D provides sensitivities arising from unsteady turbulent flows and unstructured dynamic overset meshes, while a complex-variable approach is used to compute DYMORE structural sensitivities with respect to aerodynamic loads. The multidisciplinary sensitivity analysis is conducted through integrating the sensitivity components from each discipline of the coupled system. Numerical results verify accuracy of the FUN3D/DYMORE system by conducting simulations for a benchmark rotorcraft test model and comparing solutions with established analyses and experimental data. Complex-variable implementation of sensitivity analysis of DYMORE and the coupled FUN3D/DYMORE system is verified by comparing with real-valued analysis and sensitivities. Correctness of adjoint formulations for FUN3D/DYMORE interfaces is verified by comparing adjoint-based and complex-variable sensitivities. Finally, sensitivities of the lift and drag functions obtained by complex-variable FUN3D/DYMORE simulations are compared with sensitivities computed by the multidisciplinary sensitivity analysis, which couples adjoint-based flow and grid sensitivities of FUN3D and FUN3D/DYMORE interfaces with complex-variable sensitivities of DYMORE structural responses.

Large Angle Transient Dynamics (LATDYN) user's manual

NASA Technical Reports Server (NTRS)

Abrahamson, A. Louis; Chang, Che-Wei; Powell, Michael G.; Wu, Shih-Chin; Bingel, Bradford D.; Theophilos, Paula M.

1991-01-01

A computer code for modeling the large angle transient dynamics (LATDYN) of structures was developed to investigate techniques for analyzing flexible deformation and control/structure interaction problems associated with large angular motions of spacecraft. This type of analysis is beyond the routine capability of conventional analytical tools without simplifying assumptions. In some instances, the motion may be sufficiently slow and the spacecraft (or component) sufficiently rigid to simplify analyses of dynamics and controls by making pseudo-static and/or rigid body assumptions. The LATDYN introduces a new approach to the problem by combining finite element structural analysis, multi-body dynamics, and control system analysis in a single tool. It includes a type of finite element that can deform and rotate through large angles at the same time, and which can be connected to other finite elements either rigidly or through mechanical joints. The LATDYN also provides symbolic capabilities for modeling control systems which are interfaced directly with the finite element structural model. Thus, the nonlinear equations representing the structural model are integrated along with the equations representing sensors, processing, and controls as a coupled system.

Aeroelastic Analyses of the SemiSpan SuperSonic Transport (S4T) Wind Tunnel Model at Mach 0.95

NASA Technical Reports Server (NTRS)

Hur, Jiyoung

2014-01-01

Detailed aeroelastic analyses of the SemiSpan SuperSonic Transport (S4T) wind tunnel model at Mach 0.95 with a 1.75deg fixed angle of attack are presented. First, a numerical procedure using the Computational Fluids Laboratory 3-Dimensional (CFL3D) Version 6.4 flow solver is investigated. The mesh update method for structured multi-block grids was successfully applied to the Navier-Stokes simulations. Second, the steady aerodynamic analyses with a rigid structure of the S4T wind tunnel model are reviewed in transonic flow. Third, the static analyses were performed for both the Euler and Navier-Stokes equations. Both the Euler and Navier-Stokes equations predicted a significant increase of lift forces, compared to the results from the rigid structure of the S4T wind-tunnel model, over various dynamic pressures. Finally, dynamic aeroelastic analyses were performed to investigate the flutter condition of the S4T wind tunnel model at the transonic Mach number. The condition of flutter was observed at a dynamic pressure of approximately 75.0-psf for the Navier-Stokes simulations. However, it was observed that the flutter condition occurred a dynamic pressure of approximately 47.27-psf for the Euler simulations. Also, the computational efficiency of the aeroelastic analyses for the S4T wind tunnel model has been assessed.

The influence of computational assumptions on analysing abdominal aortic aneurysm haemodynamics.

PubMed

Ene, Florentina; Delassus, Patrick; Morris, Liam

2014-08-01

The variation in computational assumptions for analysing abdominal aortic aneurysm haemodynamics can influence the desired output results and computational cost. Such assumptions for abdominal aortic aneurysm modelling include static/transient pressures, steady/transient flows and rigid/compliant walls. Six computational methods and these various assumptions were simulated and compared within a realistic abdominal aortic aneurysm model with and without intraluminal thrombus. A full transient fluid-structure interaction was required to analyse the flow patterns within the compliant abdominal aortic aneurysms models. Rigid wall computational fluid dynamics overestimates the velocity magnitude by as much as 40%-65% and the wall shear stress by 30%-50%. These differences were attributed to the deforming walls which reduced the outlet volumetric flow rate for the transient fluid-structure interaction during the majority of the systolic phase. Static finite element analysis accurately approximates the deformations and von Mises stresses when compared with transient fluid-structure interaction. Simplifying the modelling complexity reduces the computational cost significantly. In conclusion, the deformation and von Mises stress can be approximately found by static finite element analysis, while for compliant models a full transient fluid-structure interaction analysis is required for acquiring the fluid flow phenomenon. © IMechE 2014.

Development of hydraulic computer models to analyze tidal and coastal stream hydraulic conditions at highway structures : phase 2 for the Pooled Fund Study, SPR-3(22)

DOT National Transportation Integrated Search

1997-12-01

Highway structures are subjected to stream instability and foundation scour resulting from dynamic flow conditions caused by tides, currents, storm surges, and upland runoff. This phase of the study (Phase II) focused on (1) making useful modificatio...

Multi-body Dynamic Contact Analysis Tool for Transmission Design

DTIC Science & Technology

2003-04-01

frequencies were computed in COSMIC NASTRAN, and were validated against the published experimental modal analysis [17]. • Using assumed time domain... modal superposition. • Results from the structural analysis (mode shapes or forced response) were converted into IDEAS universal format (dataset 55...ARMY RESEARCH LABORATORY Multi-body Dynamic Contact Analysis Tool for Transmission Design SBIR Phase II Final Report by

Integrated Multiscale Modeling of Molecular Computing Devices. Final Report

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

Tim Schulze

2012-11-01

The general theme of this research has been to expand the capabilities of a simulation technique, Kinetic Monte Carlo (KMC) and apply it to study self-assembled nano-structures on epitaxial thin films. KMC simulates thin film growth and evolution by replacing the detailed dynamics of the system's evolution, which might otherwise be studied using molecular dynamics, with an appropriate stochastic process.

Real-time moving horizon estimation for a vibrating active cantilever

NASA Astrophysics Data System (ADS)

Abdollahpouri, Mohammad; Takács, Gergely; Rohaľ-Ilkiv, Boris

2017-03-01

Vibrating structures may be subject to changes throughout their operating lifetime due to a range of environmental and technical factors. These variations can be considered as parameter changes in the dynamic model of the structure, while their online estimates can be utilized in adaptive control strategies, or in structural health monitoring. This paper implements the moving horizon estimation (MHE) algorithm on a low-cost embedded computing device that is jointly observing the dynamic states and parameter variations of an active cantilever beam in real time. The practical behavior of this algorithm has been investigated in various experimental scenarios. It has been found, that for the given field of application, moving horizon estimation converges faster than the extended Kalman filter; moreover, it handles atypical measurement noise, sensor errors or other extreme changes, reliably. Despite its improved performance, the experiments demonstrate that the disadvantage of solving the nonlinear optimization problem in MHE is that it naturally leads to an increase in computational effort.

Predicting Real-Valued Protein Residue Fluctuation Using FlexPred.

PubMed

Peterson, Lenna; Jamroz, Michal; Kolinski, Andrzej; Kihara, Daisuke

2017-01-01

The conventional view of a protein structure as static provides only a limited picture. There is increasing evidence that protein dynamics are often vital to protein function including interaction with partners such as other proteins, nucleic acids, and small molecules. Considering flexibility is also important in applications such as computational protein docking and protein design. While residue flexibility is partially indicated by experimental measures such as the B-factor from X-ray crystallography and ensemble fluctuation from nuclear magnetic resonance (NMR) spectroscopy as well as computational molecular dynamics (MD) simulation, these techniques are resource-intensive. In this chapter, we describe the web server and stand-alone version of FlexPred, which rapidly predicts absolute per-residue fluctuation from a three-dimensional protein structure. On a set of 592 nonredundant structures, comparing the fluctuations predicted by FlexPred to the observed fluctuations in MD simulations showed an average correlation coefficient of 0.669 and an average root mean square error of 1.07 Å. FlexPred is available at http://kiharalab.org/flexPred/ .

Free energy minimization to predict RNA secondary structures and computational RNA design.

PubMed

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

Numerical modeling of the exterior-to-interior transmission of impulsive sound through three-dimensional, thin-walled elastic structures

NASA Astrophysics Data System (ADS)

Remillieux, Marcel C.; Pasareanu, Stephanie M.; Svensson, U. Peter

2013-12-01

Exterior propagation of impulsive sound and its transmission through three-dimensional, thin-walled elastic structures, into enclosed cavities, are investigated numerically in the framework of linear dynamics. A model was developed in the time domain by combining two numerical tools: (i) exterior sound propagation and induced structural loading are computed using the image-source method for the reflected field (specular reflections) combined with an extension of the Biot-Tolstoy-Medwin method for the diffracted field, (ii) the fully coupled vibro-acoustic response of the interior fluid-structure system is computed using a truncated modal-decomposition approach. In the model for exterior sound propagation, it is assumed that all surfaces are acoustically rigid. Since coupling between the structure and the exterior fluid is not enforced, the model is applicable to the case of a light exterior fluid and arbitrary interior fluid(s). The structural modes are computed with the finite-element method using shell elements. Acoustic modes are computed analytically assuming acoustically rigid boundaries and rectangular geometries of the enclosed cavities. This model is verified against finite-element solutions for the cases of rectangular structures containing one and two cavities, respectively.

Modelling of structural flexiblity in multibody railroad vehicle systems

NASA Astrophysics Data System (ADS)

Escalona, José L.; Sugiyama, Hiroyuki; Shabana, Ahmed A.

2013-07-01

This paper presents a review of recent research investigations on the computer modelling of flexible bodies in railroad vehicle systems. The paper will also discuss the influence of the structural flexibility of various components, including the wheelset, the truck frames, tracks, pantograph/catenary systems, and car bodies, on the dynamics of railroad vehicles. While several formulations and computer techniques for modelling structural flexibility are discussed in this paper, a special attention is paid to the floating frame of reference formulation which is widely used and leads to reduced-order finite-element models for flexible bodies by employing component modes synthesis techniques. Other formulations and numerical methods such as semi-analytical approaches, absolute nodal coordinate formulation, finite-segment method, boundary elements method, and discrete elements method are also discussed. This investigation is motivated by the fact that the structural flexibility can have a significant effect on the overall dynamics of railroad vehicles, ride comfort, vibration suppression and noise level reduction, lateral stability, track response to vehicle forces, stress analysis, wheel-rail contact forces, wear and crashworthiness.

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes.

PubMed

Papaleo, Elena; Tiberti, Matteo; Invernizzi, Gaetano; Pasi, Marco; Ranzani, Valeria

2011-11-01

The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures.

Structural dynamics and vibrations of damped, aircraft-type structures

NASA Technical Reports Server (NTRS)

Young, Maurice I.

1992-01-01

Engineering preliminary design methods for approximating and predicting the effects of viscous or equivalent viscous-type damping treatments on the free and forced vibration of lightly damped aircraft-type structures are developed. Similar developments are presented for dynamic hysteresis viscoelastic-type damping treatments. It is shown by both engineering analysis and numerical illustrations that the intermodal coupling of the undamped modes arising from the introduction of damping may be neglected in applying these preliminary design methods, except when dissimilar modes of these lightly damped, complex aircraft-type structures have identical or nearly identical natural frequencies. In such cases, it is shown that a relatively simple, additional interaction calculation between pairs of modes exhibiting this 'modal response' phenomenon suffices in the prediction of interacting modal damping fractions. The accuracy of the methods is shown to be very good to excellent, depending on the normal natural frequency separation of the system modes, thereby permitting a relatively simple preliminary design approach. This approach is shown to be a natural precursor to elaborate finite element, digital computer design computations in evaluating the type, quantity, and location of damping treatment.

The LATDYN user's manual

NASA Technical Reports Server (NTRS)

Housner, J. M.; Mcgowan, P. E.; Abrahamson, A. L.; Powell, M. G.

1986-01-01

The LATDYN User's Manual presents the capabilities and instructions for the LATDYN (Large Angle Transient DYNamics) computer program. The LATDYN program is a tool for analyzing the controlled or uncontrolled dynamic transient behavior of interconnected deformable multi-body systems which can undergo large angular motions of each body relative other bodies. The program accommodates large structural deformation as well as large rigid body rotations and is applicable, but not limited to, the following areas: (1) development of large flexible space structures; (2) slewing of large space structure components; (3) mechanisms with rigid or elastic components; and (4) robotic manipulations of beam members. Presently the program is limited to two dimensional problems, but in many cases, three dimensional problems can be exactly or approximately reduced to two dimensions. The program uses convected finite elements to affect the large angular motions involved in the analysis. General geometry is permitted. Detailed user input and output specifications are provided and discussed with example runstreams. To date, LATDYN has been configured for CDC/NOS and DEC VAX/VMS machines. All coding is in ANSII-77 FORTRAN. Detailed instructions regarding interfaces with particular computer operating systems and file structures are provided.

A 4DCT imaging-based breathing lung model with relative hysteresis

PubMed Central

Miyawaki, Shinjiro; Choi, Sanghun; Hoffman, Eric A.; Lin, Ching-Long

2016-01-01

To reproduce realistic airway motion and airflow, the authors developed a deforming lung computational fluid dynamics (CFD) model based on four-dimensional (4D, space and time) dynamic computed tomography (CT) images. A total of 13 time points within controlled tidal volume respiration were used to account for realistic and irregular lung motion in human volunteers. Because of the irregular motion of 4DCT-based airways, we identified an optimal interpolation method for airway surface deformation during respiration, and implemented a computational solid mechanics-based moving mesh algorithm to produce smooth deforming airway mesh. In addition, we developed physiologically realistic airflow boundary conditions for both models based on multiple images and a single image. Furthermore, we examined simplified models based on one or two dynamic or static images. By comparing these simplified models with the model based on 13 dynamic images, we investigated the effects of relative hysteresis of lung structure with respect to lung volume, lung deformation, and imaging methods, i.e., dynamic vs. static scans, on CFD-predicted pressure drop. The effect of imaging method on pressure drop was 24 percentage points due to the differences in airflow distribution and airway geometry. PMID:28260811

A 4DCT imaging-based breathing lung model with relative hysteresis

NASA Astrophysics Data System (ADS)

Miyawaki, Shinjiro; Choi, Sanghun; Hoffman, Eric A.; Lin, Ching-Long

2016-12-01

To reproduce realistic airway motion and airflow, the authors developed a deforming lung computational fluid dynamics (CFD) model based on four-dimensional (4D, space and time) dynamic computed tomography (CT) images. A total of 13 time points within controlled tidal volume respiration were used to account for realistic and irregular lung motion in human volunteers. Because of the irregular motion of 4DCT-based airways, we identified an optimal interpolation method for airway surface deformation during respiration, and implemented a computational solid mechanics-based moving mesh algorithm to produce smooth deforming airway mesh. In addition, we developed physiologically realistic airflow boundary conditions for both models based on multiple images and a single image. Furthermore, we examined simplified models based on one or two dynamic or static images. By comparing these simplified models with the model based on 13 dynamic images, we investigated the effects of relative hysteresis of lung structure with respect to lung volume, lung deformation, and imaging methods, i.e., dynamic vs. static scans, on CFD-predicted pressure drop. The effect of imaging method on pressure drop was 24 percentage points due to the differences in airflow distribution and airway geometry.

Dynamic mechanical analysis and organization/storage of data for polymetric materials

NASA Technical Reports Server (NTRS)

Rosenberg, M.; Buckley, W.

1982-01-01

Dynamic mechanical analysis was performed on a variety of temperature resistant polymers and composite resin matrices. Data on glass transition temperatures and degree of cure attained were derived. In addition a laboratory based computer system was installed and data base set up to allow entry of composite data. The laboratory CPU termed TYCHO is based on a DEC PDP 11/44 CPU with a Datatrieve relational data base. The function of TYCHO is integration of chemical laboratory analytical instrumentation and storage of chemical structures for modeling of new polymeric structures and compounds

Computational Methods for Nonlinear Dynamics Problems in Solid and Structural Mechanics: Models of Dynamic Frictional Phenomena in Metallic Structures.

DTIC Science & Technology

1986-03-31

Martins, J.A.C. and Campos , L.T. [1986], "Existence and Local Uniqueness of Solutions to Contact Problems in Elasticity with Nonlinear Friction...noisy and ttoubl esome vibt.t4ons. If the sound generated by the friction-induced oscillations of Rviolin strings may be the delight of all music lovers...formulation. See 0den and Martins - [1985] and Rabier, Martins, Oden and Campos [1986]. - It is now simple to show, in a 6o’uman manner, that, for

Optimal placement of excitations and sensors for verification of large dynamical systems

NASA Technical Reports Server (NTRS)

Salama, M.; Rose, T.; Garba, J.

1987-01-01

The computationally difficult problem of the optimal placement of excitations and sensors to maximize the observed measurements is studied within the framework of combinatorial optimization, and is solved numerically using a variation of the simulated annealing heuristic algorithm. Results of numerical experiments including a square plate and a 960 degrees-of-freedom Control of Flexible Structure (COFS) truss structure, are presented. Though the algorithm produces suboptimal solutions, its generality and simplicity allow the treatment of complex dynamical systems which would otherwise be difficult to handle.

Using directed information for influence discovery in interconnected dynamical systems

NASA Astrophysics Data System (ADS)

Rao, Arvind; Hero, Alfred O.; States, David J.; Engel, James Douglas

2008-08-01

Structure discovery in non-linear dynamical systems is an important and challenging problem that arises in various applications such as computational neuroscience, econometrics, and biological network discovery. Each of these systems have multiple interacting variables and the key problem is the inference of the underlying structure of the systems (which variables are connected to which others) based on the output observations (such as multiple time trajectories of the variables). Since such applications demand the inference of directed relationships among variables in these non-linear systems, current methods that have a linear assumption on structure or yield undirected variable dependencies are insufficient. Hence, in this work, we present a methodology for structure discovery using an information-theoretic metric called directed time information (DTI). Using both synthetic dynamical systems as well as true biological datasets (kidney development and T-cell data), we demonstrate the utility of DTI in such problems.

Theoretical predictor for candidate structure assignment from IMS data of biomolecule-related conformational space.

PubMed

Schenk, Emily R; Nau, Frederic; Fernandez-Lima, Francisco

2015-06-01

The ability to correlate experimental ion mobility data with candidate structures from theoretical modeling provides a powerful analytical and structural tool for the characterization of biomolecules. In the present paper, a theoretical workflow is described to generate and assign candidate structures for experimental trapped ion mobility and H/D exchange (HDX-TIMS-MS) data following molecular dynamics simulations and statistical filtering. The applicability of the theoretical predictor is illustrated for a peptide and protein example with multiple conformations and kinetic intermediates. The described methodology yields a low computational cost and a simple workflow by incorporating statistical filtering and molecular dynamics simulations. The workflow can be adapted to different IMS scenarios and CCS calculators for a more accurate description of the IMS experimental conditions. For the case of the HDX-TIMS-MS experiments, molecular dynamics in the "TIMS box" accounts for a better sampling of the molecular intermediates and local energy minima.

Engineering science and mechanics; Proceedings of the International Symposium, Tainan, Republic of China, December 29-31, 1981. Parts 1 & 2

NASA Astrophysics Data System (ADS)

Hsia, H.-M.; Chou, Y.-L.; Longman, R. W.

1983-07-01

The topics considered are related to measurements and controls in physical systems, the control of large scale and distributed parameter systems, chemical engineering systems, aerospace science and technology, thermodynamics and fluid mechanics, and computer applications. Subjects in structural dynamics are discussed, taking into account finite element approximations in transient analysis, buckling finite element analysis of flat plates, dynamic analysis of viscoelastic structures, the transient analysis of large frame structures by simple models, large amplitude vibration of an initially stressed thick plate, nonlinear aeroelasticity, a sensitivity analysis of a combined beam-spring-mass structure, and the optimal design and aeroelastic investigation of segmented windmill rotor blades. Attention is also given to dynamics and control of mechanical and civil engineering systems, composites, and topics in materials. For individual items see A83-44002 to A83-44061

Molecular mechanics and dynamics characterization of an in silico mutated protein: a stand-alone lab module or support activity for in vivo and in vitro analyses of targeted proteins.

PubMed

Chiang, Harry; Robinson, Lucy C; Brame, Cynthia J; Messina, Troy C

2013-01-01

Over the past 20 years, the biological sciences have increasingly incorporated chemistry, physics, computer science, and mathematics to aid in the development and use of mathematical models. Such combined approaches have been used to address problems from protein structure-function relationships to the workings of complex biological systems. Computer simulations of molecular events can now be accomplished quickly and with standard computer technology. Also, simulation software is freely available for most computing platforms, and online support for the novice user is ample. We have therefore created a molecular dynamics laboratory module to enhance undergraduate student understanding of molecular events underlying organismal phenotype. This module builds on a previously described project in which students use site-directed mutagenesis to investigate functions of conserved sequence features in members of a eukaryotic protein kinase family. In this report, we detail the laboratory activities of a MD module that provide a complement to phenotypic outcomes by providing a hypothesis-driven and quantifiable measure of predicted structural changes caused by targeted mutations. We also present examples of analyses students may perform. These laboratory activities can be integrated with genetics or biochemistry experiments as described, but could also be used independently in any course that would benefit from a quantitative approach to protein structure-function relationships. Copyright © 2013 Wiley Periodicals, Inc.

Development of Advanced Computational Aeroelasticity Tools at NASA Langley Research Center

NASA Technical Reports Server (NTRS)

Bartels, R. E.

2008-01-01

NASA Langley Research Center has continued to develop its long standing computational tools to address new challenges in aircraft and launch vehicle design. This paper discusses the application and development of those computational aeroelastic tools. Four topic areas will be discussed: 1) Modeling structural and flow field nonlinearities; 2) Integrated and modular approaches to nonlinear multidisciplinary analysis; 3) Simulating flight dynamics of flexible vehicles; and 4) Applications that support both aeronautics and space exploration.

The Dynamic Interplay between Spatialization of Written Units in Writing Activity and Functions of Tools on the Computer

ERIC Educational Resources Information Center

Huh, Joo Hee

2012-01-01

I criticize the typewriting model and linear writing structure of Microsoft Word software for writing in the computer. I problematize bodily movement in writing that the error of the software disregards. In this research, writing activity is viewed as bodily, spatial and mediated activity under the premise of the unity of consciousness and…

Derivation of improved load transformation matrices for launchers-spacecraft coupled analysis, and direct computation of margins of safety

NASA Technical Reports Server (NTRS)

Klein, M.; Reynolds, J.; Ricks, E.

1989-01-01

Load and stress recovery from transient dynamic studies are improved upon using an extended acceleration vector in the modal acceleration technique applied to structural analysis. Extension of the normal LTM (load transformation matrices) stress recovery to automatically compute margins of safety is presented with an application to the Hubble space telescope.

Modeling, Analysis, and Optimization Issues for Large Space Structures.

DTIC Science & Technology

1983-02-01

There are numerous opportunities - provided by new advances in computer hardware, firmware, software , CAD/CAM systems, computational algorithms and...Institute Department of Mechanical Engineering Dept. of Civil Engineering & Mechanics Troy, NY 12181 Drexel University Philadelphia, PA 19104 Dr...Mechanical Engineering Hampton, VA 23665 Washington, DC 20059 Dr. K. T. Alfriend Mr. Siva S. Banda Department of the Navy Flight Dynamics LaboratoryNaval

Effect of Turbulence Modeling on an Excited Jet

NASA Technical Reports Server (NTRS)

Brown, Clifford A.; Hixon, Ray

2010-01-01

The flow dynamics in a high-speed jet are dominated by unsteady turbulent flow structures in the plume. Jet excitation seeks to control these flow structures through the natural instabilities present in the initial shear layer of the jet. Understanding and optimizing the excitation input, for jet noise reduction or plume mixing enhancement, requires many trials that may be done experimentally or computationally at a significant cost savings. Numerical simulations, which model various parts of the unsteady dynamics to reduce the computational expense of the simulation, must adequately capture the unsteady flow dynamics in the excited jet for the results are to be used. Four CFD methods are considered for use in an excited jet problem, including two turbulence models with an Unsteady Reynolds Averaged Navier-Stokes (URANS) solver, one Large Eddy Simulation (LES) solver, and one URANS/LES hybrid method. Each method is used to simulate a simplified excited jet and the results are evaluated based on the flow data, computation time, and numerical stability. The knowledge gained about the effect of turbulence modeling and CFD methods from these basic simulations will guide and assist future three-dimensional (3-D) simulations that will be used to understand and optimize a realistic excited jet for a particular application.

Computationally Guided Design of Polymer Electrolytes for Battery Applications

NASA Astrophysics Data System (ADS)

Wang, Zhen-Gang; Webb, Michael; Savoie, Brett; Miller, Thomas

We develop an efficient computational framework for guiding the design of polymer electrolytes for Li battery applications. Short-times molecular dynamics (MD) simulations are employed to identify key structural and dynamic features in the solvation and motion of Li ions, such as the structure of the solvation shells, the spatial distribution of solvation sites, and the polymer segmental mobility. Comparative studies on six polyester-based polymers and polyethylene oxide (PEO) yield good agreement with experimental data on the ion conductivities, and reveal significant differences in the ion diffusion mechanism between PEO and the polyesters. The molecular insights from the MD simulations are used to build a chemically specific coarse-grained model in the spirit of the dynamic bond percolation model of Druger, Ratner and Nitzan. We apply this coarse-grained model to characterize Li ion diffusion in several existing and yet-to-be synthesized polyethers that differ by oxygen content and backbone stiffness. Good agreement is obtained between the predictions of the coarse-grained model and long-timescale atomistic MD simulations, thus providing validation of the model. Our study predicts higher Li ion diffusivity in poly(trimethylene oxide-alt-ethylene oxide) than in PEO. These results demonstrate the potential of this computational framework for rapid screening of new polymer electrolytes based on ion diffusivity.

Dynamic characterization of solid rockets

NASA Technical Reports Server (NTRS)

1973-01-01

The structural dynamics of solid rockets in-general was studied. A review is given of the modes of vibration and bending that can exist for a solid propellant rocket, and a NASTRAN computer model is included. Also studied were the dynamic properties of a solid propellant, polybutadiene-acrylic acid-acrylonitrile terpolymer, which may be used in the space shuttle rocket booster. The theory of viscoelastic materials (i.e, Poisson's ratio) was employed in describing the dynamic properties of the propellant. These studies were performed for an eventual booster stage development program for the space shuttle.

Development of methodology for horizontal axis wind turbine dynamic analysis

NASA Technical Reports Server (NTRS)

Dugundji, J.

1982-01-01

Horizontal axis wind turbine dynamics were studied. The following findings are summarized: (1) review of the MOSTAS computer programs for dynamic analysis of horizontal axis wind turbines; (2) review of various analysis methods for rotating systems with periodic coefficients; (3) review of structural dynamics analysis tools for large wind turbine; (4) experiments for yaw characteristics of a rotating rotor; (5) development of a finite element model for rotors; (6) development of simple models for aeroelastics; and (7) development of simple models for stability and response of wind turbines on flexible towers.

Computational Methods of Studying the Binding of Toxins From Venomous Animals to Biological Ion Channels: Theory and Applications

PubMed Central

Chen, Rong; Chung, Shin-Ho

2013-01-01

The discovery of new drugs that selectively block or modulate ion channels has great potential to provide new treatments for a host of conditions. One promising avenue revolves around modifying or mimicking certain naturally occurring ion channel modulator toxins. This strategy appears to offer the prospect of designing drugs that are both potent and specific. The use of computational modeling is crucial to this endeavor, as it has the potential to provide lower cost alternatives for exploring the effects of new compounds on ion channels. In addition, computational modeling can provide structural information and theoretical understanding that is not easily derivable from experimental results. In this review, we look at the theory and computational methods that are applicable to the study of ion channel modulators. The first section provides an introduction to various theoretical concepts, including force-fields and the statistical mechanics of binding. We then look at various computational techniques available to the researcher, including molecular dynamics, Brownian dynamics, and molecular docking systems. The latter section of the review explores applications of these techniques, concentrating on pore blocker and gating modifier toxins of potassium and sodium channels. After first discussing the structural features of these channels, and their modes of block, we provide an in-depth review of past computational work that has been carried out. Finally, we discuss prospects for future developments in the field. PMID:23589832

Acceleration and torque feedback for robotic control - Experimental results

NASA Technical Reports Server (NTRS)

Mclnroy, John E.; Saridis, George N.

1990-01-01

Gross motion control of robotic manipulators typically requires significant on-line computations to compensate for nonlinear dynamics due to gravity, Coriolis, centripetal, and friction nonlinearities. One controller proposed by Luo and Saridis avoids these computations by feeding back joint acceleration and torque. This study implements the controller on a Puma 600 robotic manipulator. Joint acceleration measurement is obtained by measuring linear accelerations of each joint, and deriving a computationally efficient transformation from the linear measurements to the angular accelerations. Torque feedback is obtained by using the previous torque sent to the joints. The implementation has stability problems on the Puma 600 due to the extremely high gains inherent in the feedback structure. Since these high gains excite frequency modes in the Puma 600, the algorithm is modified to decrease the gain inherent in the feedback structure. The resulting compensator is stable and insensitive to high frequency unmodeled dynamics. Moreover, a second compensator is proposed which uses acceleration and torque feedback, but still allows nonlinear terms to be fed forward. Thus, by feeding the increment in the easily calculated gravity terms forward, improved responses are obtained. Both proposed compensators are implemented, and the real time results are compared to those obtained with the computed torque algorithm.

Implications of the Turing machine model of computation for processor and programming language design

NASA Astrophysics Data System (ADS)

Hunter, Geoffrey

2004-01-01

A computational process is classified according to the theoretical model that is capable of executing it; computational processes that require a non-predeterminable amount of intermediate storage for their execution are Turing-machine (TM) processes, while those whose storage are predeterminable are Finite Automation (FA) processes. Simple processes (such as traffic light controller) are executable by Finite Automation, whereas the most general kind of computation requires a Turing Machine for its execution. This implies that a TM process must have a non-predeterminable amount of memory allocated to it at intermediate instants of its execution; i.e. dynamic memory allocation. Many processes encountered in practice are TM processes. The implication for computational practice is that the hardware (CPU) architecture and its operating system must facilitate dynamic memory allocation, and that the programming language used to specify TM processes must have statements with the semantic attribute of dynamic memory allocation, for in Alan Turing"s thesis on computation (1936) the "standard description" of a process is invariant over the most general data that the process is designed to process; i.e. the program describing the process should never have to be modified to allow for differences in the data that is to be processed in different instantiations; i.e. data-invariant programming. Any non-trivial program is partitioned into sub-programs (procedures, subroutines, functions, modules, etc). Examination of the calls/returns between the subprograms reveals that they are nodes in a tree-structure; this tree-structure is independent of the programming language used to encode (define) the process. Each sub-program typically needs some memory for its own use (to store values intermediate between its received data and its computed results); this locally required memory is not needed before the subprogram commences execution, and it is not needed after its execution terminates; it may be allocated as its execution commences, and deallocated as its execution terminates, and if the amount of this local memory is not known until just before execution commencement, then it is essential that it be allocated dynamically as the first action of its execution. This dynamically allocated/deallocated storage of each subprogram"s intermediate values, conforms with the stack discipline; i.e. last allocated = first to be deallocated, an incidental benefit of which is automatic overlaying of variables. This stack-based dynamic memory allocation was a semantic implication of the nested block structure that originated in the ALGOL-60 programming language. AGLOL-60 was a TM language, because the amount of memory allocated on subprogram (block/procedure) entry (for arrays, etc) was computable at execution time. A more general requirement of a Turing machine process is for code generation at run-time; this mandates access to the source language processor (compiler/interpretor) during execution of the process. This fundamental aspect of computer science is important to the future of system design, because it has been overlooked throughout the 55 years since modern computing began in 1048. The popular computer systems of this first half-century of computing were constrained by compile-time (or even operating system boot-time) memory allocation, and were thus limited to executing FA processes. The practical effect was that the distinction between the data-invariant program and its variable data was blurred; programmers had to make trial and error executions, modifying the program"s compile-time constants (array dimensions) to iterate towards the values required at run-time by the data being processed. This era of trial and error computing still persists; it pervades the culture of current (2003) computing practice.

Dynamic array processing for computationally intensive expert systems in CLIPS

NASA Technical Reports Server (NTRS)

Athavale, N. N.; Ragade, R. K.; Fenske, T. E.; Cassaro, M. A.

1990-01-01

This paper puts forth an architecture for implementing a loop for advanced data structure of arrays in CLIPS. An attempt is made to use multi-field variables in such an architecture to process a set of data during the decision making cycle. Also, current limitations on the expert system shells are discussed in brief in this paper. The resulting architecture is designed to circumvent the current limitations set by the expert system shell and also by the operating environment. Such advanced data structures are needed for tightly coupling symbolic and numeric computation modules.

Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2009-01-01

Structural and functional studies of the ABL and EGFR kinase domains have recently suggested a common mechanism of activation by cancer-causing mutations. However, dynamics and mechanistic aspects of kinase activation by cancer mutations that stimulate conformational transitions and thermodynamic stabilization of the constitutively active kinase form remain elusive. We present a large-scale computational investigation of activation mechanisms in the ABL and EGFR kinase domains by a panel of clinically important cancer mutants ABL-T315I, ABL-L387M, EGFR-T790M, and EGFR-L858R. We have also simulated the activating effect of the gatekeeper mutation on conformational dynamics and allosteric interactions in functional states of the ABL-SH2-SH3 regulatory complexes. A comprehensive analysis was conducted using a hierarchy of computational approaches that included homology modeling, molecular dynamics simulations, protein stability analysis, targeted molecular dynamics, and molecular docking. Collectively, the results of this study have revealed thermodynamic and mechanistic catalysts of kinase activation by major cancer-causing mutations in the ABL and EGFR kinase domains. By using multiple crystallographic states of ABL and EGFR, computer simulations have allowed one to map dynamics of conformational fluctuations and transitions in the normal (wild-type) and oncogenic kinase forms. A proposed multi-stage mechanistic model of activation involves a series of cooperative transitions between different conformational states, including assembly of the hydrophobic spine, the formation of the Src-like intermediate structure, and a cooperative breakage and formation of characteristic salt bridges, which signify transition to the active kinase form. We suggest that molecular mechanisms of activation by cancer mutations could mimic the activation process of the normal kinase, yet exploiting conserved structural catalysts to accelerate a conformational transition and the enhanced stabilization of the active kinase form. The results of this study reconcile current experimental data with insights from theoretical approaches, pointing to general mechanistic aspects of activating transitions in protein kinases. PMID:19714203

Data-driven train set crash dynamics simulation

NASA Astrophysics Data System (ADS)

Tang, Zhao; Zhu, Yunrui; Nie, Yinyu; Guo, Shihui; Liu, Fengjia; Chang, Jian; Zhang, Jianjun

2017-02-01

Traditional finite element (FE) methods are arguably expensive in computation/simulation of the train crash. High computational cost limits their direct applications in investigating dynamic behaviours of an entire train set for crashworthiness design and structural optimisation. On the contrary, multi-body modelling is widely used because of its low computational cost with the trade-off in accuracy. In this study, a data-driven train crash modelling method is proposed to improve the performance of a multi-body dynamics simulation of train set crash without increasing the computational burden. This is achieved by the parallel random forest algorithm, which is a machine learning approach that extracts useful patterns of force-displacement curves and predicts a force-displacement relation in a given collision condition from a collection of offline FE simulation data on various collision conditions, namely different crash velocities in our analysis. Using the FE simulation results as a benchmark, we compared our method with traditional multi-body modelling methods and the result shows that our data-driven method improves the accuracy over traditional multi-body models in train crash simulation and runs at the same level of efficiency.

Journal and Wave Bearing Impedance Calculation Software

NASA Technical Reports Server (NTRS)

Hanford, Amanda; Campbell, Robert

2012-01-01

The wave bearing software suite is a MALTA application that computes bearing properties for user-specified wave bearing conditions, as well as plain journal bearings. Wave bearings are fluid film journal bearings with multi-lobed wave patterns around the circumference of the bearing surface. In this software suite, the dynamic coefficients are outputted in a way for easy implementation in a finite element model used in rotor dynamics analysis. The software has a graphical user interface (GUI) for inputting bearing geometry parameters, and uses MATLAB s structure interface for ease of interpreting data. This innovation was developed to provide the stiffness and damping components of wave bearing impedances. The computational method for computing bearing coefficients was originally designed for plain journal bearings and tilting pad bearings. Modifications to include a wave bearing profile consisted of changing the film thickness profile given by an equation, and writing an algorithm to locate the integration limits for each fluid region. Careful consideration was needed to implement the correct integration limits while computing the dynamic coefficients, depending on the form of the input/output variables specified in the algorithm.

An Evaluation of the Scattering Law for Light and Heavy Water in ENDF-6 Format, Based on Experimental Data and Molecular Dynamics

NASA Astrophysics Data System (ADS)

Márquez Damián, J. I.; Granada, J. R.; Malaspina, D. C.

2014-04-01

In this work we present an evaluation in ENDF-6 format of the scattering law for light and heavy water computed using the LEAPR module of NJOY99. The models used in this evaluation are based on experimental data on light water dynamics measured by Novikov, partial structure factors obtained by Soper, and molecular dynamics calculations performed with GROMACS using a reparameterized version of the flexible SPC model by Toukan and Rahman. The models use the Egelstaff-Schofield diffusion equation for translational motion, and a continuous spectrum calculated from the velocity autocorrelation function computed with GROMACS. The scattering law for H in H2O is computed using the incoherent approximation, and the scattering law D and O in D2O are computed using the Sköld approximation for coherent scattering. The calculations show significant improvement over ENDF/B-VI and ENDF/B-VII when compared with measurements of the total cross section, differential scattering experiments and quasi-elastic neutron scattering experiments (QENS).

Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures

PubMed Central

de la Fuente, Ildefonso Martínez

2010-01-01

One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life. PMID:20957111

Integral projection models for finite populations in a stochastic environment.

PubMed

Vindenes, Yngvild; Engen, Steinar; Saether, Bernt-Erik

2011-05-01

Continuous types of population structure occur when continuous variables such as body size or habitat quality affect the vital parameters of individuals. These structures can give rise to complex population dynamics and interact with environmental conditions. Here we present a model for continuously structured populations with finite size, including both demographic and environmental stochasticity in the dynamics. Using recent methods developed for discrete age-structured models we derive the demographic and environmental variance of the population growth as functions of a continuous state variable. These two parameters, together with the expected population growth rate, are used to define a one-dimensional diffusion approximation of the population dynamics. Thus, a substantial reduction in complexity is achieved as the dynamics of the complex structured model can be described by only three population parameters. We provide methods for numerical calculation of the model parameters and demonstrate the accuracy of the diffusion approximation by computer simulation of specific examples. The general modeling framework makes it possible to analyze and predict future dynamics and extinction risk of populations with various types of structure, and to explore consequences of changes in demography caused by, e.g., climate change or different management decisions. Our results are especially relevant for small populations that are often of conservation concern.

Structural Refinement of Membrane Proteins by Restrained Molecular Dynamics and Solvent Accessibility Data

PubMed Central

Sompornpisut, Pornthep; Roux, Benoît; Perozo, Eduardo

2008-01-01

We present an approach for incorporating solvent accessibility data from electron paramagnetic resonance experiments in the structural refinement of membrane proteins through restrained molecular dynamics simulations. The restraints have been parameterized from oxygen (ΠO2) and nickel-ethylenediaminediacetic acid (ΠNiEdda) collision frequencies, as indicators of lipid or aqueous exposed spin-label sites. These are enforced through interactions between a pseudoatom representation of the covalently attached Nitroxide spin-label and virtual “solvent” particles corresponding to O2 and NiEdda in the surrounding environment. Interactions were computed using an empirical potential function, where the parameters have been optimized to account for the different accessibilities of the spin-label pseudoatoms to the surrounding environment. This approach, “pseudoatom-driven solvent accessibility refinement”, was validated by refolding distorted conformations of the Streptomyces lividans potassium channel (KcsA), corresponding to a range of 2–30 Å root mean-square deviations away from the native structure. Molecular dynamics simulations based on up to 58 electron paramagnetic resonance restraints derived from spin-label mutants were able to converge toward the native structure within 1–3 Å root mean-square deviations with minimal computational cost. The use of energy-based ranking and structure similarity clustering as selection criteria helped in the convergence and identification of correctly folded structures from a large number of simulations. This approach can be applied to a variety of integral membrane protein systems, regardless of oligomeric state, and should be particularly useful in calculating conformational changes from a known reference crystal structure. PMID:18676641

The theory of reasoned action as parallel constraint satisfaction: towards a dynamic computational model of health behavior.

PubMed

Orr, Mark G; Thrush, Roxanne; Plaut, David C

2013-01-01

The reasoned action approach, although ubiquitous in health behavior theory (e.g., Theory of Reasoned Action/Planned Behavior), does not adequately address two key dynamical aspects of health behavior: learning and the effect of immediate social context (i.e., social influence). To remedy this, we put forth a computational implementation of the Theory of Reasoned Action (TRA) using artificial-neural networks. Our model re-conceptualized behavioral intention as arising from a dynamic constraint satisfaction mechanism among a set of beliefs. In two simulations, we show that constraint satisfaction can simultaneously incorporate the effects of past experience (via learning) with the effects of immediate social context to yield behavioral intention, i.e., intention is dynamically constructed from both an individual's pre-existing belief structure and the beliefs of others in the individual's social context. In a third simulation, we illustrate the predictive ability of the model with respect to empirically derived behavioral intention. As the first known computational model of health behavior, it represents a significant advance in theory towards understanding the dynamics of health behavior. Furthermore, our approach may inform the development of population-level agent-based models of health behavior that aim to incorporate psychological theory into models of population dynamics.

The Theory of Reasoned Action as Parallel Constraint Satisfaction: Towards a Dynamic Computational Model of Health Behavior

PubMed Central

Orr, Mark G.; Thrush, Roxanne; Plaut, David C.

2013-01-01

The reasoned action approach, although ubiquitous in health behavior theory (e.g., Theory of Reasoned Action/Planned Behavior), does not adequately address two key dynamical aspects of health behavior: learning and the effect of immediate social context (i.e., social influence). To remedy this, we put forth a computational implementation of the Theory of Reasoned Action (TRA) using artificial-neural networks. Our model re-conceptualized behavioral intention as arising from a dynamic constraint satisfaction mechanism among a set of beliefs. In two simulations, we show that constraint satisfaction can simultaneously incorporate the effects of past experience (via learning) with the effects of immediate social context to yield behavioral intention, i.e., intention is dynamically constructed from both an individual’s pre-existing belief structure and the beliefs of others in the individual’s social context. In a third simulation, we illustrate the predictive ability of the model with respect to empirically derived behavioral intention. As the first known computational model of health behavior, it represents a significant advance in theory towards understanding the dynamics of health behavior. Furthermore, our approach may inform the development of population-level agent-based models of health behavior that aim to incorporate psychological theory into models of population dynamics. PMID:23671603

Hybrid Voronoi diagrams, their computation and reduction for applications in computational biochemistry.

PubMed

Manak, Martin; Zemek, Michal; Szkandera, Jakub; Kolingerova, Ivana; Papaleo, Elena; Lambrughi, Matteo

2017-06-01

Geometric models of molecular structures are often described as a set of balls, where balls represent individual atoms. The ability to describe and explore the empty space among these balls is important, e.g., in the analysis of the interaction of enzymes with substrates, ligands and solvent molecules. Voronoi diagrams from the field of computational geometry are often used here, because they provide a mathematical description of how the whole space can be divided into regions assigned to individual atoms. This paper introduces a combination of two different types of Voronoi diagrams into a new hybrid Voronoi diagram - one part of this diagram belongs to the additively weighted (aw-Voronoi) diagram and the other to the power diagram. The boundary between them is controlled by a user-defined constant (the probe radius). Both parts are computed by different algorithms, which are already known. The reduced aw-Voronoi diagram is then obtained by removing the power diagram part from the hybrid diagram. Reduced aw-Voronoi diagrams are perfectly tailored for the analysis of dynamic molecular structures, their computation is faster and storage requirements are lower than in the case of complete aw-Voronoi diagrams. Here, we showed their application to key proteins in cancer research such as p53 and ARID proteins as case study. We identified a biologically relevant cavity in p53 structural ensembles generated by molecular dynamics simulations and analyzed its accessibility, attesting the potential of our approach. This method is relevant for cancer research since it permits to depict a dynamical view of cavities and pockets in proteins that could be affected by mutations in the disease. Our approach opens novel prospects for the study of cancer-related proteins by molecular simulations and the identification of novel targets for drug design. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparative 1D and 3D numerical investigation of open-channel junction flows and energy losses

NASA Astrophysics Data System (ADS)

Luo, Hao; Fytanidis, Dimitrios K.; Schmidt, Arthur R.; García, Marcelo H.

2018-07-01

The complexity of open channel confluences stems from flow mixing, secondary circulation, post-confluence flow separation, contraction and backwater effects. These effects in turn result in a large number of parameters required to adequately quantify the junction induced hydraulic resistance and describe mean flow pattern and turbulent flow structures due to flow merging. The recent development in computing power advances the application of 3D Computational Fluid Dynamics (CFD) codes to visualize and understand the Confluence Hydrodynamic Zone (CHZ). Nevertheless, 1D approaches remain the mainstay in large drainage network or waterway system modeling considering computational efficiency and data availability. This paper presents (i) a modified 1D nonlinear dynamic model; (ii) a fully 3D non-hydrostatic, Reynolds-averaged Navier-Stokes Equations (RANS)-based, Computational Fluid Dynamics (CFD) model; (iii) an analysis of changing confluence hydrodynamics and 3D turbulent flow structure under various controls; (iv) a comparison of flow features (i.e. upstream water depths, energy losses and post-confluence contraction) predicted by 1D and 3D models; and (v) parameterization of 3D flow characteristics in 1D modeling through the computation of correction coefficients associated with contraction, energy and momentum. The present comprehensive 3D numerical investigation highlights the driving mechanisms for junction induced energy losses. Moreover, the comparative 1D and 3D study quantifies the deviation of 1D approximations and associated underlying assumptions from the 'true' resultant flow field. The study may also shed light on improving the accuracy of the 1D large network modeling through the parameterization of the complex 3D feature of the flow field and correction of interior boundary conditions at junctions of larger angles and/or with substantial lateral inflows. Moreover, the enclosed numerical investigations may enhance the understanding of the primary mechanisms contributing to hydraulic structure induced turbulent flow behavior and increased hydraulic resistance.

Towards data warehousing and mining of protein unfolding simulation data.

PubMed

Berrar, Daniel; Stahl, Frederic; Silva, Candida; Rodrigues, J Rui; Brito, Rui M M; Dubitzky, Werner

2005-10-01

The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

Parametric instabilities of rotor-support systems with application to industrial ventilators

NASA Technical Reports Server (NTRS)

Parszewski, Z.; Krodkiemski, T.; Marynowski, K.

1980-01-01

Rotor support systems interaction with parametric excitation is considered for both unequal principal shaft stiffness (generators) and offset disc rotors (ventilators). Instability regions and types of instability are computed in the first case, and parametric resonances in the second case. Computed and experimental results are compared for laboratory machine models. A field case study of parametric vibrations in industrial ventilators is reported. Computed parametric resonances are confirmed in field measurements, and some industrial failures are explained. Also the dynamic influence and gyroscopic effect of supporting structures are shown and computed.

Molecular dynamics simulation of water at mineral surfaces: Structure, dynamics, energetics and hydrogen bonding

NASA Astrophysics Data System (ADS)

Kalinichev, A. G.; Wang, J.; Kirkpatrick, R.

2006-05-01

Fundamental molecular-level understanding of the properties of aqueous mineral interfaces is of great importance for many geochemical and environmental systems. Interaction between water and mineral surfaces substantially affects the properties of both phases, including the reactivity and functionality of the substrate surface, and the structure, dynamics, and energetics of the near surface aqueous phase. Experimental studies of interfacial water structure and dynamics using surface-sensitive techniques such as sum-frequency vibrational spectroscopy or X-ray and neutron reflectivity are not always possible for many practically important substrates, and their results often require interpretation concerning the atomistic mechanisms responsible for the observed behavior. Molecular computer simulations can provide new insight into the underlying molecular- level relationships between the inorganic substrate structure and composition and the structure, ordering, and dynamics of interfacial water. We have performed a series of molecular dynamics (MD) computer simulations of aqueous interfaces with several silicates (quartz, muscovite, and talc) and hydroxides (brucite, portlandite, gibbsite, Ca/Al and Mg/Al double hydroxides) to quantify the effects of the substrate mineral structure and composition on the structural, transport, and thermodynamic properties of water on these mineral surfaces. Due to the prevalent effects of the development of well-interconnected H-bonding networks across the mineral- water interfaces, all the hydroxide surfaces (including a fully hydroxylated quartz surface) show very similar H2O density profiles perpendicular to the interface. However, the predominant orientations of the interfacial H2O molecules and their detailed 2-dimensional near-surface structure and dynamics parallel to the interface are quite different reflecting the differences in the substrate structural charge distribution and the density and orientations of the surface OH groups. The H2O density profiles and other structural and dynamic characteristics of water at the two siloxane surfaces are very different from each other and from the hydroxide surfaces, since the muscovite surface is negatively charged and hydrophilic, while the talc surface is electrostatically neutral and hydrophobic. In general, at hydrophilic neutral surfaces both donating and accepting H-bonds from the H2O molecules are contributing to the development of the interfacial H-bond network, whereas at hydrophilic but charged surfaces only accepting or donating H-bonds with H2O molecules are possible. At the hydrophobic talc surface H-bonds among H2O molecules dominate the interfacial H-bond network and the water-surface interactions are very weak. The first water layer at all substrates is well ordered parallel to the surface, reflecting substrate crystal structures and indicating the reduced translational and orientational mobility of interfacial H2O molecules. At longer time scale (~100ps) their dynamics can be decomposed into a slow, virtually frozen, regime due to the substrate- bound H2O and a faster regime of almost free water reflecting the dynamics far from the surface. At shorter times (>10ps) the two dynamical regimes are superimposed. The much higher ordering of interfacial water (compared to bulk liquid) can not be adequately described as simply "ice-like". To some extent, it rather resembles the behavior of supercooled water.

Adding dynamic rules to self-organizing fuzzy systems

NASA Technical Reports Server (NTRS)

Buhusi, Catalin V.

1992-01-01

This paper develops a Dynamic Self-Organizing Fuzzy System (DSOFS) capable of adding, removing, and/or adapting the fuzzy rules and the fuzzy reference sets. The DSOFS background consists of a self-organizing neural structure with neuron relocation features which will develop a map of the input-output behavior. The relocation algorithm extends the topological ordering concept. Fuzzy rules (neurons) are dynamically added or released while the neural structure learns the pattern. The DSOFS advantages are the automatic synthesis and the possibility of parallel implementation. A high adaptation speed and a reduced number of neurons is needed in order to keep errors under some limits. The computer simulation results are presented in a nonlinear systems modelling application.

A framework for stochastic simulations and visualization of biological electron-transfer dynamics

NASA Astrophysics Data System (ADS)

Nakano, C. Masato; Byun, Hye Suk; Ma, Heng; Wei, Tao; El-Naggar, Mohamed Y.

2015-08-01

Electron transfer (ET) dictates a wide variety of energy-conversion processes in biological systems. Visualizing ET dynamics could provide key insight into understanding and possibly controlling these processes. We present a computational framework named VizBET to visualize biological ET dynamics, using an outer-membrane Mtr-Omc cytochrome complex in Shewanella oneidensis MR-1 as an example. Starting from X-ray crystal structures of the constituent cytochromes, molecular dynamics simulations are combined with homology modeling, protein docking, and binding free energy computations to sample the configuration of the complex as well as the change of the free energy associated with ET. This information, along with quantum-mechanical calculations of the electronic coupling, provides inputs to kinetic Monte Carlo (KMC) simulations of ET dynamics in a network of heme groups within the complex. Visualization of the KMC simulation results has been implemented as a plugin to the Visual Molecular Dynamics (VMD) software. VizBET has been used to reveal the nature of ET dynamics associated with novel nonequilibrium phase transitions in a candidate configuration of the Mtr-Omc complex due to electron-electron interactions.

Membrane proteins structures: A review on computational modeling tools.

PubMed

Almeida, Jose G; Preto, Antonio J; Koukos, Panagiotis I; Bonvin, Alexandre M J J; Moreira, Irina S

2017-10-01

Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights. This review highlights the importance of membrane proteins and how computational methods are capable of overcoming challenges associated with their experimental characterization. It covers various MP structural aspects, such as lipid interactions, allostery, and structure prediction, based on methods such as Molecular Dynamics (MD) and Machine-Learning (ML). Recent developments in algorithms, tools and hybrid approaches, together with the increase in both computational resources and the amount of available data have resulted in increasingly powerful and trustworthy approaches to model MPs. Even though MPs are elementary and important in nature, the determination of their 3D structure has proven to be a challenging endeavor. Computational methods provide a reliable alternative to experimental methods. In this review, we focus on computational techniques to determine the 3D structure of MP and characterize their binding interfaces. We also summarize the most relevant databases and software programs available for the study of MPs. Copyright © 2017 Elsevier B.V. All rights reserved.

Interactions between Magnetically Levitated Vehicles and Elevated Guideway Structures

DOT National Transportation Integrated Search

1992-07-01

The dynamic performance characteristic of magnetically levitated vehicles and vehicle trains relating to ride quality and magnetic gap variations have been determined using computer simulation models for one-dimensional, two-dimensional and finite le...

In vitro flow assessment: from PC-MRI to computational fluid dynamics including fluid-structure interaction

NASA Astrophysics Data System (ADS)

Kratzke, Jonas; Rengier, Fabian; Weis, Christian; Beller, Carsten J.; Heuveline, Vincent

2016-04-01

Initiation and development of cardiovascular diseases can be highly correlated to specific biomechanical parameters. To examine and assess biomechanical parameters, numerical simulation of cardiovascular dynamics has the potential to complement and enhance medical measurement and imaging techniques. As such, computational fluid dynamics (CFD) have shown to be suitable to evaluate blood velocity and pressure in scenarios, where vessel wall deformation plays a minor role. However, there is a need for further validation studies and the inclusion of vessel wall elasticity for morphologies being subject to large displacement. In this work, we consider a fluid-structure interaction (FSI) model including the full elasticity equation to take the deformability of aortic wall soft tissue into account. We present a numerical framework, in which either a CFD study can be performed for less deformable aortic segments or an FSI simulation for regions of large displacement such as the aortic root and arch. Both of the methods are validated by means of an aortic phantom experiment. The computational results are in good agreement with 2D phase-contrast magnetic resonance imaging (PC-MRI) velocity measurements as well as catheter-based pressure measurements. The FSI simulation shows a characteristic vessel compliance effect on the flow field induced by the elasticity of the vessel wall, which the CFD model is not capable of. The in vitro validated FSI simulation framework can enable the computation of complementary biomechanical parameters such as the stress distribution within the vessel wall.

STARS: A general-purpose finite element computer program for analysis of engineering structures

NASA Technical Reports Server (NTRS)

Gupta, K. K.

1984-01-01

STARS (Structural Analysis Routines) is primarily an interactive, graphics-oriented, finite-element computer program for analyzing the static, stability, free vibration, and dynamic responses of damped and undamped structures, including rotating systems. The element library consists of one-dimensional (1-D) line elements, two-dimensional (2-D) triangular and quadrilateral shell elements, and three-dimensional (3-D) tetrahedral and hexahedral solid elements. These elements enable the solution of structural problems that include truss, beam, space frame, plane, plate, shell, and solid structures, or any combination thereof. Zero, finite, and interdependent deflection boundary conditions can be implemented by the program. The associated dynamic response analysis capability provides for initial deformation and velocity inputs, whereas the transient excitation may be either forces or accelerations. An effective in-core or out-of-core solution strategy is automatically employed by the program, depending on the size of the problem. Data input may be at random within a data set, and the program offers certain automatic data-generation features. Input data are formatted as an optimal combination of free and fixed formats. Interactive graphics capabilities enable convenient display of nodal deformations, mode shapes, and element stresses.

Spaceborne Processor Array

NASA Technical Reports Server (NTRS)

Chow, Edward T.; Schatzel, Donald V.; Whitaker, William D.; Sterling, Thomas

2008-01-01

A Spaceborne Processor Array in Multifunctional Structure (SPAMS) can lower the total mass of the electronic and structural overhead of spacecraft, resulting in reduced launch costs, while increasing the science return through dynamic onboard computing. SPAMS integrates the multifunctional structure (MFS) and the Gilgamesh Memory, Intelligence, and Network Device (MIND) multi-core in-memory computer architecture into a single-system super-architecture. This transforms every inch of a spacecraft into a sharable, interconnected, smart computing element to increase computing performance while simultaneously reducing mass. The MIND in-memory architecture provides a foundation for high-performance, low-power, and fault-tolerant computing. The MIND chip has an internal structure that includes memory, processing, and communication functionality. The Gilgamesh is a scalable system comprising multiple MIND chips interconnected to operate as a single, tightly coupled, parallel computer. The array of MIND components shares a global, virtual name space for program variables and tasks that are allocated at run time to the distributed physical memory and processing resources. Individual processor- memory nodes can be activated or powered down at run time to provide active power management and to configure around faults. A SPAMS system is comprised of a distributed Gilgamesh array built into MFS, interfaces into instrument and communication subsystems, a mass storage interface, and a radiation-hardened flight computer.

Application of foam-extend on turbulent fluid-structure interaction

NASA Astrophysics Data System (ADS)

Rege, K.; Hjertager, B. H.

2017-12-01

Turbulent flow around flexible structures is likely to induce structural vibrations which may eventually lead to fatigue failure. In order to assess the fatigue life of these structures, it is necessary to take the action of the flow on the structure into account, but also the influence of the vibrating structure on the fluid flow. This is achieved by performing fluid-structure interaction (FSI) simulations. In this work, we have investigated the capability of a FSI toolkit for the finite volume computational fluid dynamics software foam-extend to simulate turbulence-induced vibrations of a flexible structure. A large-eddy simulation (LES) turbulence model has been implemented to a basic FSI problem of a flexible wall which is placed in a confined, turbulent flow. This problem was simulated for 2.32 seconds. This short simulation required over 200 computation hours, using 20 processor cores. Thereby, it has been shown that the simulation of FSI with LES is possible, but also computationally demanding. In order to make turbulent FSI simulations with foam-extend more applicable, more sophisticated turbulence models and/or faster FSI iteration schemes should be applied.

Sequence- and structure-based computational analyses of Gram-negative tripartite efflux pumps in the context of bacterial membranes

DOE PAGES

Travers, Timothy; Wang, Katherine J.; Lopez, Cesar A.; ...

2018-02-09

Gram-negative multidrug resistance currently presents a serious threat to public health with infections effectively rendered untreatable. Multiple molecular mechanisms exist that cause antibiotic resistance and in addition, the last three decades have seen slowing rates of new drug development. In this paper, we summarize the use of various computational techniques for investigating the mechanisms of multidrug resistance mediated by Gram-negative tripartite efflux pumps and membranes. Recent work in our lab combines data-driven sequence and structure analyses to study the interactions and dynamics of these bacterial components. Computational studies can complement experimental methodologies for gaining crucial insights into combatting multidrug resistance.

Sequence- and structure-based computational analyses of Gram-negative tripartite efflux pumps in the context of bacterial membranes

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

Travers, Timothy; Wang, Katherine J.; Lopez, Cesar A.

Gram-negative multidrug resistance currently presents a serious threat to public health with infections effectively rendered untreatable. Multiple molecular mechanisms exist that cause antibiotic resistance and in addition, the last three decades have seen slowing rates of new drug development. In this paper, we summarize the use of various computational techniques for investigating the mechanisms of multidrug resistance mediated by Gram-negative tripartite efflux pumps and membranes. Recent work in our lab combines data-driven sequence and structure analyses to study the interactions and dynamics of these bacterial components. Computational studies can complement experimental methodologies for gaining crucial insights into combatting multidrug resistance.

Wind-US Flow Calculations for the M2129 S-Duct Using Structured and Unstructured Grids

NASA Technical Reports Server (NTRS)

Mohler, Stanley R., Jr.

2003-01-01

Computational Fluid Dynamics (CFD) flow solutions for the M2129 diffusing S-duct with and without vane effectors were computed by the Wind-US flow solver. Both structured and unstructured 3-D grids were used. Without vane effectors, the duct exhibited massive flow separation in both experiment and CFD. With vane effectors installed, the flow remained attached and aerodynamic losses were reduced. Total pressure recovery and distortion near the duct outlet were computed from the solutions and compared favorably to experimental values. These calculations are part of a validation effort for the Wind-US code. They also provide an example case to aid engineers in learning to use the Wind-US software.

Probabilistic Structural Analysis Methods (PSAM) for Select Space Propulsion System Components

NASA Technical Reports Server (NTRS)

1999-01-01

Probabilistic Structural Analysis Methods (PSAM) are described for the probabilistic structural analysis of engine components for current and future space propulsion systems. Components for these systems are subjected to stochastic thermomechanical launch loads. Uncertainties or randomness also occurs in material properties, structural geometry, and boundary conditions. Material property stochasticity, such as in modulus of elasticity or yield strength, exists in every structure and is a consequence of variations in material composition and manufacturing processes. Procedures are outlined for computing the probabilistic structural response or reliability of the structural components. The response variables include static or dynamic deflections, strains, and stresses at one or several locations, natural frequencies, fatigue or creep life, etc. Sample cases illustrates how the PSAM methods and codes simulate input uncertainties and compute probabilistic response or reliability using a finite element model with probabilistic methods.