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Sample records for md simulations similar

  1. Harvesting graphics power for MD simulations

    NARCIS (Netherlands)

    van Meel, J.A.; Arnold, A.; Frenkel, D.; Portegies Zwart, S.F.; Belleman, R.G.

    2008-01-01

    We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a

  2. Harvesting graphics power for MD simulations

    NARCIS (Netherlands)

    Meel, J.A. van; Arnold, A.; Frenkel, D.; Portegies Zwart, S.F.; Belleman, R.G.

    We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a

  3. MD simulation of cluster formation during sputtering

    International Nuclear Information System (INIS)

    Muramoto, T.; Okai, M.; Yamashita, Y.; Yorizane, K.; Yamamura, Y.

    2001-01-01

    The cluster ejection due to cluster impact on a solid surface is studied through molecular dynamics (MD) simulations. Simulations are performed for Cu cluster impacts on the Cu(1 1 1) surface for cluster energy 100 eV/atom, and for clusters of 6, 13, 28 and 55 atoms. Interatomic interactions are described by the AMLJ-EAM potential. The vibration energy spectrum is independent of the incident cluster size and energy. This comes from the fact that sputtered clusters become stable through the successive fragmentation of nascent large sputtered clusters. The vibration energy spectra for large sputtered clusters have a peak, whose energy corresponds to the melting temperature of Cu. The exponent of the power-law fit of the abundance distribution and the total sputtering yield for the cluster impacts are higher than that for the monatomic ion impacts with the same total energy, where the exponent δ is given by Y n ∝n δ and Y n is the yield of sputtered n-atom cluster. The exponent δ follows a unified function of the total sputtering yield, which is a monotonic increase function, and it is nearly equal to δ ∼ -3 for larger yield

  4. StandsSIM-MD: a Management Driven forest SIMulator

    Energy Technology Data Exchange (ETDEWEB)

    Barreiro, S.; Rua, J.; Tomé, M.

    2016-07-01

    Aim of the study. The existing stand level forest simulators available in Portugal were not developed with the aim of including up-to-date model versions and were limited in terms of accounting for forest management. The simulators’ platform, sIMfLOR was recently created to implement different growth models with a common philosophy. The objective was developing one easily-updatable, user-friendly, forest management and climate change sensitive simulator capable of projecting growth for the main tree species in Portugal. Area of the study: Portugal. Material and methods: The new simulator was programmed in a modular form consisting of several modules. The growth module integrates different forest growth and yield models (empirical and process-based) for the main wood production tree species in Portugal (eucalypt, umbrella and maritime pines); whereas the management module drives the growth projections along the planning horizon according to a range of forest management approaches and climate (at present only available for eucalypt). Main results: The main result is the StandsSIM-MD Management Driven simulator that overcomes the limitations of the existing stand level simulators. It is a step forward when compared to the models currently available in the sIMfLOR platform covering more tree species, stand structures and stand compositions. It is focused on end-users and it is based on similar concepts regarding the generation of required inputs and generated outputs. Research highlights: Forest Management Driven simulations approach. Multiple Prescriptions-Per-Stand functionality. StandsSIM-MD can be used to support landowners decisions on stand forest management. StandsSIM-MD simulations at regional level can be combined with optimization routines. (Author)

  5. StandsSIM-MD: a Management Driven forest SIMulator

    Directory of Open Access Journals (Sweden)

    Susana Barreiro

    2016-07-01

    Full Text Available Aim of the study: The existing stand level forest simulators available in Portugal were not developed with the aim of including up-to-date model versions and were limited in terms of accounting for forest management. The simulators’ platform, sIMfLOR was recently created to implement different growth models with a common philosophy. The objective was developing one easily-updatable, user-friendly, forest management and climate change sensitive simulator capable of projecting growth for the main tree species in Portugal. Area of the study: Portugal. Material and methods: The new simulator was programmed in a modular form consisting of several modules. The growth module integrates different forest growth and yield models (empirical and process-based for the main wood production tree species in Portugal (eucalypt, umbrella and maritime pines; whereas the management module drives the growth projections along the planning horizon according to a range of forest management approaches and climate (at present only available for eucalypt. Main results: The main result is the StandsSIM-MD Management Driven simulator that overcomes the limitations of the existing stand level simulators. It is a step forward when compared to the models currently available in the sIMfLOR platform covering more tree species, stand structures and stand compositions. It is focused on end-users and it is based on similar concepts regarding the generation of required inputs and generated outputs. Research highlights: -          Forest Management Driven simulations approach -          Multiple Prescriptions-Per-Stand functionality -          StandsSIM-MD can be used to support landowners decisions on stand forest management -          StandsSIM-MD simulations at regional level can be combined with optimization routines Keywords: Forest simulator, Forest Management Approaches; StandsSIM-MD; forest management.

  6. A molecular dynamics (MD simulation on tire-aggregate friction

    Directory of Open Access Journals (Sweden)

    Fengyan Sun

    2017-07-01

    Full Text Available The friction between tire and road surface is fundamentally depending on the molecular forces. In this paper, the nanoscale 3D contact model is employed to investigate the tire-aggregate friction mechanism. The tire and aggregate micro-structure are both constructed to evaluate the microscopic performance of tire-aggregate friction influence. Simulation results show for a high velocity, the energy dissipation of sliding on crystal structure is small, which results in a small friction coefficient; temperature will have influences on the friction coefficient, and with the increasing of velocity, the effect will gradually reduce. Keywords: Tire, Aggregate, Friction coefficient, Microscopic mechanism, MD simulation

  7. MD and BCA simulations of He and H bombardment of fuzz in bcc elements

    Science.gov (United States)

    Klaver, T. P. C.; Zhang, S.; Nordlund, K.

    2017-08-01

    We present results of MD simulations of low energy He ion bombardment of low density fuzz in bcc elements. He ions can penetrate several micrometers into sparse fuzz, which allows for a sufficient He flux through it to grow the fuzz further. He kinetic energy falls off exponentially with penetration depth. A BCA code was used to carry out the same ion bombardment on the same fuzz structures as in MD simulations, but with simpler, 10 million times faster calculations. Despite the poor theoretical basis of the BCA at low ion energies, and the use of somewhat different potentials in MD and BCA calculations, the ion penetration depths predicted by BCA are only ∼12% less than those predicted by MD. The MD-BCA differences are highly systematic and trends in the results of the two methods are very similar. We have carried out more than 200 BCA calculation runs of ion bombardment of fuzz, in which parameters in the ion bombardment process were varied. For most parameters, the results show that the ion bombardment process is quite generic. The ion species (He or H), ion mass, fuzz element (W, Ta, Mo, Fe) and fuzz element lattice parameter turned out to have a modest influence on ion penetration depths at most. An off-normal angle of incidence strongly reduces the ion penetration depth. Increasing the ion energy increases the ion penetration, but the rate by which ion energy drops off at high ion energies follows the same exponential pattern as at lower energies.

  8. Analysis of MD5 authentication in various routing protocols using simulation tools

    Science.gov (United States)

    Dinakaran, M.; Darshan, K. N.; Patel, Harsh

    2017-11-01

    Authentication being an important paradigm of security and Computer Networks require secure paths to make the flow of the data even more secure through some security protocols. So MD-5(Message Digest 5) helps in providing data integrity to the data being sent through it and authentication to the network devices. This paper gives a brief introduction to the MD-5, simulation of the networks by including MD-5 authentication using various routing protocols like OSPF, EIGRP and RIPv2. GNS3 is being used to simulate the scenarios. Analysis of the MD-5 authentication is done in the later sections of the paper.

  9. PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

    International Nuclear Information System (INIS)

    Kylasa, S.B.; Aktulga, H.M.; Grama, A.Y.

    2014-01-01

    We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors

  10. PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

    Energy Technology Data Exchange (ETDEWEB)

    Kylasa, S.B., E-mail: skylasa@purdue.edu [Department of Elec. and Comp. Eng., Purdue University, West Lafayette, IN 47907 (United States); Aktulga, H.M., E-mail: hmaktulga@lbl.gov [Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, MS 50F-1650, Berkeley, CA 94720 (United States); Grama, A.Y., E-mail: ayg@cs.purdue.edu [Department of Computer Science, Purdue University, West Lafayette, IN 47907 (United States)

    2014-09-01

    We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.

  11. Application of MD Simulations to Predict Membrane Properties of MOFs

    Directory of Open Access Journals (Sweden)

    Elda Adatoz

    2015-01-01

    Full Text Available Metal organic frameworks (MOFs are a new group of nanomaterials that have been widely examined for various chemical applications. Gas separation using MOF membranes has become an increasingly important research field in the last years. Several experimental studies have shown that thin-film MOF membranes can outperform well known polymer and zeolite membranes due to their higher gas permeances and selectivities. Given the very large number of available MOF materials, it is impractical to fabricate and test the performance of every single MOF membrane using purely experimental techniques. In this study, we used molecular simulations, Monte Carlo and Molecular Dynamics, to estimate both single-gas and mixture permeances of MOF membranes. Predictions of molecular simulations were compared with the experimental gas permeance data of MOF membranes in order to validate the accuracy of our computational approach. Results show that computational methodology that we described in this work can be used to accurately estimate membrane properties of MOFs prior to extensive experimental efforts.

  12. Water at silica/liquid water interfaces investigated by DFT-MD simulations

    Science.gov (United States)

    Gaigeot, Marie-Pierre

    This talk is dedicated to probing the microscopic structural organization of water at silica/liquid water interfaces including electrolytes by first principles DFT-based molecular dynamics simulations (DFT-MD). We will present our very recent DFT-MD simulations of electrolytic (KCl, NaCl, NaI) silica/liquid water interfaces in order to unravel the intertwined structural properties of water and electrolytes at the crystalline quartz/liquid water and amorphous silica/liquid water interfaces. DFT-MD simulations provide direct knowledge of the structural organization of water and the H-Bond network formed between the water molecules within the different water layers above the silica surface. One can furthermore extract vibrational signatures of the water molecules within the interfacial layers from the DFT-MD simulations, especially non-linear SFG (Sum Frequency generation) signatures that are active at solid/liquid interfaces. The strength of the simulated spectra is that a detailed analysis of the signatures in terms of the water/water H-Bond networks formed within the interfacial water layers and in terms of the water/silica or water/electrolytes H-Bond networks can be given. Comparisons of SFG spectra between quartz/water/electrolytes and amorphous silica/water/electrolytes interfaces allow us to definitely conclude on how the structural arrangements of liquid water at these electrolytic interfaces modulate the final spectroscopic signatures. Invited speaker.

  13. Investigation on single carbon atom transporting through the single-walled carbon nanotube by MD simulation

    International Nuclear Information System (INIS)

    Ding Yinfeng; Zhang Zhibin; Ke Xuezhi; Zhu Zhiyuan; Zhu Dezhang; Wang Zhenxia; Xu Hongjie

    2005-01-01

    The single carbon atom transporting through the single-walled carbon nanotube has been studied by molecular-dynamics (MD) simulation. We got different trajectories of the carbon atom by changing the input parameters. The simulation results indicate that the single carbon atom with low energy can transport through the carbon nanotube under some input conditions and result in different trajectories being straight line or 'rosette' or circular. (authors)

  14. Parallel Object Oriented MD Simulation Program for Long Time Simulations of Metallic Glasses and Undercooled Liquids

    Science.gov (United States)

    Böddeker, B.; Teichler, H.

    The MD simulation program TABB is motivated by the need of long time simulations for the investigation of slow processes near the glass transition of glass forming alloys. TABB is written in C++ with a high degree of flexibility: TABB allows the use of any short ranged pair potentials or EAM potentials, by generating and using a spline representation of all functions and their derivatives. TABB supports several numerical integration algorithms like the Runge-Kotta or the modified Gear-predictor-corrector algorithm of order five. The boundary conditions can be chosen to resemble the geometry of bulk materials or films. The simulation box length or the pressure can be fixed for each dimension separately. TABB may be used in isokinetic, isoenergeric or canonic (with random forces) mode. TABB contains a simple instruction interpreter to easily control the parameters and options during the simulation. The same source code can be compiled either for workstations or for parallel computers. The main optimization goal of TABB is to allow long time simulations of medium or small sized systems. To make this possible, much attention is spent on the optimized communication between the nodes. TABB uses a domain decomposition procedure. To use many nodes with a small system, the domain size has to be small compared to the range of particle interactions. In the limit of many nodes for only few atoms, the bottle neck of communication is the latency time. TABB minimizes the number of pairs of domains containing atoms that interact between these domains. This procedure minimizes the need of communication calls between pairs of nodes. TABB decides automatically, to how many, and to which directions the decomposition shall be applied. E.g., in the case of one dimensional domain decomposition, the simulation box is only split into "slabs" along a selected direction. The three dimensional domain decomposition is best with respect to the number of interacting domains only for simulations

  15. Novel 3D/VR interactive environment for MD simulations, visualization and analysis.

    Science.gov (United States)

    Doblack, Benjamin N; Allis, Tim; Dávila, Lilian P

    2014-12-18

    The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) 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 materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

  16. PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.

    Science.gov (United States)

    Scheurer, Maximilian; Rodenkirch, Peter; Siggel, Marc; Bernardi, Rafael C; Schulten, Klaus; Tajkhorshid, Emad; Rudack, Till

    2018-02-06

    Molecular dynamics (MD) simulations have become ubiquitous in all areas of life sciences. The size and model complexity of MD simulations are rapidly growing along with increasing computing power and improved algorithms. This growth has led to the production of a large amount of simulation data that need to be filtered for relevant information to address specific biomedical and biochemical questions. One of the most relevant molecular properties that can be investigated by all-atom MD simulations is the time-dependent evolution of the complex noncovalent interaction networks governing such fundamental aspects as molecular recognition, binding strength, and mechanical and structural stability. Extracting, evaluating, and visualizing noncovalent interactions is a key task in the daily work of structural biologists. We have developed PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories. PyContact is designed to facilitate this task by enabling identification of relevant noncovalent interactions in a comprehensible manner. The implementation of PyContact as a standalone application enables rapid analysis and data visualization without any additional programming requirements, and also preserves full in-program customization and extension capabilities for advanced users. The statistical analysis representation is interactively combined with full mapping of the results on the molecular system through the synergistic connection between PyContact and VMD. We showcase the capabilities and scientific significance of PyContact by analyzing and visualizing in great detail the noncovalent interactions underlying the ion permeation pathway of the human P2X 3 receptor. As a second application, we examine the protein-protein interaction network of the mechanically ultrastable cohesin-dockering complex. Copyright © 2017 Biophysical Society

  17. Microsecond MD Simulations of Nano-patterned Polymer Brushes on Self-Assembled Monolayers

    Science.gov (United States)

    Buie, Creighton; Qiu, Liming; Cheng, Kwan; Park, Soyeun

    2010-03-01

    Nano-patterned polymer brushes end-grafted onto self-assembled monolayers have gained increasing research interests due to their unique thermodynamic properties and their chemical and biomedical applications in colloids, biosensing and tissue engineering. So far, the interactions between the polymer brushes with the surrounding environments such as the floor and solvent at the nanometer length scale and microsecond time scale are still difficult to obtained experimentally and computationally. Using a Coarse-Grained MD approach, polymer brushes of different monomeric lengths, grafting density and hydrophobicity of the monomers grafted on self-assembled monolayers and in explicit solvent were studied. Molecular level information, such as lateral diffusion, transverse height and volume contour of the brushes, were calculated from our microsecond-MD simulations. Our results demonstrated the significance of the hydration of the polymer in controlling the conformational arrangement of the polymer brushes.

  18. MD simulation: determination of the physical properties and surface vaporization analysis of beryllium armours

    International Nuclear Information System (INIS)

    Prinzio, M. Di; Aquaro, D.

    2006-01-01

    The erosion of the divertor and of the first wall determined on the base of the anticipated operating conditions, is a critical issue that could affect the performance and the operating schedule of the nuclear fusion reactor ITER. This paper deals with the analysis of beryllium thermal properties by means of MD simulations, in order to better predict thermal behaviour of beryllium armoured PFCs in fusion devices. The importance of this analysis is clearly connected to thermal response evaluation of PFCs to high heat flux exposure, during off-normal events and Edge Localized Modes. The ensuing strong over-heating, in fact, produces material ablation through vaporization of surface material layers and possible loss of melting material. The overall PFCs erosion has bearings on plasma contamination, due to eroded material transport, and components lifetime, due to armour thickness reduction. An important feature of beryllium is its high vapour pressure. During thermal transients the strong vaporization keeps surface temperature relatively low but eroded thickness results high as well. Small changes in beryllium vapour pressure produce not negligible differences in thermal analyses results. On the basis of available force fields, classical Molecular Dynamics simulations have been carried out in order to better understand surface vaporization in tokamak conditions and to evaluate the effect of beryllium oxides formation. This effect has been successfully modelled by MD simulation, carried out with Moldy code. Morse stretching and bending potential for Be-O bond simulation have been used, and partial charges method, accounting for molecular polarity, has been employed. Since during short thermal transients, such as ELMs, only a few microns of Be armour will be overheated and reach melting threshold, the effective thermal conductivity is very important in determining the temperature evolution of surface layers and the ensuing erosion. Thermal conductivity can be evaluated

  19. Prediction of Osmotic Pressure of Ionic Liquids Inside a Nanoslit by MD Simulation and Continuum Approach

    Science.gov (United States)

    Moon, Gi Jong; Yang, Yu Dong; Oh, Jung Min; Kang, In Seok

    2017-11-01

    Osmotic pressure plays an important role in the processes of charging and discharging of lithium batteries. In this work, osmotic pressure of the ionic liquids confined inside a nanoslit is calculated by using both MD simulation and continuum approach. In the case of MD simulation, an ionic liquid is modeled as singly charged spheres with a short-ranged repulsive Lennard-Jones potential. The radii of the spheres are 0.5nm, reflecting the symmetry of ion sizes for simplicity. The simulation box size is 11nm×11nm×7.5nm with 1050 ion pairs. The concentration of ionic liquid is about 1.922mol/L, and the total charge on an individual wall varies from +/-60e(7.944 μm/cm2) to +/-600e(79.44 μm/cm2) . In the case of continuum approach, we classify the problems according to the correlation length and steric factor, and considered the four separate cases: 1) zero correlation length and zero steric factor, 2) zero correlation length and non-zero steric factor, 3) non-zero correlation length and zero steric factor, and 4) non-zero correlation and non-zero steric factor. Better understanding of the osmotic pressure of ionic liquids confined inside a nanoslit can be achieved by comparing the results of MD simulation and continuum approach. This research was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MSIP: Ministry of Science, ICT & Future Planning) (No. 2017R1D1A1B05035211).

  20. Dynamics of biopolymers on nanomaterials studied by quasielastic neutron scattering and MD simulations

    Science.gov (United States)

    Dhindsa, Gurpreet K.

    Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, beta-Casein and Inorganic Pyrophosphatase (IPPase). RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and functionalizable high surface area, and thus actively considered for biomedical applications. In this thesis, we utilized two tools, quasielastic neutron scattering (QENS) and Molecular Dynamics Simulations to probe the effect of ND on RNA dynamics. Our work provides fundamental understanding of how hydrated RNA motions are affected in the RNA-ND nanocomposites. From the experimental and Molecular Dynamics Simulation (MD), we found that hydrated RNA motion is faster on ND surface than a freestanding one. MD Simulation results showed that the failure of Stokes Einstein relation results the presence of dynamic heterogeneities in the biomacromolecules. Radial pair distribution function from MD Simulation confirmed that the hydrophilic nature of ND attracts more water than RNA results the de-confinement of RNA on ND. Therefore, RNA exhibits faster motion in the presence of ND than freestanding RNA. In the second project, we studied the dynamics of a natively disordered protein beta-Casein which lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of beta-Casein are explored by Quasielastic Neutron Scattering (QENS). We investigated the mean square displacement (MSD) of

  1. Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation

    Directory of Open Access Journals (Sweden)

    Yue Hou

    2017-02-01

    Full Text Available Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM experiments, Phase Dynamics Theory and Molecular Dynamics (MD Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

  2. Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation.

    Science.gov (United States)

    Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

    2017-02-21

    Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

  3. Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

    Directory of Open Access Journals (Sweden)

    Jenny Farmer

    2017-11-01

    Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.

  4. Applicability of effective fragment potential version 2 - Molecular dynamics (EFP2-MD) simulations for predicting excess properties of mixed solvents

    Science.gov (United States)

    Kuroki, Nahoko; Mori, Hirotoshi

    2018-02-01

    Effective fragment potential version 2 - molecular dynamics (EFP2-MD) simulations, where the EFP2 is a polarizable force field based on ab initio electronic structure calculations were applied to water-methanol binary mixture. Comparing EFP2s defined with (aug-)cc-pVXZ (X = D,T) basis sets, it was found that large sets are necessary to generate sufficiently accurate EFP2 for predicting mixture properties. It was shown that EFP2-MD could predict the excess molar volume. Since the computational cost of EFP2-MD are far less than ab initio MD, the results presented herein demonstrate that EFP2-MD is promising for predicting physicochemical properties of novel mixed solvents.

  5. Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

    Science.gov (United States)

    Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

    2012-07-15

    The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Structural and dynamical aspects of Streptococcus gordonii FabH through molecular docking and MD simulations.

    Science.gov (United States)

    Shamim, Amen; Abbasi, Sumra Wajid; Azam, Syed Sikander

    2015-07-01

    β-Ketoacyl-ACP-synthase III (FabH or KAS III) has become an attractive target for the development of new antibacterial agents which can overcome the multidrug resistance. Unraveling the fatty acid biosynthesis (FAB) metabolic pathway and understanding structural coordinates of FabH will provide valuable insights to target Streptococcus gordonii for curing oral infection. In this study, we designed inhibitors against therapeutic target FabH, in order to block the FAB pathway. As compared to other targets, FabH has more interactions with other proteins, located on the leading strand with higher codon adaptation index value and associated with lipid metabolism category of COG. Current study aims to gain in silico insights into the structural and dynamical aspect of S. gordonii FabH via molecular docking and molecular dynamics (MD) simulations. The FabH protein is catalytically active in dimerization while it can lock in monomeric state. Current study highlights two residues Pro88 and Leu315 that are close to each other by dimerization. The active site of FabH is composed of the catalytic triad formed by residues Cys112, His249, and Asn279 in which Cys112 is involved in acetyl transfer, while His249 and Asn279 play an active role in decarboxylation. Docking analysis revealed that among the studied compounds, methyl-CoA disulfide has highest GOLD score (82.75), binding affinity (-11 kcal/mol) and exhibited consistently better interactions. During MD simulations, the FabH structure remained stable with the average RMSD value of 1.7 Å and 1.6 Å for undocked protein and docked complex, respectively. Further, crucial hydrogen bonding of the conserved catalytic triad for exhibiting high affinity between the FabH protein and ligand is observed by RDF analysis. The MD simulation results clearly demonstrated that binding of the inhibitor with S. gordonii FabH enhanced the structure and stabilized the dimeric FabH protein. Therefore, the inhibitor has the potential to become

  7. Equilibrium Molecular Dynamics (MD Simulation Study of Thermal Conductivity of Graphene Nanoribbon: A Comparative Study on MD Potentials

    Directory of Open Access Journals (Sweden)

    Asir Intisar Khan

    2015-12-01

    Full Text Available The thermal conductivity of graphene nanoribbons (GNRs has been investigated using equilibrium molecular dynamics (EMD simulation based on Green-Kubo (GK method to compare two interatomic potentials namely optimized Tersoff and 2nd generation Reactive Empirical Bond Order (REBO. Our comparative study includes the estimation of thermal conductivity as a function of temperature, length and width of GNR for both the potentials. The thermal conductivity of graphene nanoribbon decreases with the increase of temperature. Quantum correction has been introduced for thermal conductivity as a function of temperature to include quantum effect below Debye temperature. Our results show that for temperatures up to Debye temperature, thermal conductivity increases, attains its peak and then falls off monotonically. Thermal conductivity is found to decrease with the increasing length for optimized Tersoff potential. However, thermal conductivity has been reported to increase with length using 2nd generation REBO potential for the GNRs of same size. Thermal conductivity, for the specified range of width, demonstrates an increasing trend with the increase of width for both the concerned potentials. In comparison with 2nd generation REBO potential, optimized Tersoff potential demonstrates a better modeling of thermal conductivity as well as provides a more appropriate description of phonon thermal transport in graphene nanoribbon. Such comparative study would provide a good insight for the optimization of the thermal conductivity of graphene nanoribbons under diverse conditions.

  8. Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis

    Science.gov (United States)

    Park, In-Hee; Venable, John D.; Steckler, Caitlin; Cellitti, Susan E.; Lesley, Scott A.; Spraggon, Glen; Brock, Ansgar

    2015-01-01

    Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure and dynamics. More recently, Hydrogen Exchange Mass Spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from Molecular Dynamics (MD) simulation snapshots is used to determine partitioning over bonded and non-bonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for Fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of

  9. Interaction and dynamics of homologous pairing protein 2 (HOP2) and DNA studied by MD simulation

    Science.gov (United States)

    Moktan, Hem; Pezza, Roberto; Zhou, Donghua

    2015-03-01

    The homologous pairing protein 2 (Hop2) plays an important role in meiosis and DNA repair. Together with protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. We recently determined the NMR structure of the N-terminal domain of Hop2 and proposed a model of Protein-DNA complex based on NMR chemical shift perturbations and mutagenesis studies (Moktan, J Biol Chem 2014 10.1074/jbc.M114.548180). However structure and dynamics of the complex have not been studied at the atomic level yet. Here, we used classical MD simulations to study the interactions between the N-terminal HOP2 and DNA. The simulated results indicate that helix3 (H3) interacts with DNA in major groove and wing1 (W1) interacts mostly in minor groove mainly via direct hydrogen bonds. Also it is found that binding leads to reduced fluctuations in both protein and DNA. Several water bridge interactions have been identified. The residue-wise contributions to the interaction energy were evaluated. Also the functional motion of the protein is analyzed using principal component analysis. The results confirmed the importance of H3 and W1 for the stability of the complex, which is consistent with our previous experimental studies.

  10. Atomic level insights into realistic molecular models of dendrimer-drug complexes through MD simulations

    Science.gov (United States)

    Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.

    2016-09-01

    Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an

  11. Alamethicin in lipid bilayers: combined use of X-ray scattering and MD simulations.

    Science.gov (United States)

    Pan, Jianjun; Tieleman, D Peter; Nagle, John F; Kucerka, Norbert; Tristram-Nagle, Stephanie

    2009-06-01

    We study fully hydrated bilayers of two di-monounsaturated phospholipids diC18:1PC (DOPC) and diC22:1PC with varying amounts of alamethicin (Alm). We combine the use of X-ray diffuse scattering and molecular dynamics simulations to determine the orientation of alamethicin in model lipids. Comparison of the experimental and simulated form factors shows that Alm helices are inserted transmembrane at high humidity and high concentrations, in agreement with earlier results. The X-ray scattering data and the MD simulations agree that membrane thickness changes very little up to 1/10 Alm/DOPC. In contrast, the X-ray data indicate that the thicker diC22:1PC membrane thins with added Alm, a total decrease in thickness of 4 A at 1/10 Alm/diC22:1PC. The different effect of Alm on the thickness changes of the two bilayers is consistent with Alm having a hydrophobic thickness close to the hydrophobic thickness of 27 A for DOPC; Alm is then mismatched with the 7 A thicker diC22:1PC bilayer. The X-ray data indicate that Alm decreases the bending modulus (K(C)) by a factor of approximately 2 in DOPC and a factor of approximately 10 in diC22:1PC membranes (P/L approximately 1/10). The van der Waals and fluctuational interactions between bilayers are also evaluated through determination of the anisotropic B compressibility modulus.

  12. Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor

    Directory of Open Access Journals (Sweden)

    Sandra Posch

    2016-09-01

    Full Text Available We here give information for a deeper understanding of single molecule force spectroscopy (SMFS data through the example of the blood protein von Willebrand factor (VWF. It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently developed model by Bullerjahn, Sturm, and Kroy (BSK was used for this demonstration. Further, Brownian dynamics (BD simulations, which can be utilized to estimate the lifetimes of intramolecular VWF interactions under physiological shear, are described. For interpretation and discussion of the methods and data presented here, we would like to directly point the reader to the related research paper, “Mutual A domain interactions in the force sensing protein von Willebrand Factor” (Posch et al., 2016 [1]. Keywords: Atomic force microscopy, Single molecule force spectroscopy, Molecular dynamics simulation, Brownian dynamics simulation, von Willebrand factor

  13. Coarse grained MD simulations of a fracture of filler-filled polymer nanocomposites under uniaxial elongation

    Science.gov (United States)

    Hagita, Katsumi; Morita, Hiroshi; Takano, Hiroshi

    We performed coarse grained molecular dynamics (MD) simulations based on Kremer-Grest model in order to investigate a fracture of polymer nanocomposites filled with spherical nanoparticles (NPs) under uniaxial elongation with a Poisson ratio of 0.4. In our model, the NP consists of 320 surface beads and one center bead. In order to make the NP spherical, a harmonic potential is applied to the surface particles from the center of the NP. Here, the initial volume fraction of the NPs is about 20%. The dependences of the fracture on the interactions between the NPs and polymers were examined. In order to observe the creation of nanovoids, the interaction among the polymers was set to be attractive. When the NP-polymer interaction is attractive, nanovoids appear in the bulk of polymers. On the other hand, for repulsive NP-polymer interaction, nanovoids are created at the surface between the polymers and NPs. At the same time, segregation of NPs is observed. We found that these behaviors depend on crosslink densities.

  14. MD simulations of onset of tungsten fuzz formation under helium irradiation

    International Nuclear Information System (INIS)

    Lasa, A.; Henriksson, K.O.E.; Nordlund, K.

    2013-01-01

    When helium (He) escapes a fusion reactor plasma, a tungsten (W)-based divertor may, under some conditions, form a fuzz-like nano-morphology. This is a highly undesired phenomenon for the divertor, and is not well understood. We performed molecular dynamics simulations of high fluence He and also C-seeded He (He+C) irradiation on W, focusing on the effect of the high fluence, the temperature and the impurities on the onset of the structure formation. We concluded that MD reproduces the experimentally found square root of time dependence of the surface growth. The He atomic density decreases when increasing the number of He atoms in the cell. A higher temperature causes a larger bubble growth and desorption activity, specially for the pure He irradiation cases. It also it leads to W recrystallization for the He+C irradiation cases. Carbon acts as a local He trap for small clusters or single atoms and causes a larger loss of crystallinity of the W surface

  15. MD simulation of atomic displacements in metals and metallic bilayers under low energy ion bombardment at 300 K

    International Nuclear Information System (INIS)

    Kornich, G.V.; Betz, G.; Bazhin, A.I.

    1999-01-01

    MD simulations of 100 eV Ar ion bombardment of (1 0 0) Ni and Al as well as Al/Ni bilayer crystals at 300 K have been performed and compared to previous calculations at 0 K. The Al/Ni bilayer crystal consisted of one Al layer on a (1 0 0) Ni substrate. Sputtering yields for Ni and Al/Ni show no temperature dependence, while for Al a pronounced increase with temperature was observed. The contributions of different mechanisms to the production of surface and bulk defects are discussed. The mean square displacement (MSD) of atoms is in all cases larger at 300 K as compared to 0 K. The larger MSD at 300 K is mainly due to an increase in lateral (perpendicular to the ion beam) motion of displaced atoms. Similar the number of atomic jumps, in which an atom leaves its original Wigner-Seitz cell, increases in all cases with temperature. For the pure elements the production of bulk vacancies and interstitials decreases with temperature, but the number of surface vacancies and ad-atoms increases with temperature. For the bilayer system practically no temperature dependence for defects was observed

  16. X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes

    DEFF Research Database (Denmark)

    Boscia, Alexander L.; Treece, Bradley W.; Mohammadyani, Dariush

    2014-01-01

    TMCL. Coarse grain molecular dynamics simulations confirm the experimental thickening of 2 Å for 20 mol% TMCL and locate the TMCL headgroups near the glycerol-carbonyl region of DMPC; i.e., they are sequestered below the DMPC phosphocholine headgroup. Our results suggest that TMCL plays a role similar...... to cholesterol in that it thickens and stiffens DMPC membranes, orders chains, and is positioned under the umbrella of the PC headgroup. CL may be necessary for hydrophobic matching to inner mitochondrial membrane proteins. Differential scanning calorimetry, S Xray and CGMD simulations all suggest that TMCL does......Cardiolipins (CLs) are important biologically for their unique role in biomembranes that couple phosphorylation and electron transport like bacterial plasma membranes, chromatophores, chloroplasts and mitochondria. CLs are often tightly coupled to proteins involved in oxidative phosphorylation...

  17. Simulation and similarity using models to understand the world

    CERN Document Server

    Weisberg, Michael

    2013-01-01

    In the 1950s, John Reber convinced many Californians that the best way to solve the state's water shortage problem was to dam up the San Francisco Bay. Against massive political pressure, Reber's opponents persuaded lawmakers that doing so would lead to disaster. They did this not by empirical measurement alone, but also through the construction of a model. Simulation and Similarity explains why this was a good strategy while simultaneously providing an account of modeling and idealization in modern scientific practice. Michael Weisberg focuses on concrete, mathematical, and computational models in his consideration of the nature of models, the practice of modeling, and nature of the relationship between models and real-world phenomena. In addition to a careful analysis of physical, computational, and mathematical models, Simulation and Similarity offers a novel account of the model/world relationship. Breaking with the dominant tradition, which favors the analysis of this relation through logical notions suc...

  18. MD simulation of plastic deformation nucleation in stressed crystallites under irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Korchuganov, A. V., E-mail: avkor@ispms.tsc.ru; Zolnikov, K. P., E-mail: kost@ispms.tsc.ru; Kryzhevich, D. S., E-mail: kryzhev@ispms.tsc.ru [Russian Academy of Sciences, Institute of Strength Physics and Materials Science, Siberian Branch (Russian Federation); Chernov, V. M., E-mail: VMChernov@bochvar.ru [National Research Tomsk State University (Russian Federation); Psakhie, S. G., E-mail: sp@ispms.tsc.ru [Russian Academy of Sciences, Institute of Strength Physics and Materials Science, Siberian Branch (Russian Federation)

    2016-12-15

    The investigation of plastic deformation nucleation in metals and alloys under irradiation and mechanical loading is one of the topical issues of materials science. Specific features of nucleation and evolution of the defect system in stressed and irradiated iron, vanadium, and copper crystallites were studied by molecular dynamics simulation. Mechanical loading was performed in such a way that the modeled crystallite volume remained unchanged. The energy of the primary knock-on atom initiating a cascade of atomic displacements in a stressed crystallite was varied from 0.05 to 50 keV. It was found that atomic displacement cascades might cause global structural transformations in a region far larger than the radiation-damaged area. These changes are similar to the ones occurring in the process of mechanical loading of samples. They are implemented by twinning (in iron and vanadium) or through the formation of partial dislocation loops (in copper).

  19. Accelerating all-atom MD simulations of lipids using a modified virtual-sites technique

    DEFF Research Database (Denmark)

    Loubet, Bastien; Kopec, Wojciech; Khandelia, Himanshu

    2014-01-01

    We present two new implementations of the virtual sites technique which completely suppresses the degrees of freedom of the hydrogen atoms in a lipid bilayer allowing for an increased time step of 5 fs in all-atom simulations of the CHARMM36 force field. One of our approaches uses the derivation...... of the virtual sites used in GROMACS while the other uses a new definition of the virtual sites of the CH2 groups. Our methods is tested on a DPPC (no unsaturated chain), a POPC (one unsaturated chain), and a DOPC (two unsaturated chains) lipid bilayers. We calculate various physical properties of the membrane...... of our simulations with and without virtual sites and explain the differences and similarity observed. The best agreements are obtained for the GROMACS original virtual sites on the DOPC bilayer where we get an area per lipid of 67.3 ± 0.3 A˚2 without virtual sites and 67.6 ± 0.3 A˚2 with virtual sites...

  20. Dimensional analysis, similarity, analogy, and the simulation theory

    International Nuclear Information System (INIS)

    Davis, A.A.

    1978-01-01

    Dimensional analysis, similarity, analogy, and cybernetics are shown to be four consecutive steps in application of the simulation theory. This paper introduces the classes of phenomena which follow the same formal mathematical equations as models of the natural laws and the interior sphere of restraints groups of phenomena in which one can introduce simplfied nondimensional mathematical equations. The simulation by similarity in a specific field of physics, by analogy in two or more different fields of physics, and by cybernetics in nature in two or more fields of mathematics, physics, biology, economics, politics, sociology, etc., appears as a unique theory which permits one to transport the results of experiments from the models, convenably selected to meet the conditions of researches, constructions, and measurements in the laboratories to the originals which are the primary objectives of the researches. Some interesting conclusions which cannot be avoided in the use of simplified nondimensional mathematical equations as models of natural laws are presented. Interesting limitations on the use of simulation theory based on assumed simplifications are recognized. This paper shows as necessary, in scientific research, that one write mathematical models of general laws which will be applied to nature in its entirety. The paper proposes the extent of the second law of thermodynamics as the generalized law of entropy to model life and its activities. This paper shows that the physical studies and philosophical interpretations of phenomena and natural laws cannot be separated in scientific work; they are interconnected and one cannot be put above the others

  1. Md Naimuddin

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics. Md Naimuddin. Articles written in Pramana – Journal of Physics. Volume 79 Issue 5 November 2012 pp 1255-1258 Poster Presentations. Model unspecific search for new physics in collision at s = 7 TeV · Shivali Malhotra Md Naimuddin Thomas Hebbeker Arnd Meyer ...

  2. Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study.

    Science.gov (United States)

    Dolenc, Jozica; Baron, Riccardo; Missimer, John H; Steinmetz, Michel O; van Gunsteren, Wilfred F

    2008-07-21

    The solvent structure and dynamics around ccbeta-p, a 17-residue peptide that forms a parallel three-stranded alpha-helical coiled coil in solution, was analysed through 10 ns explicit solvent molecular dynamics (MD) simulations at 278 and 330 K. Comparison with two corresponding simulations of the monomeric form of ccbeta-p was used to investigate the changes of hydration upon coiled-coil formation. Pronounced peaks in the solvent density distribution between residues Arg8 and Glu13 of neighbouring helices show the presence of water bridges between the helices of the ccbeta-p trimer; this is in agreement with the water sites observed in X-ray crystallography experiments. Interestingly, this water site is structurally conserved in many three-stranded coiled coils and, together with the Arg and Glu residues, forms part of a motif that determines three-stranded coiled-coil formation. Our findings show that little direct correlation exists between the solvent density distribution and the temporal ordering of water around the trimeric coiled coil. The MD-calculated effective residence times of up to 40 ps show rapid exchange of surface water molecules with the bulk phase, and indicate that the solvent distribution around biomolecules requires interpretation in terms of continuous density distributions rather than in terms of discrete molecules of water. Together, our study contributes to understanding the principles of three-stranded coiled-coil formation.

  3. Nanotribological behavior analysis of graphene/metal nanocomposites via MD simulations: New concepts and underlying mechanisms

    Science.gov (United States)

    Montazeri, A.; Mobarghei, A.

    2018-04-01

    In this article, we report a series of MD-based nanoindentation tests aimed to examine the nanotribological characteristics of metal-based nanocomposites in the presence of graphene sheets. To evaluate the effects of graphene/matrix interactions on the results, nickel and copper are selected as metals having strong and weak interactions with graphene, respectively. Consequently, the influence of graphene layers sliding and their distance from the sample surface on the nanoindentation outputs is thoroughly examined. Additionally, the temperature dependence of the results is deeply investigated with emphasis on the underlying mechanisms. To verify the accuracy of nanoindentation outputs, results of this method are compared with the data obtained via the tensile test. It is concluded that the nanoindentation results are closer to the values obtained by means of experimental setups. Employing these numerical-based experiments enables us to perform parametric studies to find out the dominant factors affecting the nanotribological behavior of these nanocomposites at the atomic-scale.

  4. Simulation of multi-atomic interactions in H-O-W system with the MD code CADAC

    International Nuclear Information System (INIS)

    Landman, I.S.

    2005-01-01

    For future tokamak reactors, chemical erosion of tungsten armour surfaces under impact of hot deuterium-tritium plasma that contains impurities, for instance oxygen, is an important issue. Oxygen can form volatile molecular complexes O x W y at the surface, and the retained H-atoms form the volatile complexes H x O y , which mitigates the erosion (H states for hydrogen isotopes). The plasma impact can substantially destroy the complexes. To describe this H-O-W system, the molecular dynamics (MD) code CADAC was earlier developed using only pair-atomic interactions. Now CADAC is extended for multi-body forces to simulate molecular organization of atoms near the tungsten surface. The approach uses the Abell's model of empirical bond-order potentials in addition combined, for the first time, with a valence concept. CADAC simulates chemical features using atomic valences and the Morse potentials. The new model is introduced and model parameters are estimated

  5. Do SiO 2 and carbon-doped SiO 2 nanoparticles melt? Insights from QM/MD simulations and ramifications regarding carbon nanotube growth

    Science.gov (United States)

    Page, Alister J.; Chandrakumar, K. R. S.; Irle, Stephan; Morokuma, Keiji

    2011-05-01

    Quantum chemical molecular dynamics (QM/MD) simulations of pristine and carbon-doped SiO 2 nanoparticles have been performed between 1000 and 3000 K. At temperatures above 1600 K, pristine nanoparticle SiO 2 decomposes rapidly, primarily forming SiO. Similarly, carbon-doped nanoparticle SiO 2 decomposes at temperatures above 2000 K, primarily forming SiO and CO. Analysis of the physical states of these pristine and carbon-doped SiO 2 nanoparticles indicate that they remain in the solid phase throughout decomposition. This process is therefore one of sublimation, as the liquid phase is never entered. Ramifications of these observations with respect to presently debated mechanisms of carbon nanotube growth on SiO 2 nanoparticles will be discussed.

  6. MD simulations to evaluate effects of applied tensile strain on irradiation-induced defect production at various PKA energies

    International Nuclear Information System (INIS)

    Miyashiro, S.; Fujita, S.; Okita, T.; Okuda, H.

    2012-01-01

    Highlights: ► Strain effects on defect formation were evaluated at various PKA energies by MD. ► Radiation-induced defects were increased numerically by external strain. ► Enhanced formation of larger clusters causes the numerical increase of defects. ► Strain influence on the number of defects was greatest at about 20 keV PKA. ► Cluster size, which is mostly affected by strain, was greater with higher PKA energy. - Abstract: Molecular Dynamics (MD) simulations were conducted to investigate the influence of applied tensile strain on defect production during cascade damages at various Primary Knock-on Atom (PKA) energies of 1–30 keV. When 1% strain was applied, the number of surviving defects increased at PKA energies higher than 5 keV, although they did not increase at 1 keV. The rate of increase by strain application was higher with higher PKA energy, and attained the maximum at 20 keV PKA energy with a subsequent gradual decrease at 30 keV PKA energy The cluster size, mostly affected by strain, was larger with higher PKA energy, although clusters with fewer than seven interstitials did not increase in number at any PKA energy.

  7. Unique structure and dynamics of the EphA5 ligand binding domain mediate its binding specificity as revealed by X-ray crystallography, NMR and MD simulations.

    Directory of Open Access Journals (Sweden)

    Xuelu Huan

    Full Text Available The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions with 9 ephrin-A and ephrin-B ligands initiate bidirectional signals controlling many physiological and pathological processes. Most interactions occur between receptor and ephrins of the same class, and only EphA4 can bind all A and B ephrins. To understand the structural and dynamic principles that enable Eph receptors to utilize the same jellyroll β-sandwich fold to bind ephrins, the VAPB-MSP domain, peptides and small molecules, we have used crystallography, NMR and molecular dynamics (MD simulations to determine the first structure and dynamics of the EphA5 ligand-binding domain (LBD, which only binds ephrin-A ligands. Unexpectedly, despite being unbound, the high affinity ephrin-binding pocket of EphA5 resembles that of other Eph receptors bound to ephrins, with a helical conformation over the J-K loop and an open pocket. The openness of the pocket is further supported by NMR hydrogen/deuterium exchange data and MD simulations. Additionally, the EphA5 LBD undergoes significant picosecond-nanosecond conformational exchanges over the loops, as revealed by NMR and MD simulations, but lacks global conformational exchanges on the microsecond-millisecond time scale. This is markedly different from the EphA4 LBD, which shares 74% sequence identity and 87% homology. Consequently, the unbound EphA5 LBD appears to comprise an ensemble of open conformations that have only small variations over the loops and appear ready to bind ephrin-A ligands. These findings show how two proteins with high sequence homology and structural similarity are still able to achieve distinctive binding specificities through different dynamics, which may represent a general mechanism whereby the same protein fold can serve for different functions. Our findings also suggest that a promising strategy to design agonists/antagonists with high affinity and selectivity

  8. Designing of phenol-based β-carbonic anhydrase1 inhibitors through QSAR, molecular docking, and MD simulation approach.

    Science.gov (United States)

    Ahamad, Shahzaib; Hassan, Md Imtaiyaz; Dwivedi, Neeraja

    2018-05-01

    Tuberculosis (Tb) is an airborne infectious disease caused by Mycobacterium tuberculosis. Beta-carbonic anhydrase 1 ( β-CA1 ) has emerged as one of the potential targets for new antitubercular drug development. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking, and molecular dynamics (MD) simulation approaches were performed on a series of natural and synthetic phenol-based β-CA1 inhibitors. The developed 3D-QSAR model ( r 2  = 0.94, q 2  = 0.86, and pred_r 2  = 0.74) indicated that the steric and electrostatic factors are important parameters to modulate the bioactivity of phenolic compounds. Based on this indication, we designed 72 new phenolic inhibitors, out of which two compounds (D25 and D50) effectively stabilized β-CA1 receptor and, thus, are potential candidates for new generation antitubercular drug discovery program.

  9. Conformational analysis of the Sda determinant-containing tetrasaccharide and two mimics in aqueous solution by using 1H NMR ROESY spectroscopy in combination with MD simulations

    International Nuclear Information System (INIS)

    Blanco, Jose L. Jimenez; Rooijen, Johannes J.M. van; Erbel, Paul J.A.; Leeflang, Bas R.; Kamerling, Johannis P.; Vliegenthart, Johannes F.G.

    2000-01-01

    The conformational behaviour of the spacer-linked synthetic Sd a tetrasaccharide β-d-GalpNAc-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O) (CH 2 ) 5 NH 2 (1) and the two mimics β-d-Galp-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O)(CH 2 ) 5 NH 2 (2) and β-d-GlcpNAc-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O) (CH 2 ) 5 NH 2 (3) were investigated by 1 H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. Experimental 2D 1 H ROESY cross-peak intensities (ROEs) of the tetrasaccharides were compared with calculated ROEs derived from MD trajectories using the CROSREL program. Analysis of these data indicated that the oligosaccharidic skeletons of the compounds 1-3 are rather rigid, especially the β-d-Hex(NAc)-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp fragments. The α- Neu5-Ac-(2 → 3)-β-d-Galp linkage occurred in two different energy minima in the three-dimensional structure of the compounds 1-3 in aqueous solution. Experimental data and dynamics simulations supported the finding that the higher energy rotamer (CHEAT forcefield) was abundant in compounds 1 and 3 due to the existence of a hydrogen bond between the carboxyl group of the sialic acid and the acetamido group of the terminal monosaccharide (GalNAc or GlcNAc) unit. The conformational similarity between 1 and 3 leads to the suggestion that also their activities will be alike.

  10. Solid state NMR investigations and MD simulations of triblock copolymers in lipid bilayers

    Czech Academy of Sciences Publication Activity Database

    Baerenwald, R.; Ferreira, T. M.; Ollila, Samuli; Saalwaechter, K.

    2017-01-01

    Roč. 46, Suppl 1 (2017), S117 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : solid state NMR * molecular dynamic simulations Subject RIV: BO - Biophysics

  11. MD simulation of atomic displacement cascades near chromium-rich clusters in FeCr alloy

    International Nuclear Information System (INIS)

    Tikhonchev, M.; Svetukhin, V.; Gaganidze, E.

    2013-01-01

    The paper reports simulation of cascades in Fe–9 at.%Cr binary alloy containing chromium-rich clusters. The simulation is performed by the molecular dynamics method at the initial temperature of 300 K and primary knock-on atom energy of 15 and 20 keV. Spherical clusters containing 95 at.% of Cr with diameter of 1–5 nm have been considered. The properties of cascade evolution in the presence of chromium-rich cluster are studied. It is shown that these clusters tend to dissolve in collision cascades. However, clusters with diameter of ⩾3 nm exhibit only slight modifications and can be considered stable. Parameters of small (1–2 nm) clusters can change significantly and, in some cases, a 1 nm cluster can be totally dissolved

  12. MD simulation of atomic displacement cascades near chromium-rich clusters in FeCr alloy

    Energy Technology Data Exchange (ETDEWEB)

    Tikhonchev, M., E-mail: tikhonchev@sv.ulsu.ru [Ulyanovsk State University, Research Institute of Technology, 42 Leo Tolstoy St., 432970 Ulyanovsk (Russian Federation); Svetukhin, V. [Ulyanovsk State University, Research Institute of Technology, 42 Leo Tolstoy St., 432970 Ulyanovsk (Russian Federation); Gaganidze, E. [Karlsruhe Institute of Technology, Institute for Applied Materials, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Karlsruhe (Germany)

    2013-11-15

    The paper reports simulation of cascades in Fe–9 at.%Cr binary alloy containing chromium-rich clusters. The simulation is performed by the molecular dynamics method at the initial temperature of 300 K and primary knock-on atom energy of 15 and 20 keV. Spherical clusters containing 95 at.% of Cr with diameter of 1–5 nm have been considered. The properties of cascade evolution in the presence of chromium-rich cluster are studied. It is shown that these clusters tend to dissolve in collision cascades. However, clusters with diameter of ⩾3 nm exhibit only slight modifications and can be considered stable. Parameters of small (1–2 nm) clusters can change significantly and, in some cases, a 1 nm cluster can be totally dissolved.

  13. Low-energy oxygen bombardment of silicon by MD simulations making use of a reactive force field

    International Nuclear Information System (INIS)

    Philipp, P.; Briquet, L.; Wirtz, T.; Kieffer, J.

    2011-01-01

    In the field of Secondary Ion Mass Spectrometry (SIMS), ion-matter interactions have been largely investigated by numerical simulations. For MD simulations related to inorganic samples, mostly classical force fields assuming stable bonding structure have been used. In materials science, level-three force fields capable of simulating the breaking and formation of chemical bonds have recently been conceived. One such force field has been developed by John Kieffer . This potential includes directional covalent bonds, Coulomb and dipolar interaction terms, dispersion terms, etc. Important features of this force field for simulating systems that undergo significant structural reorganization are (i) the ability to account for the redistribution of electron density upon ionization, formation, or breaking of bonds, through a charge transfer term, and (ii) the fact that the angular constraints dynamically adjust when a change in the coordination number of an atom occurs. In this paper, the modification of the force field to allow for an exact description of the sputtering process, the influence of this modification on previous results obtained for phase transitions in glasses as well as properties of particles sputtered at 250-1000 eV from a mono-crystalline silicon sample will be presented. The simulation results agree qualitatively with predictions from experiments or models. Most atoms are sputtered from the first monolayer: for an impact energy of 250 eV up to 86% of the atoms are sputtered from the first monolayer and for 750 eV, this percentage drops to 61%, with 89% of the atoms being sputtered from the first two monolayers. For sputtering yields, 250 and 500 eV results agree with experimental data, but for 750 eV sub-channelling in the pristine sample becomes more important than in experiments where samples turn amorphous under ion bombardment.

  14. Evaluation of GEOS-5 sulfur dioxide simulations during the Frostburg, MD 2010 field campaign

    Directory of Open Access Journals (Sweden)

    V. Buchard

    2014-02-01

    Full Text Available Sulfur dioxide (SO2 is a major atmospheric pollutant with a strong anthropogenic component mostly produced by the combustion of fossil fuel and other industrial activities. As a precursor of sulfate aerosols that affect climate, air quality, and human health, this gas needs to be monitored on a global scale. Global climate and chemistry models including aerosol processes along with their radiative effects are important tools for climate and air quality research. Validation of these models against in-situ and satellite measurements is essential to ascertain the credibility of these models and to guide model improvements. In this study, the Goddard Chemistry, Aerosol, Radiation, and Transport (GOCART module running on-line inside the Goddard Earth Observing System version 5 (GEOS-5 model is used to simulate aerosol and SO2 concentrations. Data taken in November 2010 over Frostburg, Maryland during an SO2 field campaign involving ground instrumentation and aircraft are used to evaluate GEOS-5 simulated SO2 concentrations. Preliminary data analysis indicated the model overestimated surface SO2 concentration, which motivated the examination of the specification of SO2 anthropogenic emission rates. As a result of this analysis, a revision of anthropogenic emission inventories in GEOS-5 was implemented, and the vertical placement of SO2 sources was updated. Results show that these revisions improve the model agreement with observations locally and in regions outside the area of this field campaign. In particular, we use the ground-based measurements collected by the United States Environmental Protection Agency (US EPA for the year 2010 to evaluate the revised model simulations over North America.

  15. Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant.

    Directory of Open Access Journals (Sweden)

    Md Zahid Kamal

    Full Text Available Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.

  16. Electroreduction Property and MD Simulation of Nitrobenzene in Ionic Liquid [BMim][Tf2N]/[BMim][BF4

    International Nuclear Information System (INIS)

    Zeng, Jianping; Zhang, Yinxu; Sun, Ruyao; Chen, Song

    2014-01-01

    Highlights: • The two different common accessible ionic liquids are mixed in a simple and economic way. • In some compound ratios, the dynamic performance of nitrobenzene is superior to either of ionic liquids. • Modification and functionalization of ionic liquids in electrochemical field is feasible. • The mass transfer of diffusion of nitrobenzene in ionic liquids can be simulated with molecular dynamics. • Molecular dynamics explains the improvement of nitrobenzene in composite ionic liquids. - Abstract: The two different common accessible ionic liquids [BMim][BF 4 ] and [BMim][Tf 2 N] were mixed each other in a simple and economic way. In some compound ratios, the dynamic performance of nitrobenzene in electric reduction was superior to that of any single kind of ionic liquid has been appeared. The interaction and mass transfer of diffusion of nitrobenzene in composite ionic liquids with different volume ratios were studied with molecular dynamics (MD) simulation. The improvement of the electroreduction performance of nitrobenzene in composite ionic liquids was verified and was tried to explain. This provides a new idea for the modification and functionalization of ionic liquids in electrochemical field. The experimental results showed that kinematic viscosity and electroconductibility of different ionic liquid systems display a regular change. And the change law has been basically unchanged after adding water. The two different functional ionic liquids were complemented each other in a simple and economic way, which has compensated for the disadvantage of mono-component ionic liquids. At 25 °C, electroreduction property of V [BMim][BF4] :V [BMim][Tf2N] = 1:1 is the best in cyclic voltammetry experiments of nitrobenzene in different composite ionic liquids. Its electrochemical behavior is significantly affected by scan rate, temperature, concentration of nitrobenzene and concentration of water. The MD simulation results showed most of interaction

  17. Simulation of multi-atomic interactions in H-O-W system with the MD code CADAC

    Energy Technology Data Exchange (ETDEWEB)

    Landman, I.S. [Forschungszentrum Karlsruhe, Institute for Pulsed Power and Microwave Technology, P.O. Box 3640, 76021 Karlsruhe (Germany)]. E-mail: igor.landman@ihm.fzk.de

    2005-11-15

    For future tokamak reactors, chemical erosion of tungsten armour surfaces under impact of hot deuterium-tritium plasma that contains impurities, for instance oxygen, is an important issue. Oxygen can form volatile molecular complexes O {sub x}W {sub y} at the surface, and the retained H-atoms form the volatile complexes H {sub x}O {sub y}, which mitigates the erosion (H states for hydrogen isotopes). The plasma impact can substantially destroy the complexes. To describe this H-O-W system, the molecular dynamics (MD) code CADAC was earlier developed using only pair-atomic interactions. Now CADAC is extended for multi-body forces to simulate molecular organization of atoms near the tungsten surface. The approach uses the Abell's model of empirical bond-order potentials in addition combined, for the first time, with a valence concept. CADAC simulates chemical features using atomic valences and the Morse potentials. The new model is introduced and model parameters are estimated.

  18. An MD simulation of interactions between self-interstitial atoms and edge dislocation in bcc transition metals

    Energy Technology Data Exchange (ETDEWEB)

    Kamiyama, H. (Aomori Public College, 153-4 Yamazaki, Goushi-zawa, Aomori 030-01 (Japan)); Rafii-Tabar, H. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan)); Kawazoe, Y. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan)); Matsui, H. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan))

    1994-09-01

    According to our model on the mechanism of dislocation bias reduction based on the interaction of dumbbell self-interstitial atoms (SIAs) with dislocation, the bias is significantly different depending on the dumbbell configuration in the dislocation strain field. A large-scale molecular dynamics (MD) simulation is performed to reveal the stability and the mechanism of diffusion of dumbbell SIAs near the edge dislocation core in bcc iron. Most SIAs take the crowdion configuration parallel to the Burgers vector in the expansion side of the dislocation. Such crowdions are stable in the temperature range of this simulation, i.e. between 373 and 473 K, making one-dimensional random to-and-fro motion parallel to the dislocation Burgers vector staying at several atomic layers below'' the dislocation core. This means that the SIA does not approach the dislocation core. These results suggest that the stable configuration of SIAs is seriously affected by the dislocation resulting in a reduction of bias factor. ((orig.))

  19. An MD simulation of interactions between self-interstitial atoms and edge dislocation in bcc transition metals

    International Nuclear Information System (INIS)

    Kamiyama, H.; Rafii-Tabar, H.; Kawazoe, Y.; Matsui, H.

    1994-01-01

    According to our model on the mechanism of dislocation bias reduction based on the interaction of dumbbell self-interstitial atoms (SIAs) with dislocation, the bias is significantly different depending on the dumbbell configuration in the dislocation strain field. A large-scale molecular dynamics (MD) simulation is performed to reveal the stability and the mechanism of diffusion of dumbbell SIAs near the edge dislocation core in bcc iron. Most SIAs take the crowdion configuration parallel to the Burgers vector in the expansion side of the dislocation. Such crowdions are stable in the temperature range of this simulation, i.e. between 373 and 473 K, making one-dimensional random to-and-fro motion parallel to the dislocation Burgers vector staying at several atomic layers ''below'' the dislocation core. This means that the SIA does not approach the dislocation core. These results suggest that the stable configuration of SIAs is seriously affected by the dislocation resulting in a reduction of bias factor. ((orig.))

  20. Bicelles and Other Membrane Mimics: Comparison of Structure, Properties, and Dynamics from MD Simulations

    DEFF Research Database (Denmark)

    Vestergaard, Mikkel; Kraft, Johan Frederik; Vosegaard, Thomas

    2015-01-01

    present molecular dynamics simulations to elucidate structural and dynamic properties of small bicelles and compare them to a large alignable bicelle, a small nanodisc, and a lipid bilayer. Properties such as lipid packing and properties related to embedding both an α-helical peptide and a transmembrane...... protein are investigated. The small bicelles are found to be very dynamic and mainly assume a prolate shape substantiating that small bicelles cannot be regarded as well-defined disclike structures. However, addition of a peptide results in an increased tendency to form disc-shaped bicelles. The small......The increased interest in studying membrane proteins has led to the development of new membrane mimics such as bicelles and nanodiscs. However, only limited knowledge is available of how these membrane mimics are affected by embedded proteins and how well they mimic a lipid bilayer. Herein, we...

  1. MD simulation of atomic displacement cascades in Fe-10 at.%Cr binary alloy

    International Nuclear Information System (INIS)

    Tikhonchev, M.; Svetukhin, V.; Kadochkin, A.; Gaganidze, E.

    2009-01-01

    Molecular dynamics simulation of atomic displacement cascades up to 20 keV has been performed in Fe-10 at.%Cr binary alloy at a temperature of 600 K. The N-body interatomic potentials of Finnis-Sinclair type were used. According to the obtained results the dependence of 'surviving' defects amount is well approximated by power function that coincides with other researchers' results. Obtained cascade efficiency for damage energy in the range from 10 to 20 keV is ∼0.2 NRT that is slightly higher than for pure α-Fe. In post-cascade area Cr fraction in interstitials is in range 2-5% that is essentially lower than Cr content in the base alloy. The results on size and amount of vacancy and interstitial clusters generated in displacement cascades are obtained. For energies of 2 keV and higher the defect cluster average size increases and it is well approximated by a linear dependence on cascade energy both for interstitials and vacancies.

  2. MD simulation of atomic displacement cascades in Fe-10 at.%Cr binary alloy

    Energy Technology Data Exchange (ETDEWEB)

    Tikhonchev, M., E-mail: tikhonchev@sv.ulsu.r [Ulyanovsk State University, Leo Tolstoy Str., 42, Ulyanovsk 432970 (Russian Federation); Joint Stock Company, ' State Scientific Center Research Institute of Atomic Reactors' , 433510 Dimitrovgrad-10 (Russian Federation); Svetukhin, V.; Kadochkin, A. [Ulyanovsk State University, Leo Tolstoy Str., 42, Ulyanovsk 432970 (Russian Federation); Gaganidze, E. [Forschungszentrum Karlsruhe, IMF II, 3640, D-76021 Karlsruhe (Germany)

    2009-12-15

    Molecular dynamics simulation of atomic displacement cascades up to 20 keV has been performed in Fe-10 at.%Cr binary alloy at a temperature of 600 K. The N-body interatomic potentials of Finnis-Sinclair type were used. According to the obtained results the dependence of 'surviving' defects amount is well approximated by power function that coincides with other researchers' results. Obtained cascade efficiency for damage energy in the range from 10 to 20 keV is approx0.2 NRT that is slightly higher than for pure alpha-Fe. In post-cascade area Cr fraction in interstitials is in range 2-5% that is essentially lower than Cr content in the base alloy. The results on size and amount of vacancy and interstitial clusters generated in displacement cascades are obtained. For energies of 2 keV and higher the defect cluster average size increases and it is well approximated by a linear dependence on cascade energy both for interstitials and vacancies.

  3. Spectroscopic and MD simulation studies on unfolding processes of mitochondrial carbonic anhydrase VA induced by urea.

    Science.gov (United States)

    Idrees, Danish; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2016-09-01

    Carbonic anhydrase VA (CAVA) is primarily expressed in the mitochondria and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis and neuronal transmission. To understand the biophysical properties of CAVA, we carried out a reversible urea-induced isothermal denaturation at pH 7.0 and 25°C. Spectroscopic probes, [θ]222 (mean residue ellipticity at 222 nm), F344 (Trp-fluorescence emission intensity at 344 nm) and Δε280 (difference absorption at 280 nm) were used to monitor the effect of urea on the structure and stability of CAVA. The urea-induced reversible denaturation curves were used to estimate [Formula: see text], Gibbs free energy in the absence of urea; Cm, the mid-point of the denaturation curve, i.e. molar urea concentration ([urea]) at which ΔGD = 0; and m, the slope (=∂ΔGD/∂[urea]). Coincidence of normalized transition curves of all optical properties suggests that unfolding/refolding of CAVA is a two-state process. We further performed 40 ns molecular dynamics simulation of CAVA to see the dynamics at different urea concentrations. An excellent agreement was observed between in silico and in vitro studies.

  4. The Unfolding MD Simulations of Cyclophilin: Analyzed by Surface Contact Networks and Their Associated Metrics

    Science.gov (United States)

    Roy, Sourav; Basu, Sankar; Dasgupta, Dipak; Bhattacharyya, Dhananjay; Banerjee, Rahul

    2015-01-01

    Currently, considerable interest exists with regard to the dissociation of close packed aminoacids within proteins, in the course of unfolding, which could result in either wet or dry moltenglobules. The progressive disjuncture of residues constituting the hydrophobic core ofcyclophilin from L. donovani (LdCyp) has been studied during the thermal unfolding of the molecule, by molecular dynamics simulations. LdCyp has been represented as a surface contactnetwork (SCN) based on the surface complementarity (Sm) of interacting residues within themolecular interior. The application of Sm to side chain packing within proteins make it a very sensitive indicator of subtle perturbations in packing, in the thermal unfolding of the protein. Network based metrics have been defined to track the sequential changes in the disintegration ofthe SCN spanning the hydrophobic core of LdCyp and these metrics prove to be highly sensitive compared to traditional metrics in indicating the increased conformational (and dynamical) flexibility in the network. These metrics have been applied to suggest criteria distinguishing DMG, WMG and transition state ensembles and to identify key residues involved in crucial conformational/topological events during the unfolding process. PMID:26545107

  5. A green process for recovery of 1-propanol/2-propanol from their aqueous solutions: Experimental and MD simulation studies

    International Nuclear Information System (INIS)

    Gupta, Bhupender S.; Taha, Mohamed; Lee, Ming-Jer

    2017-01-01

    Highlights: • A green conceptual design for separating propanols from their aqueous solutions is proposed. • TRIS is biocompatible and non-volatile and can be used as an auxiliary agent for the separation. • Isobaric VLE data for 1-propanol/2-propanol + water + TRIS were measured at 101.3 kPa. • The azeotropic compositions are significantly shifted in the presence of TRIS. • Intermolecular interactions were studied with fluorescence, COSMO-RS, and MD simulation. - Abstract: In the present study, we have found that a common and relatively inexpensive biological buffer tris(hydroxymethyl)aminomethane (TRIS) is potentially applicable to shift the azeotrope compositions of aqueous solutions of 1-propanol and 2-propanol. By taking the advantage of our findings, we are proposing a green process for the recovery of these organics from their respective aqueous solutions. In order to confirm the effect of TRIS buffer on vapor–liquid equilibrium behavior of the aqueous propanol systems, we measured the isobaric vapor–liquid equilibrium (VLE) data at 101.3 kPa for the 1-proponol + water + TRIS and 2-propanol + water + TRIS systems over the azeotropic range with various concentrations of TRIS (0.02, 0.04, 0.08, and 0.12 in mole fraction). The binary interaction parameters were obtained for TRIS with water, TRIS with 1-propanol, and TRIS with 2-propanol by correlating the new VLE data with the NRTL model. The isobaric VLE properties for the investigated propanol + water mixtures in the presence of various concentrations of TRIS were also predicted with the conductor-like screening model COSMO-RS. Based on the predicted excess molar enthalpies (H E m ) from the COSMO-RS, the interactions between all constituent pairs of molecules were estimated. To explore the mechanism of TRIS-based separation of 1-propanol/2-propanol from their aqueous solutions, the interactions between different pairs of molecules were also investigated by using fluorescence analysis and

  6. Theoretical investigation on the inclusion of TCDD with β-cyclodextrin by performing QM calculations and MD simulations

    International Nuclear Information System (INIS)

    Pan, Wenxiao; Zhang, Dongju; Zhan, Jinhua

    2011-01-01

    Highlights: → We study the inclusion mechanism of TCDD with β-CD by theoretical methods. → Clearly, the formation of inclusion complex is an energetically driven process. → The inclusion complex can be detected by IR and Raman techniques. → The results imply that β-CD may be used as a host molecule to enrich TCDD molecules. - Abstract: The rapid enrichment and detection of trace polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are currently challenging issues in the field of environmental science. In this paper, by performing quantum chemistry (QM) calculations and molecular dynamics (MD) simulations, we studied the inclusion complexation of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a representative PCDD molecule, with β-cyclodextrin (β-CD), one of the widely used compounds in supramolecular chemistry. The calculated results reveal that the stable inclusion complex can be formed in both the gas phase and solvent, which proposes that β-CD may serve as a potential substrate enriching TCDD. The calculated vibrational spectra indicate that the infrared (IR) and Raman spectroscopy may be suitable for the detection of β-CD-modified TCDD. The present theoretical results may be informative to environmental scientists who are devoting themselves to developing effective methods for detection and treatment of POPs.

  7. Assessment of hydrogen bonding effect on ionization of water from ambient to supercritical region–MD simulation approach

    International Nuclear Information System (INIS)

    Swiatla-Wojcik, D.; Mozumder, A.

    2014-01-01

    We present a novel, molecular dynamics (MD) simulation based, strategy to analyze how the degree of hydrogen bonding may influence the ionization and dissociation of water upon heating from ambient to supercritical temperatures. Calculations show a negligible change in the ionization energy up to 200 °C. At higher temperatures the ionization energy increases due to the decreasing degree of hydrogen bonding. The influence of density (pressure) is pronounced in the supercritical region. The ionization is more energy consuming in the less dense fluid. We also show that high temperature and low density may promote dissociation of the electronically excited water molecules. Implications on the initial radiation chemical yields of the hydrated electron, hydrogen atom and hydroxyl radical are discussed. - Highlights: • Up to 200 °C changes in the vertical and adiabatic ionization potentials are negligible. • At higher temperatures ionization is more energy consuming. • Ionization potential increases with decreasing density of supercritical water. • High temperature and low density promote dissociation of the excited molecules

  8. Detailed regulatory mechanism of the interaction between ZO-1 PDZ2 and connexin43 revealed by MD simulations.

    Directory of Open Access Journals (Sweden)

    Fei Xiao

    Full Text Available The gap junction protein connexin43 (Cx43 binds to the second PDZ domain of Zonula occludens-1 (ZO-1 through its C-terminal tail, mediating the regulation of gap junction plaque size and dynamics. Biochemical study demonstrated that the very C-terminal 12 residues of Cx43 are necessary and sufficient for ZO-1 PDZ2 binding and phosphorylation at residues Ser (-9 and Ser (-10 of the peptide can disrupt the association. However, only a crystal structure of ZO-1 PDZ2 in complex with a shorter 9 aa peptide of connexin43 was solved experimentally. Here, the interactions between ZO-1 PDZ2 and the short, long and phosphorylated Cx43 peptides were studied using molecular dynamics (MD simulations and free energy calculation. The short peptide bound to PDZ2 exhibits large structural variations, while the extension of three upstream residues stabilizes the peptide conformation and enhanced the interaction. Phosphorylation at Ser(-9 significantly weakens the binding and results in conformational flexibility of the peptide. Glu210 of ZO-1 PDZ2 was found to be a key regulatory point in Cx43 binding and phosphorylation induced dissociation.

  9. Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome?

    Science.gov (United States)

    Moustafa, Ibrahim M; Gohara, David W; Uchida, Akira; Yennawar, Neela; Cameron, Craig E

    2015-11-23

    The genomes of RNA viruses are relatively small. To overcome the small-size limitation, RNA viruses assign distinct functions to the processed viral proteins and their precursors. This is exemplified by poliovirus 3CD protein. 3C protein is a protease and RNA-binding protein. 3D protein is an RNA-dependent RNA polymerase (RdRp). 3CD exhibits unique protease and RNA-binding activities relative to 3C and is devoid of RdRp activity. The origin of these differences is unclear, since crystal structure of 3CD revealed "beads-on-a-string" structure with no significant structural differences compared to the fully processed proteins. We performed molecular dynamics (MD) simulations on 3CD to investigate its conformational dynamics. A compact conformation of 3CD was observed that was substantially different from that shown crystallographically. This new conformation explained the unique properties of 3CD relative to the individual proteins. Interestingly, simulations of mutant 3CD showed altered interface. Additionally, accelerated MD simulations uncovered a conformational ensemble of 3CD. When we elucidated the 3CD conformations in solution using small-angle X-ray scattering (SAXS) experiments a range of conformations from extended to compact was revealed, validating the MD simulations. The existence of conformational ensemble of 3CD could be viewed as a way to expand the poliovirus proteome, an observation that may extend to other viruses.

  10. Quasielastic neutron scattering measurements and ab initio MD-simulations on single ion motions in molten NaF

    Energy Technology Data Exchange (ETDEWEB)

    Demmel, F. [ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX (United Kingdom); Mukhopadhyay, S. [ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX (United Kingdom); Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ (United Kingdom)

    2016-01-07

    The ionic stochastic motions in the molten alkali halide NaF are investigated by quasielastic neutron scattering and first principles molecular dynamics simulation. Quasielastic neutron scattering was employed to extract the diffusion behavior of the sodium ions in the melt. An extensive first principles based simulation on a box of up to 512 particles has been performed to complement the experimental data. From that large box, a smaller 64-particle box has then been simulated over a runtime of 60 ps. A good agreement between calculated and neutron data on the level of spectral shape has been obtained. The obtained sodium diffusion coefficients agree very well. The simulation predicts a fluorine diffusion coefficient similar to the sodium one. Applying the Nernst-Einstein equation, a remarkable large cross correlation between both ions can be deduced. The velocity cross correlations demonstrate a positive correlation between the ions over a period of 0.1 ps. That strong correlation is evidence that the unlike ions do not move completely statistically independent and have a strong association over a short period of time.

  11. Prediction and analysis of the structure of hydrated Mn2+, V2+, Ti3 and Cr3 ions by means of the MD simulation methods

    International Nuclear Information System (INIS)

    Iglesias, Y.J.

    2002-01-01

    Classical Molecular dynamics (MD) and hybrid Quantum/Molecular Mechanics-Molecular Dynamics (QM/MM-MD) simulations have been performed to investigate structural properties of Mn(II), V(II), Cr(III) and Ti(III) cations in aqueous solution. The first hydration sphere in QM/MM-MD simulations is treated quantum mechanically, while the rest of the system is described by classical analytical two- and three-body potentials. The results obtained for the first hydration shell from this method are in agreement with experimental data, showing 100 % of 6 fold coordination around the ion in all cases. The results prove that non/additive contributions are mandatory for an accurate description of ion hydration. Within the QM/MM method, the inclusion of a perturbation field describing the remaining system was shown to be an accurate tool for evaluating the first shell structure, and thus to be a good alternative for systems, where the construction of a three-body correction function is difficult or too time-consuming. (author)

  12. MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding.

    Directory of Open Access Journals (Sweden)

    Kaori Asamitsu

    Full Text Available In this study, we applied molecular dynamics (MD simulation to analyze the dynamic behavior of the Tat/CycT1/CDK9 tri-molecular complex and revealed the structural changes of P-TEFb upon Tat binding. We found that Tat could deliberately change the local flexibility of CycT1. Although the structural coordinates of the H1 and H2 helices did not substantially change, H1', H2', and H3' exhibited significant changes en masse. Consequently, the CycT1 residues involved in Tat binding, namely Tat-recognition residues (TRRs, lost their flexibility with the addition of Tat to P-TEFb. In addition, we clarified the structural variation of CDK9 in complex with CycT1 in the presence or absence of Tat. Interestingly, Tat addition significantly reduced the structural variability of the T-loop, thus consolidating the structural integrity of P-TEFb. Finally, we deciphered the formation of the hidden catalytic cavity of CDK9 upon Tat binding. MD simulation revealed that the PITALRE signature sequence of CDK9 flips the inactive kinase cavity of CDK9 into the active form by connecting with Thr186, which is crucial for its activity, thus presumably recruiting the substrate peptide such as the C-terminal domain of RNA pol II. These findings provide vital information for the development of effective novel anti-HIV drugs with CDK9 catalytic activity as the target.

  13. Distinct solvent- and temperature-dependent packing arrangements of anti-parallel β-sheet polyalanines studied with solid-state 13C NMR and MD simulation.

    Science.gov (United States)

    Kametani, Shunsuke; Tasei, Yugo; Nishimura, Akio; Asakura, Tetsuo

    2017-08-09

    Polyalanine (polyA) sequences are well known as the simplest sequence that naturally forms anti-parallel β-sheets and constitute a key element in the structure of spider and wild silkworm silk fibers. We have carried out a systematic analysis of the packing of anti-parallel β-sheets for (Ala) n , n = 5, 6, 7 and 12, using primarily 13 C solid-state NMR and MD simulation. HFIP and TFA are frequently used as the dope solvents for recombinant silks, and polyA was solidified from both HFIP and TFA solutions by drying. An analysis of Ala Cβ peaks in the 13 C CP/MAS NMR spectra indicated that polyA from HFIP was mainly rectangular but polyA from TFA was mainly staggered. The transition from the rectangular to the staggered arrangement in (Ala) 6 was observed for the first time from the change in the Ala Cβ peak through heat treatment at 200 °C for 4 h. The removal of the bound water was confirmed by thermal analysis. This transition could be reproduced by MD simulation of (Ala) 6 molecules at 200 °C after removal of the bound water molecules. In this way, the origin of the stability of the different packing arrangements of polyA was clarified.

  14. Advanced Models and Algorithms for Self-Similar IP Network Traffic Simulation and Performance Analysis

    Science.gov (United States)

    Radev, Dimitar; Lokshina, Izabella

    2010-11-01

    The paper examines self-similar (or fractal) properties of real communication network traffic data over a wide range of time scales. These self-similar properties are very different from the properties of traditional models based on Poisson and Markov-modulated Poisson processes. Advanced fractal models of sequentional generators and fixed-length sequence generators, and efficient algorithms that are used to simulate self-similar behavior of IP network traffic data are developed and applied. Numerical examples are provided; and simulation results are obtained and analyzed.

  15. Calibrating and Validating a Simulation Model to Identify Drivers of Urban Land Cover Change in the Baltimore, MD Metropolitan Region

    Directory of Open Access Journals (Sweden)

    Claire Jantz

    2014-09-01

    Full Text Available We build upon much of the accumulated knowledge of the widely used SLEUTH urban land change model and offer advances. First, we use SLEUTH’s exclusion/attraction layer to identify and test different urban land cover change drivers; second, we leverage SLEUTH’s self-modification capability to incorporate a demographic model; and third, we develop a validation procedure to quantify the influence of land cover change drivers and assess uncertainty. We found that, contrary to our a priori expectations, new development is not attracted to areas serviced by existing or planned water and sewer infrastructure. However, information about where population and employment growth is likely to occur did improve model performance. These findings point to the dominant role of centrifugal forces in post-industrial cities like Baltimore, MD. We successfully developed a demographic model that allowed us to constrain the SLEUTH model forecasts and address uncertainty related to the dynamic relationship between changes in population and employment and urban land use. Finally, we emphasize the importance of model validation. In this work the validation procedure played a key role in rigorously assessing the impacts of different exclusion/attraction layers and in assessing uncertainty related to population and employment forecasts.

  16. Cryptanalysis of MD2

    DEFF Research Database (Denmark)

    Knudsen, Lars Ramkilde; Mathiassen, John Erik; Muller, Frédéric

    2010-01-01

    This paper considers the hash function MD2 which was developed by Ron Rivest in 1989. Despite its age, MD2 has withstood cryptanalytic attacks until recently. This paper contains the state-of-the-art cryptanalytic results on MD2, in particular collision and preimage attacks on the full hash...

  17. Fusion Simulation Project. Workshop Sponsored by the U.S. Department of Energy, Rockville, MD, May 16-18, 2007

    Energy Technology Data Exchange (ETDEWEB)

    Kritz, A.; Keyes, D.

    2007-05-18

    The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel [Journal of Fusion Energy 20, 135 (2001)] recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts [Journal of Fusion Energy 23, 1 (2004)]. The current FSP planning effort involved forty-six physicists, applied mathematicians and computer scientists, from twenty-one institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a three-day workshop in May 2007.

  18. Fusion Simulation Project. Workshop sponsored by the U.S. Department of Energy Rockville, MD, May 16-18, 2007

    Energy Technology Data Exchange (ETDEWEB)

    None

    2007-05-16

    The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel [Journal of Fusion Energy 20, 135 (2001)] recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts [Journal of Fusion Energy 23, 1 (2004)]. The current FSP planning effort involved forty-six physicists, applied mathematicians and computer scientists, from twenty-one institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a three-day workshop in May 2007.

  19. Fusion Simulation Project. Workshop sponsored by the U.S. Department of Energy Rockville, MD, May 16-18, 2007

    International Nuclear Information System (INIS)

    2007-01-01

    The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel (Journal of Fusion Energy 20, 135 (2001)) recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts (Journal of Fusion Energy 23, 1 (2004)). The current FSP planning effort involved forty-six physicists, applied mathematicians and computer scientists, from twenty-one institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a three-day workshop in May 2007.

  20. Fusion Simulation Project. Workshop Sponsored by the U.S. Department of Energy, Rockville, MD, May 16-18, 2007

    International Nuclear Information System (INIS)

    Kritz, A.; Keyes, D.

    2007-01-01

    The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel [Journal of Fusion Energy 20, 135 (2001)] recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts [Journal of Fusion Energy 23, 1 (2004)]. The current FSP planning effort involved forty-six physicists, applied mathematicians and computer scientists, from twenty-one institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a three-day workshop in May 2007

  1. QM/MM MD and Free Energy Simulation Study of Methyl Transfer Processes Catalyzed by PKMTs and PRMTs.

    Science.gov (United States)

    Chu, Yuzhuo; Guo, Hong

    2015-09-01

    Methyl transfer processes catalyzed by protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs) control important biological events including transcriptional regulation and cell signaling. One important property of these enzymes is that different PKMTs and PRMTs catalyze the formation of different methylated product (product specificity). These different methylation states lead to different biological outcomes. Here, we review the results of quantum mechanics/molecular mechanics molecular dynamics and free energy simulations that have been performed to study the reaction mechanism of PKMTs and PRMTs and the mechanism underlying the product specificity of the methyl transfer processes.

  2. Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations

    DEFF Research Database (Denmark)

    Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit

    2012-01-01

    Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic...... resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates...

  3. Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study.

    Science.gov (United States)

    Dhindsa, Gurpreet K; Bhowmik, Debsindhu; Goswami, Monojoy; O'Neill, Hugh; Mamontov, Eugene; Sumpter, Bobby G; Hong, Liang; Ganesh, Panchapakesan; Chu, Xiang-Qiang

    2016-09-14

    Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. Our new findings may provide new design principles for safer, improved drug delivery platforms.

  4. MD Simulation on Collision Behavior Between Nano-Scale TiO₂ Particles During Vacuum Cold Spraying.

    Science.gov (United States)

    Yao, Hai-Long; Yang, Guan-Jun; Li, Chang-Jiu

    2018-04-01

    Particle collision behavior influences significantly inter-nano particle bonding formation during the nano-ceramic coating deposition by vacuum cold spraying (or aerosol deposition method). In order to illuminate the collision behavior between nano-scale ceramic particles, molecular dynamic simulation was applied to explore impact process between nano-scale TiO2 particles through controlling impact velocities. Results show that the recoil efficiency of the nano-scale TiO2 particle is decreased with the increase of the impact velocity. Nano-scale TiO2 particle exhibits localized plastic deformation during collision at low velocities, while it is intensively deformed by collision at high velocities. This intensive deformation promotes the nano-particle adhesion rather than rebounding off. A relationship between the adhesion energy and the rebound energy is established for the bonding formation of the nano-scale TiO2 particle. The adhesion energy required to the bonding formation between nano-scale ceramic particles can be produced by high velocity collision.

  5. Comparative MD Simulations Indicate a Dual Role for Arg1323.50 in Dopamine-Dependent D2R Activation.

    Directory of Open Access Journals (Sweden)

    Ralf C Kling

    Full Text Available Residue Arg3.50 belongs to the highly conserved DRY-motif of class A GPCRs, which is located at the bottom of TM3. On the one hand, Arg3.50 has been reported to help stabilize the inactive state of GPCRs, but on the other hand has also been shown to be crucial for stabilizing active receptor conformations and mediating receptor-G protein coupling. The combined results of these studies suggest that the exact function of Arg3.50 is likely to be receptor-dependent and must be characterized independently for every GPCR. Consequently, we now present comparative molecular-dynamics simulations that use our recently described inactive-state and Gα-bound active-state homology models of the dopamine D2 receptor (D2R, which are either bound to dopamine or ligand-free, performed to identify the function of Arg1323.50 in D2R. Our results are consistent with a dynamic model of D2R activation in which Arg1323.50 adopts a dual role, both by stabilizing the inactive-state receptor conformation and enhancing dopamine-dependent D2R-G protein coupling.

  6. MD simulation of organics adsorption from aqueous solution in carbon slit-like pores. Foundations of the pore blocking effect

    International Nuclear Information System (INIS)

    Gauden, Piotr A; Terzyk, Artur P; Furmaniak, Sylwester; Zieliński, Wojciech; Włoch, Jerzy; Kowalczyk, Piotr

    2014-01-01

    The results of systematic studies of organics adsorption from aqueous solutions (at the neutral pH level) in a system of slit-like carbon pores having different sizes and oxygen groups located at the pore mouth are reported. Using molecular dynamics simulations (GROMACS package) the properties of adsorbent–adsorbate (benzene, phenol or paracetamol) as well as adsorbent–water systems are discussed. After the introduction of surface oxygen functionalities, adsorption of organic compounds decreases (in accordance with experimental data) and this is caused by the accumulation of water molecules at pore entrances. The pore blocking effect decreases with the diameter of slits and practically vanishes for widths larger than approx. 0.68 nm. We observed the increase in phenol adsorption with the rise in temperature. Moreover, adsorbed molecules occupy the external surface of the slit pores (the entrances) in the case of oxidized adsorbents. Among the studied molecules benzene, phenol and paracetamol prefer an almost flat orientation and with the rise in the pore width the number of molecules oriented in parallel decreases. The decrease or increase in temperature (with respect to 298 K) leads to insignificant changes of angular orientation of adsorbed molecules. (paper)

  7. Injector MD Days 2017

    CERN Document Server

    Rumolo, G

    2017-01-01

    The Injector Machine Development (MD) days 2017 were held on 23-24 March, 2017, at CERN with thefollowing main goals:Give a chance to the MD users to present their results and show the relevant progress made in 2016 onseveral fronts.Provide the MD users and the Operation (OP) crews with a general overview on the outcome and theimpact of all ongoing MD activities.Identify the open questions and consequently define - with priorities - a list of machine studies in theinjectors for 2017 (covering the operational beams, LHC Injectors Upgrade, High Luminosity LHC,Physics Beyond Colliders, other projects).Create the opportunity to collect and document the highlights of the 2016 MDs and define the perspectivesfor 2017.Discuss how to make best use of the MD time, in particular let the main MD user express their wishesand see whether/how OP teams can contribute to their fulfilment.

  8. Feelings of Clinician-Patient Similarity and Trust Influence Pain: Evidence From Simulated Clinical Interactions.

    Science.gov (United States)

    Losin, Elizabeth A Reynolds; Anderson, Steven R; Wager, Tor D

    2017-07-01

    Pain is influenced by many factors other than external sources of tissue damage. Among these, the clinician-patient relationship is particularly important for pain diagnosis and treatment. However, the effects of the clinician-patient relationship on pain remain underexamined. We tested the hypothesis that patients who believe they share core beliefs and values with their clinician will report less pain than patients who do not. We also measured feelings of perceived clinician-patient similarity and trust to see if these interpersonal factors influenced pain. We did so by experimentally manipulating perceptions of similarity between participants playing the role of clinicians and participants playing the role of patients in simulated clinical interactions. Participants were placed in 2 groups on the basis of their responses to a questionnaire about their personal beliefs and values, and painful thermal stimulation was used as an analog of a painful medical procedure. We found that patients reported feeling more similarity and trust toward their clinician when they were paired with clinicians from their own group. In turn, patients' positive feelings of similarity and trust toward their clinicians-but not clinicians' feelings toward patients or whether the clinician and patient were from the same group-predicted lower pain ratings. Finally, the most anxious patients exhibited the strongest relationship between their feelings about their clinicians and their pain report. These findings increase our understanding of context-driven pain modulation and suggest that interventions aimed at increasing patients' feelings of similarity to and trust in health care providers may help reduce the pain experienced during medical care. We present novel evidence that the clinician-patient relationship can affect the pain experienced during medical care. We found that "patients" in simulated clinical interactions who reported feeling more similarity and trust toward their

  9. Supramolecular architecture of 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole.3H2O: Synthesis, spectroscopic investigations, DFT computation, MD simulations and docking studies

    Science.gov (United States)

    Murthy, P. Krishna; Smitha, M.; Sheena Mary, Y.; Armaković, Stevan; Armaković, Sanja J.; Rao, R. Sreenivasa; Suchetan, P. A.; Giri, L.; Pavithran, Rani; Van Alsenoy, C.

    2017-12-01

    Crystal and molecular structure of newly synthesized compound 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole (BMMBI) has been authenticated by single crystal X-ray diffraction, FT-IR, FT-Raman, 1H NMR, 13C NMR and UV-Visible spectroscopic techniques; compile both experimental and theoretical results which are performed by DFT/B3LYP/6-311++G(d,p) method at ground state in gas phase. Visualize nature and type of intermolecular interactions and crucial role of these interactions in supra-molecular architecture has been investigated by use of a set of graphical tools 3D-Hirshfeld surfaces and 2D-fingerprint plots analysis. The title compound stabilized by strong intermolecular hydrogen bonds N⋯Hsbnd O and O⋯Hsbnd O, which are envisaged by dark red spots on dnorm mapped surfaces and weak Br⋯Br contacts envisaged by red spot on dnorm mapped surface. The detailed fundamental vibrational assignments of wavenumbers were aid by with help of Potential Energy distribution (PED) analysis by using GAR2PED program and shows good agreement with experimental values. Besides frontier orbitals analysis, global reactivity descriptors, natural bond orbitals and Mullikan charges analysis were performed by same basic set at ground state in gas phase. Potential reactive sites of the title compound have been identified by ALIE, Fukui functions and MEP, which are mapped to the electron density surfaces. Stability of BMMBI have been investigated from autoxidation process and pronounced interaction with water (hydrolysis) by using bond dissociation energies (BDE) and radial distribution functions (RDF), respectively after MD simulations. In order to identify molecule's most important reactive spots we have used a combination of DFT calculations and MD simulations. Reactivity study encompassed calculations of a set of quantities such as: HOMO-LUMO gap, MEP and ALIE surfaces, Fukui functions, bond dissociation energies and radial distribution functions. To confirm the potential

  10. Thermal evolution of nanocrystalline co-sputtered Ni–Zr alloy films: Structural, magnetic and MD simulation studies

    International Nuclear Information System (INIS)

    Bhattacharya, Debarati; Rao, T.V. Chandrasekhar; Bhushan, K.G.; Ali, Kawsar; Debnath, A.; Singh, S.; Arya, A.; Bhattacharya, S.; Basu, S.

    2015-01-01

    Monophasic and homogeneous Ni 10 Zr 7 nanocrystalline alloy films were successfully grown at room temperature by co-sputtering in an indigenously developed three-gun DC/RF magnetron sputtering unit. The films could be produced with long-range crystallographic and chemical order in the alloy, thus overcoming the widely acknowledged inherent proclivity of the glass forming Ni–Zr couple towards amorphization. Crystallinity of these alloys is a desirable feature with regard to improved efficacy in applications such as hydrogen storage, catalytic activity and nuclear reactor engineering, to name a few. Thermal stability of this crystalline phase, being vital for transition to viable applications, was investigated through systematic annealing of the alloy films at 473 K, 673 K and 923 K for various durations. While the films were stable at 473 K, the effect of annealing at 673 K was to create segregation into nanocrystalline Ni (superparamagnetic) and amorphous Ni + Zr (non-magnetic) phases. Detailed analyses of the physical and magnetic structures before and after annealing were performed through several techniques effectual in analyzing stratified configurations and the findings were all consistent with each other. Polarized neutron and X-ray reflectometry, grazing incidence x-ray diffraction, time-of-flight secondary ion mass spectroscopy and X-ray photoelectron spectroscopy were used to gauge phase separation at nanometer length scales. SQUID based magnetometry was used to investigate macroscopic magnetic properties. Simulated annealing performed on this system using molecular dynamic calculations corroborated well with the experimental results. This study provides a thorough understanding of the creation and thermal evolution of a crystalline Ni–Zr alloy. - Highlights: • Nanocrystalline Ni 10 Zr 7 alloy thin films deposited successfully by co-sputtering. • Creation of a crystalline alloy in a binary system with a tendency to amorphize. • Quantitative

  11. Thermal evolution of nanocrystalline co-sputtered Ni–Zr alloy films: Structural, magnetic and MD simulation studies

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, Debarati, E-mail: debarati@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Rao, T.V. Chandrasekhar; Bhushan, K.G. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Ali, Kawsar [Material Science Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Debnath, A. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Singh, S. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Arya, A. [Material Science Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Bhattacharya, S. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Basu, S. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2015-11-15

    Monophasic and homogeneous Ni{sub 10}Zr{sub 7} nanocrystalline alloy films were successfully grown at room temperature by co-sputtering in an indigenously developed three-gun DC/RF magnetron sputtering unit. The films could be produced with long-range crystallographic and chemical order in the alloy, thus overcoming the widely acknowledged inherent proclivity of the glass forming Ni–Zr couple towards amorphization. Crystallinity of these alloys is a desirable feature with regard to improved efficacy in applications such as hydrogen storage, catalytic activity and nuclear reactor engineering, to name a few. Thermal stability of this crystalline phase, being vital for transition to viable applications, was investigated through systematic annealing of the alloy films at 473 K, 673 K and 923 K for various durations. While the films were stable at 473 K, the effect of annealing at 673 K was to create segregation into nanocrystalline Ni (superparamagnetic) and amorphous Ni + Zr (non-magnetic) phases. Detailed analyses of the physical and magnetic structures before and after annealing were performed through several techniques effectual in analyzing stratified configurations and the findings were all consistent with each other. Polarized neutron and X-ray reflectometry, grazing incidence x-ray diffraction, time-of-flight secondary ion mass spectroscopy and X-ray photoelectron spectroscopy were used to gauge phase separation at nanometer length scales. SQUID based magnetometry was used to investigate macroscopic magnetic properties. Simulated annealing performed on this system using molecular dynamic calculations corroborated well with the experimental results. This study provides a thorough understanding of the creation and thermal evolution of a crystalline Ni–Zr alloy. - Highlights: • Nanocrystalline Ni{sub 10}Zr{sub 7} alloy thin films deposited successfully by co-sputtering. • Creation of a crystalline alloy in a binary system with a tendency to amorphize.

  12. Enhancement Corrosion Resistance of (γ-Glycidyloxypropyl-Silsesquioxane-Titanium Dioxide Films and Its Validation by Gas Molecule Diffusion Coefficients Using Molecular Dynamics (MD Simulation

    Directory of Open Access Journals (Sweden)

    Haiyan Wang

    2014-01-01

    Full Text Available Based on silsesquioxanes (SSO derived from the hydrolytic condensation of (γ-glycidyloxypropyltrimethoxysilane (GPMS and titanium tetrabutoxide (TTB, hybrid films on aluminum alloy (AA, film-GPMS-SSO (f-GS and f-GS-TTBi% (f-GSTT5%–25%, i = 5, 10, 15, 20 and 25 wt%, were prepared and tested by electrochemical measurements with typical potentiodynamic polarization curves. The Icorr values of the samples were significantly lower, comparing with the Icorr values of the f-GS, AA and f-GS modified tetraethoxysilane (TEOS in the previous study, which implies that the TTB5%–25% (TiO2 additions in the coatings indeed enhance the electrochemical corrosion resistance. Correlations between the film structures and anticorrosion properties were discussed. To validate the corresponding anticorrosion experiment results, different 3D-amorphous cubic unit cells were employed as models to investigate the self-diffusion coefficient (SDC for SO2, NO2 and H2O molecules by molecular dynamics (MD simulation. All of the SDCs calculated for SO2, NO2 and H2O diffusing in f-GSTT5%–25% cells were less than the SDCs in f-GS. These results validated the corresponding anticorrosion experiment results.

  13. Tests of peak flow scaling in simulated self-similar river networks

    Science.gov (United States)

    Menabde, M.; Veitzer, S.; Gupta, V.; Sivapalan, M.

    2001-01-01

    The effect of linear flow routing incorporating attenuation and network topology on peak flow scaling exponent is investigated for an instantaneously applied uniform runoff on simulated deterministic and random self-similar channel networks. The flow routing is modelled by a linear mass conservation equation for a discrete set of channel links connected in parallel and series, and having the same topology as the channel network. A quasi-analytical solution for the unit hydrograph is obtained in terms of recursion relations. The analysis of this solution shows that the peak flow has an asymptotically scaling dependence on the drainage area for deterministic Mandelbrot-Vicsek (MV) and Peano networks, as well as for a subclass of random self-similar channel networks. However, the scaling exponent is shown to be different from that predicted by the scaling properties of the maxima of the width functions. ?? 2001 Elsevier Science Ltd. All rights reserved.

  14. Correlations between contouring similarity metrics and simulated treatment outcome for prostate radiotherapy

    Science.gov (United States)

    Roach, D.; Jameson, M. G.; Dowling, J. A.; Ebert, M. A.; Greer, P. B.; Kennedy, A. M.; Watt, S.; Holloway, L. C.

    2018-02-01

    Many similarity metrics exist for inter-observer contouring variation studies, however no correlation between metric choice and prostate cancer radiotherapy dosimetry has been explored. These correlations were investigated in this study. Two separate trials were undertaken, the first a thirty-five patient cohort with three observers, the second a five patient dataset with ten observers. Clinical and planning target volumes (CTV and PTV), rectum, and bladder were independently contoured by all observers in each trial. Structures were contoured on T2-weighted MRI and transferred onto CT following rigid registration for treatment planning in the first trial. Structures were contoured directly on CT in the second trial. STAPLE and majority voting volumes were generated as reference gold standard volumes for each structure for the two trials respectively. VMAT treatment plans (78 Gy to PTV) were simulated for observer and gold standard volumes, and dosimetry assessed using multiple radiobiological metrics. Correlations between contouring similarity metrics and dosimetry were calculated using Spearman’s rank correlation coefficient. No correlations were observed between contouring similarity metrics and dosimetry for CTV within either trial. Volume similarity correlated most strongly with radiobiological metrics for PTV in both trials, including TCPPoisson (ρ  =  0.57, 0.65), TCPLogit (ρ  =  0.39, 0.62), and EUD (ρ  =  0.43, 0.61) for each respective trial. Rectum and bladder metric correlations displayed no consistency for the two trials. PTV volume similarity was found to significantly correlate with rectum normal tissue complication probability (ρ  =  0.33, 0.48). Minimal to no correlations with dosimetry were observed for overlap or boundary contouring metrics. Future inter-observer contouring variation studies for prostate cancer should incorporate volume similarity to provide additional insights into dosimetry during analysis.

  15. Identification of 253Md

    International Nuclear Information System (INIS)

    Kadkhodayan, B.; Czerwinski, K.R.; Kreek, S.A.; Hannink, N.J.; Gregorich, K.E.; Lee, D.M.; Nurmia, M.J.; Hoffman, D.C.; Hall, H.L.

    1992-01-01

    We have measured the half-life and production cross section of the new isotope 253 Md, produced via the 243 Am( 13 C,3n) reaction. Isolation of Md from other activities was accomplished using elution with ammonium α-hydroxyisobutyrate from a cation exchange resin column. Experiments were performed with different irradiation time intervals, but the chemical separation always began and ended at exactly the same length of time after the end of irradiation. All separations with the same irradation lengths were combined and analyzed for growth and decay of the 3.0-d 253 Fm daughter and 20.47-d 253 Es, granddaugther of 253 Md. The amount of 253 Es in each fraction depends on the length of each irradiation and the 253 Md half-life. An increase in the length of irradiation will cause a corresponding increase in the amount of the new isotope 253 Md and hence, in the amount of 253 Es produced, provided the length of irradiations are not very long compared to the half-life of 253 Md. In this way, the Md half-life was estimated to be about 6 minutes with a production cross section of the order of 50 nb. (orig.)

  16. Toward a Rational Design of Bioactive Glasses with Optimal Structural Features: Composition–Structure Correlations Unveiled by Solid-State NMR and MD Simulations

    Science.gov (United States)

    2013-01-01

    The physiological responses of silicate-based bioactive glasses (BGs) are known to depend critically on both the P content (nP) of the glass and its silicate network connectivity (N̅BOSi). However, while the bioactivity generally displays a nonmonotonic dependence on nP itself, recent work suggest that it is merely the net orthophosphate content that directly links to the bioactivity. We exploit molecular dynamics (MD) simulations combined with 31P and 29Si solid-state nuclear magnetic resonance (NMR) spectroscopy to explore the quantitative relationships between N̅BOSi, nP, and the silicate and phosphate speciations in a series of Na2O–CaO–SiO2–P2O5 glasses spanning 2.1 ≤ N̅BOSi ≤ 2.9 and variable P2O5 contents up to 6.0 mol %. The fractional population of the orthophosphate groups remains independent of nP at a fixed N̅BOSi-value, but is reduced slightly as N̅BOSi increases. Nevertheless, P remains predominantly as readily released orthophosphate ions, whose content may be altered essentially independently of the network connectivity, thereby offering a route to optimize the glass bioactivity. We discuss the observed composition-structure links in relation to known composition-bioactivity correlations, and define how Na2O–CaO–SiO2–P2O5 compositions exhibiting an optimal bioactivity can be designed by simultaneously altering three key parameters: the silicate network connectivity, the (ortho)phosphate content, and the nNa/nCa molar ratio. PMID:24364818

  17. Characterization of the immersion properties of the peripheral membrane anchor of the FATC domain of the kinase "target of rapamycin" by NMR, oriented CD spectroscopy, and MD simulations.

    Science.gov (United States)

    Sommer, Lisa A M; Janke, J Joel; Bennett, W F Drew; Bürck, Jochen; Ulrich, Anne S; Tieleman, D Peter; Dames, Sonja A

    2014-05-08

    The multidomain ser/thr kinase "target of rapamycin" (TOR) centrally controls eukaryotic growth and metabolism. The C-terminal FATC domain is important for TOR regulation and was suggested to directly mediate TOR-membrane interactions. Here, we present a detailed characterization of the membrane immersion properties of the oxidized and reduced yeast TOR1 FATC domain (2438-2470 = y1fatc). The immersion depth was characterized by NMR-monitored interaction studies with DPC micelles containing paramagnetically tagged 5- or 16-doxyl stearic acid (5-/16-SASL) and by analyzing the paramagnetic relaxation enhancement (PRE) from Mn(2+) in the solvent. Complementary MD-simulations of micellar systems in the absence and presence of protein showed that 5-/16-SASL can move in the micelle and that 16-SASL can bend such that the doxyl group is close to the headgroup region and not deep in the interior as commonly assumed. Based on oriented CD (OCD) data, the single α-helix of oxidized/reduced y1fatc has an angle to the membrane normal of ∼30-60°/∼35-65° in neutral and ∼5-35°/∼0-30° in negatively charged bilayers. The presented experimentally well-founded models help to better understand how this redox-sensitive peripheral membrane anchor may be part of a network of protein-protein and protein-membrane interactions regulating TOR localization at different cellular membranes. Moreover, the presented work provides a good methodological reference for the structural characterization of other peripherally membrane associating proteins.

  18. Muscular Dystrophy (MD)

    Science.gov (United States)

    ... patients may need assisted ventilation to treat respiratory muscle weakness and a pacemaker for cardiac abnormalities. View Full Treatment Information Definition The muscular dystrophies (MD) are a group of more than 30 ...

  19. ProtoMD: A prototyping toolkit for multiscale molecular dynamics

    Science.gov (United States)

    Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.

    2016-05-01

    ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.

  20. The discovery of 260Md and the decay properties of 258Fm, 258m,gMd and 259Md

    International Nuclear Information System (INIS)

    Lougheed, R.W.; Hulet, E.K.; Dougan, R.J.; Wild, J.F.; Dupzyk, R.J.; Henderson, C.M.; Moody, K.J.; Hahn, R.L.; Suemmerer, K.; Bethune, G.

    1986-01-01

    We have discovered a new neutron-rich isotope, 260 Md, from 18 O and 22 Ne bombardments of 254 Es. We observed a spontaneous-fission (SF) activity with a half-life of 32 days in electromagnetically separated fractions with mass number 260 from these bombardments and we measured the mass and kinetic energy distributions of this SF activity. The mass distribution was symmetric with the principal energy peak at a total kinetic energy (TKE) of 234 MeV, similar to previous observations for heavy fermium isotopes. Surprisingly, we also observed a smaller symmetric component with a TKE of 195 MeV. We interpret these two peaks in the TKE distribution as arising from two types of fission in the same nucleus, or bimodal fission. The observed fission activity may be either from the SF decay of 260 Md or from 260 Fm which would arise from electron-capture (EC) decay of 260 Md. We have eliminated the possible β - decay of 260 Md by measuring β - -SF time correlations for the decay of 260 Md and we plan to determine whether 260 Md decays by EC by measuring time correlations between fermium X-rays and SF events. We also measured various properties of the heavy fermium and mendelevium isotopes and obtained 1. more accurate cross-sections for the neutron-rich mendelevium isotopes which we use to predict the production rates of yet undiscovered nuclides, 2. improved half-life measurements for 258m,g Md and 259 Md, 3. confirmation of the EC decay of 258m Md by measurement of the fermium X-rays preceding the SF decay of 258 Fm and 4. very substantially improved mass and TKE distributions for the SF decay of 258 Fm and 259 Md. (orig.)

  1. Self-similarity and turbulence characteristics of wind turbine wakes via large-eddy simulation (Invited)

    Science.gov (United States)

    Xie, S.; Archer, C. L.

    2013-12-01

    In this study, a new large-eddy simulation code, the Wind Turbine and Turbulence Simulator (WiTTS), is developed to study the wake generated from a single wind turbine in the neutral ABL. The WiTTS formulation is based on a scale-dependent Lagrangian dynamical model of the sub-grid shear stress and uses actuator lines to simulate the effects of the rotating blades. WiTTS is first tested against wind tunnel experiments and then used to study the commonly-used assumptions of self-similarity and axis-symmetry of the wake under neutral conditions for a variety of wind speeds and turbine properties. The mean velocity deficit shows good self-similarity properties following a normal distribution in the horizontal plane at the hub-height level. Self-similarity is a less valid approximation in the vertical near the ground, due to strong wind shear and ground effects. The mean velocity deficit is strongly dependent on the thrust coefficient or induction factor. A new relationship is proposed to model the mean velocity deficit along the centerline at the hub-height level to fit the LES results piecewise throughout the wake. A logarithmic function is used in the near and intermediate wake regions whereas a power function is used in the far-wake. These two functions provide a better fit to both simulated and observed wind velocity deficits than other functions previously used in wake models such as WAsP. The wind shear and impact with the ground cause an anisotropy in the expansion of the wake such that the wake grows faster horizontally than vertically. The wake deforms upon impact with the ground and spreads laterally. WiTTS is also used to study the turbulence characteristics in the wake. Aligning with the mean wind direction, the streamwise component of turbulence intensity is the dominant among the three components and thus it is further studied. The highest turbulence intensity occurs near the top-tip level. The added turbulence intensity increases fast in the near

  2. Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-D-Enantiomer of Alzheimer’s β-Amyloid Peptide: Relevance to the Ion Channel Mechanism of AD Pathology

    Science.gov (United States)

    Connelly, Laura; Arce, Fernando Teran; Jang, Hyunbum; Capone, Ricardo; Kotler, Samuel A.; Ramachandran, Srinivasan; Kagan, Bruce L.; Nussinov, Ruth; Lal, Ratnesh

    2012-01-01

    Alzheimer’s disease (AD) is a protein misfolding disease characterized by a build-up of β-amyloid (Aβ) peptide as senile plaques, uncontrolled neurodegeneration, and memory loss. AD pathology is linked to the destabilization of cellular ionic homeostasis and involves Aβ peptide-plasma membrane interactions. In principle, there are two possible ways through which disturbance of the ionic homeostasis can take place: directly, where the Aβ peptide either inserts into the membrane and creates ion-conductive pores or destabilizes the membrane organization; or, indirectly, where the Aβ peptide interacts with existing cell membrane receptors. To distinguish between these two possible types of Aβ-membrane interactions, we took advantage of the biochemical tenet that ligand-receptor interactions are stereospecific; L-amino acid peptides, but not their D-counterparts, bind to cell membrane receptors. However, with respect to the ion channel-mediated mechanism, like L-amino acids, D-amino acid peptides will also form ion channel-like structures. Using atomic force microscopy (AFM) we imaged the structures of both D- and L-enantiomers of the full length Aβ1-42 when reconstituted in lipid bilayers. AFM imaging shows that both L- and D-Aβ isomers form similar channel-like structures. Molecular dynamics (MD) simulations support the AFM imaged 3D structures. Earlier we have shown that D-Aβ1-42 channels conduct ions similarly to their L-counter parts. Taken together, our results support the direct mechanism of Aβ ion channel-mediated destabilization of ionic homeostasis rather than the indirect mechanism through Aβ interaction with membrane receptors. PMID:22217000

  3. On the scale similarity in large eddy simulation. A proposal of a new model

    International Nuclear Information System (INIS)

    Pasero, E.; Cannata, G.; Gallerano, F.

    2004-01-01

    Among the most common LES models present in literature there are the Eddy Viscosity-type models. In these models the subgrid scale (SGS) stress tensor is related to the resolved strain rate tensor through a scalar eddy viscosity coefficient. These models are affected by three fundamental drawbacks: they are purely dissipative, i.e. they cannot account for back scatter; they assume that the principal axes of the resolved strain rate tensor and SGS stress tensor are aligned; and that a local balance exists between the SGS turbulent kinetic energy production and its dissipation. Scale similarity models (SSM) were created to overcome the drawbacks of eddy viscosity-type models. The SSM models, such as that of Bardina et al. and that of Liu et al., assume that scales adjacent in wave number space present similar hydrodynamic features. This similarity makes it possible to effectively relate the unresolved scales, represented by the modified Cross tensor and the modified Reynolds tensor, to the smallest resolved scales represented by the modified Leonard tensor] or by a term obtained through multiple filtering operations at different scales. The models of Bardina et al. and Liu et al. are affected, however, by a fundamental drawback: they are not dissipative enough, i.e they are not able to ensure a sufficient energy drain from the resolved scales of motion to the unresolved ones. In this paper it is shown that such a drawback is due to the fact that such models do not take into account the smallest unresolved scales where the most dissipation of turbulent SGS energy takes place. A new scale similarity LES model that is able to grant an adequate drain of energy from the resolved scales to the unresolved ones is presented. The SGS stress tensor is aligned with the modified Leonard tensor. The coefficient of proportionality is expressed in terms of the trace of the modified Leonard tensor and in terms of the SGS kinetic energy (computed by solving its balance equation). The

  4. Similarities and differences of serotonin and its precursors in their interactions with model membranes studied by molecular dynamics simulation

    Science.gov (United States)

    Wood, Irene; Martini, M. Florencia; Pickholz, Mónica

    2013-08-01

    In this work, we report a molecular dynamics (MD) simulations study of relevant biological molecules as serotonin (neutral and protonated) and its precursors, tryptophan and 5-hydroxy-tryptophan, in a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC). The simulations were carried out at the fluid lamellar phase of POPC at constant pressure and temperature conditions. Two guest molecules of each type were initially placed at the water phase. We have analyzed, the main localization, preferential orientation and specific interactions of the guest molecules within the bilayer. During the simulation run, the four molecules were preferentially found at the water-lipid interphase. We found that the interactions that stabilized the systems are essentially hydrogen bonds, salt bridges and cation-π. None of the guest molecules have access to the hydrophobic region of the bilayer. Besides, zwitterionic molecules have access to the water phase, while protonated serotonin is anchored in the interphase. Even taking into account that these simulations were done using a model membrane, our results suggest that the studied molecules could not cross the blood brain barrier by diffusion. These results are in good agreement with works that show that serotonin and Trp do not cross the BBB by simple diffusion.

  5. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

    Science.gov (United States)

    2015-01-01

    The reliability of free energy simulations (FES) is limited by two factors: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect

  6. mdFoam+: Advanced molecular dynamics in OpenFOAM

    Science.gov (United States)

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

    2018-03-01

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

  7. Similar simulation study on the characteristics of the electric potential response to coal mining

    Science.gov (United States)

    Niu, Yue; Li, Zhonghui; Kong, Biao; Wang, Enyuan; Lou, Quan; Qiu, Liming; Kong, Xiangguo; Wang, Jiali; Dong, Mingfu; Li, Baolin

    2018-02-01

    An electric potential (EP) can be generated during the failure process of coal and rock. In this article, a similar physical model of coal rock was built and the characteristics of the EP responding to the process of coal mining were studied. The results showed that, at the early mining stage, the structure of coal rock strata were stable in the simulation model, the support stress of overlying coal rock strata was low and the maximum subsidence was little, while the EP change was less. With the advancement of the working face, the support stress of the overlying coal rock strata in the mined-out area changed dramatically, the maximum subsidence increased constantly, the deformation and destruction were aggravated, and cracks expanded continuously. Meanwhile, the EP response was significant with fluctuation. When significant macro damage appeared in coal rock strata, the EP signal fluctuation was violent. The overlying coal rock strata were influenced by gravity and mining activity. During the mining process, the crack growth and the friction, together with slip between coal and rock particles, resulted in the response of EP. The change in EP was closely related to the damage state and stress distribution of the coal rock strata. EP monitoring has the advantages of accurate reflection and strong anti-interference in the field. Therefore, with further study, an EP monitoring method could be applied for monitoring and early warning of coal and rock dynamic disaster, and risk evaluation in the future. The strength of the EP and its fluctuation degree could serve as the key discrimination indexes.

  8. Developing the MD Explorer

    Science.gov (United States)

    Howie, Philip V.

    1993-04-01

    The MD Explorer is an eight-seat twin-turbine engine helicopter which is being developed using integrated product definition (IPD) team methodology. New techniques include NOTAR antitorque system for directional control, a composite fuselage, an all-composite bearingless main rotor, and digital cockpit displays. Three-dimensional CAD models are the basis of the entire Explorer design. Solid models provide vendor with design clarification, removing much of the normal drawing interpretation errors.

  9. Similarity, Self-Esteem and Reactions to Aid in a Simulated Decision Making Task.

    Science.gov (United States)

    esteem - low self esteem recipients were the three experimental factors. The effect of these experimental variables on the recipients self -perceptions...The study explored the effects of the overall similarity between donor and recipient of resistance and the recipient’s level of self - esteem on his...reactions to being helped. A 2 x 2 x 2 factorial between subjects design was employed in which aid-no aid, similar donor-dissimilar donor and high self

  10. Self-Similarity and helical symmetry in vortex generator flow simulations

    DEFF Research Database (Denmark)

    Fernandez, U.; Velte, Clara Marika; Réthoré, Pierre-Elouan

    2014-01-01

    According to experimental observations, the vortices generated by vortex generators have previously been observed to be self-similar for both the axial (uz) and azimuthal (uӨ) velocity profiles. Further, the measured vortices have been observed to obey the criteria for helical symmetry...

  11. A close examination of the structure and dynamics of HC(NH2)2PbI3by MD simulations and group theory

    KAUST Repository

    Carignano, M. A.; Saeed, Y.; Aravindh, S. Assa; Roqan, Iman S.; Even, J.; Katan, C.

    2016-01-01

    The formamidinium lead iodide hybrid perovskite is studied using first principles molecular dynamics simulations and further analyzed using group theory. The simulations are performed on large supercells containing 768 atoms under isothermal

  12. Md-miR156ab and Md-miR395 Target WRKY Transcription Factors to Influence Apple Resistance to Leaf Spot Disease.

    Science.gov (United States)

    Zhang, Qiulei; Li, Yang; Zhang, Yi; Wu, Chuanbao; Wang, Shengnan; Hao, Li; Wang, Shengyuan; Li, Tianzhong

    2017-01-01

    MicroRNAs (miRNAs) are key regulators of gene expression that post-transcriptionally regulate transcription factors involved in plant physiological activities. Little is known about the effects of miRNAs in disease resistance in apple ( Malus × domestica ). We globally profiled miRNAs in the apple cultivar Golden Delicious (GD) infected or not with the apple leaf spot fungus Alternaria alternaria f. sp. mali (ALT1), and identified 58 miRNAs that exhibited more than a 2-fold upregulation upon ALT1 infection. We identified a pair of miRNAs that target protein-coding genes involved in the defense response against fungal pathogens; Md-miR156ab targets a novel WRKY transcription factor, MdWRKYN1, which harbors a TIR and a WRKY domain. Md-miR395 targets another transcription factor, MdWRKY26, which contains two WRKY domains. Real-time PCR analysis showed that Md-miR156ab and Md-miR395 levels increased, while MdWRKYN1 and MdWRKY26 expression decreased in ALT1-inoculated GD leaves; furthermore, the overexpression of Md-miR156ab and Md-miR395 resulted in a significant reduction in MdWRKYN1 and MdWRKY26 expression. To investigate whether these miRNAs and their targets play a crucial role in plant defense, we overexpressed MdWRKYN1 or knocked down Md-miR156ab activity, which in both cases enhanced the disease resistance of the plants by upregulating the expression of the WRKY-regulated pathogenesis-related (PR) protein-encoding genes MdPR3-1, MdPR3-2, MdPR4, MdPR5, MdPR10-1 , and MdPR10-2 . In a similar analysis, we overexpressed MdWRKY26 or suppressed Md-miR395 activity, and found that many PR protein-encoding genes were also regulated by MdWRKY26 . In GD, ALT-induced Md-miR156ab and Md-miR395 suppress MdWRKYN1 and MdWRKY26 expression, thereby decreasing the expression of some PR genes, and resulting in susceptibility to ALT1.

  13. Hydro-epidemiology of Chronic Kidney Disease(CKD) in Sri Lanka and Its Similarities to the CKD Epidemic in Meso-America.Sarath Gunatilake M.D, Dr. P.H, Professor, California State University, Long Beach California

    Science.gov (United States)

    Illangasekera, T.; Gunatilake, S.

    2015-12-01

    Over 2000 years ago Sri Lanka was known as the granary of the east. This distinction was achieved with a massive rice production aided by an efficient irrigation system. The basic structural unit of this irrigation system -with thousands of man-made lakes- was a large reservoir collecting rain water from tributaries and redistributing it to a cascade of rice paddy farms. The rice cultivation used organic fertilizer and natural pesticides made from ancient Ayurvedic recipes. The sociopolitical changes initiated in the county in 1977 resulted in a modernized agricultural economy with the renovation of the old irrigation system. Heavy use of pesticides, mostly Glyphosate (brand name "Round Up") with government subsidized cheap synthetic fertilizer (mostly triple phosphate) contaminated with heavy metals, including Arsenic and Cadmium, became a common practice. As a result, the shallow aquifers in the lowest lying areas, recharged by the irrigation water, was contaminated with Calcium, Magnesium phosphates, and the heavy metals, rendering the drinking water from shallow wells in these areas, extremely hard and unpalatable. The practice of drinking water from the shallow wells in low lying areas, most of which are abandoned now, and the use and spraying of pesticides particularly Glyphosate (often without proper personal protective equipment) have been identified in a case control study, as the main risk factors responsible for a massive epidemic of Chronic Kidney Disease (CKD) affecting 450,000 young farmers, resulting in 23,000 deaths. It is hypothesized that the Glyphosate chelates heavy metals delivering it to the kidney, with contaminated drinking water and food, causing progressive kidney damage. The same irrigation system that contributed to past prosperity has now become a scourge within the realm of a modernized agriculture. Climatic variations, global warming and severe dehydration also have been identified as contributory factors. Similar CKD epidemic killing

  14. SU-F-P-51: Similarity Analysis of the Linear Accelerator Machines Based On Clinical Simulation

    International Nuclear Information System (INIS)

    Li, K

    2016-01-01

    Purpose: To evaluate the clinical rationale for Truebeam and Trilogy Linac machines from Varian Medical System as exchangeable treatment modalities in the same radiation oncology department. Methods: Intensity Modulated Radiotherapy (IMRT) plans for different diseases were selected for this study. These disease sites included brain, head and neck, breast, lung, and prostate. The parameters selected for this study were the energy amount, Monitor Unit (MU); dose coverage of target reflected by prescription isodose volume(PIV); dose spillage described by the volume of 50% isodoseline of the prescription; and dose homogeneities represented by the maximum dose (MaxD) and the minimum dose (MinD) of target volume (TV) and critical structure (CS). Each percentage difference between the values of these parameters formed an element of a matrix, which was called Similarity Comparison Matrix(SCM). The elements of the SCM were then simplified by dimensional conversion algorithm, which was used to determine clinical similarity between two machines through a single value. Results: For the selected clinical cases in this study, the average percentage differences between Trilogy and Truebeam in MU was 0.28% with standard deviation(SD) 0.66%, PIV was 0.23% with SD 0.20%, Volume at 50% prescription dose was 0.31% with SD at 0.78%, MaxD at TV is 0.26% with SD 0.35%, MinD at TV is −0.04% with SD 0.51%, MaxD in CS is −0.53% with SD 0.92%, and MinD in CS 3.31%, with SD at 2.89%. The sum, product, geometric and harmonic mean for the matrix elements were 19.0%, 0.00%, 0.19%, and 0.00%. Conclusion: A method to compare two machines in clinical level was developed and some reference values were calculated for decision-making in clinical practice, and this strategy could be expanded to different clinical applications.

  15. SU-F-P-51: Similarity Analysis of the Linear Accelerator Machines Based On Clinical Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Li, K [Associates In Medical Physics, Lanham, MD (United States); John R Marsh Cancer Center (United States)

    2016-06-15

    Purpose: To evaluate the clinical rationale for Truebeam and Trilogy Linac machines from Varian Medical System as exchangeable treatment modalities in the same radiation oncology department. Methods: Intensity Modulated Radiotherapy (IMRT) plans for different diseases were selected for this study. These disease sites included brain, head and neck, breast, lung, and prostate. The parameters selected for this study were the energy amount, Monitor Unit (MU); dose coverage of target reflected by prescription isodose volume(PIV); dose spillage described by the volume of 50% isodoseline of the prescription; and dose homogeneities represented by the maximum dose (MaxD) and the minimum dose (MinD) of target volume (TV) and critical structure (CS). Each percentage difference between the values of these parameters formed an element of a matrix, which was called Similarity Comparison Matrix(SCM). The elements of the SCM were then simplified by dimensional conversion algorithm, which was used to determine clinical similarity between two machines through a single value. Results: For the selected clinical cases in this study, the average percentage differences between Trilogy and Truebeam in MU was 0.28% with standard deviation(SD) 0.66%, PIV was 0.23% with SD 0.20%, Volume at 50% prescription dose was 0.31% with SD at 0.78%, MaxD at TV is 0.26% with SD 0.35%, MinD at TV is −0.04% with SD 0.51%, MaxD in CS is −0.53% with SD 0.92%, and MinD in CS 3.31%, with SD at 2.89%. The sum, product, geometric and harmonic mean for the matrix elements were 19.0%, 0.00%, 0.19%, and 0.00%. Conclusion: A method to compare two machines in clinical level was developed and some reference values were calculated for decision-making in clinical practice, and this strategy could be expanded to different clinical applications.

  16. Verina Morton Jones, MD.

    Science.gov (United States)

    Rishworth, Susan K

    2012-01-01

    The purpose of this historical article is to demonstrate, as the biography of Verina Morton Jones, MD, is uncovered, the difficulties inherent in researching original source material on the lives of 19th- and early 20th-century African American physicians as well as the great benefits derived from doing this research. The procedures used include basic archival research and close examination of published materials about her in the past, in conjunction with oral history. Original correspondence from Dr Morton Jones to her niece and nephew is used to illustrate events in her life and the thoughts and attitudes she expressed. Some of these thoughts and attitudes reflect those current situations in which African Americans found themselves, and others are quite unique, no doubt owing to her privileged position in the African American community. The principle conclusions reached include the great benefits derived from doing this kind of research, as difficult and time-consuming as that may be, with the enhanced knowledge and appreciation of the heritage of African American physicians, and insights into American social history during this period.

  17. Harold E. Varmus, MD.

    Science.gov (United States)

    Varmus, H E

    1995-06-01

    On November 19, 1993, the Senate approved the nomination of Harold E. Varmus, MD, as Director of the National Institutes of Health (NIH). Varmus, who received the 1989 Nobel Prize in Medicine, brought unquestioned credentials as a scientist to the NIH. Despite his limited background as an administrator, Varmus has received high marks from most observers for improving the morale of NIH staffers and implementing streamlined procedures in the grant review process. His tenure has not been free of controversy, however. Many clinical researchers have long felt there is a bias in NIH study sections against patient-oriented research. A recent study sponsored by the Division of Research Grants confirmed the lower success rate of patient-oriented research proposals, but the outcome of these findings remains unclear. Faced with mounting political pressure for a balanced budget, and the resultant reduction of funding to many branches of government, Varmus has been a strong voice for non-targeted investigator initiated research. Interviewed in his office in Building One on the NIH campus in Bethesda, Maryland, Varmus discussed the state of patient oriented research, the evolving role of the NIH in supporting science, and just where the money to pay for it should be found.

  18. ADT fast losses MD

    CERN Document Server

    Priebe, A; Dehning, B; Redaelli, S; Salvachua Ferrando, BM; Sapinski, M; Solfaroli Camillocci, M; Valuch, D

    2013-01-01

    The fast beam losses in the order of 1 ms are expected to be a potential major luminosity limitation for higher beam energies after the LHC long shutdown (LS1). Therefore a Quench Test is planned in the winter 2013 to estimate the quench limit in this timescale and revise the current models. This experiment was devoted to determination the LHC Transverse Damper (ADT) as a system for fast losses induction. A non-standard operation of the ADT was used to develop the beam oscillation instead of suppressing them. The sign flip method had allowed us to create the fast losses within several LHC turns at 450 GeV during the previous test (26th March 2012). Thus, the ADT could be potentially used for the studies of the UFO ("Unidentied Falling Object") impact on the cold magnets. Verification of the system capability and investigations of the disturbed beam properties were the main objectives of this MD. During the experiment, the pilot bunches of proton beam were excited independently in the horizontal and vertical ...

  19. Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs

    Czech Academy of Sciences Publication Activity Database

    Krepl, Miroslav; Clery, A.; Blatter, M.; Allain, F.H.T.; Šponer, Jiří

    2016-01-01

    Roč. 44, č. 13 (2016), s. 6452-6470 ISSN 0305-1048 Institutional support: RVO:68081707 Keywords : molecular- dynamics simulations * particle mesh ewald * pre-ribosomal-rna Subject RIV: BO - Biophysics Impact factor: 10.162, year: 2016

  20. The molecular mechanism of bisphenol A (BPA as an endocrine disruptor by interacting with nuclear receptors: insights from molecular dynamics (MD simulations.

    Directory of Open Access Journals (Sweden)

    Lanlan Li

    Full Text Available Bisphenol A (BPA can interact with nuclear receptors and affect the normal function of nuclear receptors in very low doses, which causes BPA to be one of the most controversial endocrine disruptors. However, the detailed molecular mechanism about how BPA interferes the normal function of nuclear receptors is still undiscovered. Herein, molecular dynamics simulations were performed to explore the detailed interaction mechanism between BPA with three typical nuclear receptors, including hERα, hERRγ and hPPARγ. The simulation results and calculated binding free energies indicate that BPA can bind to these three nuclear receptors. The binding affinities of BPA were slightly lower than that of E2 to these three receptors. The simulation results proved that the binding process was mainly driven by direct hydrogen bond and hydrophobic interactions. In addition, structural analysis suggested that BPA could interact with these nuclear receptors by mimicking the action of natural hormone and keeping the nuclear receptors in active conformations. The present work provided the structural evidence to recognize BPA as an endocrine disruptor and would be important guidance for seeking safer substitutions of BPA.

  1. Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

    Science.gov (United States)

    Mishra, S. B.; Nanda, B. R. K.

    2017-05-01

    Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

  2. Data supporting beta-amyloid dimer structural transitions and protein–lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures

    Directory of Open Access Journals (Sweden)

    Sara Y. Cheng

    2016-06-01

    Full Text Available This data article supports the research article entitled “Maximally Asymmetric Transbilayer Distribution of Anionic Lipids Alters the Structure and interaction with Lipids of an Amyloidogenic Protein Dimer Bound to the Membrane Surface” [1]. We describe supporting data on the binding kinetics, time evolution of secondary structure, and residue-contact maps of a surface-absorbed beta-amyloid dimer protein on different membrane surfaces. We further demonstrate the sorting of annular and non-annular regions of the protein/lipid bilayer simulation systems, and the correlation of lipid-number mismatch and surface area per lipid mismatch of asymmetric lipid membranes.

  3. Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

    Science.gov (United States)

    Odinokov, A. V.; Leontyev, I. V.; Basilevsky, M. V.; Petrov, N. Ch.

    2011-01-01

    Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD-PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.

  4. A close examination of the structure and dynamics of HC(NH2)2PbI3by MD simulations and group theory

    KAUST Repository

    Carignano, M. A.

    2016-06-22

    The formamidinium lead iodide hybrid perovskite is studied using first principles molecular dynamics simulations and further analyzed using group theory. The simulations are performed on large supercells containing 768 atoms under isothermal and fully anisotropic isobaric conditions. Two trajectories, one at 300 K and another at 450 K, were extended for over 50 ps in order to perform a detailed assessment of the rotational dynamics of organic cations. The characteristic rotations of the cation are analyzed by defining two rotation axes. It is found that the formamidinium molecules rotate preferentially around the direction parallel to the line connecting the two nitrogen atoms. The rotational dynamics shows some characteristics already observed in methylammonium lead iodide, like the heterogeneous dynamics at room temperature that disappears at 450 K. The orientational probability of the molecules is explored in terms of an expansion in cubic harmonics up to the 12th order. It reveals a strong directionality at room temperature that relaxes when increasing the temperature. These findings are further rationalized using Landau and group theories suggesting a mixed displacive/order-disorder structural instability at lower temperatures.

  5. MD SIMULATION STUDIES TO INVESTIGATE ISO-ENERGETIC CONFORMATIONAL BEHAVIOUR OF MODIFIED NUCLEOSIDES M2G AND M22G PRESENT IN tRNA

    Directory of Open Access Journals (Sweden)

    Rohit S Bavi

    2013-02-01

    Full Text Available Modified nucleic acid bases are most commonly found in tRNA. These may contain modifications from simple methylation to addition of bulky groups. Methylation of the four canonical nucleotide bases at a wide variety of positions is particularly prominent among the known modification. Methylation of N2 group of guanine is a relatively common modification in tRNA and rRNA. N2-methylguanosine (m2G is the second most often encountered nucleoside in E. coli tRNAs. N2, N2-dimethylguanosine (m22G is found in the majority of eukaryotic tRNAs and involved in forming base pair interactions with adjacent bases. Hence, in order to understand the structural significance of these methylated nucleic acid bases we have carried out molecular dynamics simulation to see the salvation effect. The results obtained shows iso-energetic conformational behaviors for m2G and m22G. The simulation trajectory of m2G shows regular periodical fluctuations suggesting that m2G is equally stable as either s-cis or s-trans rotamers. The two rotamers of m2G may interact canonically or non-canonically with opposite base as s-trans m2G26:C/A/U44 and s-cis m2G26:A/U44. The free rotations around the C-N bond could be the possible reason for these iso-energetic conformations. Dimethylation of G has almost no influence on base pairing with either A or U. Thus, these results reveal that modified nucleosides m2G and m22G may play an important role to prevent tRNA from adopting the unusual mitochondrial like conformation.

  6. Structural, stability, dynamic and binding properties of the ALS-causing T46I mutant of the hVAPB MSP domain as revealed by NMR and MD simulations.

    Directory of Open Access Journals (Sweden)

    Shixiong Lua

    Full Text Available T46I is the second mutation on the hVAPB MSP domain which was recently identified from non-Brazilian kindred to cause a familial amyotrophic lateral sclerosis (ALS. Here using CD, NMR and molecular dynamics (MD simulations, we characterized the structure, stability, dynamics and binding capacity of the T46I-MSP domain. The results reveal: 1 unlike P56S which we previously showed to completely eliminate the native MSP structure, T46I leads to no significant disruption of the native secondary and tertiary structures, as evidenced from its far-UV CD spectrum, as well as Cα and Cβ NMR chemical shifts. 2 Nevertheless, T46I does result in a reduced thermodynamic stability and loss of the cooperative urea-unfolding transition. As such, the T46I-MSP domain is more prone to aggregation than WT at high protein concentrations and temperatures in vitro, which may become more severe in the crowded cellular environments. 3 T46I only causes a 3-fold affinity reduction to the Nir2 peptide, but a significant elimination of its binding to EphA4. 4 EphA4 and Nir2 peptide appear to have overlapped binding interfaces on the MSP domain, which strongly implies that two signaling networks may have a functional interplay in vivo. 5 As explored by both H/D exchange and MD simulations, the MSP domain is very dynamic, with most loop residues and many residues on secondary structures highly fluctuated or/and exposed to bulk solvent. Although T46I does not alter overall dynamics, it does trigger increased dynamics of several local regions of the MSP domain which are implicated in binding to EphA4 and Nir2 peptide. Our study provides the structural and dynamic understanding of the T46I-causing ALS; and strongly highlights the possibility that the interplay of two signaling networks mediated by the FFAT-containing proteins and Eph receptors may play a key role in ALS pathogenesis.

  7. A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A.

    Science.gov (United States)

    Sobieraj, M; Krzyśko, K A; Jarmuła, A; Kalinowski, M W; Lesyng, B; Prokopowicz, M; Cieśla, J; Gojdź, A; Kierdaszuk, B

    2015-04-01

    Predicting FRET pathways in proteins using computer simulation techniques is very important for reliable interpretation of experimental data. A novel and relatively simple methodology has been developed and applied to purine nucleoside phosphorylase (PNP) complexed with a fluorescent ligand - formycin A (FA). FRET occurs between an excited Tyr residue (D*) and FA (A). This study aims to interpret experimental data that, among others, suggests the absence of FRET for the PNPF159A mutant in complex with FA, based on novel theoretical methodology. MD simulations for the protein molecule containing D*, and complexed with A, are carried out. Interactions of D* with its molecular environment are accounted by including changes of the ESP charges in S1, compared to S0, and computed at the SCF-CI level. FRET probability W F depends on the inverse six-power of the D*-A distance, R da . The orientational factor 0 < k(2) < 4 between D* and A is computed and included in the analysis. Finally W F is time-averaged over the MD trajectories resulting in its mean value. The red-shift of the tyrosinate anion emission and thus lack of spectral overlap integral and thermal energy dissipation are the reasons for the FRET absence in the studied mutants at pH 7 and above. The presence of the tyrosinate anion results in a competitive energy dissipation channel and red-shifted emission, thus in consequence in the absence of FRET. These studies also indicate an important role of the phenyl ring of Phe159 for FRET in the wild-type PNP, which does not exist in the Ala159 mutant, and for the effective association of PNP with FA. In a more general context, our observations point out very interesting and biologically important properties of the tyrosine residue in its excited state, which may undergo spontaneous deprotonation in the biomolecular systems, resulting further in unexpected physical and/or biological phenomena. Until now, this observation has not been widely discussed in the

  8. Oil-soluble and water-soluble BTPhens and their europium complexes in octanol/water solutions: interface crossing studied by MD and PMF simulations.

    Science.gov (United States)

    Benay, G; Wipff, G

    2013-01-31

    Bistriazinyl-phenantroline "BTPhen" ligands L display the remarkable feature to complex trivalent lanthanide and actinide ions, with a marked selectivity for the latter. We report on molecular dynamics studies of tetrasubstituted X(4)BTPhens: L(4+) (X = (+)Et(3)NCH(2)-), L(4-) (X = (-)SO(3)Ph-), and L(0) (X = CyMe(4)) and their complexes with Eu(III) in binary octanol/water solutions. Changes in free energies upon interface crossing are also calculated for typical solutes by potential of mean force PMF simulations. The ligands and their complexes partition, as expected, to either the aqueous or the oil phase, depending on the "solubilizing" group X. Furthermore, most of them are found to be surface active. The water-soluble L(4+) and L(4-) ligands and their (L)Eu(NO(3))(3) complexes adsorb at the aqueous side of the interface, more with L(4-) than with L(4+). The oil soluble ligand L(0) is not surface active in its endo-endo form but adsorbs on the oil side of the interface in its most polar endo-exo form, as well as in its protonated L(0)H(+) and complexed (L(0))Eu(NO(3))(3) states. Furthermore, comparing PMFs of the Eu(III) complexes with and without nitric acid shows that acidifying the aqueous phase has different effects, depending on the ligand charge. In particular, acid promotes the Eu(III) extraction by L(0) via the (L(0))(2)Eu(NO(3))(2+) complex, as observed experimentally. Overall, the results point to the importance of interfacial adsorption for the liquid-liquid extraction of trivalent lanthanide and actinide cations by BTPhens and analogues.

  9. Spontaneous fission of 259Md

    International Nuclear Information System (INIS)

    Hulet, E.K.; Wild, J.F.; Lougheed, R.W.; Baisden, P.A.; Landrum, J.H.; Dougan, R.J.; Mustafa, M.; Ghiorso, A.; Nitschke, J.M.

    1979-01-01

    The mass and kinetic energy distributions of fission fragments from the spontaneous fission of th newly discovered nuclide 259 Md were obtained. 259 Md was identified as the E. C. daughter of 259 No, and was found to decay entirely (> 95%) by spontaneous fission with a 95-min half-life. From the kinetic energies measured for 397 pairs of coincident fragments, a mass distribution was derived that is symmetric with sigma = 13 amu. 259 Md, together with 258 Fm and 259 Fm, form a select group of three nuclides whose mass division in spontaneous fission is highly symmetric. Unlike the total-kinetic-energy (TKE) distributions of 258 Fm and 259 Fm, which peak at approx. = to 240 MeV, this distribution for 259 Md is broad and is 50 MeV lower in energy. Analysis of the mass and energy distributions shows that events near mass symmetry also exhibit a broad TKE distribution, with one-third of the symmetric events having TKEs less than 200 MeV. The associated of low TKEs with symmetric mass division in the fission of very heavy actinides is anomalous and inconsistent with theories based upon the emergence of fragment shells near the scission point. Either three-body fragmentation or peculiar fragment shapes are assumed as the cause for the large consumption of Coulomb energy observed for a significant fraction of symmetric fissions in 259 Md. 6 figures

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

    Science.gov (United States)

    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.

  11. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

    Science.gov (United States)

    Hofer, Thomas S.; Hünenberger, Philippe H.

    2018-06-01

    The absolute intrinsic hydration free energy GH+,w a t ◦ of the proton, the surface electric potential jump χwa t ◦ upon entering bulk water, and the absolute redox potential VH+,w a t ◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na+) and potassium (K+) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potential-summation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for GH+,w a t ◦, χwa t ◦, and VH+,w a t ◦, reported with statistical errors based on a confidence interval of 99%. The values obtained

  12. MD 2179: Scraping of off-momentum halo after injection

    CERN Document Server

    Garcia Morales, Hector; Patecki, Marcin; Wretborn, Sven Joel; CERN. Geneva. ATS Department

    2018-01-01

    In this MD, a beam scraping was performed using the momentum primary collimator in IR3 where dispersion is high. A second scraping was performed using a TCSG in IR7 where dispersion is almost negligible. In such a way, we aim to disentangle the contribution of off-momentum particles to halo population. These scrapings will provide useful information to better understand the usual off-momentum losses we see at the start of the ramp. The MD results would also be used to benchmark simulations of off-momentum beam losses in order to gain confidence in simulation models.

  13. Singaporean college students overpour drinks similar to Western populations: influence of peer presence in a simulated alcohol-pouring task.

    Science.gov (United States)

    Zandy, Shannon L; Pang, Joyce S; Ho, Moon-Ho Ringo; Matthews, Douglas B

    2013-11-01

    College drinking is a global health concern. However, most studies originate from countries with high alcohol consumption. In the United States, college students overpour a standard alcoholic drink, yet it is unclear if this remains true in countries with low alcohol consumption. Additionally, in college, peer influence is the greatest predictor of drinking behavior, yet it is unknown if social norms affect how students pour drinks. This study examined how male college students, in a country with low alcohol consumption, define standard drinks, and if the presence of an unfamiliar peer affects how students pour during a simulated alcohol-pouring task. Male undergraduate students (n = 105) underwent baseline assessments of impulsivity, self-monitoring, religiosity, and drinking characteristics. Participants poured fluid into empty cups of different sizes to equal a standard serving of beer or shot of liquor. There were 2 groups based on gender of experimenter. Within each group, participants were randomly assigned to Alone or Dyad condition. In the Alone condition, students were instructed to pour only for themselves. In the Dyad condition, students were instructed to pour for themselves and the experimenter. The volumes poured by the students were compared with standards used in Singapore and the United States. Collapsed across container size, students overpoured shots by 50% and beer by 100% when compared to the standard drink definition in Singapore. When using a more liberal definition, students overpoured beer by 25%, but did not overpour shots. In the presence of an unfamiliar peer, overpouring decreased by 10% for beer. The current data show that college students, in a country with low alcohol consumption, overestimate standard alcoholic drinks similar to their Western counterparts and use social norms to determine how much to pour for a drink when confronted with an unfamiliar peer. Efforts toward creating internationally recognized standard drink

  14. Developing improved MD codes for understanding processive cellulases

    International Nuclear Information System (INIS)

    Crowley, M F; Nimlos, M R; Himmel, M E; Uberbacher, E C; Iii, C L Brooks; Walker, R C

    2008-01-01

    The mechanism of action of cellulose-degrading enzymes is illuminated through a multidisciplinary collaboration that uses molecular dynamics (MD) simulations and expands the capabilities of MD codes to allow simulations of enzymes and substrates on petascale computational facilities. There is a class of glycoside hydrolase enzymes called cellulases that are thought to decrystallize and processively depolymerize cellulose using biochemical processes that are largely not understood. Understanding the mechanisms involved and improving the efficiency of this hydrolysis process through computational models and protein engineering presents a compelling grand challenge. A detailed understanding of cellulose structure, dynamics and enzyme function at the molecular level is required to direct protein engineers to the right modifications or to understand if natural thermodynamic or kinetic limits are in play. Much can be learned about processivity by conducting carefully designed molecular dynamics (MD) simulations of the binding and catalytic domains of cellulases with various substrate configurations, solvation models and thermodynamic protocols. Most of these numerical experiments, however, will require significant modification of existing code and algorithms in order to efficiently use current (terascale) and future (petascale) hardware to the degree of parallelism necessary to simulate a system of the size proposed here. This work will develop MD codes that can efficiently use terascale and petascale systems, not just for simple classical MD simulations, but also for more advanced methods, including umbrella sampling with complex restraints and reaction coordinates, transition path sampling, steered molecular dynamics, and quantum mechanical/molecular mechanical simulations of systems the size of cellulose degrading enzymes acting on cellulose

  15. Cavity Voltage Phase Modulation MD

    CERN Document Server

    Mastoridis, Themistoklis; Molendijk, John; Timko, Helga; CERN. Geneva. ATS Department

    2016-01-01

    The LHC RF/LLRF system is currently configured for extremely stable RF voltage to minimize transient beam loading effects. The present scheme cannot be extended beyond nominal beam current since the demanded power would exceed the peak klystron power and lead to saturation. A new scheme has therefore been proposed: for beam currents above nominal (and possibly earlier), the cavity phase modulation by the beam will not be corrected (transient beam loading), but the strong RF feedback and One-Turn Delay feedback will still be active for loop and beam stability in physics. To achieve this, the voltage set point will be adapted for each bunch. The goal of this MD was to test a new algorithm that would adjust the voltage set point to achieve the cavity phase modulation that would minimize klystron forward power.

  16. Similarity and Difference between the South Atlantic Convergence Zone and the Baiu Frontal Zone Simulated by an AGCM

    OpenAIRE

    Kozo, NINOMIYA; Frontier Research Center for Global Change, Japan Agency for Marine-Earth Science and Technology

    2007-01-01

    Features of the South Atlantic convergence zone (SACZ) and the Baiu frontal zone (BFZ) simulated by an AGCM (T106L56: a primitive equation spectral model which has 56 σ-levels and triangular spectral truncation at wave-number 106) are studied. The 24-year integration, from 1979 to 2002, by the model constrained by observed sea-surface temperature and sea-ice distribution, is used for this study. The detailed analysis is made for the typical case of SACZ and BFZ selected from data in 1985-1996...

  17. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

    Science.gov (United States)

    Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

    2017-10-12

    Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

  18. Molecular dynamics simulation of melting of finite and infinite size silicene

    OpenAIRE

    Min, Tjun Kit; Yoon, Tiem Leong; Lim, Thong Leng

    2017-01-01

    We report the melting temperature of free-standing silicene by carrying out molecular dynamics (MD) simulation experiments using optimzed Stillinger-Weber (SW) potential by Zhang {\\it et al.}. The melting scenario of a free-standing silicene is well captured visually in our MD simulations. The data are systematically analyzed using a few qualitatively different indicators, including caloric curve, radial distribution function and a numerical indicator known as `global similarity index'. The o...

  19. Property Analysis of Exfoliated Graphite Nanoplatelets Modified Asphalt Model Using Molecular Dynamics (MD Method

    Directory of Open Access Journals (Sweden)

    Hui Yao

    2017-01-01

    Full Text Available This Molecular Dynamics (MD simulation paper presents a physical property comparison study between exfoliated graphite nanoplatelets (xGNP modified and control asphalt models, including density, glass transition temperature, viscosity and thermal conductivity. The three-component control asphalt model consists of asphaltenes, aromatics, and saturates based on previous references. The xGNP asphalt model was built by incorporating an xGNP and control asphalt model and controlling mass ratios to represent the laboratory prepared samples. The Amber Cornell Extension Force Field (ACEFF was used with assigned molecular electro-static potential (ESP charge from NWChem analysis. After optimization and ensemble relaxation, the properties of the control and xGNP modified asphalt models were computed and analyzed using the MD method. The MD simulated results have a similar trend as the test results. The property analysis showed that: (1 the density of the xGNP modified model is higher than that of the control model; (2 the glass transition temperature of the xGNP modified model is closer to the laboratory data of the Strategic Highway Research Program (SHRP asphalt binders than that of the control model; (3 the viscosities of the xGNP modified model at different temperatures are higher than those of the control model, and it coincides with the trend in the laboratory data; (4 the thermal conductivities of the xGNP modified asphalt model are higher than those of the control asphalt model at different temperatures, and it is consistent with the trend in the laboratory data.

  20. First thoughts on MD priorities for 2012

    CERN Document Server

    Zimmermann, F; Assmann, R

    2012-01-01

    In 2012, 22 days of beam time will be allocated for LHC MDs. In this paper, after recalling the 2011 LHC MD experience, the MD rrequests for 2012 are reviewed. Three primary MD themes for 2012 can be identified: 1)pushing performance in 2012, 2)preparing for 2014/15, and 3)towards maximum luminosity. Example topics include emittance growth in collision or enhanced satellites for theme 1), 25 ns operation for 2), and ATS optics for 3). Structures lists of MD requests and topics for each theme as well as some initial thoughts on the MD priorities are presented. For certain topics, "start-of-fill MDs" are proposed in order to most efficiently use of the available beam time.

  1. Graphical user interface based computer simulation of self-similar modes of a paraxial slow self-focusing laser beam for saturating plasma nonlinearities

    International Nuclear Information System (INIS)

    Batra, Karuna; Mitra, Sugata; Subbarao, D.; Sharma, R.P.; Uma, R.

    2005-01-01

    The task for the present study is to make an investigation of self-similarity in a self-focusing laser beam both theoretically and numerically using graphical user interface based interactive computer simulation model in MATLAB (matrix laboratory) software in the presence of saturating ponderomotive force based and relativistic electron quiver based plasma nonlinearities. The corresponding eigenvalue problem is solved analytically using the standard eikonal formalism and the underlying dynamics of self-focusing is dictated by the corrected paraxial theory for slow self-focusing. The results are also compared with computer simulation of self-focusing by the direct fast Fourier transform based spectral methods. It is found that the self-similar solution obtained analytically oscillates around the true numerical solution equating it at regular intervals. The simulation results are the main ones although a feasible semianalytical theory under many assumptions is given to understand the process. The self-similar profiles are called as self-organized profiles (not in a strict sense), which are found to be close to Laguerre-Gaussian curves for all the modes, the shape being conserved. This terminology is chosen because it has already been shown from a phase space analysis that the width of an initially Gaussian beam undergoes periodic oscillations that are damped when any absorption is added in the model, i.e., the beam width converges to a constant value. The research paper also tabulates the specific values of the normalized phase shift for solutions decaying to zero at large transverse distances for first three modes which can, however, be extended to higher order modes

  2. MD2036: UFO Dynamics Studies and UFO Fast Detection

    CERN Document Server

    Belanger, Philippe; Valette, Matthieu; Lindstrom, Bjorn Hans Filip; Grob, Laura Katharina; Schmidt, Rudiger; Wollmann, Daniel

    2017-01-01

    UFOs are one of the remaining unknown related to LHC operation. Therefore, improving the understanding of UFO dynamics and validating the developed models against direct beam measurements is of fundamental importance in view of LHC operation at 7 TeV and with HL-LHC beam intensities. If not understood, UFOs could also be a showstopper for future machines such as FCC. This MD demonstrates new methods to study the dynamic behaviour of a calibrated UFO, simulated by the interaction of wire scanners with the beam. The events created during the MD were monitored using diamond BLMs in IR7, providing bunch-by-bunch resolution measurements. The analysis presented herein shows that blown-up bunches can be used to identify the plane of movement of UFOs, that bunch profiles and bunch sizes can be measured with dBLMs with good precision, that simulation of expected losses are in good agreement with measurements for oscillating bunches and that the space resolution of the acquisition system used during the MD is about 10 ...

  3. Visible implant elastomer (VIE) tagging and simulated predation risk elicit similar physiological stress responses in three-spined stickleback Gasterosteus aculeatus.

    Science.gov (United States)

    Fürtbauer, I; King, A J; Heistermann, M

    2015-05-01

    The effect of visible implant elastomer (VIE) tagging on the immediate physiological stress response was tested in female three-spined stickleback Gasterosteus aculeatus, using non-invasive waterborne cortisol analysis. Post-tagging cortisol levels were significantly higher compared with pretreatment baseline concentrations; however, when comparing post-tagging cortisol levels with cortisol levels after exposure to a simulated aerial predator, no significant differences were found. This study indicates that VIE tagging elicits a physiological stress response similar to those occurring in the everyday lives of this important biological model organism. © 2015 The Fisheries Society of the British Isles.

  4. Angiotensin II induces kidney inflammatory injury and fibrosis through binding to myeloid differentiation protein-2 (MD2).

    Science.gov (United States)

    Xu, Zheng; Li, Weixin; Han, Jibo; Zou, Chunpeng; Huang, Weijian; Yu, Weihui; Shan, Xiaoou; Lum, Hazel; Li, Xiaokun; Liang, Guang

    2017-03-21

    Growing evidence indicates that angiotensin II (Ang II), a potent biologically active product of RAS, is a key regulator of renal inflammation and fibrosis. In this study, we tested the hypothesis that Ang II induces renal inflammatory injury and fibrosis through interaction with myeloid differentiation protein-2 (MD2), the accessory protein of toll-like receptor 4 (TLR4) of the immune system. Results indicated that in MD2 -/- mice, the Ang II-induced renal fibrosis, inflammation and kidney dysfunction were significantly reduced compared to control Ang II-infused wild-type mice. Similarly, in the presence of small molecule MD2 specific inhibitor L6H21 or siRNA-MD2, the Ang II-induced increases of pro-fibrotic and pro-inflammatory molecules were prevented in tubular NRK-52E cells. MD2 blockade also inhibited activation of NF-κB and ERK. Moreover, MD2 blockade prevented the Ang II-stimulated formation of the MD2/TLR4/MyD88 signaling complex, as well as the increased surface binding of Ang II in NRK-52E cells. In addition, Ang II directly bound recombinant MD2 protein, rather than TLR4 protein. We conclude that MD2 is a significant contributor in the Ang II-induced kidney inflammatory injury in chronic renal diseases. Furthermore, MD2 inhibition could be a new and important therapeutic strategy for preventing progression of chronic renal diseases.

  5. Unification and extension of the similarity scaling criteria and mixing transition for studying astrophysics using high energy density laboratory experiments or numerial simulations

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Y

    2006-08-21

    The Euler similarity criteria for laboratory experiments and time-dependent mixing transition are important concepts introduced recently for application to prediction and analysis of astrophysical phenomena. However Euler scaling by itself provides no information on the distinctive spectral range of high Reynolds number turbulent flows found in astrophysics situations. On the other hand, time-dependent mixing transition gives no indication on whether a flow that just passed the mixing transition is sufficient to capture all of the significant dynamics of the complete astrophysical spectral range. In this paper, a new approach, based on additional insight gained from review of Navier-Stokes turbulence theory, is developed. It allows for revelations about the distinctive spectral scale dynamics associated with high Reynolds number astrophysical flows. From this perspective, we caution that the energy containing range of the turbulent flow measured in a laboratory setting must not be unintentionally contaminated in such a way that the interactive influences of this spectral scale range in the corresponding astrophysical situation cannot be faithfully represented. In this paper we introduce the concept of a minimum state as the lowest Reynolds number turbulent flow that a time-dependent mixing transition must achieve to fulfill this objective. Later in the paper we show that the Reynolds number of the minimum state may be determined as 1.6 x 10{sup 5}. Our efforts here can be viewed as a unification and extension of the concepts of both similarity scaling and transient mixing transition concepts. At the last the implications of our approach in planning future intensive laser experiments or massively parallel numerical simulations are discussed. A systematic procedure is outlined so that as the capabilities of the laser interaction experiments and supporting results from detailed numerical simulations performed in recently advanced supercomputing facilities increase

  6. Unification and extension of the similarity scaling criteria and mixing transition for studying astrophysics using high energy density laboratory experiments or numerical simulations

    International Nuclear Information System (INIS)

    Zhou Ye

    2007-01-01

    The Euler similarity criteria for laboratory experiments and time-dependent mixing transition are important concepts introduced recently for application to prediction and analysis of astrophysical phenomena. However, Euler scaling by itself provides no information on the distinctive spectral range of high Reynolds number turbulent flows found in astrophysics situations. On the other hand, time-dependent mixing transition gives no indication on whether a flow that just passed the mixing transition is sufficient to capture all of the significant dynamics of the complete astrophysical spectral range. In this paper, a new approach, based on additional insight gained from review of Navier-Stokes turbulence theory, is developed. It allows for revelations about the distinctive spectral scale dynamics associated with high Reynolds number astrophysical flows. From this perspective, the energy-containing range of the turbulent flow measured in a laboratory setting must not be unintentionally contaminated in such a way that the interactive influences of this spectral scale range in the corresponding astrophysical situation cannot be faithfully represented. In this paper, the concept of a minimum state is introduced as the lowest Reynolds number turbulent flow that a time-dependent mixing transition must achieve to fulfill this objective. Later in the paper, the Reynolds number of the minimum state is determined as 1.6x10 5 . The temporal criterion for the minimum state is also obtained. The efforts here can be viewed as a unification and extension of the concepts of both similarity scaling and transient mixing transition concepts. Finally, the implications of our approach in planning future intensive laser experiments or massively parallel numerical simulations are discussed. A systematic procedure is outlined so that as the capabilities of the laser interaction experiments and supporting results from detailed numerical simulations performed in recently advanced

  7. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields

    Czech Academy of Sciences Publication Activity Database

    Havrila, Marek; Zgarbová, M.; Jurečka, P.; Banáš, P.; Krepl, Miroslav; Otyepka, M.; Šponer, Jiří

    2015-01-01

    Roč. 119, č. 49 (2015), s. 15176-15190 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DIMERIZATION INITIATION SITE * QUANTUM-CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 3.187, year: 2015

  8. Simulation-based multiprofessional obstetric anaesthesia training conducted in situ versus off-site leads to similar individual and team outcomes: a randomised educational trial

    NARCIS (Netherlands)

    Sorensen, J.L.; Vleuten, C. van der; Rosthoj, S.; Ostergaard, D.; Leblanc, V.; Johansen, M.; Ekelund, K.; Starkopf, L.; Lindschou, J.; Gluud, C.; Weikop, P.; Ottesen, B.

    2015-01-01

    OBJECTIVE: To investigate the effect of in situ simulation (ISS) versus off-site simulation (OSS) on knowledge, patient safety attitude, stress, motivation, perceptions of simulation, team performance and organisational impact. DESIGN: Investigator-initiated single-centre randomised superiority

  9. 75 FR 47203 - Airworthiness Directives; McDonnell Douglas Corporation Model MD-11 and MD-11F Airplanes Equipped...

    Science.gov (United States)

    2010-08-05

    ... Airworthiness Directives; McDonnell Douglas Corporation Model MD- 11 and MD-11F Airplanes Equipped With General... Sec. 39.13 by adding the following new AD: 2010-16-03 McDonnell Douglas Corporation: Amendment 39... applies to McDonnell Douglas Corporation Model MD-11 and MD-11F airplanes, certified in any category...

  10. MD2190: Q" Stabilization during injection

    CERN Document Server

    Schenk, Michael; Li, Kevin Shing Bruce; Malina, Lukas; Metral, Elias; Tomas Garcia, Rogelio; CERN. Geneva. ATS Department

    2018-01-01

    This MD is a follow-up study of MD1831, where single bunches were stabilized against impedance-driven instabilities at 6.5 TeV in the LHC with Q''. The goals are (i) to explore whether an amplitude detuning free Q'' knob can be implemented at injection energy, and (ii) whether Q'' can provide beam stability at injection, where the beams suffer mostly from electron cloud effects. Ideally, this would relax the use of the Landau octupoles and may help in preserving the beam quality by reducing dynamic aperture limitations originating from the octupoles. The MD has been split into two parts: First, optics corrections were put in place to minimize beta-beating and linear coupling introduced by the knobs. The corrections were achieved by means of orbit bumps and skew quadrupole knobs. Machine safety was then validated with loss maps. While the betatron loss maps were approved, the off-momentum maps showed a priori unexpected losses in several arcs and the MD was stopped at this point for reasons of machine protecti...

  11. MD2725: 16L2 aperture measurement

    CERN Document Server

    Mirarchi, Daniele; Rossi, Roberto; CERN. Geneva. ATS Department

    2018-01-01

    Dumps induced by sudden increase of losses in the half-cell 16L2 have been a serious machine limitation during the 2017 run. The aim of this MD was to perform local aperture measurements in order to assess differences after the beam screen regeneration, compared to first measurements in 2017.

  12. Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-XL protein: clues for its ability to bind diverse BH3 ligands from MD simulations.

    Directory of Open Access Journals (Sweden)

    Dilraj Lama

    Full Text Available Bcl-XL is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-XL interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-XL were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-XL to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-XL remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-XL.

  13. MD-11 PCA - Research flight team photo

    Science.gov (United States)

    1995-01-01

    On Aug. 30, 1995, a the McDonnell Douglas MD-11 transport aircraft landed equipped with a computer-assisted engine control system that has the potential to increase flight safety. In landings at NASA Dryden Flight Research Center, Edwards, California, on August 29 and 30, the aircraft demonstrated software used in the aircraft's flight control computer that essentially landed the MD-11 without a need for the pilot to manipulate the flight controls significantly. In partnership with McDonnell Douglas Aerospace (MDA), with Pratt & Whitney and Honeywell helping to design the software, NASA developed this propulsion-controlled aircraft (PCA) system following a series of incidents in which hydraulic failures resulted in the loss of flight controls. This new system enables a pilot to operate and land the aircraft safely when its normal, hydraulically-activated control surfaces are disabled. This August 29, 1995, photo shows the MD-11 team. Back row, left to right: Tim Dingen, MDA pilot; John Miller, MD-11 Chief pilot (MDA); Wayne Anselmo, MD-11 Flight Test Engineer (MDA); Gordon Fullerton, PCA Project pilot; Bill Burcham, PCA Chief Engineer; Rudey Duran, PCA Controls Engineer (MDA); John Feather, PCA Controls Engineer (MDA); Daryl Townsend, Crew Chief; Henry Hernandez, aircraft mechanic; Bob Baron, PCA Project Manager; Don Hermann, aircraft mechanic; Jerry Cousins, aircraft mechanic; Eric Petersen, PCA Manager (Honeywell); Trindel Maine, PCA Data Engineer; Jeff Kahler, PCA Software Engineer (Honeywell); Steve Goldthorpe, PCA Controls Engineer (MDA). Front row, left to right: Teresa Hass, Senior Project Management Analyst; Hollie Allingham (Aguilera), Senior Project Management Analyst; Taher Zeglum, PCA Data Engineer (MDA); Drew Pappas, PCA Project Manager (MDA); John Burken, PCA Control Engineer.

  14. Molecular cloning and functional analysis of a blue light receptor gene MdCRY2 from apple (Malus domestica).

    Science.gov (United States)

    Li, Yuan-Yuan; Mao, Ke; Zhao, Cheng; Zhao, Xian-Yan; Zhang, Rui-Fen; Zhang, Hua-Lei; Shu, Huai-Rui; Hao, Yu-Jin

    2013-04-01

    MdCRY2 was isolated from apple fruit skin, and its function was analyzed in MdCRY2 transgenic Arabidopsis. The interaction between MdCRY2 and AtCOP1 was found by yeast two-hybrid and BiFC assays. Cryptochromes are blue/ultraviolet-A (UV-A) light receptors involved in regulating various aspects of plant growth and development. Investigations of the structure and functions of cryptochromes in plants have largely focused on Arabidopsis (Arabidopsis thaliana), tomato (Solanum lycopersicum), pea (Pisum sativum), and rice (Oryza sativa). However, no data on the function of CRY2 are available in woody plants. In this study, we isolated a cryptochrome gene, MdCRY2, from apple (Malus domestica). The deduced amino acid sequences of MdCRY2 contain the conserved N-terminal photolyase-related domain and the flavin adenine dinucleotide (FAD) binding domain, as well as the C-terminal DQXVP-acidic-STAES (DAS) domain. Relationship analysis indicates that MdCRY2 shows the highest similarity to the strawberry FvCRY protein. The expression of MdCRY2 is induced by blue/UV-A light, which represents a 48-h circadian rhythm. To investigate the function of MdCRY2, we overexpressed the MdCRY2 gene in a cry2 mutant and wild type (WT) Arabidopsis, assessed the phenotypes of the resulting transgenic plants, and found that MdCRY2 functions to regulate hypocotyl elongation, root growth, flower initiation, and anthocyanin accumulation. Furthermore, we examined the interaction between MdCRY2 and AtCOP1 using a yeast two-hybrid assay and a bimolecular fluorescence complementation assay. These data provide functional evidence for a role of blue/UV-A light-induced MdCRY2 in controlling photomorphogenesis in apple.

  15. Molecular Cloning and Expression Analysis of a Hexokinase Gene, MdHXK1 in Apple

    Directory of Open Access Journals (Sweden)

    Jin Zhao

    2016-03-01

    Full Text Available A hexokinase gene named MdHXK1 (MDP0000309677 was cloned from ‘Gala’ apple (Malus × domestica Borkh.. Sequence analysis showed that the MdHXK1 gene was 1 497 bp long and encoded 499 amino acids. The predicted molecular mass of this protein was 54.05 kD, and the pI was 5.76. A phylogenetic tree indicated apple MdHXK1 exhibited the highest sequence similarity to Pyrus bretschneideri PbHXK1. Analysis of the functional domain showed that the MdHXK1 protein included two conserved kinase domains. The prediction of subcellular localization suggested that the MdHXK1 protein was mainly localized in the cytoplasm. There was an indication that MdHXK1 existed as one copy in the apple genome by Southern blotting. Silico analysis suggested that the promoter sequence contained several typical cis-acting elements, including defense, sugar signaling and phytohormone responsive elements. Quantitative real-time PCR analysis demonstrated that the MdHXK1 gene was mainly expressed in stem and flower tissues. During the development of apple fruits, the expression of the MdHXK1 gene initially increased and then decreased. The changes on Glc phosphorylation relative activity and glucose concentration showed the same trend. In addition, the expression of this gene was induced by salt stress, low temperature, and abscisic acid (ABA. Finally, we obtained and purified the fused MdHXK1 protein by recombinant prokaryotic expression. Studies have demonstrated that MdHXK1 may participate in sugar metabolism in apple fruits. Enzyme encoded by MdHXK1 is a key factor in the mediation of sugar accumulation. Recently, researchers on hexokinase at home and abroad mainly focused on model plants, such as Arabidopsis, tobacco and rice, but orchard fruit like apple were underresearched. Our research established the foundation for the further study of the functions of MdHXK1.

  16. Exploring intentions of physician-scientist trainees: factors influencing MD and MD/PhD interest in research careers.

    Science.gov (United States)

    Kwan, Jennifer M; Daye, Dania; Schmidt, Mary Lou; Conlon, Claudia Morrissey; Kim, Hajwa; Gaonkar, Bilwaj; Payne, Aimee S; Riddle, Megan; Madera, Sharline; Adami, Alexander J; Winter, Kate Quinn

    2017-07-11

    Prior studies have described the career paths of physician-scientist candidates after graduation, but the factors that influence career choices at the candidate stage remain unclear. Additionally, previous work has focused on MD/PhDs, despite many physician-scientists being MDs. This study sought to identify career sector intentions, important factors in career selection, and experienced and predicted obstacles to career success that influence the career choices of MD candidates, MD candidates with research-intense career intentions (MD-RI), and MD/PhD candidates. A 70-question survey was administered to students at 5 academic medical centers with Medical Scientist Training Programs (MSTPs) and Clinical and Translational Science Awards (CTSA) from the NIH. Data were analyzed using bivariate or multivariate analyses. More MD/PhD and MD-RI candidates anticipated or had experienced obstacles related to balancing academic and family responsibilities and to balancing clinical, research, and education responsibilities, whereas more MD candidates indicated experienced and predicted obstacles related to loan repayment. MD/PhD candidates expressed higher interest in basic and translational research compared to MD-RI candidates, who indicated more interest in clinical research. Overall, MD-RI candidates displayed a profile distinct from both MD/PhD and MD candidates. MD/PhD and MD-RI candidates experience obstacles that influence their intentions to pursue academic medical careers from the earliest training stage, obstacles which differ from those of their MD peers. The differences between the aspirations of and challenges facing MD, MD-RI and MD/PhD candidates present opportunities for training programs to target curricula and support services to ensure the career development of successful physician-scientists.

  17. Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes MdSAUR37, MdPP2CH and MdALMTII.

    Science.gov (United States)

    Jia, Dongjie; Shen, Fei; Wang, Yi; Wu, Ting; Xu, Xuefeng; Zhang, Xinzhong; Han, Zhenhai

    2018-05-11

    Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, we identified four genome-wide major QTLs responsible for apple fruit acidity by MapQTL and BSA-seq analyses using two independent pedigree-based populations. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37, and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits. In addition, MdPP2CH inactivated three vacuolar H + -ATPases (MdVHA-A3, MdVHA-B2 and MdVHA-D2) and one aluminium-activated malate transporter (MdALMTII) via dephosphorylation and negatively influenced fruit malate accumulation. The dephosphotase activity of MdPP2CH was suppressed by MdSAUR37, which implied a higher hierarchy of genetic interaction. Therefore, the MdSAUR37/MdPP2CH/MdALMTII chain cascaded hierarchical epistatic genetic effects to precisely determine apple fruit malate content. An A/G SNP (-1010) on MdMYB44 promoter region from a major QTL (qtl08.1) was closely associated with fruit malate content. The predicted phenotype values (PPVs) were estimated using the tentative genotype values of the gene markers, and the PPVs were significantly correlated with the observed phenotype values. Our findings provide an insight into plant genome-based selection in apples and will aid in conducting research to understand the physiological fundamentals of quantitative genetics. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  18. MD on UFOs at MKIs and MKQs

    CERN Document Server

    Baer, T; Bartmann, W; Bracco, C; Carlier, E; Dehning, B; Garrel, N; Goddard, B; Jackson, S; Jimenez, M; Kain, V; Mertens, V; Misiowiec, M; Nordt, A; Papotti, G; Uythoven, J; Wenninger, J; Zerlauth, M; Zamantzas, C; Zimmermann, F

    2012-01-01

    UFOs ("Unidentified Falling Objects") are expected to be one of the major known performance limitation of the LHC. In this MD, the production mechanism and the dynamics of UFOs at the injection kicker magnets (MKIs) and the tune kicker magnets (MKQs) were studied. This was done by pulsing the MKIs and MKQs on a gap in the partly filled machine. During the MD, in total 58 UFO-type beam loss patterns were observed directly after pulsing the MKIs. None were observed after pulsing the MKQs, which provides important input for possible mitigation strategies. The temporal and spatial distribution of the UFO events could be determined by using a dedicated BLM Study Buffer, the implications for the UFO dynamics are discussed.

  19. Simulation-based multiprofessional obstetric anaesthesia training conducted in situ versus off-site leads to similar individual and team outcomes

    DEFF Research Database (Denmark)

    Sørensen, Jette Led; van der Vleuten, Cees; Rosthøj, Susanne

    2015-01-01

    choice question test. EXPLORATORY OUTCOMES: Individual outcomes: scores on the Safety Attitudes Questionnaire, stress measurements (State-Trait Anxiety Inventory, cognitive appraisal and salivary cortisol), Intrinsic Motivation Inventory and perceptions of simulations. Team outcome: video assessment......OBJECTIVE: To investigate the effect of in situ simulation (ISS) versus off-site simulation (OSS) on knowledge, patient safety attitude, stress, motivation, perceptions of simulation, team performance and organisational impact. DESIGN: Investigator-initiated single-centre randomised superiority...... educational trial. SETTING: Obstetrics and anaesthesiology departments, Rigshospitalet, University of Copenhagen, Denmark. PARTICIPANTS: 100 participants in teams of 10, comprising midwives, specialised midwives, auxiliary nurses, nurse anaesthetists, operating theatre nurses, and consultant doctors...

  20. Molecular dynamics simulation of impact test

    International Nuclear Information System (INIS)

    Akahoshi, Y.; Schmauder, S.; Ludwig, M.

    1998-01-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  1. Molecular dynamics simulation of impact test

    Energy Technology Data Exchange (ETDEWEB)

    Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

    1998-11-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  2. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

    DEFF Research Database (Denmark)

    Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

    2008-01-01

    . Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...

  3. MD Test of a Ballistic Optics

    CERN Document Server

    Garcia-Tabares Valdivieso, Ana; Salvachua Ferrando, Belen Maria; Skowronski, Piotr Krzysztof; Solfaroli Camillocci, Matteo; Tomas Garcia, Rogelio; Wenninger, Jorg; Coello De Portugal - Martinez Vazquez, Jaime Maria; CERN. Geneva. ATS Department

    2016-01-01

    The ballistic optics is designed to improve the understanding of optical errors and BPM systematic effects in the critical triplet region. The particularity of that optics is that the triplet is switched off, effectively transforming the triplets on both sides of IR1 and IR5 into drift spaces. Advantage can be taken from that fact to localize better errors in the Q4-Q5-triplet region. During this MD this new optics was tested for the first time at injection with beam 2.

  4. QM/MM-MD simulations of conjugated polyelectrolytes

    DEFF Research Database (Denmark)

    Sjöqvist, Jonas; Linares, Mathieu; Mikkelsen, Kurt Valentin

    2014-01-01

    A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field desc...

  5. Simulation-based multiprofessional obstetric anaesthesia training conducted in situ versus off-site leads to similar individual and team outcomes: a randomised educational trial

    Science.gov (United States)

    Sørensen, Jette Led; van der Vleuten, Cees; Rosthøj, Susanne; Østergaard, Doris; LeBlanc, Vicki; Johansen, Marianne; Ekelund, Kim; Starkopf, Liis; Lindschou, Jane; Gluud, Christian; Weikop, Pia; Ottesen, Bent

    2015-01-01

    Objective To investigate the effect of in situ simulation (ISS) versus off-site simulation (OSS) on knowledge, patient safety attitude, stress, motivation, perceptions of simulation, team performance and organisational impact. Design Investigator-initiated single-centre randomised superiority educational trial. Setting Obstetrics and anaesthesiology departments, Rigshospitalet, University of Copenhagen, Denmark. Participants 100 participants in teams of 10, comprising midwives, specialised midwives, auxiliary nurses, nurse anaesthetists, operating theatre nurses, and consultant doctors and trainees in obstetrics and anaesthesiology. Interventions Two multiprofessional simulations (clinical management of an emergency caesarean section and a postpartum haemorrhage scenario) were conducted in teams of 10 in the ISS versus the OSS setting. Primary outcome Knowledge assessed by a multiple choice question test. Exploratory outcomes Individual outcomes: scores on the Safety Attitudes Questionnaire, stress measurements (State-Trait Anxiety Inventory, cognitive appraisal and salivary cortisol), Intrinsic Motivation Inventory and perceptions of simulations. Team outcome: video assessment of team performance. Organisational impact: suggestions for organisational changes. Results The trial was conducted from April to June 2013. No differences between the two groups were found for the multiple choice question test, patient safety attitude, stress measurements, motivation or the evaluation of the simulations. The participants in the ISS group scored the authenticity of the simulation significantly higher than did the participants in the OSS group. Expert video assessment of team performance showed no differences between the ISS versus the OSS group. The ISS group provided more ideas and suggestions for changes at the organisational level. Conclusions In this randomised trial, no significant differences were found regarding knowledge, patient safety attitude, motivation or stress

  6. An unusual dimeric structure and assembly for TLR4 regulator RP105-MD-1

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Sung-il; Hong, Minsun; Wilson, Ian A [Scripps

    2011-11-16

    RP105-MD-1 modulates the TLR4-MD-2-mediated, innate immune response against bacterial lipopolysaccharide (LPS). The crystal structure of the bovine 1:1 RP105-MD-1 complex bound to a putative endogenous lipid at 2.9 Å resolution shares a similar overall architecture to its homolog TLR4-MD-2 but assembles into an unusual 2:2 homodimer that differs from any other known TLR-ligand assembly. The homodimer is assembled in a head-to-head orientation that juxtaposes the N-terminal leucine-rich repeats (LRRs) of the two RP105 chains, rather than the usual tail-to-tail configuration of C-terminal LRRs in ligand-activated TLR dimers, such as TLR1-TRL2, TLR2-TLR6, TLR3-TLR3 and TLR4-TLR4. Another unusual interaction is mediated by an RP105-specific asparagine-linked glycan, which wedges MD-1 into the co-receptor binding concavity on RP105. This unique mode of assembly represents a new paradigm for TLR complexes and suggests a molecular mechanism for regulating LPS responses.

  7. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

    Science.gov (United States)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  8. Shallow boron dopant on silicon An MD study

    International Nuclear Information System (INIS)

    Perez-Martin, A. Mari Carmen; Jimenez-Rodriguez, Jose J.; Jimenez-Saez, Jose Carlos

    2004-01-01

    Low energy boron bombardment of silicon has been simulated at room temperature by molecular dynamics (MD). Tersoff potential T3 was used in the simulation smoothly linked up with the universal potential. The boron-silicon (B-Si) interaction was simulated according to Tersoff potential for SiC but modified to account for the B-Si interaction. The algorithm can distinguish a B from a Si neighbour. Si-c, with (2 x 1) surface reconstruction, was bombarded with boron at 200 and 500 eV. These energies were initially chosen as good representative values of the low energy range. Reliable results require of a reasonable good statistic so that 1000-impact points were chosen uniformly distributed over a representative area of a 2 x 1 surface. The distribution of mean projected range for B is given. All kinds of point defect were looked for in a Si damaged target after bombardment. Energetically stable substitutional and interstitial configurations are presented and the relative appearances of the different types of interstitials, for both Si and B, are given. It is also determined the mean length of the distance to the first neighbours of defects

  9. MD-11 PCA - First Landing at Edwards

    Science.gov (United States)

    1995-01-01

    This McDonnell Douglas MD-11 approaches the first landing ever of a transport aircraft under engine power only on Aug. 29, 1995, at NASA's Dryden Flight Research Center, Edwards, California. The milestone flight, flown by NASA research pilot and former astronaut Gordon Fullerton, was part of a NASA project to develop a computer-assisted engine control system that enables a pilot to land a plane safely when it normal control surfaces are disabled. The Propulsion-Controlled Aircraft (PCA) system uses standard autopilot controls already present in the cockpit, together with the new programming in the aircraft's flight control computers. The PCA concept is simple--for pitch control, the program increases thrust to climb and reduces thrust to descend. To turn right, the autopilot increases the left engine thrust while decreasing the right engine thrust. The initial Propulsion-Controlled Aircraft studies by NASA were carried out at Dryden with a modified twin-engine F-15 research aircraft.

  10. MD-11 PCA - Research flight team egress

    Science.gov (United States)

    1995-01-01

    This McDonnell Douglas MD-11 has parked on the flightline at NASA's Dryden Flight Research Center, Edwards, California, following its completion of the first and second landings ever performed by a transport aircraft under engine power only (on Aug. 29, 1995). The milestone flight, with NASA research pilot and former astronaut Gordon Fullerton at the controls, was part of a NASA project to develop a computer-assisted engine control system that enables a pilot to land a plane safely when its normal control surfaces are disabled. Coming down the steps from the aircraft are Gordon Fullerton (in front), followed by Bill Burcham, Propulsion Controlled Aircraft (PCA) project engineer at Dryden; NASA Dryden controls engineer John Burken; John Feather of McDonnell Douglas; and Drew Pappas, McDonnell Douglas' project manager for PCA.

  11. An Efficient Hybrid DSMC/MD Algorithm for Accurate Modeling of Micro Gas Flows

    KAUST Repository

    Liang, Tengfei

    2013-01-01

    Aiming at simulating micro gas flows with accurate boundary conditions, an efficient hybrid algorithmis developed by combining themolecular dynamics (MD) method with the direct simulationMonte Carlo (DSMC)method. The efficiency comes from the fact that theMD method is applied only within the gas-wall interaction layer, characterized by the cut-off distance of the gas-solid interaction potential, to resolve accurately the gas-wall interaction process, while the DSMC method is employed in the remaining portion of the flow field to efficiently simulate rarefied gas transport outside the gas-wall interaction layer. A unique feature about the present scheme is that the coupling between the two methods is realized by matching the molecular velocity distribution function at the DSMC/MD interface, hence there is no need for one-toone mapping between a MD gas molecule and a DSMC simulation particle. Further improvement in efficiency is achieved by taking advantage of gas rarefaction inside the gas-wall interaction layer and by employing the "smart-wall model" proposed by Barisik et al. The developed hybrid algorithm is validated on two classical benchmarks namely 1-D Fourier thermal problem and Couette shear flow problem. Both the accuracy and efficiency of the hybrid algorithm are discussed. As an application, the hybrid algorithm is employed to simulate thermal transpiration coefficient in the free-molecule regime for a system with atomically smooth surface. Result is utilized to validate the coefficients calculated from the pure DSMC simulation with Maxwell and Cercignani-Lampis gas-wall interaction models. ©c 2014 Global-Science Press.

  12. Wettability of graphitic-carbon and silicon surfaces: MD modeling and theoretical analysis

    International Nuclear Information System (INIS)

    Ramos-Alvarado, Bladimir; Kumar, Satish; Peterson, G. P.

    2015-01-01

    The wettability of graphitic carbon and silicon surfaces was numerically and theoretically investigated. A multi-response method has been developed for the analysis of conventional molecular dynamics (MD) simulations of droplets wettability. The contact angle and indicators of the quality of the computations are tracked as a function of the data sets analyzed over time. This method of analysis allows accurate calculations of the contact angle obtained from the MD simulations. Analytical models were also developed for the calculation of the work of adhesion using the mean-field theory, accounting for the interfacial entropy changes. A calibration method is proposed to provide better predictions of the respective contact angles under different solid-liquid interaction potentials. Estimations of the binding energy between a water monomer and graphite match those previously reported. In addition, a breakdown in the relationship between the binding energy and the contact angle was observed. The macroscopic contact angles obtained from the MD simulations were found to match those predicted by the mean-field model for graphite under different wettability conditions, as well as the contact angles of Si(100) and Si(111) surfaces. Finally, an assessment of the effect of the Lennard-Jones cutoff radius was conducted to provide guidelines for future comparisons between numerical simulations and analytical models of wettability

  13. Orbit Feedback Operation with RCBX (MD 1209)

    CERN Document Server

    Wenninger, Jorg; Nisbet, David; Ponce, Laurette; Louro Alves, Diogo Miguel; CERN. Geneva. ATS Department

    2017-01-01

    The LHC Orbit Feedback (OFB) is able to drive any orbit corrector circuit (COD) to steer the LHC orbit. But during the first feedback tests in 2010, all attempts to use the common triplet orbit correctors (MCBX) failed because the QPS system installed to protect those magnets triggered power aborts as soon as the OFB steered the beam with those CODs. The reason was most likely the violation of the RCBX circuit acceleration limits. For this reason the MCBX orbit correctors were never driven by the OFB in regular operation. Although the performance of the OFB is generally excellent, the quality of the beam steering around IRs could be improved if the OFB could correct the orbit with the MCBX to counteract locally triplet quadrupole movements. The aim of this MD was to make a new attempt to use the MCBX in the OFB. The test was successful at injection (no circuit trip) and failed during the ramp (QPS power abort). The PC voltages and QPS Ures signals revealed the presence of voltage spikes with a period of 10~s...

  14. Simultaneous ion and neutral evaporation in aqueous nanodrops: experiment, theory, and molecular dynamics simulations.

    Science.gov (United States)

    Higashi, Hidenori; Tokumi, Takuya; Hogan, Christopher J; Suda, Hiroshi; Seto, Takafumi; Otani, Yoshio

    2015-06-28

    We use a combination of tandem ion mobility spectrometry (IMS-IMS, with differential mobility analyzers), molecular dynamics (MD) simulations, and analytical models to examine both neutral solvent (H2O) and ion (solvated Na(+)) evaporation from aqueous sodium chloride nanodrops. For experiments, nanodrops were produced via electrospray ionization (ESI) of an aqueous sodium chloride solution. Two nanodrops were examined in MD simulations: a 2500 water molecule nanodrop with 68 Na(+) and 60 Cl(-) ions (an initial net charge of z = +8), and (2) a 1000 water molecule nanodrop with 65 Na(+) and 60 Cl(-) ions (an initial net charge of z = +5). Specifically, we used MD simulations to examine the validity of a model for the neutral evaporation rate incorporating both the Kelvin (surface curvature) and Thomson (electrostatic) influences, while both MD simulations and experimental measurements were compared to predictions of the ion evaporation rate equation of Labowsky et al. [Anal. Chim. Acta, 2000, 406, 105-118]. Within a single fit parameter, we find excellent agreement between simulated and modeled neutral evaporation rates for nanodrops with solute volume fractions below 0.30. Similarly, MD simulation inferred ion evaporation rates are in excellent agreement with predictions based on the Labowsky et al. equation. Measurements of the sizes and charge states of ESI generated NaCl clusters suggest that the charge states of these clusters are governed by ion evaporation, however, ion evaporation appears to have occurred with lower activation energies in experiments than was anticipated based on analytical calculations as well as MD simulations. Several possible reasons for this discrepancy are discussed.

  15. 77 FR 5201 - Drawbridge Operation Regulation; Bear Creek, Dundalk, MD

    Science.gov (United States)

    2012-02-02

    ...-AA09 Drawbridge Operation Regulation; Bear Creek, Dundalk, MD AGENCY: Coast Guard, DHS. ACTION: Notice... operation of the Baltimore County highway bridge at Wise Avenue across Bear Creek, mile 3.4, between Dundalk... Avenue across Bear Creek, mile 3.4 between Dundalk and Sparrows Point, MD. This change would require the...

  16. MD290: Q4 IP6 Quench Level

    CERN Document Server

    Bednarek, Mateusz Jakub; Lechner, Anton; CERN. Geneva. ATS Department

    2016-01-01

    The detailed program proposed for the LHC Machine Development concerning a quench induced by fast losses on the MQY.4L6 quadrupole is presented. The merit of the MD, the necessary modifications of the machine protection systems are presented together with a preliminary analysis of the MD results.

  17. Chosen-Prefix Collisions for MD5 and Applications

    NARCIS (Netherlands)

    M.M.J. Stevens (Marc); A.K. Lenstra (Arjen); B. de Weger (Benne)

    2012-01-01

    textabstractWe present a novel, automated way to find differential paths for MD5. Its main application is in the construction of \\emph{chosen-prefix collisions}. We have shown how, at an approximate expected cost of $2^{39}$ calls to the MD5 compression function, for any two chosen

  18. Waiting time distribution in M/D/1 queueing systems

    DEFF Research Database (Denmark)

    Iversen, Villy Bæk; Staalhagen, Lars

    1999-01-01

    The well-known formula for the waiting time distribution of M/D/1 queueing systems is numerically unsuitable when the load is close to 1.0 and/or the results for a large waiting time are required. An algorithm for any load and waiting time is presented, based on the state probabilities of M/D/1...

  19. Temperature dependence of gafchromic MD-55 dosimeter

    International Nuclear Information System (INIS)

    Klassen, Norman V.; Zwan, Len van der; Cygler, Joanna

    1997-01-01

    Objective: Gafchromic MD-55 is a fairly new, thin film dosimeter that develops a blue color (λ max = 676 nm) when irradiated with ionizing radiation. The increase in absorbance is nearly proportional to the absorbed dose. MD-55 can be used for high precision dosimetry if care is taken to assure reproducible film orientation in the spectrophotometer as well as temperature control during both irradiation and reading. In order to achieve the maximum sensitivity of this dosimeter the readings of the optical density should be taken at λ max . It was reported for another type of Gafchromic film (DM-1260), that both λ max and ε max decrease with an increase in the temperature of the spectrophotometer. The purpose of this study was to characterize the reading temperature dependence of the new type of Gafchromic film available on the market and to find optimal conditions for using it for high precision dosimetry. Materials and Methods: Irradiations were carried out using 60 Co gamma rays from an Eldorado irradiator. The dosimeters were sandwiched in a lucite phantom with 4.4 mm build-up and irradiated in the center of a 10 cm x 10 cm field at 1 meter from the source. The temperature during irradiations was 22 deg. C. The dose rate was about 0.68 Gy/min. Measurements of optical density were made using a Cary 210 spectrophotometer. A bandpass of 3.5 nm was used. The temperature of the baseplate of the sample holder was regulated to +/-0.05 deg. C and measured by a probe lying on the baseplate. In all cases, values of OD were only recorded after they had come to a constant value, which was reached within 5 minutes of inserting the dosimeter into the sample chamber of the spectrophotometer. Results: The temperature dependence of the OD at 676 nm was measured in 2 studies using 6 dosimeters that had received 0, 1.0, 3.5, 6.2, 14.5 Gy. Readings were taken at 7 temperatures between 18.8 and 28.1 deg. C. By returning to the initial temperature several hours later, it was found

  20. Simulations

    CERN Document Server

    Ngada, Narcisse

    2015-06-15

    The complexity and cost of building and running high-power electrical systems make the use of simulations unavoidable. The simulations available today provide great understanding about how systems really operate. This paper helps the reader to gain an insight into simulation in the field of power converters for particle accelerators. Starting with the definition and basic principles of simulation, two simulation types, as well as their leading tools, are presented: analog and numerical simulations. Some practical applications of each simulation type are also considered. The final conclusion then summarizes the main important items to keep in mind before opting for a simulation tool or before performing a simulation.

  1. What's new in management discussion and analysis (MD and A)

    International Nuclear Information System (INIS)

    Bradley, N.M.

    1998-01-01

    Disclosure obligations under the management and discussion analysis (MD and A) with respect to uncertainties regarding the millennium bug were discussed from a legal perspective. The year 2000 problem stems from the use of only two digits to represent the year in the date field throughout most computer programs, rendering computers unable to differentiate between the year 1900 and the year 2000. Companies should be aware that specific requirements have been imposed by securities regulators in Canada and the United States over and above the general continuous disclosure requirements. These new requirements are designed to assist companies to minimize their liability, and at the same time to motivate them to make progress in their Y2K efforts. Details of CSA Staff Notice 41-301 and 51-302 entitled 'The year 2000 challenge - Disclosure issues' and similar U.S. Securities and Stock Exchange requirements are reviewed. Specific examples of Y2K disclosure issues in the Canadian petroleum industry are described. 23 refs

  2. The Structural Basis for Lipid and Endotoxin Binding in RP105-MD-1, and Consequences for Regulation of Host Lipopolysaccharide Sensitivity.

    Science.gov (United States)

    Ortiz-Suarez, Maite L; Bond, Peter J

    2016-01-05

    MD-1 is a member of the MD-2-related lipid-recognition (ML) family, and associates with RP105, a cell-surface protein that resembles Toll-like receptor 4 (TLR4). The RP105⋅MD-1 complex has been proposed to play a role in fine-tuning the innate immune response to endotoxin such as bacterial lipopolysaccharide (LPS) via TLR4⋅MD-2, but controversy surrounds its mechanism. We have used atomically detailed simulations to reveal the structural basis for ligand binding and consequent functional dynamics of MD-1 and the RP105 complex. We rationalize reports of endogenous phospholipid binding, by showing that they prevent collapse of the malleable MD-1 fold, before refining crystallographic models and uncovering likely binding modes for LPS analogs. Subsequent binding affinity calculations reveal that endotoxin specificity arises from the entropic cost of expanding the MD-1 cavity to accommodate bulky lipid tails, and support the role of MD-1 as a "sink" that sequesters endotoxin from TLR4 and stabilizes RP105/TLR4 interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Synergistic Applications of MD and NMR for the Study of Biological Systems

    Directory of Open Access Journals (Sweden)

    Olivier Fisette

    2012-01-01

    same time, theoretical and computational approaches gain in reliability and their field of application widens. In this short paper, we discuss recent advances in the areas of solution nuclear magnetic resonance (NMR spectroscopy and molecular dynamics (MD simulations that were made possible by the combination of both methods, that is, through their synergistic use. We present the main NMR observables and parameters that can be computed from simulations, and how they are used in a variety of complementary applications, including dynamics studies, model-free analysis, force field validation, and structural studies.

  4. A New Trajectory Similarity Measure for GPS Data

    KAUST Repository

    Ismail, Anas; Vigneron, Antoine E.

    2016-01-01

    We present a new algorithm for measuring the similarity between trajectories, and in particular between GPS traces. We call this new similarity measure the Merge Distance (MD). Our approach is robust against subsampling and supersampling. We perform experiments to compare this new similarity measure with the two main approaches that have been used so far: Dynamic Time Warping (DTW) and the Euclidean distance. © 2015 ACM.

  5. A New Trajectory Similarity Measure for GPS Data

    KAUST Repository

    Ismail, Anas

    2016-08-08

    We present a new algorithm for measuring the similarity between trajectories, and in particular between GPS traces. We call this new similarity measure the Merge Distance (MD). Our approach is robust against subsampling and supersampling. We perform experiments to compare this new similarity measure with the two main approaches that have been used so far: Dynamic Time Warping (DTW) and the Euclidean distance. © 2015 ACM.

  6. Preparing MD-PhD students for clinical rotations: navigating the interface between PhD and MD training.

    Science.gov (United States)

    Goldberg, Charles; Insel, Paul A

    2013-06-01

    Many aspects of MD-PhD training are not optimally designed to prepare students for their future roles as translational clinician-scientists. The transition between PhD research efforts and clinical rotations is one hurdle that must be overcome. MD-PhD students have deficits in clinical skills compared with those of their MD-only colleagues at the time of this transition. Reimmersion programs (RPs) targeted to MD-PhD students have the potential to help them navigate this transition.The authors draw on their experience creating and implementing an RP that incorporates multiple types of activities (clinical exam review, objective structured clinical examination, and supervised practice in patient care settings) designed to enhance the participants' skills and readiness for clinical efforts. On the basis of this experience, they note that MD-PhD students' time away from the clinical environment negatively affects their clinical skills, causing them to feel underprepared for clinical rotations. The authors argue that participation in an RP can help students feel more comfortable speaking with and examining patients and decrease their anxiety regarding clinical encounters. The authors propose that RPs can have positive outcomes for improving the transition from PhD to clinical MD training in dual-degree programs. Identifying and addressing this and other transitions need to be considered to improve the educational experience of MD-PhD students.

  7. MD1003 (high-dose biotin) for the treatment of progressive multiple sclerosis: A randomised, double-blind, placebo-controlled study.

    Science.gov (United States)

    Tourbah, Ayman; Lebrun-Frenay, Christine; Edan, Gilles; Clanet, Michel; Papeix, Caroline; Vukusic, Sandra; De Sèze, Jerome; Debouverie, Marc; Gout, Olivier; Clavelou, Pierre; Defer, Gilles; Laplaud, David-Axel; Moreau, Thibault; Labauge, Pierre; Brochet, Bruno; Sedel, Frédéric; Pelletier, Jean

    2016-11-01

    Treatment with MD1003 (high-dose biotin) showed promising results in progressive multiple sclerosis (MS) in a pilot open-label study. To confirm the efficacy and safety of MD1003 in progressive MS in a double-blind, placebo-controlled study. Patients (n = 154) with a baseline Expanded Disability Status Scale (EDSS) score of 4.5-7 and evidence of disease worsening within the previous 2 years were randomised to 12-month MD1003 (100 mg biotin) or placebo thrice daily, followed by 12-month MD1003 for all patients. The primary endpoint was the proportion of patients with disability reversal at month 9, confirmed at month 12, defined as an EDSS decrease of ⩾1 point (⩾0.5 for EDSS 6-7) or a ⩾20% decrease in timed 25-foot walk time compared with the best baseline among screening or randomisation visits. A total of 13 (12.6%) MD1003-treated patients achieved the primary endpoint versus none of the placebo-treated patients (p = 0.005). MD1003 treatment also reduced EDSS progression and improved clinical impression of change compared with placebo. Efficacy was maintained over follow-up, and the safety profile of MD1003 was similar to that of placebo. MD1003 achieves sustained reversal of MS-related disability in a subset of patients with progressive MS and is well tolerated. © The Author(s), 2016.

  8. MD and FFM Electron Broadening for Warm and Dense Hydrogen Plasmas

    International Nuclear Information System (INIS)

    Ferri, S.; Calisti, A.; Mosse, C.; Talin, B.; Gonzalez, M. A.; Gigosos, M. A.

    2006-01-01

    Direct integration of the semi-classical evolution equation based on Molecular Dynamics simulations (MD) and the Frequency Fluctuation Model (FFM) have long been used to synthesize spectra accounting for ion dynamics. Cross comparisons of these approaches generally show results in good agreement. Recently, interest in low temperature (Te ∼ 1eV) and high density (Ne ∼ 1018 cm-3) hydrogen plasma spectroscopy has motivated extended applications of FFM. Arising discrepancies were found to originate in electron collision operators suggesting an improper use of impact approximations for warm and dense plasma conditions. In order to clarify this point, new useful cross comparisons between MD and FFM have been carried out for electron broadening

  9. A COMPARISON OF SEMANTIC SIMILARITY MODELS IN EVALUATING CONCEPT SIMILARITY

    Directory of Open Access Journals (Sweden)

    Q. X. Xu

    2012-08-01

    Full Text Available The semantic similarities are important in concept definition, recognition, categorization, interpretation, and integration. Many semantic similarity models have been established to evaluate semantic similarities of objects or/and concepts. To find out the suitability and performance of different models in evaluating concept similarities, we make a comparison of four main types of models in this paper: the geometric model, the feature model, the network model, and the transformational model. Fundamental principles and main characteristics of these models are introduced and compared firstly. Land use and land cover concepts of NLCD92 are employed as examples in the case study. The results demonstrate that correlations between these models are very high for a possible reason that all these models are designed to simulate the similarity judgement of human mind.

  10. 75 FR 80744 - Airworthiness Directives; McDonnell Douglas Corporation Model DC-9-81 (MD-81), DC-9-82 (MD-82...

    Science.gov (United States)

    2010-12-23

    ...-1203; Directorate Identifier 2010-NM-168-AD] RIN 2120-AA64 Airworthiness Directives; McDonnell Douglas... amends Sec. 39.13 by adding the following new airworthiness directive (AD): McDonnell Douglas Corporation... Douglas Corporation Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD-83), DC-9-87 (MD-87) and MD-88...

  11. Annual International Meeting on Medical Simulation (5th); Simulating Change Together, Held at the Radisson Miami Florida, on January 13-16, 2005

    Science.gov (United States)

    2005-02-01

    Challenging Superiors in the Healthcare Environment: The Two-Challenge Center for Medical Simulation Rule IMMS Singh Shashank Trauma and Awareness Pen...Rochester * Dallas Rochester MN Rochester NY Dallas TX SMartin Eason MD JD Marc Horowitz MD - Swati Argarwal, MD ETSU University of NM Stanford...Murphy, MD Simluation-based training allows educators in medicine to finally Swati Argarwal, MD address the needs of the adult learner. This high

  12. Milestone report on MD potential development for uranium silicide

    International Nuclear Information System (INIS)

    Yu, Jianguo; Zhang, Yongfeng; Hales, Jason Dean

    2016-01-01

    This report summarizes the progress on the interatomic potential development of triuranium-disilicide (U 3 Si 2 ) for molecular dynamics (MD) simulations. The development is based on the Tersoff type potentials for single element U and Si. The Si potential is taken from the literature and a Tersoff type U potential is developed in this project. With the primary focus on the U 3 Si 2 phase, some other U-Si systems such as U 3 Si are also included as a test of the transferability of the potentials for binary U-Si phases. Based on the potentials for unary U and Si, two sets of parameters for the binary U-Si system are developed using the Tersoff mixing rules and the cross-term fitting, respectively. The cross-term potential is found to give better results on the enthalpy of formation, lattice constants and elastic constants than those produced by the Tersoff mixing potential, with the reference data taken from either experiments or density functional theory (DFT) calculations. In particular, the results on the formation enthalpy and lattice constants for the U 3 Si 2 phase and lattice constants for the high temperature U 3 Si (h-U 3 Si) phase generated by the cross-term potential agree well with experimental data. Reasonable agreements are also reached on the elastic constants of U 3 Si 2 , on the formation enthalpy for the low temperature U 3 Si (m-U 3 Si) and h-U 3 Si phases, and on the lattice constants of m-U 3 Si phase. All these phases are predicted to be mechanically stable. The unary U potential is tested for three metallic U phases (α, β, γ). The potential is found capable to predict the cohesive energies well against experimental data for all three phases. It matches reasonably with previous experiments on the lattice constants and elastic constants of αU.

  13. Fluids density functional theory and initializing molecular dynamics simulations of block copolymers

    Science.gov (United States)

    Brown, Jonathan R.; Seo, Youngmi; Maula, Tiara Ann D.; Hall, Lisa M.

    2016-03-01

    Classical, fluids density functional theory (fDFT), which can predict the equilibrium density profiles of polymeric systems, and coarse-grained molecular dynamics (MD) simulations, which are often used to show both structure and dynamics of soft materials, can be implemented using very similar bead-based polymer models. We aim to use fDFT and MD in tandem to examine the same system from these two points of view and take advantage of the different features of each methodology. Additionally, the density profiles resulting from fDFT calculations can be used to initialize the MD simulations in a close to equilibrated structure, speeding up the simulations. Here, we show how this method can be applied to study microphase separated states of both typical diblock and tapered diblock copolymers in which there is a region with a gradient in composition placed between the pure blocks. Both methods, applied at constant pressure, predict a decrease in total density as segregation strength or the length of the tapered region is increased. The predictions for the density profiles from fDFT and MD are similar across materials with a wide range of interfacial widths.

  14. Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding.

    Directory of Open Access Journals (Sweden)

    Aruna Rajan

    2010-04-01

    Full Text Available Recent advances in computing technology have enabled microsecond long all-atom molecular dynamics (MD simulations of biological systems. Methods that can distill the salient features of such large trajectories are now urgently needed. Conventional clustering methods used to analyze MD trajectories suffer from various setbacks, namely (i they are not data driven, (ii they are unstable to noise and changes in cut-off parameters such as cluster radius and cluster number, and (iii they do not reduce the dimensionality of the trajectories, and hence are unsuitable for finding collective coordinates. We advocate the application of principal component analysis (PCA and a non-metric multidimensional scaling (nMDS method to reduce MD trajectories and overcome the drawbacks of clustering. To illustrate the superiority of nMDS over other methods in reducing data and reproducing salient features, we analyze three complete villin headpiece folding trajectories. Our analysis suggests that the folding process of the villin headpiece is structurally heterogeneous.

  15. New Similarity Functions

    DEFF Research Database (Denmark)

    Yazdani, Hossein; Ortiz-Arroyo, Daniel; Kwasnicka, Halina

    2016-01-01

    spaces, in addition to their similarity in the vector space. Prioritized Weighted Feature Distance (PWFD) works similarly as WFD, but provides the ability to give priorities to desirable features. The accuracy of the proposed functions are compared with other similarity functions on several data sets....... Our results show that the proposed functions work better than other methods proposed in the literature....

  16. Phoneme Similarity and Confusability

    Science.gov (United States)

    Bailey, T.M.; Hahn, U.

    2005-01-01

    Similarity between component speech sounds influences language processing in numerous ways. Explanation and detailed prediction of linguistic performance consequently requires an understanding of these basic similarities. The research reported in this paper contrasts two broad classes of approach to the issue of phoneme similarity-theoretically…

  17. Serpins in fruit and vegetative tissues of apple (Malus domestica): expression of four serpins with distinct reactive centres and characterisation of a major inhibitory seed form, MdZ1b

    DEFF Research Database (Denmark)

    Hejgaard, Jørn; Laing, W.A.; Marttila, S.

    2005-01-01

    in a wide variety of tissues, including developing and mature fruits, seeds and vegetative buds as well as developing, mature and senescing leaves. Analysis of 46 sequences, most full-length, identified serpins with four distinct reactive centres belonging to two subfamilies (MdZ1 and MdZ2) with similar...

  18. 3MdB: the Mexican Million Models database

    Science.gov (United States)

    Morisset, C.; Delgado-Inglada, G.

    2014-10-01

    The 3MdB is an original effort to construct a large multipurpose database of photoionization models. This is a more modern version of a previous attempt based on Cloudy3D and IDL tools. It is accessed by MySQL requests. The models are obtained using the well known and widely used Cloudy photoionization code (Ferland et al, 2013). The database is aimed to host grids of models with different references to identify each project and to facilitate the extraction of the desired data. We present here a description of the way the database is managed and some of the projects that use 3MdB. Anybody can ask for a grid to be run and stored in 3MdB, to increase the visibility of the grid and the potential side applications of it.

  19. Methodological issues in lipid bilayer simulations

    NARCIS (Netherlands)

    Anezo, C; de Vries, AH; Holtje, HD; Tieleman, DP; Marrink, SJ

    2003-01-01

    Methodological issues in molecular dynamics (MD) simulations, such as the treatment of long-range electrostatic interactions or the type of pressure coupling, have important consequences for the equilibrium properties observed. We report a series of long (up to 150 ns) MD simulations of

  20. Report from LHC MD 2171: Amplitude dependent closest tune approach from normal and skew octupoles

    CERN Document Server

    Maclean, Ewen Hamish; Persson, Tobias Hakan Bjorn; Carlier, Felix Simon; CERN. Geneva. ATS Department

    2018-01-01

    Simulation-based studies predict significant amplitude-dependent closest tune approach can be generated by skew octupole sources in conjunction with their normal octupolar counterparts. This has the potential to significantly influence Landau damping at small β∗, where skew octupole errors in the experimental IRs, together with b4 introduced by the Landau octupoles, is predicted to cause large distortion of the tune footprint. This MD aimed to perform a first exploration of these predictions with beam, by enhancing skew octupole sources in the IRs at injection and measuring amplitude detuning with free kicks in the plane approaching the coupling resonance.

  1. Swiss national MD-PhD-program: an outcome analysis.

    Science.gov (United States)

    Kuehnle, Katrin; Winkler, David T; Meier-Abt, Peter J

    2009-09-19

    This study aims at a first evaluation of the outcome of the Swiss national MD-PhD program during the last 16 years. One hundred and twenty six former and current students in the Swiss national MD-PhD program were surveyed via a Web-based questionnaire in September 2007. Twenty-four questions assessed information regarding participant demographics, information on the PhD thesis and publication activity, current positions and research activity, as well as participant's opinions, attitudes and career goals. Eighty questionnaires were received from 126 MD-PhD students and graduates (63.5% response rate). The responders consisted of present students (36%), former graduates (56%), and dropouts (8%). The percentage of women in the program was 23%, and the average duration of the program was 4.2 +/- 1.4 years. Research interests were predominantly in the fields of neuroscience, immunology, molecular biology and cancer research. A considerable portion of the MD-PhD graduates had an excellent publication record stemming from their PhD research work, and 89% were planning to continue a research-orientated career. Over 50% of those MD-PhD graduates completing their thesis before 2002 had already reached an assistant or full professor position at the time of the survey. Nearly all participants considered the MD-PhD training helpful to their career and high quality standards were assigned to the acquired practical and intellectual skills. However, criticism was expressed concerning the general mentoring and the career related mentoring. Moreover, general mentoring and career related mentoring were significantly less well perceived in research groups employing more than seven PhD students at the same time. The MD-PhD students and graduates surveyed were satisfied with their education and most of them continued a research-orientated career. Regarding the overall positive evaluation, this study supports the view that MD-PhD graduates are well qualified for a successful career in

  2. BayesMD: flexible biological modeling for motif discovery

    DEFF Research Database (Denmark)

    Tang, Man-Hung Eric; Krogh, Anders; Winther, Ole

    2008-01-01

    We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained on trans......We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained...

  3. Comparative simulations of microjetting using atomistic and continuous approaches in the presence of viscosity and surface tension

    Science.gov (United States)

    Durand, O.; Jaouen, S.; Soulard, L.; Heuzé, O.; Colombet, L.

    2017-10-01

    We compare, at similar scales, the processes of microjetting and ejecta production from shocked roughened metal surfaces by using atomistic and continuous approaches. The atomistic approach is based on very large scale molecular dynamics (MD) simulations with systems containing up to 700 × 106 atoms. The continuous approach is based on Eulerian hydrodynamics simulations with adaptive mesh refinement; the simulations take into account the effects of viscosity and surface tension, and the equation of state is calculated from the MD simulations. The microjetting is generated by shock-loading above its fusion point a three-dimensional tin crystal with an initial sinusoidal free surface perturbation, the crystal being set in contact with a vacuum. Several samples with homothetic wavelengths and amplitudes of defect are simulated in order to investigate the influence of viscosity and surface tension of the metal. The simulations show that the hydrodynamic code reproduces with very good agreement the profiles, calculated from the MD simulations, of the ejected mass and velocity along the jet. Both codes also exhibit a similar fragmentation phenomenology of the metallic liquid sheets ejected, although the fragmentation seed is different. We show in particular, that it depends on the mesh size in the continuous approach.

  4. Apple MdACS6 Regulates Ethylene Biosynthesis During Fruit Development Involving Ethylene-Responsive Factor.

    Science.gov (United States)

    Li, Tong; Tan, Dongmei; Liu, Zhi; Jiang, Zhongyu; Wei, Yun; Zhang, Lichao; Li, Xinyue; Yuan, Hui; Wang, Aide

    2015-10-01

    Ethylene biosynthesis in plants involves different 1-aminocyclopropane-1-carboxylic acid synthase (ACS) genes. The regulation of each ACS gene during fruit development is unclear. Here, we characterized another apple (Malus×domestica) ACS gene, MdACS6. The transcript of MdACS6 was observed not only in fruits but also in other tissues. During fruit development, MdACS6 was initiated at a much earlier stage, whereas MdACS3a and MdACS1 began to be expressed at 35 d before harvest and immediateley after harvest, respectively. Moreover, the enzyme activity of MdACS6 was significantly lower than that of MdACS3a and MdACS1, accounting for the low ethylene biosynthesis in young fruits. Overexpression of MdACS6 (MdACS6-OE) by transient assay in apple showed enhanced ethylene production, and MdACS3a was induced in MdACS6-OE fruits but not in control fruits. In MdACS6 apple fruits silenced by the virus-induced gene silencing (VIGS) system (MdACS6-AN), neither ethylene production nor MdACS3a transcript was detectable. In order to explore the mechanism through which MdACS3a was induced in MdACS6-OE fruits, we investigated the expression of apple ethylene-responsive factor (ERF) genes. The results showed that the expression of MdERF2 was induced in MdACS6-OE fruits and inhibited in MdACS6-AN fruits. Yeast one-hybrid assay showed that MdERF2 protein could bind to the promoter of MdACS3a. Moreover, down-regulation of MdERF2 in apple flesh callus led to a decrease of MdACS3a expression, demonstrating the regulation of MdERF2 on MdACS3a. The mechanism through which MdACS6 regulates the action of MdACS3a was discussed. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  5. Molecular similarity measures.

    Science.gov (United States)

    Maggiora, Gerald M; Shanmugasundaram, Veerabahu

    2011-01-01

    Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.

  6. Apple (Malus domestica) MdERF2 negatively affects ethylene biosynthesis during fruit ripening by suppressing MdACS1 transcription.

    Science.gov (United States)

    Li, Tong; Jiang, Zhongyu; Zhang, Lichao; Tan, Dongmei; Wei, Yun; Yuan, Hui; Li, Tianlai; Wang, Aide

    2016-12-01

    Ripening in climacteric fruit requires the gaseous phytohormone ethylene. Although ethylene signaling has been well studied, knowledge of the transcriptional regulation of ethylene biosynthesis is still limited. Here we show that an apple (Malus domestica) ethylene response factor, MdERF2, negatively affects ethylene biosynthesis and fruit ripening by suppressing the transcription of MdACS1, a gene that is critical for biosynthesis of ripening-related ethylene. Expression of MdERF2 was suppressed by ethylene during ripening of apple fruit, and we observed that MdERF2 bound to the promoter of MdACS1 and directly suppressed its transcription. Moreover, MdERF2 suppressed the activity of the promoter of MdERF3, a transcription factor that we found to bind to the MdACS1 promoter, thereby increasing MdACS1 transcription. We determined that the MdERF2 and MdERF3 proteins directly interact, and this interaction suppresses the binding of MdERF3 to the MdACS1 promoter. Moreover, apple fruit with transiently downregulated MdERF2 expression showed higher ethylene production and faster ripening. Our results indicate that MdERF2 negatively affects ethylene biosynthesis and fruit ripening in apple by suppressing the transcription of MdACS1 via multiple mechanisms, thereby acting as an antagonist of positive ripening regulators. Our findings offer a deep understanding of the transcriptional regulation of ethylene biosynthesis during climacteric fruit ripening. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  7. Sex similarities and differences in risk factors for recurrence of major depression.

    Science.gov (United States)

    van Loo, Hanna M; Aggen, Steven H; Gardner, Charles O; Kendler, Kenneth S

    2017-11-27

    Major depression (MD) occurs about twice as often in women as in men, but it is unclear whether sex differences subsist after disease onset. This study aims to elucidate potential sex differences in rates and risk factors for MD recurrence, in order to improve prediction of course of illness and understanding of its underlying mechanisms. We used prospective data from a general population sample (n = 653) that experienced a recent episode of MD. A diverse set of potential risk factors for recurrence of MD was analyzed using Cox models subject to elastic net regularization for males and females separately. Accuracy of the prediction models was tested in same-sex and opposite-sex test data. Additionally, interactions between sex and each of the risk factors were investigated to identify potential sex differences. Recurrence rates and the impact of most risk factors were similar for men and women. For both sexes, prediction models were highly multifactorial including risk factors such as comorbid anxiety, early traumas, and family history. Some subtle sex differences were detected: for men, prediction models included more risk factors concerning characteristics of the depressive episode and family history of MD and generalized anxiety, whereas for women, models included more risk factors concerning early and recent adverse life events and socioeconomic problems. No prominent sex differences in risk factors for recurrence of MD were found, potentially indicating similar disease maintaining mechanisms for both sexes. Course of MD is a multifactorial phenomenon for both males and females.

  8. Similarity Measure of Graphs

    Directory of Open Access Journals (Sweden)

    Amine Labriji

    2017-07-01

    Full Text Available The topic of identifying the similarity of graphs was considered as highly recommended research field in the Web semantic, artificial intelligence, the shape recognition and information research. One of the fundamental problems of graph databases is finding similar graphs to a graph query. Existing approaches dealing with this problem are usually based on the nodes and arcs of the two graphs, regardless of parental semantic links. For instance, a common connection is not identified as being part of the similarity of two graphs in cases like two graphs without common concepts, the measure of similarity based on the union of two graphs, or the one based on the notion of maximum common sub-graph (SCM, or the distance of edition of graphs. This leads to an inadequate situation in the context of information research. To overcome this problem, we suggest a new measure of similarity between graphs, based on the similarity measure of Wu and Palmer. We have shown that this new measure satisfies the properties of a measure of similarities and we applied this new measure on examples. The results show that our measure provides a run time with a gain of time compared to existing approaches. In addition, we compared the relevance of the similarity values obtained, it appears that this new graphs measure is advantageous and  offers a contribution to solving the problem mentioned above.

  9. Processes of Similarity Judgment

    Science.gov (United States)

    Larkey, Levi B.; Markman, Arthur B.

    2005-01-01

    Similarity underlies fundamental cognitive capabilities such as memory, categorization, decision making, problem solving, and reasoning. Although recent approaches to similarity appreciate the structure of mental representations, they differ in the processes posited to operate over these representations. We present an experiment that…

  10. Judgments of brand similarity

    NARCIS (Netherlands)

    Bijmolt, THA; Wedel, M; Pieters, RGM; DeSarbo, WS

    This paper provides empirical insight into the way consumers make pairwise similarity judgments between brands, and how familiarity with the brands, serial position of the pair in a sequence, and the presentation format affect these judgments. Within the similarity judgment process both the

  11. Milestone report on MD potential development for uranium silicide

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Jianguo [Idaho National Lab. (INL), Idaho Falls, ID (United States). Fuel Modeling and Simulation Dept.; Zhang, Yongfeng [Idaho National Lab. (INL), Idaho Falls, ID (United States). Fuel Modeling and Simulation Dept.; Hales, Jason Dean [Idaho National Lab. (INL), Idaho Falls, ID (United States). Fuel Modeling and Simulation Dept.

    2016-03-01

    This report summarizes the progress on the interatomic potential development of triuranium-disilicide (U3Si2) for molecular dynamics (MD) simulations. The development is based on the Tersoff type potentials for single element U and Si. The Si potential is taken from the literature and a Tersoff type U potential is developed in this project. With the primary focus on the U3Si2 phase, some other U-Si systems such as U3Si are also included as a test of the transferability of the potentials for binary U-Si phases. Based on the potentials for unary U and Si, two sets of parameters for the binary U-Si system are developed using the Tersoff mixing rules and the cross-term fitting, respectively. The cross-term potential is found to give better results on the enthalpy of formation, lattice constants and elastic constants than those produced by the Tersoff mixing potential, with the reference data taken from either experiments or density functional theory (DFT) calculations. In particular, the results on the formation enthalpy and lattice constants for the U3Si2 phase and lattice constants for the high temperature U3Si (h-U3Si) phase generated by the cross-term potential agree well with experimental data. Reasonable agreements are also reached on the elastic constants of U3Si2, on the formation enthalpy for the low temperature U3Si (m-U3Si) and h-U3Si phases, and on the lattice constants of m-U3Si phase. All these phases are predicted to be mechanically stable. The unary U potential is tested for three metallic U phases (α, β, γ). The potential is found capable to predict the cohesive energies well against experimental data for all three phases. It matches reasonably with previous experiments on the lattice constants and elastic constants of αU.

  12. 76 FR 51887 - Safety Zone; Patuxent River, Patuxent River, MD

    Science.gov (United States)

    2011-08-19

    ...-AA00 Safety Zone; Patuxent River, Patuxent River, MD AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is establishing a temporary safety zone during the ``NAS Patuxent River... held over certain waters of the Patuxent River adjacent to Patuxent River, Maryland from September 1...

  13. Thomas Secker M.D.: Archbishop and man-midwife.

    Science.gov (United States)

    Morgan-Guy, John

    2018-05-01

    This paper provides a biographical outline of the career of Thomas Secker, MD, who from 1758-68 was Archbishop of Canterbury. Although much has been written on Secker, this study seeks to highlight his training in medicine, which has been largely overlooked hitherto by historians.

  14. A pilot study of MD (psychiatry) theses-based research.

    Science.gov (United States)

    Srivastava, Shrikant; Agarwal, Vivek; Subramanyam, Alka; Srivastava, Mona; Sathyanarayana Rao, T S; Rao, G Prasad; Khurana, Hitesh; Singh, Archana

    2018-01-01

    Undertaking a research project is mandatory for MD Psychiatry trainees. The present study was undertaken to assess the type of research activity being undertaken as part of MD Psychiatry dissertation, and its contribution to national and international literature. Three medical colleges supplied the data about the topic, names of the supervisor and the candidate, collaboration, funding accrued, and publication details of MD-based research carried out between years 2000 and 2010 inclusive; 95 records were collected for the final analysis. The details of the publications provided were cross-checked on the internet, which would have taken care of missed publications as well. Most studies were single-point assessment clinical studies. Only 2 studies had been funded, 11 had collaboration with other departments within the same institute, and 5 had inter-institute collaborations. Majority of the studies were not published. Only 30 were published as full paper and 9 as abstracts. Of these 30 full publications, only 3 were published in journals having JCI impact factor values (1.4, 1.3, and 1.4, respectively). The main finding of this pilot study was that MD-based research has low contribution to the national and international literature, and those articles which are published are in low impact journals. Suggestions for modifying this state of affairs are discussed.

  15. Find an Orthopaedic Foot and Ankle MD/DO

    Science.gov (United States)

    ... All Site Content AOFAS / FootCareMD / Find a Surgeon Find a Foot & Ankle Orthopaedic Surgeon Page Content Who ... your prescribed treatment (surgical and/or non-surgical) ​ Find a Surgeon ​ Click here to find a foot ...

  16. The semantic similarity ensemble

    Directory of Open Access Journals (Sweden)

    Andrea Ballatore

    2013-12-01

    Full Text Available Computational measures of semantic similarity between geographic terms provide valuable support across geographic information retrieval, data mining, and information integration. To date, a wide variety of approaches to geo-semantic similarity have been devised. A judgment of similarity is not intrinsically right or wrong, but obtains a certain degree of cognitive plausibility, depending on how closely it mimics human behavior. Thus selecting the most appropriate measure for a specific task is a significant challenge. To address this issue, we make an analogy between computational similarity measures and soliciting domain expert opinions, which incorporate a subjective set of beliefs, perceptions, hypotheses, and epistemic biases. Following this analogy, we define the semantic similarity ensemble (SSE as a composition of different similarity measures, acting as a panel of experts having to reach a decision on the semantic similarity of a set of geographic terms. The approach is evaluated in comparison to human judgments, and results indicate that an SSE performs better than the average of its parts. Although the best member tends to outperform the ensemble, all ensembles outperform the average performance of each ensemble's member. Hence, in contexts where the best measure is unknown, the ensemble provides a more cognitively plausible approach.

  17. Simulation

    DEFF Research Database (Denmark)

    Gould, Derek A; Chalmers, Nicholas; Johnson, Sheena J

    2012-01-01

    Recognition of the many limitations of traditional apprenticeship training is driving new approaches to learning medical procedural skills. Among simulation technologies and methods available today, computer-based systems are topical and bring the benefits of automated, repeatable, and reliable p...... performance assessments. Human factors research is central to simulator model development that is relevant to real-world imaging-guided interventional tasks and to the credentialing programs in which it would be used....

  18. Gender similarities and differences.

    Science.gov (United States)

    Hyde, Janet Shibley

    2014-01-01

    Whether men and women are fundamentally different or similar has been debated for more than a century. This review summarizes major theories designed to explain gender differences: evolutionary theories, cognitive social learning theory, sociocultural theory, and expectancy-value theory. The gender similarities hypothesis raises the possibility of theorizing gender similarities. Statistical methods for the analysis of gender differences and similarities are reviewed, including effect sizes, meta-analysis, taxometric analysis, and equivalence testing. Then, relying mainly on evidence from meta-analyses, gender differences are reviewed in cognitive performance (e.g., math performance), personality and social behaviors (e.g., temperament, emotions, aggression, and leadership), and psychological well-being. The evidence on gender differences in variance is summarized. The final sections explore applications of intersectionality and directions for future research.

  19. Direct Numerical Simulations of Concentration and Temperature Polarization in Direct Contact Membrane Distillation

    Science.gov (United States)

    Lou, Jincheng; Tilton, Nils

    2017-11-01

    Membrane distillation (MD) is a method of desalination with boundary layers that are challenging to simulate. MD is a thermal process in which warm feed and cool distilled water flow on opposite sides of a hydrophobic membrane. The temperature difference causes water to evaporate from the feed, travel through the membrane, and condense in the distillate. Two challenges to MD are temperature and concentration polarization. Temperature polarization represents a reduction in the transmembrane temperature difference due to heat transfer through the membrane. Concentration polarization describes the accumulation of solutes near the membrane. These phenomena reduce filtration and lead to membrane fouling. They are difficult to simulate due to the coupling between the velocity, temperature, and concentration fields on the membrane. Unsteady regimes are particularly challenging because noise at the outlets can pollute the near-membrane flow fields. We present the development of a finite-volume method for the simulation of fluid flow, heat, and mass transport in MD systems. Using the method, we perform a parametric study of the polarization boundary layers, and show that the concentration boundary layer shows self-similar behavior that satisfies power laws for the downstream growth. Funded by the U.S. Bureau of Reclamation.

  20. Theoretical analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach

    Science.gov (United States)

    Yoshida, Norio; Higashi, Masahiro; Motoki, Hideyoshi; Hirota, Shun

    2018-01-01

    The structural stability of a cytochrome c domain-swapped dimer compared with that of the monomer was investigated by molecular dynamics (MD) simulations and by three-dimensional reference interaction site model (3D-RISM) theory. The structural fluctuation and structural energy of cytochrome c were treated by MD simulations, and the solvation thermodynamics was treated by 3D-RISM theory. The domain-swapped dimer state is slightly less stable than the monomer state, which is consistent with experimental observations; the total free energy difference is calculated as 25 kcal mol-1. The conformational change and translational/rotational entropy change contribute to the destabilization of the dimer, whereas the hydration and vibrational entropy contribute to the stabilization. Further analyses on the residues located at the hinge loop for swapping were conducted, and the results reveal details at the molecular level of the structural and interaction changes upon dimerization.

  1. Simulation

    CERN Document Server

    Ross, Sheldon

    2006-01-01

    Ross's Simulation, Fourth Edition introduces aspiring and practicing actuaries, engineers, computer scientists and others to the practical aspects of constructing computerized simulation studies to analyze and interpret real phenomena. Readers learn to apply results of these analyses to problems in a wide variety of fields to obtain effective, accurate solutions and make predictions about future outcomes. This text explains how a computer can be used to generate random numbers, and how to use these random numbers to generate the behavior of a stochastic model over time. It presents the statist

  2. Similarity or difference?

    DEFF Research Database (Denmark)

    Villadsen, Anders Ryom

    2013-01-01

    While the organizational structures and strategies of public organizations have attracted substantial research attention among public management scholars, little research has explored how these organizational core dimensions are interconnected and influenced by pressures for similarity....... In this paper I address this topic by exploring the relation between expenditure strategy isomorphism and structure isomorphism in Danish municipalities. Different literatures suggest that organizations exist in concurrent pressures for being similar to and different from other organizations in their field......-shaped relation exists between expenditure strategy isomorphism and structure isomorphism in a longitudinal quantitative study of Danish municipalities....

  3. Simulation of dense colloids

    NARCIS (Netherlands)

    Herrmann, H.J.; Harting, J.D.R.; Hecht, M.; Ben-Naim, E.

    2008-01-01

    We present in this proceeding recent large scale simulations of dense colloids. On one hand we simulate model clay consisting of nanometric aluminum oxide spheres in water using realistic DLVO potentials and a combination of MD and SRD. We find pronounced cluster formation and retrieve the shear

  4. Comparing Harmonic Similarity Measures

    NARCIS (Netherlands)

    de Haas, W.B.; Robine, M.; Hanna, P.; Veltkamp, R.C.; Wiering, F.

    2010-01-01

    We present an overview of the most recent developments in polyphonic music retrieval and an experiment in which we compare two harmonic similarity measures. In contrast to earlier work, in this paper we specifically focus on the symbolic chord description as the primary musical representation and

  5. Similarity analysis between quantum images

    Science.gov (United States)

    Zhou, Ri-Gui; Liu, XingAo; Zhu, Changming; Wei, Lai; Zhang, Xiafen; Ian, Hou

    2018-06-01

    Similarity analyses between quantum images are so essential in quantum image processing that it provides fundamental research for the other fields, such as quantum image matching, quantum pattern recognition. In this paper, a quantum scheme based on a novel quantum image representation and quantum amplitude amplification algorithm is proposed. At the end of the paper, three examples and simulation experiments show that the measurement result must be 0 when two images are same, and the measurement result has high probability of being 1 when two images are different.

  6. Hybrid method coupling molecular dynamics and Monte Carlo simulations to study the properties of gases in microchannels and nanochannels

    NARCIS (Netherlands)

    Nedea, S.V.; Frijns, A.J.H.; Steenhoven, van A.A.; Markvoort, Albert. J.; Hilbers, P.A.J.

    2005-01-01

    We combine molecular dynamics (MD) and Monte Carlo (MC) simulations to study the properties of gas molecules confined between two hard walls of a microchannel or nanochannel. The coupling between MD and MC simulations is introduced by performing MD near the boundaries for accuracy and MC in the bulk

  7. MD210 Note: Creation of Hollow Bunches in the PSB

    CERN Document Server

    Oeftiger, Adrian; Findlay, Alan James; Hancock, Steven; Rumolo, Giovanni; CERN. Geneva. ATS Department

    2016-01-01

    MD210 aims for the creation of longitudinally hollow bunches in the CERN PS Booster. The first three sessions have been carried out using the radial loop feedback system in order to drive the beam on a dipolar parametric resonance (instead of the phase loop). It has been found that the damping by the phase loop inhibits the excitation of the resonance to a major extent. The hollow distributions generated under these circumstances fail to reach a satisfying bunching factor. Nonetheless, proving the principally successful application of this technique to the PS Booster promises good results once the phase loop system supports trim functions. The approach, actions and detailed results of the first three MD sessions are presented in this paper.

  8. Postgraduate research training: the PhD and MD thesis.

    Science.gov (United States)

    Higginson, I; Corner, J

    1996-04-01

    Higher research degrees, such as the PhD, MPhil and MD, have existed within universities for 80 years or more, although the differences between the MD and PhD remain confused. A higher research degree training provides individuals with greater research knowledge and skills, and benefits the specialty. Concern exists about the levels of supervision sometimes provided, failure to complete degrees, and the variable levels of research knowledge and skills attained. We propose that higher research degrees in palliative care have four functions: extending personal scholarship, generating knowledge, training for the individual and contributing to the growth of the specialty. Such an approach may include: a formalised first year with taught components such as in research MSc programmes, formal supervision and progress assessment. In palliative care, clinical and academic approaches need greater integration. Multiprofessional learning is essential. To allow individuals to undertake higher research degree programmes, fellowships or specific funding are needed.

  9. MD study of pyrimidine base damage on DNA and its recognition by repair enzyme

    International Nuclear Information System (INIS)

    Pinak, M.

    2000-01-01

    The molecular dynamics (MD) simulation was used on the study of two specific damages of pyrimidine bases of DNA. Pyrimidine bases are major targets either of free radicals induced by ionizing radiation in DNA surrounding environment or UV radiation. Thymine dimer (TD) is UV induced damage, in which two neighboring thymines in one strand are joined by covalent bonds of C(5)-C(5) and C(6)-C(6) atoms of thymines. Thymine glycol (TG) is ionizing radiation induced damage in which the free water radical adds to unsaturated bond C(5)-C(6) of thymine. Both damages are experimentally suggested to be mutagenetic and carcinogenic unless properly repaired by repair enzymes. In the case of MD of TD, there is detected strong kink around the TD site that is not observed in native DNA. In addition there is observed the different value of electrostatic energy at the TD site - negative '-10 kcal/mol', in contrary to nearly neutral value of native thymine site. Structural changes and specific electrostatic energy - seems to be important for proper recognition of TD damaged site, formation of DNA-enzyme complex and thus for subsequent repair of DNA. In the case of TG damaged DNA there is major structural distortion at the TG site, mainly the increased distance between TG and the C5' of adjacent nucleotide. This enlarged gap between the neighboring nucleotides may prevent the insertion of complementary base during replication causing the replication process to stop. In which extend this structural feature together with energy properties of TG contributes to the proper recognition of TG by repair enzyme Endonuclease III is subject of further computational MD study. (author)

  10. Towards automatic coupling corrections with DOROS BPMs (MD750)

    CERN Document Server

    Persson, Tobias Hakan Bjorn; Langner, Andy Sven; Lefevre, Thibaut; Maclean, Ewen Hamish; Malina, Lukas; Olexa, Jakub; Skowronski, Piotr Krzysztof; Garcia-Tabares Valdivieso, Ana; Coello De Portugal - Martinez Vazquez, Jaime Maria; Tomas Garcia, Rogelio; CERN. Geneva. ATS Department

    2015-01-01

    BPMs close to IP1 and IP5 have been equipped with the new DOROS (Diode ORbit OScillation) system which provides precise orbit and turn-by-turn data [1]. In this MD-note we report on the rst measurements with the DOROS system to measure the transverse coupling. Furthermore, we compare the results and the performance of the system to the normal BPMs.

  11. MD 349: Impedance Localization with AC-dipole

    CERN Document Server

    Biancacci, Nicolo; Metral, Elias; Salvant, Benoit; Papotti, Giulia; Persson, Tobias Hakan Bjorn; Tomas Garcia, Rogelio; CERN. Geneva. ATS Department

    2016-01-01

    The purpose of this MD is to measure the distribution of the transverse impedance of the LHC by observing the phase advance variation with intensity between the machine BPMs. Four injected bunches with different intensities are excited with an AC dipole and the turn by turn data is acquired from the BPM system. Through post-processing analysis the phase variation along the machine is depicted and, from this information, first conclusions of the impedance distribution can be drawn.

  12. MD 1691: Active halo control using tune ripple at injection

    CERN Document Server

    Garcia Morales, Hector; Bruce, Roderik; Redaelli, Stefano; Fitterer, Miriam; Fiascaris, Maria; Nisbet, David; Thiesen, Hugues; Valentino, Gianluca; Xu, Chen; CERN. Geneva. ATS Department

    2017-01-01

    In this MD we performed halo excitation through tune ripple. This consists in an excitation that introduces new resonance sidebands around the existing resonance lines. In presence of sufficient detuning with amplitude, these sidebands can in principle affect only the dynamics of the halo particles at large amplitudes. Tune ripple was induced through a current modulation of the warm trim quadrupoles in IR7. This is the first time this method is experimentally tested at the LHC.

  13. Review of 40-year MD theses in Medical Oncology

    International Nuclear Information System (INIS)

    Zeeneldin, A.; Diyaa, A.; Elgammal, M.; Buhoush, W.; Manar Moneer, M.

    2014-01-01

    Background and objective: It is almost 40 years since the foundation of the Medical Oncology (MO) Department. We aimed to appraise the clinical research to fulfill the Medical Doctorate (MD) degree in MO at the National Cancer Institute, Cairo University (NCI, CU). Methods: This review included 62 MD theses containing 66 studies. They were reviewed regarding aims, type of study, clinical trial phase, design and methodology, statistical tests, results, limitations, consent and IRB approval. Theses were grouped into 3 periods: 1970-1989, 1990-1999 and 2000- 2008. Results: Almost 76% of the studies were interventional and 24% were observational. Informed consent and Institutional Review Board approval were mentioned in 18 and 2 studies, respectively. While all studies mentioned the aims, none, clearly mentioned the research question. Outcomes were mainly efficacy followed by safety. Study design was inadequately considered, especially in 70’s–80’s period (p = 0.038). Median sample size and study duration were almost stable through the three periods (p = 0.441, 0.354, respectively). Most of the studies used both descriptive and analytical statistical methods. In a descending order, researched cancers were lymphoma, breast, leukemia, liver, urinary bladder, lung and colorectal. The commonest stages researched were IV and III. The number of studies focused on assessing biomarkers, biomarkers plus drugs/procedures, drugs and procedures are 20, 20, 16 and 6, respectively. Conclusion: With time, research within MD theses in MO increased quantitatively and qualitatively. Improvements were noticeable in documentation of study design.

  14. MD Anderson's Population Health Approaches to Cancer Prevention.

    Science.gov (United States)

    Foxhall, Lewis; Moreno, Mark; Hawk, Ernest

    2018-02-01

    Texas's size and unique population demographics present challenges to addressing the state's cancer burden. The University of Texas MD Anderson Cancer Center is one of 69 National Cancer Institute-designated cancer centers across the United States. While these centers traditionally have focused on research, education and training, and providing research-driven patient care, they are in a unique position to collaboratively advance population health through cancer control. Unlike the traditional academic model of a three-legged stool representing research, education, and patient care, MD Anderson's mission includes a fourth leg that incorporates population health approaches. MD Anderson has leveraged state- and national-level data and freely available resources to develop population-health priorities and a set of evidence-based actions across policy, public and professional education, and community-based clinical service domains to address these priorities. Population health approaches complement dissemination and implementation research and treatment, and will be increasingly needed to address the growing cancer burden in Texas and the nation.

  15. The hydration enthalpies of Md3+ and Lr3+

    International Nuclear Information System (INIS)

    Bruechle, W.; Schaedel, M.; Scherer, U.W.; Kratz, J.V.

    1987-10-01

    Lawrencium (3-min 260 Lr) and lighter actinides were produced in the bombardement of a 249 Bk target with 18 O ions and loaded onto a cation exchange column in 0.05 M α-hydroxy-isobutyrate solution at pH = 4.85 together with the radioactive lanthanide tracers 166 Ho, 171 Er, and 171 Tm. In elutions with 0.12 M α-hydroxy-isobutyrate solution (pH = 4.85) trivalent Lr was eluted exactly together with the Er tracer and Md close to Ho. Lr elutes much later than expected based on the known elution positions of the lighter actinides and the expected analogy to the elution positions of the homologous lanthanides. From the measured elution positions, ionic radii were calculated for Lr 3+ and Md 3+ . Semiempirical models allow the calculation of the heat of hydration from the ionic radii, resulting in ΔH hyd ≅ - 3654 kJ/mol for Md 3+ and ΔH hyd ≅ - 3689 kJ/mol for Lr 3+ . (orig.)

  16. Multi-Device to Multi-Device (MD2MD Content-Centric Networking Based on Multi-RAT Device

    Directory of Open Access Journals (Sweden)

    Cheolhoon Kim

    2017-11-01

    Full Text Available This paper proposes a method whereby a device can transmit and receive information using a beacon, and also describes application scenarios for the proposed method. In a multi-device to multi-device (MD2MD content-centric networking (CCN environment, the main issue involves searching for and connecting to nearby devices. However, if a device can’t find another device that satisfies its requirements, the connection is delayed due to the repetition of processes. It is possible to rapidly connect to a device without repetition through the selection of the optimal device using the proposed method. Consequently, the proposed method and scenarios are advantageous in that they enable efficient content identification and delivery in a content-centric Internet of Things (IoT environment, in which multiple mobile devices coexist.

  17. Rhodotorula taiwanensis MD1149 produces hypoacetylated PEFA compounds with increased surface activity compared to Rhodotorula babjevae MD1169

    Science.gov (United States)

    Rubinfeld, Bonnee; Leif, Roald; Mulcahy, Heather; Dugan, Lawrence; Souza, Brian

    2018-01-01

    Biosurfactants have several desirable characteristics in the industrial sector: detergency, antimicrobial effects, skin hydration, and emulsibility. Several yeast glycolipids are currently being utilized in these capacities: sophorolipids, ustilagic acid, and mannosylerythritol lipids (MELs). An emerging class of glycolipids, termed polyol esters of fatty acids (PEFA), have recently been reported for Rhodotorula babjevae, a basidiomycetous yeast species that secretes hyperacetylated congeners of PEFA (typically with 3–6 acetylation modifications). While screening Rhodotorula species for surfactant production, we identified a new environmental isolate identified as Rhodotorula taiwanensis MD1149 that dropped the surface tension of the liquid medium, indicating that it produced a potent biosurfactant. Acid depolymerization of the purified biosurfactants, followed by gas chromatography-mass spectrometry (GC-MS) analysis revealed that the biosurfactants were composed of PEFA compounds composed mainly of mannitol and arabitol esters of 3-hydroxy fatty acid, 3-methoxy fatty acid, and fatty acids with a single double bond; chain lengths were mainly C16 and C18. Liquid chromatography-mass spectrometry (LC-MS) confirmed the predicted accurate mass of these compounds. Interestingly, PEFA compounds produced by Rhodotorula taiwanensis MD1149 were more surface active due to their hypoacetylation profile (0–4 acetylation modifications) compared to Rhodotorula babjevae MD1169. These disparate surface active properties, based on acetylation, change the hydrophilic-lipophilic balance (HLB) of these compounds, and their potential utility within industrial applications. PMID:29293588

  18. Rhodotorula taiwanensis MD1149 produces hypoacetylated PEFA compounds with increased surface activity compared to Rhodotorula babjevae MD1169.

    Science.gov (United States)

    Lyman, Mathew; Rubinfeld, Bonnee; Leif, Roald; Mulcahy, Heather; Dugan, Lawrence; Souza, Brian

    2018-01-01

    Biosurfactants have several desirable characteristics in the industrial sector: detergency, antimicrobial effects, skin hydration, and emulsibility. Several yeast glycolipids are currently being utilized in these capacities: sophorolipids, ustilagic acid, and mannosylerythritol lipids (MELs). An emerging class of glycolipids, termed polyol esters of fatty acids (PEFA), have recently been reported for Rhodotorula babjevae, a basidiomycetous yeast species that secretes hyperacetylated congeners of PEFA (typically with 3-6 acetylation modifications). While screening Rhodotorula species for surfactant production, we identified a new environmental isolate identified as Rhodotorula taiwanensis MD1149 that dropped the surface tension of the liquid medium, indicating that it produced a potent biosurfactant. Acid depolymerization of the purified biosurfactants, followed by gas chromatography-mass spectrometry (GC-MS) analysis revealed that the biosurfactants were composed of PEFA compounds composed mainly of mannitol and arabitol esters of 3-hydroxy fatty acid, 3-methoxy fatty acid, and fatty acids with a single double bond; chain lengths were mainly C16 and C18. Liquid chromatography-mass spectrometry (LC-MS) confirmed the predicted accurate mass of these compounds. Interestingly, PEFA compounds produced by Rhodotorula taiwanensis MD1149 were more surface active due to their hypoacetylation profile (0-4 acetylation modifications) compared to Rhodotorula babjevae MD1169. These disparate surface active properties, based on acetylation, change the hydrophilic-lipophilic balance (HLB) of these compounds, and their potential utility within industrial applications.

  19. Alpha-gamma decay studies of 253No and its daughter products 253Md, 249Fm

    International Nuclear Information System (INIS)

    Hessberger, F.P.; Antalic, S.; Kalaninova, Z.; Saro, S.; Venhart, M.; Ackermann, D.; Heinz, S.; Kindler, B.; Kojouharov, I.; Kuusiniemi, P.; Lommel, B.; Mann, R.; Sulignano, B.; Hofmann, S.; Streicher, B.; Leino, M.; Nishio, K.

    2012-01-01

    Nuclear structure and decay of the isotope 253 No and its decay products 249 Fm and 253 Md were investigated by means of α - γ spectroscopy. Besides the established strong γ transitions from the 9/2 - [734] Nilsson level in 249 Fm, populated predominantly by the α decay of 253 No, into the ground-state (gs) rotational band, a couple of weaker γ lines (58.3, 129.2, 209.3 and 669.5keV) were observed and placed into the 249 Fm level scheme. The transition from the 7/2 - level in 249 Es, populated by the α decay of 253 Md, into the 9/2 + member of the gs rotational band, so far established for other odd-mass Es isotopes, was observed clearly. GEANT4 simulations were performed to investigate the influence of energy summing between α particles and conversion electrons (CE) on the shape of the α spectra at different implantation energies, leading to evidence for a weak α decay branch of 253 No into the gs of 249 Fm or the ground-state rotational band, respectively. (orig.)

  20. MdMYB9 and MdMYB11 are involved in the regulation of the JA-induced biosynthesis of anthocyanin and proanthocyanidin in apples.

    Science.gov (United States)

    An, Xiu-Hong; Tian, Yi; Chen, Ke-Qin; Liu, Xiao-Juan; Liu, Dan-Dan; Xie, Xing-Bin; Cheng, Cun-Gang; Cong, Pei-Hua; Hao, Yu-Jin

    2015-04-01

    Anthocyanin and proanthocyanidin (PA) are important secondary metabolites and beneficial to human health. Their biosynthesis is induced by jasmonate (JA) treatment and regulated by MYB transcription factors (TFs). However, which and how MYB TFs regulate this process is largely unknown in apple. In this study, MdMYB9 and MdMYB11 which were induced by methyl jasmonate (MeJA) were functionally characterized. Overexpression of MdMYB9 or MdMYB11 promoted not only anthocyanin but also PA accumulation in apple calluses, and the accumulation was further enhanced by MeJA. Subsequently, yeast two-hybrid, pull-down and bimolecular fluorescence complementation assays showed that both MYB proteins interact with MdbHLH3. Moreover, Jasmonate ZIM-domain (MdJAZ) proteins interact with MdbHLH3. Furthermore, chromatin immunoprecipitation-quantitative PCR and yeast one-hybrid assays demonstrated that both MdMYB9 and MdMYB11 bind to the promoters of ANS, ANR and LAR, whereas MdbHLH3 is recruited to the promoters of MdMYB9 and MdMYB11 and regulates their transcription. In addition, transient expression assays indicated that overexpression of MdJAZ2 inhibits the recruitment of MdbHLH3 to the promoters of MdMYB9 and MdMYB11. Our findings provide new insight into the mechanism of how MeJA regulates anthocyanin and PA accumulation in apple. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  1. 76 FR 5686 - Drawbridge Operation Regulation; Pocomoke River, Pocomoke City, MD

    Science.gov (United States)

    2011-02-02

    ... Operation Regulation; Pocomoke River, Pocomoke City, MD AGENCY: Coast Guard, DHS. ACTION: Notice of... River, mile 15.6, at Pocomoke City, MD. The deviation restricts the operation of the draw span to.... The Route 675 Bridge across Pocomoke River, mile 15.6 at Pocomoke City MD, has a vertical clearance in...

  2. 75 FR 49992 - Peter W.S. Grigg, M.D.; Revocation of Registration

    Science.gov (United States)

    2010-08-16

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration Peter W.S. Grigg, M.D.; Revocation of... Order to Show Cause and Immediate Suspension of Registration to Peter W.S. Grigg, M.D. (Respondent), of... Registration, BG2107856, issued to Peter W.S. Grigg, M.D., be, and it hereby is, revoked. This Order is...

  3. 77 FR 7182 - Scott W. Houghton, M.D.; Decision and Order

    Science.gov (United States)

    2012-02-10

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 12-09] Scott W. Houghton, M.D... CFR 0.100(b), I order that DEA Certificate of Registration BH8796077, issued to Scott W. Houghton, M.D., be, and it hereby is, revoked. I further order that any pending application of Scott W. Houghton, M.D...

  4. 76 FR 48898 - Robert Leigh Kale, M.D., Decision and Order

    Science.gov (United States)

    2011-08-09

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration Robert Leigh Kale, M.D., Decision and Order... Enforcement Administration, issued an Order to Show Cause to Robert Leigh Kale, M.D. (Registrant), of Fort... Certificate of Registration, BK9514375, issued to Robert Leigh Kale, M.D., be, and it hereby is, revoked. I...

  5. 76 FR 20032 - Thomas E. Mitchell, M.D.; Dismissal of Proceeding

    Science.gov (United States)

    2011-04-11

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 10-7] Thomas E. Mitchell, M.D... Control, Drug Enforcement Administration, issued an Order to Show Cause to Thomas E. Mitchell, M.D....100(b) and 0.104, I hereby order that the Order to Show Cause issued to Thomas E. Mitchell, M.D., be...

  6. Computer Simulation Studies of Trishomocubane Heptapeptide of ...

    African Journals Online (AJOL)

    As part of an extension on the cage peptide chemistry, the present work involves an assessment of the conformational profile of trishomocubane heptapeptide of the type Ac-Ala3-Tris-Ala3-NHMe using molecular dynamics (MD) simulations. All MD protocols were explored within the framework of a molecular mechanics ...

  7. The ABCs of molecular dynamics simulations on B-DNA, circa 2012

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... Introduction ... methods and applications of MD simulations to nucleic acids. ... access to high-performance computing, all-atom MD on DNA ... Specifically, the focus in this article is (a) ... of MD on DNA using AMBER came with the development ..... python-based tool for managing this task on widely.

  8. Review of 40-year MD theses in medical oncology.

    Science.gov (United States)

    Zeeneldin, Ahmed; Diyaa, Amira; Moneer, Manar; Elgammal, Mosaad; Buhoush, Wafa

    2014-09-01

    It is almost 40 years since the foundation of the Medical Oncology (MO) Department. We aimed to appraise the clinical research to fulfill the Medical Doctorate (MD) degree in MO at the National Cancer Institute, Cairo University (NCI, CU). This review included 62 MD theses containing 66 studies. They were reviewed regarding aims, type of study, clinical trial phase, design and methodology, statistical tests, results, limitations, consent and IRB approval. Theses were grouped into 3 periods: 1970-1989, 1990-1999 and 2000-2008. Almost 76% of the studies were interventional and 24% were observational. Informed consent and Institutional Review Board approval were mentioned in 18 and 2 studies, respectively. While all studies mentioned the aims, none, clearly mentioned the research question. Outcomes were mainly efficacy followed by safety. Study design was inadequately considered, especially in 70's-80's period (p=0.038). Median sample size and study duration were almost stable through the three periods (p=0.441, 0.354, respectively). Most of the studies used both descriptive and analytical statistical methods. In a descending order, researched cancers were lymphoma, breast, leukemia, liver, urinary bladder, lung and colorectal. The commonest stages researched were IV and III. The number of studies focused on assessing biomarkers, biomarkers plus drugs/procedures, drugs and procedures are 20, 20, 16 and 6, respectively. With time, research within MD theses in MO increased quantitatively and qualitatively. Improvements were noticeable in documentation of study design. Copyright © 2014. Production and hosting by Elsevier B.V.

  9. Radioprotective and radiotherapeutic properties of biotechnological agent MD2

    International Nuclear Information System (INIS)

    Sobol, C.V.; Komar, V.E.; Sobol, Y.T.

    1996-01-01

    In recent years as the result of nuclear testing and accidents at nuclear power plants such as Chernobyl, etc. radiation exposure has become a major issue in various parts of the world. Experience of recent nuclear accidents has shown there is no effective treatment for patients expose to doses of radiation that result in fatal hematopoietic failure and /or secondary infections. Therefore, agents that are effective when administered after irradiation, are of great interest. In this study, the possibility of using biotechnological agent MD2 after lethal total body irradiation (TBI) and radiotherapy has been demonstrated. In addition, the considerable radioprotection without toxic effect can be obtained. (author)

  10. Similar or different?

    DEFF Research Database (Denmark)

    Cornér, Solveig; Pyhältö, Kirsi; Peltonen, Jouni

    2018-01-01

    Previous research has identified researcher community and supervisory support as key determinants of the doctoral journey contributing to students’ persistence and robustness. However, we still know little about cross-cultural variation in the researcher community and supervisory support experien...... counter partners, whereas the Finnish students perceived lower levels of instrumental support than the Danish students. The findings imply that seemingly similar contexts hold valid differences in experienced social support and educational strategies at the PhD level....... experienced by PhD students within the same discipline. This study explores the support experiences of 381 PhD students within the humanities and social sciences from three research-intensive universities in Denmark (n=145) and Finland (n=236). The mixed methods design was utilized. The data were collected...... counter partners. The results also indicated that the only form of support in which the students expressed more matched support than mismatched support was informational support. Further investigation showed that the Danish students reported a high level of mismatch in emotional support than their Finnish...

  11. Extension of the M-D model for treating stress drops in salt

    International Nuclear Information System (INIS)

    Munson, D.E.; DeVries, K.L.; Fossum, A.F.; Callahan, G.D.

    1993-01-01

    Development of the multimechanism deformation (M-D) constitutive model for steady state creep, which incorporates irreversible workhardening and recovery transient strains, was motivated by the need to predict very long term closures in underground rooms for radioactive waste repositories in salt. The multimechanism deformation model for the creep deformation of salt is extended to treat the response of salt to imposed stress drops. Stress drop tests produce a very distinctive behavior where both reversible elastic strain and reversible time dependent strain occur. These transient strains are negative compared to the positive transient strains produced by the normal creep workhardening and recovery processes. A simple micromechanical evolutionary process is defined to account for the accumulation of these reversible strains, and their subsequent release with decreases in stress. A number of experimental stress drop tests for various stress drop magnitudes and temperatures are adequately simulated with the model

  12. pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins.

    Directory of Open Access Journals (Sweden)

    Priyanka Prakash

    2015-10-01

    Full Text Available Probe-based or mixed solvent molecular dynamics simulation is a useful approach for the identification and characterization of druggable sites in drug targets. However, thus far the method has been applied only to soluble proteins. A major reason for this is the potential effect of the probe molecules on membrane structure. We have developed a technique to overcome this limitation that entails modification of force field parameters to reduce a few pairwise non-bonded interactions between selected atoms of the probe molecules and bilayer lipids. We used the resulting technique, termed pMD-membrane, to identify allosteric ligand binding sites on the G12D and G13D oncogenic mutants of the K-Ras protein bound to a negatively charged lipid bilayer. In addition, we show that differences in probe occupancy can be used to quantify changes in the accessibility of druggable sites due to conformational changes induced by membrane binding or mutation.

  13. An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine Deaminase

    International Nuclear Information System (INIS)

    Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

    2008-01-01

    We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases. TM and MA were partly supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan.MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE

  14. Full-Scale Crash Test of an MD-500 Helicopter

    Science.gov (United States)

    Littell, Justin

    2011-01-01

    A full-scale crash test was successfully conducted in March 2010 of an MD-500 helicopter at NASA Langley Research Center s Landing and Impact Research Facility. The reasons for conducting this test were threefold: 1 To generate data to be used with finite element computer modeling efforts, 2 To study the crashworthiness features typically associated with a small representative helicopter, and 3 To compare aircraft response to data collected from a previously conducted MD-500 crash test, which included an externally deployable energy absorbing (DEA) concept. Instrumentation on the airframe included accelerometers on various structural components of the airframe; and strain gages on keel beams, skid gear and portions of the skin. Three Anthropomorphic Test Devices and a specialized Human Surrogate Torso Model were also onboard to collect occupant loads for evaluation with common injury risk criteria. This paper presents background and results from this crash test conducted without the DEA concept. These results showed accelerations of approximately 30 to 50 g on the airframe at various locations, little energy attenuation through the airframe, and moderate to high probability of occupant injury for a variety of injury criteria.

  15. MD1878: Operation with primary collimators at tighter settings

    CERN Document Server

    AUTHOR|(CDS)2078850; Amorim, David; Biancacci, Nicolo; Bruce, Roderik; Buffat, Xavier; Carver, Lee Robert; Fiascaris, Maria; Mereghetti, Alessio; Redaelli, Stefano; Rossi, Roberto; Salvachua Ferrando, Belen Maria; Soderen, Martin; Trad, Georges; CERN. Geneva. ATS Department

    2017-01-01

    Primary (TCP) collimators of the betatron cleaning insertion determine the betatron cut of the LHC beam. During the 2016 they were set at 5.5 nominal beam sigmas at 6.5 TeV (i.e. by using a normalized emittance ε* = 3:5 μm is used). Reducing their settings is a possible way to push the ß* at the LHC, which depends on the collimation hierarchy. This study aims at understanding possible limitations of operating the LHC with tighter settings of the primary collimators. This is a crucial input to the choice of operational configuration in terms of ß* at the LHC as well as at the HL-LHC. This study follows a successful MD done in block 3 to understand limitations from TCP impedance [1]. The outcome of this MD can also have an impact for the design of the FCC collimation system, which is currently based on the present TCP gaps. Studies of beam stability as a function of octupole current, transverse feedback gain (ADT) and transverse separation at the IPs were also carried out.

  16. Simulation study of transfer characteristics for spacer-filled membrane distillation desalination modules

    International Nuclear Information System (INIS)

    Chang, Hsuan; Hsu, Jian-An; Chang, Cheng-Liang; Ho, Chii-Dong; Cheng, Tung-Wen

    2017-01-01

    Highlights: • A 3D CFD model takes in transmembrane heat and mass transfer developed. • DCMD modules using spacer-filled and empty channels for desalination simulated. • Fluid flow, heat transfer and mass transfer profiles revealed. • Correlations of friction factor and Nusselt number developed. - Abstract: Membrane distillation (MD) is an emerging and promising membrane separation process, which can directly utilize renewable thermal energy or low-grade waste heat, for applications in water or wastewater treatment and food industry. However, a major drawback of MD process is its low energy efficiency. Spacer is the most suggested and studied eddy promoter to enhance the heat and mass transfer, which further improves both the separation and the energy utilization performance, of MD processes. This paper presents the results of a 3D computational fluid dynamics (CFD) simulation of DCMD (direct contact membrane distillation) modules using channels with and without spacers for desalination application. The model employs permeable wall boundary condition to take into account the transmembrane heat and mass transfer and simulates the entire module length. The simulation reveals similar fluctuating distributions of temperature polarization coefficient, transmembrane heat and mass fluxes as well as the shear stress on the membrane surface along the entire module length. Correlations have been developed for friction factor and average Nusselt number. These correlations are useful for the analysis and design of DCMD modules. The extent of heat transfer enhancement by spacers depends on the geometry of spacers and the Reynolds number of fluid.

  17. [Professor Frantisek Por MD and Professor Robert Klopstock MD, students at Budapest and Prague Faculties of Medicine].

    Science.gov (United States)

    Mydlík, M; Derzsiová, K

    2010-11-01

    Professor Frantisek Por MD and Professor Robert Klopstock MD were contemporaries, both born in 1899, one in Zvolen, the other in Dombovar, at the time of Austro-Hungarian Monarchy. Prof. Por attended the Faculty of Medicine in Budapest from 1918 to 1920, and Prof. Klopstock studied at the same place between 1917 and 1919. From 1920 until graduation on 6th February 1926, Prof. Por continued his studies at the German Faculty of Medicine, Charles University in Prague. Prof. Klopstock had to interrupt his studies in Budapest due to pulmonary tuberculosis; he received treatment at Tatranske Matliare where he befriended Franz Kafka. Later, upon Kafka's encouragement, he changed institutions and continued his studies at the German Faculty of Medicine, Charles University in Prague, where he graduated the first great go. It is very likely that, during their studies in Budapest and Prague, both professors met repeatedly, even though their life paths later separated. Following his graduation, Prof. Por practiced as an internist in Prague, later in Slovakia, and from 1945 in Kosice. In 1961, he was awarded the title of university professor of internal medicine at the Faculty of Medicine, Pavol Jozef Safarik University in Kosice, where he practiced until his death in 1980. Prof. Klopstock continued his studies in Kiel and Berlin. After his graduation in 1933, he practiced in Berlin as a surgeon and in 1938 left for USA. In 1962, he was awarded the title of university professor of pulmonary surgery in NewYork, where he died in 1972.

  18. Molecular Simulation towards Efficient and Representative Subsurface Reservoirs Modeling

    KAUST Repository

    Kadoura, Ahmad Salim

    2016-01-01

    This dissertation focuses on the application of Monte Carlo (MC) molecular simulation and Molecular Dynamics (MD) in modeling thermodynamics and flow of subsurface reservoir fluids. At first, MC molecular simulation is proposed as a promising method

  19. A eural etwork Model for Dynamics Simulation

    African Journals Online (AJOL)

    Nafiisah

    Results 5 - 18 ... situations, such as a dynamic environment (e.g., a molecular dynamics (MD) simulation whereby an atom constantly changes its local environment and number ..... of systems including both small clusters and bulk structures. 7.

  20. Computer Simulation Studies of Trishomocubane Heptapeptide of ...

    African Journals Online (AJOL)

    NICO

    Trishomocubane, molecular dynamics, Amber, CLASICO, β-turn, α-helical. 1. Introduction .... MD simulations of Ac-Ala3-Tris-Ala3-NHMe explicitly in MEOH. 3. Results and .... worthwhile to group all conformations into clusters according to.

  1. molecular dynamics simulations and quantum chemical calculations

    African Journals Online (AJOL)

    ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.

  2. Transport and characterization of ambient biological aerosol near Laurel, MD

    Science.gov (United States)

    Santarpia, J. L.; Cunningham, D.; Gilberry, J.; Kim, S.; Smith, E. E.; Ratnesar-Shumate, S.; Quizon, J.

    2010-09-01

    Bacterial aerosol have been observed and studied in the ambient environment since the mid nineteenth century. These studies have sought to provide a better understanding of the diversity, variability and factors that control the biological aerosol population. In this study, we show comparisons between diversity of culturable bacteria and fungi, using culture and clinical biochemical tests, and 16S rRNA diversity using Affymetrix PhyloChips. Comparing the culturable fraction and surveying the total 16S rRNA of each sample provides a comprehensive look at the bacterial population studied and allows comparison with previous studies. Thirty-six hour back-trajectories of the air parcels sampled, over the two day period beginning 4 November 2008, provide information on the sources of aerosol sampled on the campus of Johns Hopkins University Applied Physics Laboratory in Laurel, MD. This study indicates that back-trajectory modeling of air parcels may provide insights into the observed diversity of biological aerosol.

  3. A workshop on leadership for MD/PhD students

    Directory of Open Access Journals (Sweden)

    Mark D. Cannon

    2011-08-01

    Full Text Available Success in academic medicine requires scientific and clinical aptitude and the ability to lead a team effectively. Although combined MD/PhD training programs invest considerably in the former, they often do not provide structured educational opportunities in leadership, especially as applied to investigative medicine. To fill a critical knowledge gap in physician-scientist training, the Vanderbilt Medical Scientist Training Program (MSTP developed a biennial two-day workshop in investigative leadership. MSTP students worked in partnership with content experts to develop a case-based curriculum and deliver the material. In its initial three offerings in 2006, 2008, and 2010, the workshop was judged by MSTP student attendees to be highly effective. The Vanderbilt MSTP Leadership Workshop offers a blueprint for collaborative student-faculty interactions in curriculum design and a new educational modality for physician-scientist training.

  4. Jules Stein, MD: Ophthalmologist, Entertainment Magnate, and Advocate for Vision.

    Science.gov (United States)

    Straatsma, Bradley R; Weeks, David F

    2016-04-01

    To report the lifetime activities and accomplishments of Jules Stein, MD. Retrospective review. Assessment of published and unpublished biographical material. Jules Stein combined his love of music and medicine with organizational skills to achieve successive careers as a musician, an ophthalmologist, an entertainment magnate, and an advocate for vision. To preserve vision, he founded Research to Prevent Blindness, founded the Jules Stein Eye Institute at the University of California, Los Angeles, and led a multiyear campaign to establish the National Eye Institute. With successive careers and extraordinary achievements, Jules Stein created an enduring legacy of benefits to ophthalmology, vision research, and the prevention of blindness. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

  5. Medicinal Cannabis in California: An Interview with Igor Grant, MD.

    Science.gov (United States)

    Piomelli, Daniele; Grant, Igor

    2016-01-01

    Dr. Igor Grant, MD, is distinguished professor and chair of psychiatry and director of the HIV Neurobehavioral Research Program and the Center for Medicinal Cannabis Research at the University of California, San Diego. Dr. Grant is a neuropsychiatrist who graduated from the University of British Columbia School of Medicine (1966), and received specialty training in psychiatry at the University of Pennsylvania (1967-1971), and additional training in neurology at the Institute of Neurology (1980-1981), London, U.K. Dr. Grant's academic interests focus on the effects of various diseases on brain and behavior, with an emphasis on translational studies in HIV, and drugs of abuse. He has contributed to ∼700 scholarly publications and is principal investigator of several NIH studies, including an NIDA P50 (Translational Methamphetamine AIDS Research Center-TMARC), and is codirector of the HIV Neurobehavioral Research Center (HNRC).

  6. LHC β*-reach MD: aperture measurements at small β*

    CERN Document Server

    Fuster Martinez, Nuria; Redaelli, Stefano; CERN. Geneva. ATS Department

    2017-01-01

    During this MD, performed on the 25th of July 2017, we measured the LHC aperture at top energy for β*=30 cm using the Transverse Damper (ADT) blow-up method. These measurements are part of the standard commissioning of an optics and have been performed in order to provide early on inputs for a possible change of β* later in 2017, as envisaged previously to fully profit from the additional margins introduced by the rematched phase advance between dump kickers and the TCTs (Target Collimator Tertiary). In addition to the aperture measurements, two other commissioning important tests were performed: loss maps for the nominal TCTs settings and an asynchronous dump validation with tighter TCT gaps.

  7. Luminosity Anti-leveling with Crossing Angle (MD 1669)

    CERN Document Server

    Gorzawski, Arkadiusz; Ponce, Laurette; Salvachua Ferrando, Belen Maria; Wenninger, Jorg; CERN. Geneva. ATS Department

    2016-01-01

    A significant fraction of the LHC luminosity ($\\sim$30\\% in 2016) is lost due to the presence (and necessity) of the crossing angles at the IPs. At the LHC the crossing angle is typically set to a value that provides sufficient separation of the beams at the start of fills for the peak bunch intensities. As the bunch intensity decays during a fill, it is possible to reduce the crossing angle and recover some luminosity. A smooth crossing angle reduction procedure must be developed to take advantage of this option during stable beam operation. During this MD a smooth procedure for luminosity leveling with crossing angle was tested. It was demonstrated that the orbit was well controlled, beam losses were low and the offset leveled experiments ALICE and LHCb were not affected by crossing angle leveling in ATLAS and CMS.

  8. Report from LHC MD 2158: IR-nonlinear studies

    CERN Document Server

    Maclean, Ewen Hamish; Cruz Alaniz, Emilia; Dalena, Barbara; Dilly, Joschua Werner; Fol, Elena; Giovannozzi, Massimo; Hofer, Michael; Malina, Lukas; Persson, Tobias Hakan Bjorn; Coello De Portugal - Martinez Vazquez, Jaime Maria; Skowronski, Piotr Krzysztof; Solfaroli Camillocci, Matteo; Tomas Garcia, Rogelio; Garcia-Tabares Valdivieso, Ana; Wegscheider, Andreas; CERN. Geneva. ATS Department

    2018-01-01

    For the first time the LHC is running for luminosity-production with local corrections for nonlinear errors in the ATLAS and CMS insertions. While a major step forward in LHC optics commissioning strategy (and one which has yielded clear operational benefits) considerable challenges remain to be overcome, both in regard to the optimization of LHC optics and in order to ensure successful commissioning of the High-Luminosity LHC. MD 2158 sought to follow up several aspects of the 2017 nonlinear optics commissioning which are not yet understood, and by enhancing sextupole and dodecapole sources in the ATLAS and CMS insertions explore the prospects for linear and nonlinear optics commissioning in the HL-LHC.

  9. MD 979: Beta-beating measurements on colliding beams

    CERN Document Server

    Goncalves Jorge, Patrik; Pieloni, Tatiana; Buffat, Xavier; Carlier, Felix Simon; Coello De Portugal - Martinez Vazquez, Jaime Maria; Fol, Elena; Langner, Andy Sven; Medina Medrano, Luis Eduardo; Olexa, Jakub; Tomas Garcia, Rogelio; Valuch, Daniel; Wegscheider, Andreas; CERN. Geneva. ATS Department

    2017-01-01

    The HL-LHC high brightness beams will give a large β-beating due to the head-on and long-range interactions since a beam-beam parameter of 0.01 per Interaction Point (IP) is expected. The β-heating induced by two head-on collision reaches 15%. A third IP, i.e. IP8, could bring the β-heating up to 24%. The aim of the Machine Development (MD) study was to test optics measurements with AC dipole and ADT on colliding beams at injection and to implement a correction of the β-heating due to to head-on collision in the two experiments IP1&5. Int his note, we summarize the first results of this test performed in the LHC.

  10. Leonard F. Peltier, MD, PhD, 1920-2003.

    Science.gov (United States)

    Reckling, Frederick W; Lo Vecchio, Janolyn G; Reckling, JoAnn B

    2004-05-01

    Leonard F. Peltier, MD, PhD, was an orthopaedic surgeon, academician, administrator, laboratory investigator, historian, and mentor. His career spanned nearly six decades, beginning with graduate education at the University of Minnesota (UM) under the auspices of Owen H. Wangensteen, MD, PhD. In addition to obtaining a PhD in physiology in the UM Graduate School, he completed general and orthopaedic surgery residencies and attained board certification in each specialty. He served in the US Army Occupation Force Medical Corps in Germany just after World War II. In 1957, at 37 years old, he assumed the chairmanship of the orthopaedic training program at the University of Kansas. In 1971, he couldn't resist the opportunity to become one of the founding members of the "start-up" University of Arizona College of Medicine, accepting an appointment as chair of the new orthopaedic training program, where he remained until his retirement in 1990. He took clinical problems to the laboratory, and made important scientific contributions, particularly in the area of fat embolism and in using calcium sulfate (plaster of Paris) to fill bone defects. He served on governing boards of national professional organizations and presided over the American Association for the Surgery of Trauma from 1980-1981. Throughout his career, he was fascinated by, and published extensively in, the history of medicine arena. Known fondly as "the professor" to many of his residents and colleagues, he had a pragmatic, honest, upbeat, and often humorous approach to life's challenges, valuing personal integrity above other virtues. He explored various eclectic interests far beyond his professional contributions while maintaining his family as a central priority. With his exemplary productivity and interests in the surgical and laboratory sciences, history of medicine, appreciation of fine arts, and perceptive and effective interactions with family, friends, patients, and colleagues, the memory of Leonard

  11. Proteomics and SSH analyses of ALA-promoted fruit coloration and evidence for the involvement of a MADS-box gene, MdMADS1

    Directory of Open Access Journals (Sweden)

    Xinxin Feng

    2016-11-01

    Full Text Available Skin color is a key quality attribute of fruits and how to improve fruit coloration has long been a major concern. 5-Aminolevulinic acid (ALA, a natural plant growth regulator, can significantly increase anthocyanin accumulation in fruit skin and therefore effectively improve coloration of many fruits, including apple. However, the molecular mechanism how ALA stimulates anthocyanin accumulation in fruit skin remains unknown. Here, we investigated the impact of ALA on apple skin at the protein and mRNA levels. A total of 85 differentially expressed proteins in apple skins between ALA and water treatment (control were identified by complementary gel-based and gel-freeseparation techniques. Most of these differentially expressed proteins were up-regulated by ALA. Function analysis suggested that 87.06% of the ALA-responsive proteins were associated with fruit ripening. To further screen ALA-responsive regulators, we constructed a subtracted cDNA library (tester: ALA treatment; driver: control and obtained 104 differentially expressed unigenes, of which 38 unigenes were indicators for the fruit ripening-related gene. The differentially changed proteins and transcripts did not correspond well at an individual level, but showed similar regulated direction in function at the pathway level. Among the identified fruit ripening-related genes, the expression of MdMADS1, a developmental transcription regulator of fruit ripening, was positively correlated with expression of anthocyanin biosynthetic genes (MdCHS, MdDFR, MdLDOX and MdUFGT in apple skin under ALA treatment. Moreover, overexpression of MdMADS1 enhanced anthocyanin content in transformed apple calli, which was further enhanced by ALA. The anthocyanin content in MdMADS1-silenced calli was less than that in the control with ALA treatment, but higher than that without ALA treatment. These results indicated that MdMADS1 is involved in ALA-induced anthocyanin accumulation. In addition, anthocyanin

  12. Trends in MD/PhD Graduates Entering Psychiatry: Assessing the Physician-Scientist Pipeline.

    Science.gov (United States)

    Arbuckle, Melissa R; Luo, Sean X; Pincus, Harold Alan; Gordon, Joshua A; Chung, Joyce Y; Chavez, Mark; Oquendo, Maria A

    2018-06-01

    The goal of this study was to identify trends in MD/PhD graduates entering psychiatry, to compare these trends with other specialties, and to review strategies for enhancing the physician-scientist pipeline. Data on 226,588 medical students graduating from Liaison Committee on Medical Education accredited programs between 1999 and 2012 (6626 MD/PhDs) were used to evaluate the number, percentage, and proportion of MD/PhDs entering psychiatry in comparison with other specialties (neurology, neurosurgery, internal medicine, family medicine, and radiation oncology). Linear regression and multiple linear regression determined whether these values increased over time and varied by sex. Over 14 years, an average of 18 MD/PhDs (range 13-29) enrolled in psychiatry each year. The number of MD/PhDs going into psychiatry significantly increased, although these gains were modest (less than one additional MD/PhD per year). The proportion of students entering psychiatry who were MD/PhDs varied between 2.9 and 5.9 per 100 residents, with no significant change over time. There was also no change in the percentage of MD/PhDs entering psychiatry from among all MD/PhD graduates. The rate of increase in the number of MD/PhDs going into psychiatry did not differ significantly from other specialties except for family medicine, which is decreasing. The rate of MD/PhDs going into psychiatry was higher for women, suggesting closure of the sex gap in 17 years. Despite the increase in the number of MD/PhDs entering psychiatry, these numbers remain low. Expanding the cohort of physician-scientists dedicated to translational research in psychiatry will require a multipronged approach.

  13. Hybrid classical/quantum simulation for infrared spectroscopy of water

    Science.gov (United States)

    Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro

    2018-05-01

    We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.

  14. Correlation of simulated TEM images with irradiation induced damage

    International Nuclear Information System (INIS)

    Schaeublin, R.; Almeida, P. de; Almazouzi, A.; Victoria, M.

    2000-01-01

    Crystal damage induced by irradiation is investigated using transmission electron microscopy (TEM) coupled to molecular dynamics (MD) calculations. The displacement cascades are simulated for energies ranging from 10 to 50 keV in Al, Ni and Cu and for times of up to a few tens of picoseconds. Samples are then used to perform simulations of the TEM images that one could observe experimentally. Diffraction contrast is simulated using a method based on the multislice technique. It appears that the cascade induced damage in Al imaged in weak beam exhibits little contrast, which is too low to be experimentally visible, while in Ni and Cu a good contrast is observed. The number of visible clusters is always lower than the actual one. Conversely, high resolution TEM (HRTEM) imaging allows most of the defects contained in the sample to be observed, although experimental difficulties arise due to the low contrast intensity of the smallest defects. Single point defects give rise in HTREM to a contrast that is similar to that of cavities. TEM imaging of the defects is discussed in relation to the actual size of the defects and to the number of clusters deduced from MD simulations

  15. Molecular interactions between single layered MoS2 and biological molecules† †Electronic supplementary information (ESI) available: SFG data analysis methods, spectral fitting parameters, additional spectra, CD spectrum, and details about MD simulation methods. See DOI: 10.1039/c7sc04884j

    Science.gov (United States)

    Xiao, Minyu; Wei, Shuai; Li, Yaoxin; Jasensky, Joshua; Chen, Junjie; Brooks, Charles L.

    2017-01-01

    Two-dimensional (2D) materials such as graphene, molybdenum disulfide (MoS2), tungsten diselenide (WSe2), and black phosphorous are being developed for sensing applications with excellent selectivity and high sensitivity. In such applications, 2D materials extensively interact with various analytes including biological molecules. Understanding the interfacial molecular interactions of 2D materials with various targets becomes increasingly important for the progression of better-performing 2D-material based sensors. In this research, molecular interactions between several de novo designed alpha-helical peptides and monolayer MoS2 have been studied. Molecular dynamics simulations were used to validate experimental data. The results suggest that, in contrast to peptide–graphene interactions, peptide aromatic residues do not interact strongly with the MoS2 surface. It is also found that charged amino acids are important for ensuring a standing-up pose for peptides interacting with MoS2. By performing site-specific mutations on the peptide, we could mediate the peptide–MoS2 interactions to control the peptide orientation on MoS2. PMID:29675220

  16. Combined spectroscopic, DFT, TD-DFT and MD study of newly synthesized thiourea derivative

    Science.gov (United States)

    Menon, Vidya V.; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Bielenica, Anna; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, Christian

    2018-03-01

    A novel thiourea derivative, 1-(3-bromophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (ANF-22) is synthesized and characterized by FTIR, FT-Raman and NMR spectroscopy experimentally and theoretically. A detailed conformational analysis of the title molecule has been conducted in order to locate the lowest energy geometry, which was further subjected to the detailed investigation of spectroscopic, reactive, degradation and docking studies by density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Time dependent DFT (TD-DFT) calculations have been used also in order to simulate UV spectra and investigate charge transfer within molecule. Natural bond orbital analysis has been performed analyzing the charge delocalization and using HOMO and LUMO energies the electronic properties are analyzed. Molecular electrostatic potential map is used for the quantitative measurement of active sites in the molecule. In order to determine the locations possibly prone to electrophilic attacks we have calculated average local ionization energies and mapped them to the electron density surface. Further insight into the local reactivity properties have been obtained by calculation of Fukui functions, also mapped to the electron density surface. Possible degradation properties by the autoxidation mechanism have been assessed by calculations of bond dissociation energies for hydrogen abstraction. Atoms of title molecule with significant interactions with water molecules have been determined by calculations of radial distribution functions. The title compound can be a lead compound for developing new analgesic drug.

  17. Scalar Similarity for Relaxed Eddy Accumulation Methods

    Science.gov (United States)

    Ruppert, Johannes; Thomas, Christoph; Foken, Thomas

    2006-07-01

    The relaxed eddy accumulation (REA) method allows the measurement of trace gas fluxes when no fast sensors are available for eddy covariance measurements. The flux parameterisation used in REA is based on the assumption of scalar similarity, i.e., similarity of the turbulent exchange of two scalar quantities. In this study changes in scalar similarity between carbon dioxide, sonic temperature and water vapour were assessed using scalar correlation coefficients and spectral analysis. The influence on REA measurements was assessed by simulation. The evaluation is based on observations over grassland, irrigated cotton plantation and spruce forest. Scalar similarity between carbon dioxide, sonic temperature and water vapour showed a distinct diurnal pattern and change within the day. Poor scalar similarity was found to be linked to dissimilarities in the energy contained in the low frequency part of the turbulent spectra ( definition.

  18. Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations

    Science.gov (United States)

    Ge, Yushu; van der Kamp, Marc; Malaisree, Maturos; Liu, Dan; Liu, Yi; Mulholland, Adrian J.

    2017-11-01

    Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.

  19. Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations.

    Science.gov (United States)

    Ge, Yushu; van der Kamp, Marc; Malaisree, Maturos; Liu, Dan; Liu, Yi; Mulholland, Adrian J

    2017-11-01

    Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.

  20. MD simulations and QM/MM calculations show that single-site mutations of cytochrome P450BM3 alter the active site’s complexity and the chemoselectivity of oxidation without changing the active species† †Electronic supplementary information (ESI) available: The RMS deviation of the protein during 100 ns (and 200 ns) of simulation and the total QM/MM and ZPE energies, as well as the Cartesian coordinates of all of the computed species. See DOI: 10.1039/c7sc01932g

    Science.gov (United States)

    Dubey, Kshatresh Dutta; Wang, Binju; Vajpai, Manu

    2017-01-01

    It is a long-standing mechanistic consensus that the mutation of the proton-shuttle mediator Threonine (T) in Cytochrome P450 enzymes severs the water channel and thereby quenches the formation of the active species: the high-valent iron(iv)-oxo porphyrin π-cation radical species, compound I (Cpd I). Using MD simulations and hybrid QM/MM calculations of P450BM3 we demonstrate that this is not the case. Thus, while the original water channel is disrupted in the T268A mutant of the enzyme, a new channel is formed that generates Cpd I. With this new understanding, we address the puzzling regiochemical and kinetic-isotope effect (KIE) results (Volz et al., J. Am. Chem. Soc., 2002, 124, 9724–9725) on the sulfoxidation and N-dealkylation of dimethyl-(4-methylsulfanyl-phenyl)-amine by wild type (WT) P450BM3 and its T268A vs. F87A mutants. We show that the observed variable ratio of S/Me oxidation for these enzymes, vis-à-vis the constant KIE, originates from Cpd I being the sole oxidant. Thus, while the conserved KIE probes the conserved nature of the transition state, the variable regiochemical S/Me ratio reflects the active-site reorganization in the mutants: the shifted location of the new water channel in T268A tightens the binding of the S-end by Cpd I and increases the S/Me ratio, whereas the absence of π-interaction with the S-end in F87A creates a looser binding that lowers the S/Me ratio. Our results match the experimental findings. As such, this study sheds light on puzzling experimental results, and may shift a central paradigm in P450 research. The broader implication on enzymatic research is that a single-site mutation is not a localised alteration but one that may lead to a profound change in the active site, sufficiently so as to change the chemoselectivity of catalyzed reactions. PMID:29568477

  1. MD-11 PCA - View of aircraft on ramp

    Science.gov (United States)

    1995-01-01

    This McDonnell Douglas MD-11 is taxiing to a position on the flightline at NASA's Dryden Flight Research Center, Edwards, California, following its completion of the first and second landings ever performed by a transport aircraft under engine power only (on Aug. 29, 1995). The milestone flight, with NASA research pilot and former astronaut Gordon Fullerton at the controls, was part of a NASA project to develop a computer-assisted engine control system that enables a pilot to land a plane safely when its normal control surfaces are disabled. The Propulsion-Controlled Aircraft (PCA) system uses standard autopilot controls already present in the cockpit, together with the new programming in the aircraft's flight control computers. The PCA concept is simple. For pitch control, the program increases thrust to climb and reduces thrust to descend. To turn right, the autopilot increases the left engine thrust while decreasing the right engine thrust. The initial Propulsion-Controlled Aircraft studies by NASA were carried out at Dryden with a modified twin-engine F-15 research aircraft.

  2. MD-11 PCA - Closeup view of aircraft on ramp

    Science.gov (United States)

    1995-01-01

    This McDonnell Douglas MD-11 has taxied to a position on the flightline at NASA's Dryden Flight Research Center, Edwards, California, following its completion of the first and second landings ever performed by a transport aircraft under engine power only (on Aug. 29, 1995). The milestone flight, with NASA research pilot and former astronaut Gordon Fullerton at the controls, was part of a NASA project to develop a computer-assisted engine control system that enables a pilot to land a plane safely when its normal control surfaces are disabled. The Propulsion-Controlled Aircraft (PCA) system uses standard autopilot controls already present in the cockpit, together with the new programming in the aircraft's flight control computers. The PCA concept is simple. For pitch control, the program increases thrust to climb and reduces thrust to descend. To turn right, the autopilot increases the left engine thrust while decreasing the right engine thrust. The initial Propulsion-Controlled Aircraft studies by NASA were carried out at Dryden with a modified twin-engine F-15 research aircraft.

  3. MD#1182: Calibration of diamond particle detectors in IP6

    CERN Document Server

    Valette, Matthieu; Lindstrom, Bjorn Hans Filip; Wiesner, Christoph

    2017-01-01

    In case of an asynchronous beam dump with a fully filled LHC machine it is expected that all standard ionisation chamber Beam Loss Monitors (IC BLM) around the LHC dumping region in IP6 will be saturated. Diamond Beam Loss Monitors (dBLM) were therefore installed next to the movable dump protection absorber (TCDQ) downstream of the extraction kickers. These detectors allow resolving losses at a nanosecond timescale and with an dynamic range of several orders of magnitude; thus, allowing to know the number of nominal bunches impacting the TCDQ. After a first series of calibrations using asynchronous beam dump tests, an experiment was conducted during MD#1182 to demonstrate the possibility of resolving a nominal bunch hitting the TCDQ. The impact parameter of the bunches on the TCDQ was first scanned using probe bunches with lower intensity then tests were done with nominal bunches (1.1e11 p/bunch) at injection energy. High energy calibration of the losses was also attempted unsuccessfully. Due to different beh...

  4. 76 FR 81826 - Drawbridge Operation Regulation; Pocomoke River, Pocomoke City, MD

    Science.gov (United States)

    2011-12-29

    ... Operation Regulation; Pocomoke River, Pocomoke City, MD AGENCY: Coast Guard, DHS. ACTION: Notice of... River, mile 15.6, at Pocomoke City, MD. The deviation restricts the operation of the draw span to... five hours advance notice is given. The Route 675 Bridge across Pocomoke River, mile 15.6 at Pocomoke...

  5. Possibilities of production of neutron-rich Md isotopes in multi-nucleon transfer reactions

    Energy Technology Data Exchange (ETDEWEB)

    Mun, Myeong-Hwan; Lee, Young-Ouk [Korea Atomic Energy Research Institue, Daejeon (Korea, Republic of); Adamian, G.G.; Antonenko, N.V. [Joint Institute for Nuclear Research, Dubna (Russian Federation)

    2016-12-15

    The possibilities of production of yet unknown neutron-rich isotopes of Md are explored in several multi-nucleon transfer reactions with actinide targets and stable and radioactive beams. The projectile-target combinations and bombarding energies are suggested to produce new neutron-rich isotopes of Md in future experiments. (orig.)

  6. 77 FR 29692 - Segun M. Rasaki, M.D.; Decision and Order

    Science.gov (United States)

    2012-05-18

    ... CFR 1316.67. Dated: May 4, 2012. Michele M. Leonhart, Administrator. Paul E. Soeffing, Esq., for the... reinstatement.'' Stuart A. Bergman, M.D., 70 Fed. Reg. 33,193 (DEA 2005); Roger A. Rodriguez, M.D., 70 Fed. Reg...

  7. 78 FR 47412 - Tyson D. Quy, M.D.; Decision and Order

    Science.gov (United States)

    2013-08-05

    ... Green, Jr., M.D., 59 FR 51,453 (DEA 1994); David E. Trawick, D.D.S., 53 FR 5,326 (DEA 1988). Here, the...) (ten years); Norman Alpert, M.D., 58 FR 67,420, 67,421 (DEA 1993) (seven years). Here, the conditions...

  8. 75 FR 76688 - Drawbridge Operation Regulation; Isle of Wight (Sinepuxent) Bay, Ocean City, MD

    Science.gov (United States)

    2010-12-09

    ..., mile 0.5, at Ocean City, with a vertical clearance of 13 feet above mean high tide in the closed...-AA09 Drawbridge Operation Regulation; Isle of Wight (Sinepuxent) Bay, Ocean City, MD AGENCY: Coast... Ocean City, MD. This proposed rule will require any mariner requesting an opening in the evening hours...

  9. 76 FR 17673 - Bienvenido Tan, M.D.; Denial of Application

    Science.gov (United States)

    2011-03-30

    ... (alprazolam) to help him sleep. Id. at 64. R.E. opted to buy the drugs from Respondent's dispensary and... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 09-12] Bienvenido Tan, M.D... Control, Drug Enforcement Administration, issued an Order to Show Cause to Bienvenido Tan, M.D...

  10. 76 FR 15214 - Special Local Regulations for Marine Events; Potomac River, Charles County, MD

    Science.gov (United States)

    2011-03-21

    ...-AA08 Special Local Regulations for Marine Events; Potomac River, Charles County, MD AGENCY: Coast Guard... for Marine Events; Potomac River, Charles County, MD'' in the Federal Register (76 FR 1381). We... follows: Sec. 100.35-T05-1113 Special Local Regulations for Marine Events; Potomac River, Charles County...

  11. 77 FR 6708 - Special Local Regulations for Marine Events; Potomac River, Charles County, MD

    Science.gov (United States)

    2012-02-09

    ...-AA08 Special Local Regulations for Marine Events; Potomac River, Charles County, MD AGENCY: Coast Guard... River, Charles County, MD. (a) Regulated area. The following location is a regulated area: All waters of... local regulations during the ``Potomac River Sharkfest Swim'' amateur swim, a marine event to be held on...

  12. 76 FR 1381 - Special Local Regulations for Marine Events; Potomac River, Charles County, MD

    Science.gov (United States)

    2011-01-10

    ...-AA08 Special Local Regulations for Marine Events; Potomac River, Charles County, MD AGENCY: Coast Guard... Regulations for Marine Events; Potomac River, Charles County, MD. (a) Regulated area. The following location... local regulations during the ``Potomac River Sharkfest Swim'' amateur swim, a marine event to be held on...

  13. 33 CFR 110.70a - Northeast River, North East, Md.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Northeast River, North East, Md. 110.70a Section 110.70a Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.70a Northeast River, North East, Md. The water...

  14. Functional Characterization of the Apple RING E3 Ligase MdMIEL1 in Transgenic Arabidopsis

    Directory of Open Access Journals (Sweden)

    Jianping AN

    2017-03-01

    Full Text Available E3 ubiquitin ligases are involved in various physiological processes, and they play pivotal roles in growth and development. In this study, we identified a previously unknown gene in the apple fruit (Malus × domestica and named it MdMIEL1. The MdMIEL1 gene encoded a protein that contained a zinc-finger domain at its N-terminus and a RING-finger motif at its C-terminus. To investigate MdMIEL1 functions, we generated transgenic Arabidopsis lines expressing the MdMIEL1 gene under the control of the Cauliflower mosaic virus 35S promoter. Interestingly, ectopic expression of MdMIEL1 in Arabidopsis produced multiple phenotypes, including early germination, early flowering and a lateral root number increase relative to wild-type plants. Further analysis indicated that MdMIEL1 regulated lateral root initiation by increasing auxin accumulation in the roots. In a word, these results suggest that, MdMIEL1 as a novel RING-finger ubiquitin ligase influences plant growth and development, and highlight that MdMIEL1 regulates lateral root growth.

  15. 77 FR 35021 - Kwan Bo Jin, M.D.; Decision and Order

    Science.gov (United States)

    2012-06-12

    ...] DEA registration is not appropriate.'' Anibal P. Herrera, M.D., 61 FR 65,075, 65,078 (DEA 1996); see... ``there were serious questions as to the integrity of the registrant.'' Anibal P. Herrera, M.D., 61 FR 65...

  16. Characterization of the conformational space of a triple-stranded beta-sheet forming peptide with molecular dynamics simulations

    NARCIS (Netherlands)

    Soto, P; Colombo, G

    2004-01-01

    Molecular dynamics (MD) simulations have been performed on a series of mutants of the 20 amino acid peptide Betanova in order to critically assess the ability of MD simulations to reproduce the folding and stability of small beta-sheet-forming peptides on currently accessible timescales. Simulations

  17. Molecular dynamics simulation of a phospholipid membrane

    NARCIS (Netherlands)

    Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.

    We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in

  18. William Bradley Coley, MD, and the phenomenon of spontaneous regression

    Directory of Open Access Journals (Sweden)

    Vernon LF

    2018-04-01

    Full Text Available Leonard F Vernon Sherman College of Chiropractic, Spartanburg, SC, USA Abstract: The standard definition of spontaneous regression (SR of cancer is as follows, “…when a malignant tumor partially or completely disappears without treatment or in the presence of therapy which is considered inadequate to exert a significant influence on neoplastic disease.” SR is also known as Saint Peregrine tumor, the name taken from a young priest, Peregrine Laziosi (1260 [5]–1345, exact date is unknown, who had been diagnosed with a tumor of the tibia. The mass eventually grew so large that it broke through the skin and became severely infected. The available treatment for this condition was limited to amputation. Historical records report that on the day of surgery, physicians found that the tumor had disappeared and reportedly never returned. To date, the medical literature consists only of individual case studies and overviews of this phenomenon. The most cited work on the subject was done by surgeons Tilden Everson and Warren Cole who reviewed 176 published cases of SR from 1900 to 1960. While a percentage of these were found not to be cases of SR, there remained a number of unexplained cases. A frequent theme in many cases of SR is the co-occurrence of infection. Given the current interest in immunotherapy in the treatment of cancer, this article discusses one of the very early pioneers of this theory, William Bradley Coley, MD, a surgeon who was clearly ahead of his time. Ostracized by colleagues for his belief that stimulation of the immune system could in fact produce a regression of cancer, Coley remained convinced that his theory was right and, while he was not familiar with cytokines such as tumor necrosis factor (TNF, interferons, and streptokinase, he knew instinctively that an innate immune response was taking place. Keywords: autoimmunity, cancer, fever, infection, immunotherapy, tumor, cytokines

  19. Expression Analysis of the MdCIbHLH1 Gene in Apple Flower Buds and Seeds in the Process of Dormancy

    Directory of Open Access Journals (Sweden)

    Yiran Ren

    2016-03-01

    Full Text Available A bHLH transcription factor that is induced by low temperature was found in apple (Malus × domestica Borkh.. To understand the sequence characteristics of the gene, bioinformatics analysis was performed. Furthermore, gene expression patterns of the laminated apple seeds and lateral flower buds were analyzed during the period of dormancy release with semi-quantitative RT-PCR. Based on secondary structure predictions, the results showed that the MdCIbHLH1 protein structure mainly included α-helix and random coil, while β-sheet and extended strand content was less. Semi-quantitative RT-PCR analysis showed that the expression patterns of MdCIbHLH1 were similar in laminated apple seeds and lateral flower buds during the period of dormancy release. Before dormancy release, expression levels of MdCIbHLH1 were high and gradually decreased during the period of dormancy release. These results indicated that MdCIbHLH1 might play an important role during dormancy release in apple seeds and apple buds.

  20. Molecular dynamics simulation for PBR pebble tracking simulation via a random walk approach using Monte Carlo simulation.

    Science.gov (United States)

    Lee, Kyoung O; Holmes, Thomas W; Calderon, Adan F; Gardner, Robin P

    2012-05-01

    Using a Monte Carlo (MC) simulation, random walks were used for pebble tracking in a two-dimensional geometry in the presence of a biased gravity field. We investigated the effect of viscosity damping in the presence of random Gaussian fluctuations. The particle tracks were generated by Molecular Dynamics (MD) simulation for a Pebble Bed Reactor. The MD simulations were conducted in the interaction of noncohesive Hertz-Mindlin theory where the random walk MC simulation has a correlation with the MD simulation. This treatment can easily be extended to include the generation of transient gamma-ray spectra from a single pebble that contains a radioactive tracer. Then the inverse analysis thereof could be made to determine the uncertainty of the realistic measurement of transient positions of that pebble by any given radiation detection system designed for that purpose. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. The baryonic self similarity of dark matter

    International Nuclear Information System (INIS)

    Alard, C.

    2014-01-01

    The cosmological simulations indicates that dark matter halos have specific self-similar properties. However, the halo similarity is affected by the baryonic feedback. By using momentum-driven winds as a model to represent the baryon feedback, an equilibrium condition is derived which directly implies the emergence of a new type of similarity. The new self-similar solution has constant acceleration at a reference radius for both dark matter and baryons. This model receives strong support from the observations of galaxies. The new self-similar properties imply that the total acceleration at larger distances is scale-free, the transition between the dark matter and baryons dominated regime occurs at a constant acceleration, and the maximum amplitude of the velocity curve at larger distances is proportional to M 1/4 . These results demonstrate that this self-similar model is consistent with the basics of modified Newtonian dynamics (MOND) phenomenology. In agreement with the observations, the coincidence between the self-similar model and MOND breaks at the scale of clusters of galaxies. Some numerical experiments show that the behavior of the density near the origin is closely approximated by a Einasto profile.

  2. Analysis of quasielastic neutron scattering (QENS) data of discotic systems using different molecular dynamics (MD) models

    International Nuclear Information System (INIS)

    Kruglova, O.; Mulder, F.M.; Picken, S.J.; Stride, J.; Kearley, G.J.

    2004-01-01

    Discotic molecules are composed of an aromatic core surrounded by aliphatic chains. These molecules are of importance because they can form columns in which the π orbitals of neighbouring molecules overlap leading to conductivity along the column. These materials find applications in molecular electronics and recently--with record quantum efficiencies--in photo voltaics. Because the correlation time of the electron (or hole) hopping is in the picosecond region, molecular dynamics on this timescale is of central importance. We have recently shown that these dynamics, which is easily measured by quasielastic neutron scattering (QENS), can be understood with a rather simple 'short single-column' model via an MD simulation that reproduces the measured QENS spectra. Before progressing to the larger technologically important systems we must understand any fortuitous error cancellations that may cause the simple model to reproduce the experimental signal so well. By taking a very simple discotic, hexamethyltriphenylene (HMT), we are able to compare QENS data with three types of models: simple column, cluster and periodic. It transpires that the cluster model cannot properly accommodate inter column interactions, and a fairly modest periodic model overcomes this problem and the tendency for un-physical harmonic modes along the column

  3. Using Engine Thrust for Emergency Flight Control: MD-11 and B-747 Results

    Science.gov (United States)

    Burcham, Frank W., Jr.; Maine, Trindel A.; Burken, John J.; Bull, John

    1998-01-01

    With modern digital control systems, using engine thrust for emergency flight control to supplement or replace failed aircraft normal flight controls has become a practical consideration. The NASA Dryden Flight Research Center has developed a propulsion-controlled aircraft (PCA) system in which computer-controlled engine thrust provides emergency flight control. An F-15 and an MD-11 airplane have been landed without using any flight control surfaces. Preliminary studies have also been conducted that show that engines on only one wing can provide some flight control capability if the lateral center of gravity can be shifted toward the side of the airplane that has the operating engine(s). Simulator tests of several airplanes with no flight control surfaces operating and all engines out on the left wing have all shown positive control capability within the available range of lateral center-of-gravity offset. Propulsion-controlled aircraft systems that can operate without modifications to engine control systems, thus allowing PCA technology to be installed on less capable airplanes or at low cost, are also desirable. Further studies have examined simplified 'PCA Lite' and 'PCA Ultralite' concepts in which thrust control is provided by existing systems such as auto-throttles or a combination of existing systems and manual pilot control.

  4. Renewing the Respect for Similarity

    Directory of Open Access Journals (Sweden)

    Shimon eEdelman

    2012-07-01

    Full Text Available In psychology, the concept of similarity has traditionally evoked a mixture of respect, stemmingfrom its ubiquity and intuitive appeal, and concern, due to its dependence on the framing of the problemat hand and on its context. We argue for a renewed focus on similarity as an explanatory concept, bysurveying established results and new developments in the theory and methods of similarity-preservingassociative lookup and dimensionality reduction — critical components of many cognitive functions, aswell as of intelligent data management in computer vision. We focus in particular on the growing familyof algorithms that support associative memory by performing hashing that respects local similarity, andon the uses of similarity in representing structured objects and scenes. Insofar as these similarity-basedideas and methods are useful in cognitive modeling and in AI applications, they should be included inthe core conceptual toolkit of computational neuroscience.

  5. Apple F-box Protein MdMAX2 Regulates Plant Photomorphogenesis and Stress Response

    Directory of Open Access Journals (Sweden)

    Jian-Ping An

    2016-11-01

    Full Text Available MAX2 (MORE AXILLARY GROWTH2 is involved in diverse physiological processes, including photomorphogenesis, the abiotic stress response, as well as karrikin and strigolactone signaling-mediated shoot branching. In this study, MdMAX2, an F-box protein that is a homolog of Arabidopsis MAX2, was identified and characterized. Overexpression of MdMAX2 in apple calli enhanced the accumulation of anthocyanin. Ectopic expression of MdMAX2 in Arabidopsis exhibited photomorphogenesis phenotypes, including increased anthocyanin content and decreased hypocotyl length. Further study indicated that MdMAX2 might promote plant photomorphogenesis by affecting the auxin signaling as well as other plant hormones. Transcripts of MdMAX2 were noticeably up-regulated in response to NaCl and Mannitol treatments. Moreover, compared with the wild type, the MdMAX2-overexpressing apple calli and Arabidopsis exhibited increased tolerance to salt and drought stresses. Taken together, these results suggest that MdMAX2 plays a positive regulatory role in plant photomorphogenesis and stress response.

  6. Sustainable water recovery from oily wastewater via forward osmosis-membrane distillation (FO-MD).

    Science.gov (United States)

    Zhang, Sui; Wang, Peng; Fu, Xiuzhu; Chung, Tai-Shung

    2014-04-01

    This study proposed and investigated a hybrid forward osmosis - membrane distillation (FO-MD) system for sustainable water recovery from oily wastewater by employing lab-fabricated FO and MD hollow fiber membranes. Stable oil-in-water emulsions of different concentrations with small droplet sizes (oil droplets and partial permeation of acetic acid could be achieved. Finally, an integrated FO-MD system was developed to treat the oily wastewater containing petroleum, surfactant, NaCl and acetic acid at 60 °C in the batch mode. The water flux in FO undergoes three-stage decline due to fouling and reduction in osmotic driving force, but is quite stable in MD regardless of salt concentration. Oily wastewater with relatively high salinity could be effectively recovered by the FO-MD hybrid system while maintaining large water flux, at least 90% feed water recovery could be readily attained with only trace amounts of oil and salts, and the draw solution was re-generated for the next rounds of FO-MD run. Interestingly, significant amount of acetic acid was also retained in the permeate for further reuse as a chemical additive during the production of crude oil. The work has demonstrated that not only water but also organic additives in the wastewater could be effectively recovered by FO-MD systems for reuse or other utilizations. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Molecular dynamics simulations with electronic stopping can reproduce experimental sputtering yields of metals impacted by large cluster ions

    Science.gov (United States)

    Tian, Jiting; Zhou, Wei; Feng, Qijie; Zheng, Jian

    2018-03-01

    An unsolved problem in research of sputtering from metals induced by energetic large cluster ions is that molecular dynamics (MD) simulations often produce sputtering yields much higher than experimental results. Different from the previous simulations considering only elastic atomic interactions (nuclear stopping), here we incorporate inelastic electrons-atoms interactions (electronic stopping, ES) into MD simulations using a friction model. In this way we have simulated continuous 45° impacts of 10-20 keV C60 on a Ag(111) surface, and found that the calculated sputtering yields can be very close to the experimental results when the model parameter is appropriately assigned. Conversely, when we ignore the effect of ES, the yields are much higher, just like the previous studies. We further expand our research to the sputtering of Au induced by continuous keV C60 or Ar100 bombardments, and obtain quite similar results. Our study indicates that the gap between the experimental and the simulated sputtering yields is probably induced by the ignorance of ES in the simulations, and that a careful treatment of this issue is important for simulations of cluster-ion-induced sputtering, especially for those aiming to compare with experiments.

  8. NMR solution structures and MD-simulation of procyanidin B1, B2, and C1

    Science.gov (United States)

    Procyanidins are polyphenols associated with a variety of benefits to the health of both plants and animals. Procyanidins provide increased defense against microbes, act as strong antioxidants, and may decrease the incidence of cancer. Key to understanding how procyanidins function requires understa...

  9. Efficient approach to obtain free energy gradient using QM/MM MD simulation

    International Nuclear Information System (INIS)

    Asada, Toshio; Koseki, Shiro; Ando, Kanta

    2015-01-01

    The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means of FEG and the nudged elastic band (NEB) method

  10. MD simulation of pair correlation function and static structure of charged colloidal suspensions

    NARCIS (Netherlands)

    Allahyarov, E.A.; Schram, P.P.J.M.; Trigger, S.A.

    1996-01-01

    On the basis of molecular dynamics the radial distribution function (r.d.f.) of colloidal plasma is calculated by using the effective macroion interaction in TPS-form. The vital importance of the minimum in the potential, which is a consequences of the strong counterion-macroion interaction, is

  11. Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations

    NARCIS (Netherlands)

    Deplazes, Evelyne; Louhivuori, Martti; Jayatilaka, Dylan; Marrink, Siewert J.; Corry, Ben

    The mechanosensitive channel of large conductance (MscL) has become a model system in which to understand mechanosensation, a process involved in osmoregulation and many other physiological functions. While a high resolution closed state structure is available, details of the open structure and the

  12. Sputtering from swift-ion trails in LiF: A hybrid PIC/MD simulation

    Energy Technology Data Exchange (ETDEWEB)

    Cherednikov, Yaroslav; Sun, Si Neng; Urbassek, Herbert M., E-mail: urbassek@rhrk.uni-kl.de

    2013-11-15

    We model the sputtering of a LiF crystal induced by swift-ion impact. The impinging ion creates a trail of doubly ionized F{sup +} ions, while simultaneously the corresponding electrons are set free. Ions move according to molecular dynamics, while excited electrons are treated by a particle-in-cell scheme. We treat the recombination time of electrons as a free parameter in our model. We find that the energy distribution of sputtered ions consists of 2 groups: a low-energy group centered at <1 eV, and a high-energy group at 7–8 eV. Fast ions (mainly Li{sup +}) are emitted early; these charge the surface negatively. Later, larger cluster ions and also neutral LiF molecules are emitted. Emission occurs at low angles to the surface normal. A jet along the normal direction can be observed, which is due to the electric field building up at the track surface. With increasing recombination time, processes are colder; sputtering decreases and the non-thermal jet structure becomes stronger.

  13. Characterization of an Autophagy-related Gene MdATG8i from apple

    Directory of Open Access Journals (Sweden)

    Ping eWang

    2016-05-01

    Full Text Available Nutrient deficiencies restrict apple (Malus sp. tree growth and productivity in Northwest China. The process of autophagy, a conserved degradation pathway in eukaryotic cells, has important roles in nutrient-recycling and helps improve plant performance during periods of nutrient-starvation. Little is known about the functioning of autophagy-related genes (ATGs in apple. In this study, one of the ATG8 gene family members MdATG8i was isolated from M. domestica. MdATG8i has conserved putative tubulin binding sites and ATG7 interaction domains. A 1865-bp promoter region cloned from apple genome DNA was predicated to have cis-regulatory elements responsive to light, environmental stresses and hormones. MdATG8i transcriptions were induced in response to leaf senescence, nitrogen depletion, and oxidative stress. At cellular level, MdATG8i protein was expressed in the nucleus and cytoplasm of onion epidermal cells. Yeast two-hybrid tests showed that MdATG8i could interact with MdATG7a and MdATG7b. In Arabidopsis, its heterologous expression was associated with enhanced vegetative growth, leaf senescence, and tolerance to nitrogen- and carbon-starvation. MdATG8i-overexpressing ‘Orin’ apple callus lines also displayed improved tolerance to nutrient-limited conditions. Our results demonstrate that MdATG8i protein could function in autophagy in a conserved way, as a positive regulator in the response to nutrient-starvation.

  14. Tutorial: Determination of thermal boundary resistance by molecular dynamics simulations

    Science.gov (United States)

    Liang, Zhi; Hu, Ming

    2018-05-01

    Due to the high surface-to-volume ratio of nanostructured components in microelectronics and other advanced devices, the thermal resistance at material interfaces can strongly affect the overall thermal behavior in these devices. Therefore, the thermal boundary resistance, R, must be taken into account in the thermal analysis of nanoscale structures and devices. This article is a tutorial on the determination of R and the analysis of interfacial thermal transport via molecular dynamics (MD) simulations. In addition to reviewing the commonly used equilibrium and non-equilibrium MD models for the determination of R, we also discuss several MD simulation methods which can be used to understand interfacial thermal transport behavior. To illustrate how these MD models work for various interfaces, we will show several examples of MD simulation results on thermal transport across solid-solid, solid-liquid, and solid-gas interfaces. The advantages and drawbacks of a few other MD models such as approach-to-equilibrium MD and first-principles MD are also discussed.

  15. The core competencies of James Marion Sims, MD.

    Science.gov (United States)

    Straughn, J Michael; Gandy, Roy E; Rodning, Charles B

    2012-07-01

    The concept of core competencies in graduate medical education was introduced by the Accreditation Council for Graduate Medical Education of the American Medical Association to semiquantitatively assess the professional performance of students, residents, practitioners, and faculty. Many aspects of the career of J. Marion Sims, MD, are exemplary of those core competencies: MEDICAL KNOWLEDGE: Author of the first American textbook related to gynecology. MEDICAL CARE: Innovator of the Sims' Vaginal Speculum, Sims' Position, Sims' Test, and vesico-/rectovaginal fistulorrhaphy; advocated abdominal exploration for penetrating wounds; performed the first cholecystostomy. PROFESSIONALISM: Served as President of the New York Academy of Medicine, the American Medical Association, and the American Gynecologic Society. INTERPERSONAL RELATIONSHIPS/COMMUNICATION: Cared for the indigent, hearthless, indentured, disenfranchised; served as consulting surgeon to the Empress Eugénie (France), the Duchess of Hamilton (Scotland), the Empress of Austria, and other royalty of the aristocratic Houses of Europe; accorded the National Order of the Legion of Honor. PRACTICE-BASED LEARNING: Introduction of silver wire sutures; adoption of the principles of asepsis/antisepsis; adoption of the principles of general anesthesia. SYSTEMS-BASED PRACTICE: Established the Woman's Hospital, New York City, New York, the predecessor of the Memorial Sloan-Kettering Center for the Treatment of Cancer and Allied Diseases; organized the Anglo-American Ambulance Corps under the patronage of Napoleon III. What led him to a life of clinical and humanitarian service? First, he was determined to succeed. His formal medical/surgical education was perhaps the best available to North Americans during that era. Second, he was courageous in experimentation and innovation, applying new developments in operative technique, asepsis/antisepsis, and general anesthesia. Third, his curiosity was not burdened by rigid

  16. Differential host response to LPS variants in amniochorion and the TLR4/MD-2 system in Macaca nemestrina

    Science.gov (United States)

    Chang, Justine; Jain, Sumita; Carl, David J.; Paolella, Louis; Darveau, Richard P.; Gravett, Michael G.; Waldorf, Kristina M. Adams

    2010-01-01

    OBJECTIVES Microbial-specific factors are likely critical in determining whether bacteria trigger preterm labor. Structural variations in lipopolysaccharide (LPS), a component of gram-negative bacteria, can determine whether LPS has an inflammatory (agonist) or anti-inflammatory (antagonist) effect through Toll-like receptor 4 (TLR4). Our objective was to determine whether amniochorion can discriminate between LPS variants in a nonhuman primate model. We also cloned Macaca nemestrina TLR4 and MD-2 and compared this complex functionally to the human homologue to establish whether nonhuman primates could be used to study TLR4 signaling in preterm birth. STUDY DESIGN Amniochorion explants from M. nemestrina were stimulated with a panel of LPS variants for 24 hours. Supernatants were analyzed for IL-1β, TNF-α, IL-6, IL-8 and prostaglandins E2 and F2α. Tissue expression of TLR1, 2, 4, 6, MyD88 and NF-kB was studied by RT-PCR. M. nemestrina TLR4 and MD2 genes were cloned and compared with their human counterparts in a recombinant TLR4 signaling system to determine LPS sensitivity. RESULTS LPS variants differentially stimulated cytokines and prostaglandins, which was not related to transcriptional changes of TLR4 or other TLRs. Nearly all elements of LPS binding and TLR4 leucine-rich repeats were conserved between humans and M. nemestrina. TLR4/MD-2 signaling complexes from both species were equally sensitive to LPS variants. CONCLUSIONS LPS variants elicit a hierarchical inflammatory response within amniochorion that may contribute to preterm birth. LPS sensitivity is similar between M. nemestrina and humans, validating M. nemestrina as an appropriate model to study TLR4 signaling in preterm birth. PMID:20619890

  17. MD#1826: Measurement of Quench Heater vertical kick

    CERN Document Server

    Valette, Matthieu; Lindstrom, Bjorn Hans Filip; Bortot, Lorenzo; Fernandez Navarro, Alejandro; Schmidt, Rudiger; Verweij, Arjan

    2018-01-01

    Following the observation of vertical orbit oscillations of the LHC beam between the detection of a (beam induced) quench of an LHC main dipole and the beam dump, a study was started to verify that the orbit distortions are caused by the firing of the quench heaters (QH). Simulation of the magnetic field generated by the discharge of the QH and its effect on the beam confirmed it was the most likely cause. A dedicated experiment with 450 GeV proton beams was performed to validate the simulation results. The results are presented below and compared to the simulations. Furthermore, estimates on the effect of quench heater firing in superconducting magnets other than the studied LHC main dipoles on the circulating proton beams in LHC and the future HL-LHC are discussed.

  18. LHC MD2877: Beam-beam long range impact on coupling measurements

    CERN Document Server

    Wenninger, Jorg; Carlier, Felix Simon; Coello De Portugal - Martinez Vazquez, Jaime Maria; Fuchsberger, Kajetan; Hostettler, Michi; Persson, Tobias Hakan Bjorn; Tomas Garcia, Rogelio; Valuch, Daniel; Garcia-Tabares Valdivieso, Ana; CERN. Geneva. ATS Department

    2018-01-01

    The LHC is now operating with a tune separation of ∼0.004 in collision. This puts tight constraints on the allowed transverse coupling since a |C−| larger than a fraction of the fractional tune split may lead to beam instabilities. In the last years a new tool based on the ADT used in a similar way as an AC-dipole to excite the beam was developed. The ADT AC-dipole gives coherent oscillations without increasing the beam emittance. These oscillations are analyzed automatically to obtain the value of the coupling. A coupling measurement campaign was done in 2017 and while the correction converged and stayed rather constant over time it was observed that depending on the target bunch and filling scheme the results could vary by Δ|C−| ∼ 0.002. In this MD report we investigated 3 different bunches, one with Long Range Beam-Beam (LRBB) in IPs 1 and 5, one with LRBB in all IPs and one with no LRBB. The results indicate that there are differences in coupling between the bunches experiencing different LR...

  19. Osmotically and thermally isolated forward osmosis-membrane distillation (fo-md) integrated module for water treatment applications

    KAUST Repository

    Ghaffour, Noreddine

    2016-09-01

    An integrated forward osmosis-membrane distillation (FO-MD) module and systems and methods incorporating the module is disclosed providing higher efficiencies and using less energy. The FO-MD module is osmotically and thermally isolated. The isolation can prevent mixing of FO draw solution/FO permeate and MD feed, and minimize dilution of FO draw solution and cooling of MD feed. The module provides MD feed solution and FO draw solution streams that flow in the same module but are separated by an isolation barrier. The osmotically and thermally isolated FO-MD integrated module, systems and methods offer higher driving forces of both FO and MD processes, higher recovery, and wider application than previously proposed hybrid FO- MD systems.

  20. Osmotically and thermally isolated forward osmosis-membrane distillation (fo-md) integrated module for water treatment applications

    KAUST Repository

    Ghaffour, NorEddine; Francis, Lijo; Li, Zhenyu; Valladares, Rodrigo; Alsaadi, Ahmad S.; Ghdaib, Muhannad Abu; Amy, Gary L.

    2016-01-01

    An integrated forward osmosis-membrane distillation (FO-MD) module and systems and methods incorporating the module is disclosed providing higher efficiencies and using less energy. The FO-MD module is osmotically and thermally isolated. The isolation can prevent mixing of FO draw solution/FO permeate and MD feed, and minimize dilution of FO draw solution and cooling of MD feed. The module provides MD feed solution and FO draw solution streams that flow in the same module but are separated by an isolation barrier. The osmotically and thermally isolated FO-MD integrated module, systems and methods offer higher driving forces of both FO and MD processes, higher recovery, and wider application than previously proposed hybrid FO- MD systems.

  1. MD 2485: Active halo control using narrowband and colored noise excitations

    CERN Document Server

    Garcia Morales, Hector; Kotzian, Gerd; Maclean, Ewen Hamish; Redaelli, Stefano; Valuch, Daniel; Wagner, Joschka; CERN. Geneva. ATS Department

    2018-01-01

    This MD note summarizes the actions carried out during the MD 2485 on Active halo control using narrowband and colored noise excitations. The goal of the MD was to repeat some promising cases already tested in the past and introduce a new excitation type based on applying a colored noise. Although we were able to repeat some cases using a narrowband excitation, due to a problem with the waveform generator, the colored noise excitation could not be accomplished as expected. In any case, we provide some results that may be useful for future MDs.

  2. Self-similar cosmological models

    Energy Technology Data Exchange (ETDEWEB)

    Chao, W Z [Cambridge Univ. (UK). Dept. of Applied Mathematics and Theoretical Physics

    1981-07-01

    The kinematics and dynamics of self-similar cosmological models are discussed. The degrees of freedom of the solutions of Einstein's equations for different types of models are listed. The relation between kinematic quantities and the classifications of the self-similarity group is examined. All dust local rotational symmetry models have been found.

  3. Self-similar factor approximants

    International Nuclear Information System (INIS)

    Gluzman, S.; Yukalov, V.I.; Sornette, D.

    2003-01-01

    The problem of reconstructing functions from their asymptotic expansions in powers of a small variable is addressed by deriving an improved type of approximants. The derivation is based on the self-similar approximation theory, which presents the passage from one approximant to another as the motion realized by a dynamical system with the property of group self-similarity. The derived approximants, because of their form, are called self-similar factor approximants. These complement the obtained earlier self-similar exponential approximants and self-similar root approximants. The specific feature of self-similar factor approximants is that their control functions, providing convergence of the computational algorithm, are completely defined from the accuracy-through-order conditions. These approximants contain the Pade approximants as a particular case, and in some limit they can be reduced to the self-similar exponential approximants previously introduced by two of us. It is proved that the self-similar factor approximants are able to reproduce exactly a wide class of functions, which include a variety of nonalgebraic functions. For other functions, not pertaining to this exactly reproducible class, the factor approximants provide very accurate approximations, whose accuracy surpasses significantly that of the most accurate Pade approximants. This is illustrated by a number of examples showing the generality and accuracy of the factor approximants even when conventional techniques meet serious difficulties

  4. Dynamic similarity in erosional processes

    Science.gov (United States)

    Scheidegger, A.E.

    1963-01-01

    A study is made of the dynamic similarity conditions obtaining in a variety of erosional processes. The pertinent equations for each type of process are written in dimensionless form; the similarity conditions can then easily be deduced. The processes treated are: raindrop action, slope evolution and river erosion. ?? 1963 Istituto Geofisico Italiano.

  5. Automatic learning algorithm for the MD-logic artificial pancreas system.

    Science.gov (United States)

    Miller, Shahar; Nimri, Revital; Atlas, Eran; Grunberg, Eli A; Phillip, Moshe

    2011-10-01

    Applying real-time learning into an artificial pancreas system could effectively track the unpredictable behavior of glucose-insulin dynamics and adjust insulin treatment accordingly. We describe a novel learning algorithm and its performance when integrated into the MD-Logic Artificial Pancreas (MDLAP) system developed by the Diabetes Technology Center, Schneider Children's Medical Center of Israel, Petah Tikva, Israel. The algorithm was designed to establish an initial patient profile using open-loop data (Initial Learning Algorithm component) and then make periodic adjustments during closed-loop operation (Runtime Learning Algorithm component). The MDLAP system, integrated with the learning algorithm, was tested in seven different experiments using the University of Virginia/Padova simulator, comprising adults, adolescents, and children. The experiments included simulations using the open-loop and closed-loop control strategy under nominal and varying insulin sensitivity conditions. The learning algorithm was automatically activated at the end of the open-loop segment and after every day of the closed-loop operation. Metabolic control parameters achieved at selected time points were compared. The percentage of time glucose levels were maintained within 70-180 mg/dL for children and adolescents significantly improved when open-loop was compared with day 6 of closed-loop control (Psignificantly reduced by approximately sevenfold (Psignificant reduction in the Low Blood Glucose Index (P<0.001). The new algorithm was effective in characterizing the patient profiles from open-loop data and in adjusting treatment to provide better glycemic control during closed-loop control in both conditions. These findings warrant corroboratory clinical trials.

  6. Personalized recommendation with corrected similarity

    International Nuclear Information System (INIS)

    Zhu, Xuzhen; Tian, Hui; Cai, Shimin

    2014-01-01

    Personalized recommendation has attracted a surge of interdisciplinary research. Especially, similarity-based methods in applications of real recommendation systems have achieved great success. However, the computations of similarities are overestimated or underestimated, in particular because of the defective strategy of unidirectional similarity estimation. In this paper, we solve this drawback by leveraging mutual correction of forward and backward similarity estimations, and propose a new personalized recommendation index, i.e., corrected similarity based inference (CSI). Through extensive experiments on four benchmark datasets, the results show a greater improvement of CSI in comparison with these mainstream baselines. And a detailed analysis is presented to unveil and understand the origin of such difference between CSI and mainstream indices. (paper)

  7. Towards Personalized Medicine: Leveraging Patient Similarity and Drug Similarity Analytics

    Science.gov (United States)

    Zhang, Ping; Wang, Fei; Hu, Jianying; Sorrentino, Robert

    2014-01-01

    The rapid adoption of electronic health records (EHR) provides a comprehensive source for exploratory and predictive analytic to support clinical decision-making. In this paper, we investigate how to utilize EHR to tailor treatments to individual patients based on their likelihood to respond to a therapy. We construct a heterogeneous graph which includes two domains (patients and drugs) and encodes three relationships (patient similarity, drug similarity, and patient-drug prior associations). We describe a novel approach for performing a label propagation procedure to spread the label information representing the effectiveness of different drugs for different patients over this heterogeneous graph. The proposed method has been applied on a real-world EHR dataset to help identify personalized treatments for hypercholesterolemia. The experimental results demonstrate the effectiveness of the approach and suggest that the combination of appropriate patient similarity and drug similarity analytics could lead to actionable insights for personalized medicine. Particularly, by leveraging drug similarity in combination with patient similarity, our method could perform well even on new or rarely used drugs for which there are few records of known past performance. PMID:25717413

  8. High-Performance Modeling of Carbon Dioxide Sequestration by Coupling Reservoir Simulation and Molecular Dynamics

    KAUST Repository

    Bao, Kai; Yan, Mi; Allen, Rebecca; Salama, Amgad; Lu, Ligang; Jordan, Kirk E.; Sun, Shuyu; Keyes, David E.

    2015-01-01

    The present work describes a parallel computational framework for carbon dioxide (CO2) sequestration simulation by coupling reservoir simulation and molecular dynamics (MD) on massively parallel high-performance-computing (HPC) systems

  9. Structural Analysis of Molten NaNO3 by Molecular Dynamics Simulation

    Science.gov (United States)

    Tahara, Shuta; Toyama, Hiroshi; Shimakura, Hironori; Fukami, Takanori

    2017-08-01

    MD simulation for molten NaNO3 has been performed by using the Born-Mayer-Huggins-type potentials. The new structural features of molten NaNO3 are investigated by several analytical methods. The coordination-number and bond-angle distributions are similar to those of simple molten salts such as NaCl except for the variation caused by the different size of the anion and cation. Na+ ions are attracted toward O- ions, and get separated from N+ ions by Coulomb interactions. The distribution of the dihedral angle between NO3 - plannar ionic molecules has also been investigated.

  10. In-situ Air Temperature and Relative Humidity in Greenbelt, MD, 2013-2015

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set describes the temperature and relative humidity at 12 locations around Goddard Space Flight Center in Greenbelt MD at 15 minute intervals between...

  11. 75 FR 8193 - Jeri Hassman, M.D.; Denial of Application

    Science.gov (United States)

    2010-02-23

    ... is buying drugs on the street. Id. at 1006. With respect to requests for early refills, Dr. Hare... Part II Department of Justice Drug Enforcement Administration Jeri Hassman, M.D.; Denial of...; [[Page 8194

  12. Metabolic engineering of apple by overexpression of the MdMyb10 gene

    Directory of Open Access Journals (Sweden)

    Khaled A.L. Rihani

    2017-06-01

    In the present study, the flavonoid pathway was successfully modified in apple by overexpressing the MdMyb10 transcription factor to validate the hypothesis of increased effect on plant disease resistance.

  13. 78 FR 32556 - Safety Zone; 2013 Ocean City Air Show, Atlantic Ocean; Ocean City, MD

    Science.gov (United States)

    2013-05-31

    ... FR Federal Register NPRM Notice of Proposed Rulemaking A. Regulatory History and Information The... Atlantic Ocean in Ocean City, MD. In recent years, there have been unfortunate instances of jets and planes...

  14. Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

    Science.gov (United States)

    Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao

    2018-02-01

    Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.

  15. Multi-Scale Simulation of High Energy Density Ionic Liquids

    National Research Council Canada - National Science Library

    Voth, Gregory A

    2007-01-01

    The focus of this AFOSR project was the molecular dynamics (MD) simulation of ionic liquid structure, dynamics, and interfacial properties, as well as multi-scale descriptions of these novel liquids (e.g...

  16. Image fusion in craniofacial virtual reality modeling based on CT and 3dMD photogrammetry.

    Science.gov (United States)

    Xin, Pengfei; Yu, Hongbo; Cheng, Huanchong; Shen, Shunyao; Shen, Steve G F

    2013-09-01

    The aim of this study was to demonstrate the feasibility of building a craniofacial virtual reality model by image fusion of 3-dimensional (3D) CT models and 3 dMD stereophotogrammetric facial surface. A CT scan and stereophotography were performed. The 3D CT models were reconstructed by Materialise Mimics software, and the stereophotogrammetric facial surface was reconstructed by 3 dMD patient software. All 3D CT models were exported as Stereo Lithography file format, and the 3 dMD model was exported as Virtual Reality Modeling Language file format. Image registration and fusion were performed in Mimics software. Genetic algorithm was used for precise image fusion alignment with minimum error. The 3D CT models and the 3 dMD stereophotogrammetric facial surface were finally merged into a single file and displayed using Deep Exploration software. Errors between the CT soft tissue model and 3 dMD facial surface were also analyzed. Virtual model based on CT-3 dMD image fusion clearly showed the photorealistic face and bone structures. Image registration errors in virtual face are mainly located in bilateral cheeks and eyeballs, and the errors are more than 1.5 mm. However, the image fusion of whole point cloud sets of CT and 3 dMD is acceptable with a minimum error that is less than 1 mm. The ease of use and high reliability of CT-3 dMD image fusion allows the 3D virtual head to be an accurate, realistic, and widespread tool, and has a great benefit to virtual face model.

  17. STRATEGI PEMASARAN PUBLIC RELATIONS MD ENTERTAINMENT PADA PEMASARAN FILM HABIBIE & AINUN

    OpenAIRE

    Trisna Adi Permana; Lilis Puspitasari

    2015-01-01

    Tujuan penelitian ini adalah untuk mengetahui perencanaan, implementasi serta evaluasi dari strategi Marketing Public Relations yang ditetapkan PR MD Entertainment pada film Habibie & Ainun pada tahun 2012-2013. Metode yang dilakukan adalah metode deskriptif yang bertujuan melukiskan secara sistematis fakta atau karakteristik populasi tertentu atau bidang tertentu secara faktual dan cermat. Hasil penelitian menunjukan PR MD Entertainment telah melakukan tahapan-tahapan atau Teknik...

  18. Strategi Pemasaran Public Relations Md Entertainment Pada Pemasaran Film Habibie & Ainun

    OpenAIRE

    Permana, Trisna Adi; Puspitasari, Lilis

    2015-01-01

    Tujuan penelitian ini adalah untuk mengetahui perencanaan, implementasi serta evaluasi dari strategiMarketing Public Relations yang ditetapkan PR MD Entertainment pada film Habibie & Ainun pada tahun2012-2013. Metode yang dilakukan adalah metode deskriptif yang bertujuan melukiskan secara sistematisfakta atau karakteristik populasi tertentu atau bidang tertentu secara faktual dan cermat. Hasil penelitianmenunjukan PR MD Entertainment telah melakukan tahapan-tahapan atau Teknik PR pada film Ha...

  19. Summary of LHC MD 369: DOROS vs WBTN in IR Stripline BPMs

    CERN Document Server

    Draskovic, Drasko; Calvo Giraldo, Eva; Olexa, Jakub; Gasior, Marek; CERN. Geneva. ATS Department

    2015-01-01

    The aim of this MD is to quantify the impact of the stripline beam position monitor (BPM) directivity with two acquisition chain electronics systems, WBTN (Wide Band Time Normalizer) and DOROS (Diode ORbit and Oscillation System). This impact depends on the relative position and intensity of the two beams at the location of the monitor. This note explains all the procedures of the LHC MD 369, which took place on 20/07/2015 and presents the obtained results.

  20. Structural Effects of Some Relevant Missense Mutations on the MECP2-DNA Binding: A MD Study Analyzed by Rescore+, a Versatile Rescoring Tool of the VEGA ZZ Program.

    Science.gov (United States)

    Pedretti, Alessandro; Granito, Cinzia; Mazzolari, Angelica; Vistoli, Giulio

    2016-09-01

    DNA methylation plays key roles in mammalian cells and is modulated by a set of proteins which recognize symmetrically methylated nucleotides. Among them, the protein MECP2 shows multifunctional roles repressing and/or activating genes by binding to both methylated and unmethylated regions of the genome. The interest for this protein markedly increased from the observation that its mutations are the primary cause of Rett syndrome, a neurodevelopmental disorder which causes mental retardation in young females. Thus, the present study is aimed to investigate the effects of some of these known pathogenic missense mutations (i.e. R106Q, R106W, R111G, R133C and R133H) on the MECP2 folding and DNA binding by molecular dynamics simulations. The effects of the simulated mutations are also parameterized by using a here proposed new tool, named Rescore+, implemented in the VEGA ZZ suite of programs, which calculates a set of scoring functions on all frames of a trajectory or on all complexes contained in a database thus allowing an easy rescoring of results coming from MD or docking simulations. The obtained results revealed that the reported loss of the MECP2 function induced by the simulated mutations can be ascribed to both stabilizing and destabilizing effect on DNA binding. The study confirms that MD simulations are particularly useful to rationalize and predict the mutation effects offering insightful information for diagnostics and drug design. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Development of a quantum chemical molecular dynamics tribochemical simulator and its application to tribochemical reaction dynamics of lubricant additives

    International Nuclear Information System (INIS)

    Onodera, T; Tsuboi, H; Hatakeyama, N; Endou, A; Miyamoto, A; Miura, R; Takaba, H; Suzuki, A; Kubo, M

    2010-01-01

    Tribology at the atomistic and molecular levels has been theoretically studied by a classical molecular dynamics (MD) method. However, this method inherently cannot simulate the tribochemical reaction dynamics because it does not consider the electrons in nature. Although the first-principles based MD method has recently been used for understanding the chemical reaction dynamics of several molecules in the tribology field, the method cannot simulate the tribochemical reaction dynamics of a large complex system including solid surfaces and interfaces due to its huge computation costs. On the other hand, we have developed a quantum chemical MD tribochemical simulator on the basis of a hybrid tight-binding quantum chemical/classical MD method. In the simulator, the central part of the chemical reaction dynamics is calculated by the tight-binding quantum chemical MD method, and the remaining part is calculated by the classical MD method. Therefore, the developed tribochemical simulator realizes the study on tribochemical reaction dynamics of a large complex system, which cannot be treated by using the conventional classical MD or the first-principles MD methods. In this paper, we review our developed quantum chemical MD tribochemical simulator and its application to the tribochemical reaction dynamics of a few lubricant additives

  2. A novel energy conversion based method for velocity correction in molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Hanhui [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Collaborative Innovation Center of Advanced Aero-Engine, Hangzhou 310027 (China); Liu, Ningning [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Ku, Xiaoke, E-mail: xiaokeku@zju.edu.cn [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Fan, Jianren [State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027 (China)

    2017-05-01

    Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

  3. A novel energy conversion based method for velocity correction in molecular dynamics simulations

    International Nuclear Information System (INIS)

    Jin, Hanhui; Liu, Ningning; Ku, Xiaoke; Fan, Jianren

    2017-01-01

    Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

  4. [Similarity system theory to evaluate similarity of chromatographic fingerprints of traditional Chinese medicine].

    Science.gov (United States)

    Liu, Yongsuo; Meng, Qinghua; Jiang, Shumin; Hu, Yuzhu

    2005-03-01

    The similarity evaluation of the fingerprints is one of the most important problems in the quality control of the traditional Chinese medicine (TCM). Similarity measures used to evaluate the similarity of the common peaks in the chromatogram of TCM have been discussed. Comparative studies were carried out among correlation coefficient, cosine of the angle and an improved extent similarity method using simulated data and experimental data. Correlation coefficient and cosine of the angle are not sensitive to the differences of the data set. They are still not sensitive to the differences of the data even after normalization. According to the similarity system theory, an improved extent similarity method was proposed. The improved extent similarity is more sensitive to the differences of the data sets than correlation coefficient and cosine of the angle. And the character of the data sets needs not to be changed compared with log-transformation. The improved extent similarity can be used to evaluate the similarity of the chromatographic fingerprints of TCM.

  5. MdCOP1 Ubiquitin E3 Ligases Interact with MdMYB1 to Regulate Light-Induced Anthocyanin Biosynthesis and Red Fruit Coloration in Apple1[W][OA

    Science.gov (United States)

    Li, Yuan-Yuan; Mao, Ke; Zhao, Cheng; Zhao, Xian-Yan; Zhang, Hua-Lei; Shu, Huai-Rui; Hao, Yu-Jin

    2012-01-01

    MdMYB1 is a crucial regulator of light-induced anthocyanin biosynthesis and fruit coloration in apple (Malus domestica). In this study, it was found that MdMYB1 protein accumulated in the light but degraded via a ubiquitin-dependent pathway in the dark. Subsequently, the MdCOP1-1 and MdCOP1-2 genes were isolated from apple fruit peel and were functionally characterized in the Arabidopsis (Arabidopsis thaliana) cop1-4 mutant. Yeast (Saccharomyces cerevisiae) two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays showed that MdMYB1 interacts with the MdCOP1 proteins. Furthermore, in vitro and in vivo experiments indicated that MdCOP1s are necessary for the ubiquitination and degradation of MdMYB1 protein in the dark and are therefore involved in the light-controlled stability of the MdMYB1 protein. Finally, a viral vector-based transformation approach demonstrated that MdCOP1s negatively regulate the peel coloration of apple fruits by modulating the degradation of the MdMYB1 protein. Our findings provide new insight into the mechanism by which light controls anthocyanin accumulation and red fruit coloration in apple and even other plant species. PMID:22855936

  6. Domain similarity based orthology detection.

    Science.gov (United States)

    Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich

    2015-05-13

    Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at http://www.bornberglab.org/pages/porthoda .

  7. Structure and dynamics of solvated Ba(II) in dilute aqueous solution - an ab initio QM/MM MD approach

    International Nuclear Information System (INIS)

    Hofer, Thomas S.; Rode, Bernd M.; Randolf, Bernhard R.

    2005-01-01

    Structural properties of the hydrated Ba(II) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at double zeta HF quantum mechanical level. The first shell coordination number was found to be 9.3, and several other structural parameters such as angular distribution functions, radial distribution functions and tilt- and θ-angle distributions allowed the full characterization of the hydration structure of the Ba(II) ion in dilute aqueous solution. Velocity autocorrelation functions were used to calculate librational and vibrational motions, ion-ligand motions as well as reorientation times. Different dynamical parameters such as water reorientation, mean ligand residence time, the number of ligand exchange processes and rate constants were also analyzed and the ligand exchange rate constant for the first shell was determined as k = 5.3 x 10 10 s -1

  8. Determination of two- and three-body correlation functions in ionic solutions by means of MD and EXAFS investigations

    International Nuclear Information System (INIS)

    D'Angelo, P.; Pavel, N.V.

    1999-01-01

    The solvation structure of Sr 2+ ions in acetonitrile has been studied by x-ray absorption spectroscopy (XAS) and molecular dynamics (MD) simulations. The extended x-ray absorption fine structure (EXAFS) above the Sr K-edge has been interpreted in the framework of the multiple scattering (MS) formalism and, for the first time, clear evidence of MS contributions has been found for non-complexing ions in solution. Molecular dynamics has been used to generate the partial pair g(r) and the three-body g(r 1 , r 2 , θ) distribution functions from which a model χ(k) has been constructed. An excellent agreement has been found between the theoretical and experimental data. This result demonstrates the ability of the XAS technique in probing three-body correlation functions in solutions. (au)

  9. Ratio of geometric means to analyze continuous outcomes in meta-analysis: comparison to mean differences and ratio of arithmetic means using empiric data and simulation.

    Science.gov (United States)

    Friedrich, Jan O; Adhikari, Neill K J; Beyene, Joseph

    2012-07-30

    Meta-analyses pooling continuous outcomes can use mean differences (MD), standardized MD (MD in pooled standard deviation units, SMD), or ratio of arithmetic means (RoM). Recently, ratio of geometric means using ad hoc (RoGM (ad hoc) ) or Taylor series (RoGM (Taylor) ) methods for estimating variances have been proposed as alternative effect measures for skewed continuous data. Skewed data are suggested for summary measures of clinical parameters restricted to positive values which have large coefficients of variation (CV). Our objective was to compare performance characteristics of RoGM (ad hoc) and RoGM (Taylor) to MD, SMD, and RoM. We used empiric data from systematic reviews reporting continuous outcomes and selected from each the meta-analysis with the most and at least 5 trials (Cochrane Database [2008, Issue 1]). We supplemented this with simulations conducted with representative parameters. Pooled results were calculated using each effect measure. Of the reviews, 232/5053 met the inclusion criteria. Empiric data and simulation showed that RoGM (ad hoc) exhibits more extreme treatment effects and greater heterogeneity than all other effect measures. Compared with MD, SMD, and RoM, RoGM (Taylor) exhibits similar treatment effects, more heterogeneity when CV ≤0.7, and less heterogeneity when CV > 0.7. In conclusion, RoGM (Taylor) may be considered for pooling continuous outcomes in meta-analysis when data are skewed, but RoGM (ad hoc) should not be used. However, clinicians' lack of familiarity with geometric means combined with acceptable performance characteristics of RoM in most situations suggests that RoM may be the preferable ratio method for pooling continuous outcomes in meta-analysis. Copyright © 2012 John Wiley & Sons, Ltd.

  10. Similarity measures for face recognition

    CERN Document Server

    Vezzetti, Enrico

    2015-01-01

    Face recognition has several applications, including security, such as (authentication and identification of device users and criminal suspects), and in medicine (corrective surgery and diagnosis). Facial recognition programs rely on algorithms that can compare and compute the similarity between two sets of images. This eBook explains some of the similarity measures used in facial recognition systems in a single volume. Readers will learn about various measures including Minkowski distances, Mahalanobis distances, Hansdorff distances, cosine-based distances, among other methods. The book also summarizes errors that may occur in face recognition methods. Computer scientists "facing face" and looking to select and test different methods of computing similarities will benefit from this book. The book is also useful tool for students undertaking computer vision courses.

  11. MD#1826: Measurement of Quench Heater vertical kick

    OpenAIRE

    Valette, Matthieu; Wollmann, Daniel; Lindstrom, Bjorn Hans Filip; Bortot, Lorenzo; Fernandez Navarro, Alejandro; Schmidt, Rudiger; Verweij, Arjan

    2018-01-01

    Following the observation of vertical orbit oscillations of the LHC beam between the detection of a (beam induced) quench of an LHC main dipole and the beam dump, a study was started to verify that the orbit distortions are caused by the firing of the quench heaters (QH). Simulation of the magnetic field generated by the discharge of the QH and its effect on the beam confirmed it was the most likely cause. A dedicated experiment with 450 GeV proton beams was performed to validate the simulati...

  12. Revisiting Inter-Genre Similarity

    DEFF Research Database (Denmark)

    Sturm, Bob L.; Gouyon, Fabien

    2013-01-01

    We revisit the idea of ``inter-genre similarity'' (IGS) for machine learning in general, and music genre recognition in particular. We show analytically that the probability of error for IGS is higher than naive Bayes classification with zero-one loss (NB). We show empirically that IGS does...... not perform well, even for data that satisfies all its assumptions....

  13. Fast business process similarity search

    NARCIS (Netherlands)

    Yan, Z.; Dijkman, R.M.; Grefen, P.W.P.J.

    2012-01-01

    Nowadays, it is common for organizations to maintain collections of hundreds or even thousands of business processes. Techniques exist to search through such a collection, for business process models that are similar to a given query model. However, those techniques compare the query model to each

  14. Glove boxes and similar containments

    International Nuclear Information System (INIS)

    Anon.

    1975-01-01

    According to the present invention a glove box or similar containment is provided with an exhaust system including a vortex amplifier venting into the system, the vortex amplifier also having its main inlet in fluid flow connection with the containment and a control inlet in fluid flow connection with the atmosphere outside the containment. (U.S.)

  15. Monitoring Urban Stream Restoration Efforts in Relation to Flood Behavior Along Minebank Run, Towson, MD

    Science.gov (United States)

    Lee, G.; Miller, A. J.

    2017-12-01

    Urban stream restoration efforts are commonly undertaken to combat channel degradation and restore natural stream hydrology. We examine changes in flood patterns along an approximately 1.5-mile reach of Minebank Run, located in Towson, MD, by comparing pre-restoration morphology from surveys conducted in 2001, post-restoration morphology in 2007, and current conditions in 2017 following damage to the restoration project from persistent flooding. Hydraulic modeling was conducted in HEC-RAS 2D using three alternative scenarios: 1) topographic contours from a 2001 survey of pre-restoration topography combined with 2005 LiDAR, 2) 2007 survey combined with 2005 LiDAR data representing the post-restoration channel morphology, and 3) a March 2017 DEM of current channel conditions. The 2017 DEM was created using Structure from Motion (SfM) from high resolution 4K video collected via Unmanned Aerial Vehicle (UAV) flights at a resolution of 0.05 meters. Flood hydrographs from a USGS stream gage located within the study reach as well as a simulated hydrograph of the 100-year storm event were routed through the pre-restoration, post-restoration, and current modeled terrain and analyzed for changes in water-surface elevation and depth, inundation extent, 2-d velocity fields, and translation vs. attenuation of the flood wave to assess the net impact on potential flood hazards. In addition, our study demonstrates that SfM is a quick and inexpensive method for collecting topographic data for hydrologic modeling, assessing stream characteristics including channel bed roughness, and for examining short term changes of channel morphology at a very fine scale.

  16. Effect of salinity and temperature on treatment of concentrated wastewater from RO by FO-MD

    Science.gov (United States)

    Zhou, Yingru; Huang, Manhong; Deng, Qian

    2018-02-01

    In this study the appropriate temperature of the membrane distillation (MD) hot side (the permeation flux of MD was controlled by adjusting the hot side temperature) was selected according to the water flux of FO process so that the water transfer rate on both sides of FO and MD was consistent and the FO-MD process could be stable operation. When the salt concentration of feed solution was 30, 55, 80 and 100 g/L, the desalination rates changed little, which were 99.1%, 98.4%, 98.9% and 98.7%, respectively. The removal rate of COD was 93.8%, 94.2%, 91.6% and 92.7% which also changed little like the desalination rates. The removal rate of chromaticity increased with the increase of salinity, which attained 96.6%, 97.0%, 97.2% and 97.9%, respectively. This study proved that salinity of the feed solution affected little on the removal rate of contaminants but great on the water flux, with the increase of salinity from 30 to 100 g/L, the water flux was 6.05, 4.81, 4.33 and 3.87 LMH with the appropriate temperature (67.5±0.5, 64.5±0.5, 62.5±0.5 and 60.5±0.5 °C) of MD hot side. In a word, FO-MD was first used to treat the high salinity RO water with over 30 g/L total dissolved solids (TDS), FO-MD was a promising new process for high salinity wastewater treatment, and the hybrid system can solve the problem of lower draw solution concentration, and the high-quality production water will be obtained directly by this hybrid system with low membrane fouling tendency.

  17. Pengaruh Brand Ambassador Terhadap Minat Beli Konsumen MD Clinic By Lazeta

    Directory of Open Access Journals (Sweden)

    Nurvita Septya Ningrum

    2016-10-01

    Full Text Available This research at MD Clinic by Lazeta which is in the beauty services that offer health care and facial, under of PT. Medina Global Care. MD Cilinic by Lazeta use the brand ambassador of introducing their products. The selection of brand ambassador motivated by positive image brought by the celebrities. Brand ambassadors chosen by the company as a symbol or a marker to represent the wishes and needs of prospective customers. MD Clinic by Lazeta choose Syahnaz as a brand ambassador for their products which is expected to to represent the product of MD Clinic by Lazeta, so the message can be understood by the consumer, who eventually would to lead the purchase intention. The purpose of this research was to investigate the influence of brand ambassadors on consumer purchase intention MD Clinic by Lazeta, Study on Business Administration Students year in 2103 Telkom University. Researchers used quantitative research methods. This research is population research, because all population is being respondent in this research. Populations of this research are 137 respondents. Collecting data in this research is conducted by using questionnaire distributed to all respondents, which all Students on Business Administration Telkom University who knows the MD Clinic by Lazeta. Data were analyzed using simple regression analysis and descriptive analysis.The results showed that the Brand Ambassador impact of consumer purchase intention on MD Clinic by Lazeta at the Students on Business Administration Telkom University years in 2013. Based on the calculation of the coefficient of determination (R2 can be seen the influence of brand ambassador variable (X on purchase intention (Y is 42.9%. While the remaining 57.1% is influenced by other factors which not examined in this research such as, pricing, marketing strategy and others.

  18. Measuring structural similarity in large online networks.

    Science.gov (United States)

    Shi, Yongren; Macy, Michael

    2016-09-01

    Structural similarity based on bipartite graphs can be used to detect meaningful communities, but the networks have been tiny compared to massive online networks. Scalability is important in applications involving tens of millions of individuals with highly skewed degree distributions. Simulation analysis holding underlying similarity constant shows that two widely used measures - Jaccard index and cosine similarity - are biased by the distribution of out-degree in web-scale networks. However, an alternative measure, the Standardized Co-incident Ratio (SCR), is unbiased. We apply SCR to members of Congress, musical artists, and professional sports teams to show how massive co-following on Twitter can be used to map meaningful affiliations among cultural entities, even in the absence of direct connections to one another. Our results show how structural similarity can be used to map cultural alignments and demonstrate the potential usefulness of social media data in the study of culture, politics, and organizations across the social and behavioral sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. The small ubiquitin-like modifier E3 ligase MdSIZ1 promotes anthocyanin accumulation by sumoylating MdMYB1 under low-temperature conditions in apple.

    Science.gov (United States)

    Zhou, Li-Jie; Li, Yuan-Yuan; Zhang, Rui-Fen; Zhang, Chun-Ling; Xie, Xing-Bin; Zhao, Cheng; Hao, Yu-Jin

    2017-10-01

    MdMYB1 acts as a crucial component of the MYB-bHLH-WD40 complex to regulate anthocyanin biosynthesis in red-skinned apples (Malus domestica), but little is known about its post-translational regulation. Here, a small ubiquitin-like modifier E3 ligase MdSIZ1 was screened out as an MdMYB1-interacting protein with a yeast two-hybridization approach. The interaction between MdSIZ1 and MdMYB1 was further verified with pull-down and CoIP assays. Furthermore, it was found that MdSIZ1 directly sumoylated MdMYB1 proteins in vivo and in vitro, especially under moderately low temperature (17 °C) conditions, and that this sumoylation was required for MdMYB1 protein stability. Moreover, the transcription level of MdSIZ1 gene was remarkably induced by low temperature and phosphorus deficiency, and MdSIZ1 overexpression exerted a large positive influence on anthocyanin accumulation and red fruit coloration, suggesting its important role in the regulation of anthocyanin biosynthesis under stress conditions. Our findings reveal an important role for a small ubiquitin-like modifier modification of MYB transcription factors in regulation of anthocyanin biosynthesis in plants. © 2017 John Wiley & Sons Ltd.

  20. An Alfven eigenmode similarity experiment

    International Nuclear Information System (INIS)

    Heidbrink, W W; Fredrickson, E; Gorelenkov, N N; Hyatt, A W; Kramer, G; Luo, Y

    2003-01-01

    The major radius dependence of Alfven mode stability is studied by creating plasmas with similar minor radius, shape, magnetic field (0.5 T), density (n e ≅3x10 19 m -3 ), electron temperature (1.0 keV) and beam ion population (near-tangential 80 keV deuterium injection) on both NSTX and DIII-D. The major radius of NSTX is half the major radius of DIII-D. The super-Alfvenic beam ions that drive the modes have overlapping values of v f /v A in the two devices. Observed beam-driven instabilities include toroidicity-induced Alfven eigenmodes (TAE). The stability threshold for the TAE is similar in the two devices. As expected theoretically, the most unstable toroidal mode number n is larger in DIII-D

  1. Compressional Alfven Eigenmode Similarity Study

    Science.gov (United States)

    Heidbrink, W. W.; Fredrickson, E. D.; Gorelenkov, N. N.; Rhodes, T. L.

    2004-11-01

    NSTX and DIII-D are nearly ideal for Alfven eigenmode (AE) similarity experiments, having similar neutral beams, fast-ion to Alfven speed v_f/v_A, fast-ion pressure, and shape of the plasma, but with a factor of 2 difference in the major radius. Toroidicity-induced AE with ˜100 kHz frequencies were compared in an earlier study [1]; this paper focuses on higher frequency AE with f ˜ 1 MHz. Compressional AE (CAE) on NSTX have a polarization, dependence on the fast-ion distribution function, frequency scaling, and low-frequency limit that are qualitatively consistent with CAE theory [2]. Global AE (GAE) are also observed. On DIII-D, coherent modes in this frequency range are observed during low-field (0.6 T) similarity experiments. Experiments will compare the CAE stability limits on DIII-D with the NSTX stability limits, with the aim of determining if CAE will be excited by alphas in a reactor. Predicted differences in the frequency splitting Δ f between excited modes will also be used. \\vspace0.25em [1] W.W. Heidbrink, et al., Plasmas Phys. Control. Fusion 45, 983 (2003). [2] E.D. Fredrickson, et al., Princeton Plasma Physics Laboratory Report PPPL-3955 (2004).

  2. The molecular mechanism underlying anthocyanin metabolism in apple using the MdMYB16 and MdbHLH33 genes.

    Science.gov (United States)

    Xu, Haifeng; Wang, Nan; Liu, Jingxuan; Qu, Changzhi; Wang, Yicheng; Jiang, Shenghui; Lu, Ninglin; Wang, Deyun; Zhang, Zongying; Chen, Xuesen

    2017-05-01

    MdMYB16 forms homodimers and directly inhibits anthocyanin synthesis via its C-terminal EAR repressor. It weakened the inhibitory effect of MdMYB16 on anthocyanin synthesis when overexpressing MdbHLH33 in callus overexpressing MdMYB16. MdMYB16 could interact with MdbHLH33. Anthocyanins are strong antioxidants that play a key role in the prevention of cardiovascular disease, cancer, and diabetes. The germplasm of Malus sieversii f. neidzwetzkyana is important for the study of anthocyanin metabolism. To date, only limited studies have examined the negative regulatory mechanisms underlying anthocyanin synthesis in apple. Here, we analyzed the relationship between anthocyanin levels and MdMYB16 expression in mature Red Crisp 1-5 apple (M. domestica) fruit, generated an evolutionary tree, and identified an EAR suppression sequence and a bHLH binding motif of the MdMYB16 protein using protein sequence analyses. Overexpression of MdMYB16 or MdMYB16 without bHLH binding sequence (LBSMdMYB16) in red-fleshed callus inhibited MdUFGT and MdANS expression and anthocyanin synthesis. However, overexpression of MdMYB16 without the EAR sequence (LESMdMYB16) in red-fleshed callus had no inhibitory effect on anthocyanin. The yeast one-hybrid assay showed that MdMYB16 and LESMdMYB16 interacted the promoters of MdANS and MdUFGT, respectively. Yeast two-hybrid, pull-down, and bimolecular fluorescence complementation assays showed that MdMYB16 formed homodimers and interacted with MdbHLH33, however, the LBSMdMYB16 could not interact with MdbHLH33. We overexpressed MdbHLH33 in callus overexpressing MdMYB16 and found that it weakened the inhibitory effect of MdMYB16 on anthocyanin synthesis. Together, these results suggested that MdMYB16 and MdbHLH33 may be important part of the regulatory network controlling the anthocyanin biosynthetic pathway.

  3. NBodyLab: A Testbed for Undergraduates Utilizing a Web Interface to NEMO and MD-GRAPE2 Hardware

    Science.gov (United States)

    Johnson, V. L.; Teuben, P. J.; Penprase, B. E.

    An N-body simulation testbed called NBodyLab was developed at Pomona College as a teaching tool for undergraduates. The testbed runs under Linux and provides a web interface to selected back-end NEMO modeling and analysis tools, and several integration methods which can optionally use an MD-GRAPE2 supercomputer card in the server to accelerate calculation of particle-particle forces. The testbed provides a framework for using and experimenting with the main components of N-body simulations: data models and transformations, numerical integration of the equations of motion, analysis and visualization products, and acceleration techniques (in this case, special purpose hardware). The testbed can be used by students with no knowledge of programming or Unix, freeing such students and their instructor to spend more time on scientific experimentation. The advanced student can extend the testbed software and/or more quickly transition to the use of more advanced Unix-based toolsets such as NEMO, Starlab and model builders such as GalactICS. Cosmology students at Pomona College used the testbed to study collisions of galaxies with different speeds, masses, densities, collision angles, angular momentum, etc., attempting to simulate, for example, the Tadpole Galaxy and the Antenna Galaxies. The testbed framework is available as open-source to assist other researchers and educators. Recommendations are made for testbed enhancements.

  4. [MD PhD programs: Providing basic science education for ophthalmologists].

    Science.gov (United States)

    Spaniol, K; Geerling, G

    2015-06-01

    Enrollment in MD PhD programs offers the opportunity of a basic science education for medical students and doctors. These programs originated in the USA where structured programs have been offered for many years, but now German universities also run MD PhD programs. The MD PhD programs provided by German universities were investigated regarding entrance requirements, structure and financing modalities. An internet and telephone-based search was carried out. Out of 34 German universities 22 offered MD PhD programs. At 15 of the 22 universities a successfully completed course of studies in medicine was required for enrollment, 7 programs admitted medical students in training and 7 programs required a medical doctoral thesis, which had to be completed with at least a grade of magna cum laude in 3 cases. Financing required scholarships in many cases. Several German universities currently offer MD PhD programs; however, these differ considerably regarding entrance requirements, structure and financing. A detailed analysis investigating the success rates of these programs (e.g. successful completion and career paths of graduates) would be of benefit.

  5. Opinion of stakeholders on existing curriculum for postgraduate (MD) course in Pharmacology: A survey.

    Science.gov (United States)

    Badyal, Dinesh K; Daniel, Sujit R

    2016-10-01

    To survey the opinion about various curricular components of Doctor of Medicine (MD) pharmacology curriculum in India by stakeholders, including faculty and students. An online survey was done to evaluate the various curricular components of MD pharmacology curriculum being used in India. A total of 393 respondents including faculty, MD students, and other stakeholders completed the survey. The survey was developed using SurveyMonkey platform and link to survey was E-mailed to stakeholders. The results were expressed as percentages. There was a balanced representation of respondents from various designations, teaching experience, regions, and age groups. Most of the respondents (83%) were aware of the MD pharmacology curriculum. However, they reported that it is more inclined to knowledge domain. About half of respondents (53%) said that animal experiments are being used. The most common teaching methods mentioned are seminars (98.5%), journal clubs (95%), and practical exercises by postgraduates (73%), but there is less use of newer methods (25%) in theory and less of clinical pharmacology exercise (39%) in practical classes. The log books are maintained but not assessed regularly. Internal assessment is sparingly used. The MD pharmacology curriculum needs to be made uniform at the national level and updated to include the newer methods in teaching-learning and assessment. There should be sharing of newer methods at a common platform implemented at the national level.

  6. Crystal twinning of human MD-2 recognizing endotoxin cores of lipopolysaccharide

    International Nuclear Information System (INIS)

    Ohto, Umeharu; Satow, Yoshinori

    2008-01-01

    Twinned crystals of humaan MD-2 are transformed into single crystals with cryoprotectant optimization. Twinning of crystals causes overlapping of two or more reciprocal lattice points, and hence structure amplitudes for a single crystalline domain are hardly obtained from X-ray diffraction intensities. MD-2 protein forms a stable complex with Toll-like receptor 4 and recognizes bacterial lipopolysaccharide (LPS). Excessive immune responses activated by LPS cause septic shocks. Saccharide-trimmed human MD-2 crystallizes in the tetragonal form with apparent Laue symmetry of 4/mmm, and diffraction intensities from these crystals indicate crystal twinning. The crystal consists of two different domains, A and B. The c A axis of domain A coincides with the c B axis of domain B with a smaller lattice, and the a A axis corresponds to the (a B + b B ) axis. This twinning severely imposes difficulty in structure determination. Through optimization of cryoprotectant, domain A was thoroughly transformed into domain B. The crystal containing only domain B is in space group P4 1 2 1 2 with one MD-2 molecule in the asymmetric unit. The structure of this form of MD-2 as well as its complex with antiendotoxic lipid IVa was successfully determined using the multiple isomorphous replacement method

  7. Center of excellence for mobile sensor data-to-knowledge (MD2K).

    Science.gov (United States)

    Kumar, Santosh; Abowd, Gregory D; Abraham, William T; al'Absi, Mustafa; Beck, J Gayle; Chau, Duen Horng; Condie, Tyson; Conroy, David E; Ertin, Emre; Estrin, Deborah; Ganesan, Deepak; Lam, Cho; Marlin, Benjamin; Marsh, Clay B; Murphy, Susan A; Nahum-Shani, Inbal; Patrick, Kevin; Rehg, James M; Sharmin, Moushumi; Shetty, Vivek; Sim, Ida; Spring, Bonnie; Srivastava, Mani; Wetter, David W

    2015-11-01

    Mobile sensor data-to-knowledge (MD2K) was chosen as one of 11 Big Data Centers of Excellence by the National Institutes of Health, as part of its Big Data-to-Knowledge initiative. MD2K is developing innovative tools to streamline the collection, integration, management, visualization, analysis, and interpretation of health data generated by mobile and wearable sensors. The goal of the big data solutions being developed by MD2K is to reliably quantify physical, biological, behavioral, social, and environmental factors that contribute to health and disease risk. The research conducted by MD2K is targeted at improving health through early detection of adverse health events and by facilitating prevention. MD2K will make its tools, software, and training materials widely available and will also organize workshops and seminars to encourage their use by researchers and clinicians. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  8. Evaluation of hydroacid complex in the forward osmosis–membrane distillation (FO–MD) system for desalination

    KAUST Repository

    Wang, Peng; Cui, Yue; Ge, Qingchun; Fern Tew, Tjin; Chung, Neal Tai-Shung

    2015-01-01

    The incorporation of membrane distillation (MD) into forward osmosis (FO) provides process sustainability to regenerate the draw solution and to produce clean water simultaneously. However, the reverse salt flux is the major hurdle in the FO-MD system because it not only reduces the effective osmotic driving force across the membrane but also increases the replenishment cost and scaling issue. For the first time, a hydroacid complex with abundant hydrophilic groups and ionic species is evaluated as the draw solutes in the hybrid FO-MD system consisting of multi-bore PVDF MD membranes for seawater/brackish desalination. In order to evaluate the practicality of the hydroacid complex in the FO-MD system, FO and MD experiments were conducted at elevated temperatures and concentrations. The hydroacid complex has displayed desired properties such as high solubility, low viscosity, excellent thermal stability and minimal reverse salt flux suitable for FO and MD operations. FO-MD desalination process was demonstrated with a highest seawater desalination flux of 6/32 LMH (FO/MD). This study may open up the prospective of employing the hydroacid complex as the draw solute in FO-MD hybrid systems for seawater /brackish desalination. © 2015 Elsevier B.V.

  9. Evaluation of hydroacid complex in the forward osmosis–membrane distillation (FO–MD) system for desalination

    KAUST Repository

    Wang, Peng

    2015-11-01

    The incorporation of membrane distillation (MD) into forward osmosis (FO) provides process sustainability to regenerate the draw solution and to produce clean water simultaneously. However, the reverse salt flux is the major hurdle in the FO-MD system because it not only reduces the effective osmotic driving force across the membrane but also increases the replenishment cost and scaling issue. For the first time, a hydroacid complex with abundant hydrophilic groups and ionic species is evaluated as the draw solutes in the hybrid FO-MD system consisting of multi-bore PVDF MD membranes for seawater/brackish desalination. In order to evaluate the practicality of the hydroacid complex in the FO-MD system, FO and MD experiments were conducted at elevated temperatures and concentrations. The hydroacid complex has displayed desired properties such as high solubility, low viscosity, excellent thermal stability and minimal reverse salt flux suitable for FO and MD operations. FO-MD desalination process was demonstrated with a highest seawater desalination flux of 6/32 LMH (FO/MD). This study may open up the prospective of employing the hydroacid complex as the draw solute in FO-MD hybrid systems for seawater /brackish desalination. © 2015 Elsevier B.V.

  10. MdHB1 down-regulation activates anthocyanin biosynthesis in the white-fleshed apple cultivar 'Granny Smith'.

    Science.gov (United States)

    Jiang, Yonghua; Liu, Cuihua; Yan, Dan; Wen, Xiaohong; Liu, Yanli; Wang, Haojie; Dai, Jieyu; Zhang, Yujie; Liu, Yanfei; Zhou, Bin; Ren, Xiaolin

    2017-02-01

    Coloration in apple (Malus×domestica) flesh is mainly caused by the accumulation of anthocyanin. Anthocyanin is biosynthesized through the flavonoid pathway and regulated by MYB, bHLH, and WD40 transcription factors (TFs). Here, we report that the HD-Zip I TF MdHB1 was also involved in the regulation of anthocyanin accumulation. MdHB1 silencing caused the accumulation of anthocyanin in 'Granny Smith' flesh, whereas its overexpression reduced the flesh content of anthocyanin in 'Ballerina' (red-fleshed apple). Moreover, flowers of transgenic tobacco (Nicotiana tabacum 'NC89') overexpressing MdHB1 showed a remarkable reduction in pigmentation. Transient promoter activation assays and yeast one-hybrid results indicated that MdHB1 indirectly inhibited expression of the anthocyanin biosynthetic genes encoding dihydroflavonol-4-reductase (DFR) and UDP-glucose:flavonoid 3-O-glycosyltransferase (UFGT). Yeast two-hybrid and bimolecular fluorescence complementation determined that MdHB1 acted as a homodimer and could interact with MYB, bHLH, and WD40 in the cytoplasm, consistent with its cytoplasmic localization by green fluorescent protein fluorescence observations. Together, these results suggest that MdHB1 constrains MdMYB10, MdbHLH3, and MdTTG1 to the cytoplasm, and then represses the transcription of MdDFR and MdUFGT indirectly. When MdHB1 is silenced, these TFs are released to activate the expression of MdDFR and MdUFGT and also anthocyanin biosynthesis, resulting in red flesh in 'Granny Smith'. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  11. Similarity flows in relativistic hydrodynamics

    International Nuclear Information System (INIS)

    Blaizot, J.P.; Ollitrault, J.Y.

    1986-01-01

    In ultra-relativistic heavy ion collisions, one expects in particular to observe a deconfinement transition leading to a formation of quark gluon plasma. In the framework of the hydrodynamic model, experimental signatures of such a plasma may be looked for as observable consequences of a first order transition on the evolution of the system. In most of the possible scenario, the phase transition is accompanied with discontinuities in the hydrodynamic flow, such as shock waves. The method presented in this paper has been developed to treat without too much numerical effort such discontinuous flow. It relies heavily on the use of similarity solutions of the hydrodynamic equations

  12. Vision-Augmented Molecular Dynamics Simulation of Nanoindentation

    Directory of Open Access Journals (Sweden)

    Rajab Al-Sayegh

    2015-01-01

    Full Text Available We present a user-friendly vision-augmented technique to carry out atomic simulation using hand gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of carrying out molecular dynamics simulation in a more efficient way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by simulating the crystal anisotropy of crystalline silicon during nanoindentation. A long-range (Screened bond order Tersoff potential energy function was used during the simulation which revealed the value of hardness and elastic modulus being similar to what has been found previously from the experiments. We anticipate that our proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.

  13. D-score: a search engine independent MD-score.

    Science.gov (United States)

    Vaudel, Marc; Breiter, Daniela; Beck, Florian; Rahnenführer, Jörg; Martens, Lennart; Zahedi, René P

    2013-03-01

    While peptides carrying PTMs are routinely identified in gel-free MS, the localization of the PTMs onto the peptide sequences remains challenging. Search engine scores of secondary peptide matches have been used in different approaches in order to infer the quality of site inference, by penalizing the localization whenever the search engine similarly scored two candidate peptides with different site assignments. In the present work, we show how the estimation of posterior error probabilities for peptide candidates allows the estimation of a PTM score called the D-score, for multiple search engine studies. We demonstrate the applicability of this score to three popular search engines: Mascot, OMSSA, and X!Tandem, and evaluate its performance using an already published high resolution data set of synthetic phosphopeptides. For those peptides with phosphorylation site inference uncertainty, the number of spectrum matches with correctly localized phosphorylation increased by up to 25.7% when compared to using Mascot alone, although the actual increase depended on the fragmentation method used. Since this method relies only on search engine scores, it can be readily applied to the scoring of the localization of virtually any modification at no additional experimental or in silico cost. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Self-similar gravitational clustering

    International Nuclear Information System (INIS)

    Efstathiou, G.; Fall, S.M.; Hogan, C.

    1979-01-01

    The evolution of gravitational clustering is considered and several new scaling relations are derived for the multiplicity function. These include generalizations of the Press-Schechter theory to different densities and cosmological parameters. The theory is then tested against multiplicity function and correlation function estimates for a series of 1000-body experiments. The results are consistent with the theory and show some dependence on initial conditions and cosmological density parameter. The statistical significance of the results, however, is fairly low because of several small number effects in the experiments. There is no evidence for a non-linear bootstrap effect or a dependence of the multiplicity function on the internal dynamics of condensed groups. Empirical estimates of the multiplicity function by Gott and Turner have a feature near the characteristic luminosity predicted by the theory. The scaling relations allow the inference from estimates of the galaxy luminosity function that galaxies must have suffered considerable dissipation if they originally formed from a self-similar hierarchy. A method is also developed for relating the multiplicity function to similar measures of clustering, such as those of Bhavsar, for the distribution of galaxies on the sky. These are shown to depend on the luminosity function in a complicated way. (author)

  15. Combination of advanced encryption standard 256 bits with md5 to secure documents on android smartphone

    Science.gov (United States)

    Pasaribu, Hendra; Sitanggang, Delima; Rizki Damanik, Rudolfo; Rudianto Sitompul, Alex Chandra

    2018-04-01

    File transfer by using a smartphone has some security issues like data theft by irresponsible parties. To improve the quality of data security systems on smartphones, in this research the integration of AES 256 bit algorithm by using MD5 hashing is proposed. The use of MD5 aims to increase the key strength of the encryption and decryption process of document files. The test results show that the proposed method can increase the key strength of the encryption and decryption process in the document file. Encryption and decryption time by using AES and MD5 combination is faster than using AES only on *.txt file type and reverse results for *.docx, *.xlsx, *.pptx and *.pdf file files.

  16. MD1271: Effect of low frequency noise on the evolution of the emittance and halo population

    CERN Document Server

    Fitterer, Miriam; Valishev, Alexander; Bruce, Roderik; Hofle, Wolfgang; Hostettler, Michi; Papadopoulou, Parthena Stefania; Papotti, Giulia; Papaphilippou, Yannis; Pellegrini, Dario; Trad, Georges; Valuch, Daniel; Valentino, Gianluca; Wagner, Joschka; Cai, Xu; CERN. Geneva. ATS Department

    2018-01-01

    For the High Luminosity upgrade the β* in IR1 and IR5 will be further reduced compared to the current LHC. As the β* decreases the β-functions in the inner triplet (IT) increase resulting in a higher sensitivity of the HL-LHC to ground motion in the IT region or to increases of the low frequency noise. Noise can in general lead to emittance growth and higher halo population and diffusion rate. However, it is usually assumed in the literature that only frequencies close to the betatron frequencies and sidebands have an effect on the emittance and tail population. To test this theory, an MD was carried out to observe if also low frequency noise can lead to emittance growth and stronger halo population and diffusion. This MD conducted on 24.08.2016 follows a previous MD on 05.11.2015/06.11.2015

  17. Molecular Dynamics Simulations of Escherichia coli Ammonia Channel AmtB

    DEFF Research Database (Denmark)

    Nygaard, Thomas Pedersen

    2007-01-01

    p°a s°akaldte styrede MD simuleringer, hvor NH3 og NH+4 blev trukket igennem kanalen. Selve mekanismen, som involverer ovenfor nævnte A162 og D160, blev dernæst testet vha. af en special type MD simulering, hvor dele af systemet behandles kvantemekanisk. Den foresl°aede mekanisme kunne dog hverken...

  18. MD/MBA programs in the United States: evidence of a change in health care leadership.

    Science.gov (United States)

    Larson, David B; Chandler, Maria; Forman, Howard P

    2003-03-01

    Managerial sciences are playing an increasingly prominent role in the organization and delivery of health care. Despite popular media reports that a rising number of physicians are acquiring a background in this discipline through MD/MBA (medical and master of business administration) programs, no recent study has verified this. This study measured changes in the number and nature of the affiliations between management and medicine in the form of MD/MBA programs in the United States. Surveys of admission officers of 125 U.S. allopathic medical schools and of the overseers of each joint MD/MBA degree program were administered in May-October 2001. Main outcome measures included program growth, curriculum and degree requirements, application and admission requirements, and program leadership and organization. The number of MD/MBA programs grew from six to 33 between 1993 and 2001, and 17 more medical schools were considering establishing the joint-degree program. Ten, 15, and 20 programs produced 27, 42, and 61 graduates in 1999, 2000, and 2001, respectively, and over 100 students were expected to graduate per year when all 33 programs matured. Program structures and oversight indicate a spectrum of philosophies regarding the appropriate level of integration of the two degrees. MD/MBA programs apparently attempt to complement medical education with management education rather than the converse. The growth in the numbers of MD/MBA programs and participants indicates rising cooperation between medical and business schools and increasing interest in management education early in the careers of graduating physicians.

  19. The AINTEGUMENTA genes, MdANT1 and MdANT2, are associated with the regulation of cell production during fruit growth in apple (Malus × domestica Borkh.).

    Science.gov (United States)

    Dash, Madhumita; Malladi, Anish

    2012-06-25

    Fruit growth in apple (Malus × domestica Borkh.) is mediated by cell production and expansion. Genes involved in regulating these processes and thereby fruit growth, are not well characterized. We hypothesized that the apple homolog(s) of AINTEGUMENTA (ANT), an APETALA2-repeat containing transcription factor, regulates cell production during fruit growth in apple. Two ANT genes, MdANT1 and MdANT2, were isolated from apple and their expression was studied during multiple stages of fruit development. MdANT1 and MdANT2 expression was high during early fruit growth coincident with the period of cell production, rapidly declined during exit from cell production, and remained low during the rest of fruit development. The effects of increase in carbohydrate availability during fruit growth were characterized. Increase in carbohydrate availability enhanced fruit growth largely through an increase in cell production. Expression of MdANT1 and MdANT2 increased sharply by up to around 5-fold in response to an increase in carbohydrate availability. Expression of the ANT genes was compared across two apple genotypes, 'Gala' and 'Golden Delicious Smoothee' (GS), which differ in the extent of fruit growth, largely due to differences in cell production. In comparison to 'Gala', the larger fruit-size genotype, GS, displayed higher levels and a longer duration of MdANT1 and MdANT2 expression. Expression of the ANTs and cell cycle genes in the fruit core and cortex tissues isolated using laser capture microdissection was studied. During early fruit growth, expression of the MdANTs was higher within the cortex, the tissue that constitutes the majority of the fruit. Additionally, MdANT1 and MdANT2 expression was positively correlated with that of A- and B-type CYCLINS, B-type CYCLIN-DEPENDENT-KINASES (CDKBs) and MdDEL1. Multiple lines of evidence from this study suggest that MdANT1 and MdANT2 regulate cell production during fruit growth in apple. ANTs may coordinate the expression of

  20. Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.

    Science.gov (United States)

    Chen, Yunjie; Roux, Benoît

    2014-09-21

    Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

  1. Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal

    Science.gov (United States)

    Chen, Yunjie; Roux, Benoît

    2014-09-01

    Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

  2. Seniority bosons from similarity transformations

    International Nuclear Information System (INIS)

    Geyer, H.B.

    1986-01-01

    The requirement of associating in the boson space seniority with twice the number of non-s bosons defines a similarity transformation which re-expresses the Dyson pair boson images in terms of seniority bosons. In particular the fermion S-pair creation operator is mapped onto an operator which, unlike the pair boson image, does not change the number of non-s bosons. The original results of Otsuka, Arima and Iachello are recovered by this procedure while at the same time they are generalized to include g-bosons or even bosons with J>4 as well as any higher order boson terms. Furthermore the seniority boson images are valid for an arbitrary number of d- or g-bosons - a result which is not readily obtainable within the framework of the usual Marumori- or OAI-method

  3. Fatigue life estimation of MD36 and MD523 bogies based on damage accumulation and random fatigue theory

    International Nuclear Information System (INIS)

    Younesian, Davood; Solhmirzaei, Ali; Gachloo, Alireza

    2009-01-01

    Bogies are one of the multifunctional parts of trains which are extremely subjected to random loads. This type of oscillating and random excitation arises from irregularities of the track including rail surface vertical roughness, rail joints, variance in super-elevation, and also wheel imperfections like wheel flats and unbalancy. Since most of the prementioned sources have random nature, a random based theory should be applied for fatigue life estimation of the bogie frame. Two methods of fatigue life estimation are investigated in this paper. The first approach which is being implemented in time domain is based on the damage accumulation (DA) approach. Using Monte-Carlo simulation algorithm, the rail surface roughness is generated. Finite element (FE) model of the bogie is subjected to the generated random excitation in the first approach and the stress time histories are obtained, and consequently the fatigue life is estimated by using the rain-flow algorithm. In the second approach, the fatigue life is estimated in frequency domain. Power spectral density (PSD) of the stress is obtained by using the FE model of the bogie frame and the fatigue life is estimated using Rayleigh technique in random fatigue theory. A comprehensive parametric study is carried out and effects of different parameters like the train speeds and level of the rail surface vertical roughness on the estimated fatigue life are investigated

  4. A molecular dynamics simulation code ISIS

    International Nuclear Information System (INIS)

    Kambayashi, Shaw

    1992-06-01

    Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)

  5. Studying pressure denaturation of a protein by molecular dynamics simulations.

    Science.gov (United States)

    Sarupria, Sapna; Ghosh, Tuhin; García, Angel E; Garde, Shekhar

    2010-05-15

    Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This "unfolding-up-on-squeezing" is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results-that pressure denatured states are water-swollen, and theoretical results-that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states-their water-swollen nature, retention of secondary structure, and overall compactness-mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately -60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500-2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties

  6. Overexpression of a repressor MdMYB15L negatively regulates anthocyanin and cold tolerance in red-fleshed callus.

    Science.gov (United States)

    Xu, Haifeng; Yang, Guanxian; Zhang, Jing; Wang, Yicheng; Zhang, Tianliang; Wang, Nan; Jiang, Shenghui; Zhang, Zongying; Chen, Xuesen

    2018-04-14

    The cold-induced metabolic pathway and anthocyanin biosynthesis play important roles in plant growth. In this study, we identified a bHLH binding motif in the MdMYB15L protein using protein sequence analyses. Yeast two-hybrid and pull-down assays showed that MdMYB15L could interact with MdbHLH33. Overexpressing MdMYB15L in red-fleshed callus inhibited the expression of MdCBF2 and resulted in reduced cold tolerance but did not affect anthocyanin levels. Chip-PCR and EMSA analysis showed that MdMYB15L could bind the type II cis-acting element found in the MdCBF2 promoter. Overexpressing MdMYB15L in red-fleshed callus overexpressing MdbHLH33 also reduced cold tolerance and reduced MdbHLH33-induced anthocyanin biosynthesis. Knocking out the bHLH binding sequence of MdMYB15L (LBSMdMYB15L) prevented LBSMdMYB15L from interacting with MdbHLH33. Overexpressing LBSMdMYB15L in red-fleshed callus overexpressing MdbHLH33 also reduced cold tolerance and reduced MdbHLH33-induced anthocyanin biosynthesis. Together, these results suggested that an apple repressor MdMYB15L might play a key role in the cold signaling and anthocyanin metabolic pathways. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Humanized TLR4/MD-2 mice reveal LPS recognition differentially impacts susceptibility to Yersinia pestis and Salmonella enterica.

    Directory of Open Access Journals (Sweden)

    Adeline M Hajjar

    Full Text Available Although lipopolysaccharide (LPS stimulation through the Toll-like receptor (TLR-4/MD-2 receptor complex activates host defense against Gram-negative bacterial pathogens, how species-specific differences in LPS recognition impact host defense remains undefined. Herein, we establish how temperature dependent shifts in the lipid A of Yersinia pestis LPS that differentially impact recognition by mouse versus human TLR4/MD-2 dictate infection susceptibility. When grown at 37°C, Y. pestis LPS is hypo-acylated and less stimulatory to human compared with murine TLR4/MD-2. By contrast, when grown at reduced temperatures, Y. pestis LPS is more acylated, and stimulates cells equally via human and mouse TLR4/MD-2. To investigate how these temperature dependent shifts in LPS impact infection susceptibility, transgenic mice expressing human rather than mouse TLR4/MD-2 were generated. We found the increased susceptibility to Y. pestis for "humanized" TLR4/MD-2 mice directly paralleled blunted inflammatory cytokine production in response to stimulation with purified LPS. By contrast, for other Gram-negative pathogens with highly acylated lipid A including Salmonella enterica or Escherichia coli, infection susceptibility and the response after stimulation with LPS were indistinguishable between mice expressing human or mouse TLR4/MD-2. Thus, Y. pestis exploits temperature-dependent shifts in LPS acylation to selectively evade recognition by human TLR4/MD-2 uncovered with "humanized" TLR4/MD-2 transgenic mice.

  8. Humanized TLR4/MD-2 mice reveal LPS recognition differentially impacts susceptibility to Yersinia pestis and Salmonella enterica.

    Science.gov (United States)

    Hajjar, Adeline M; Ernst, Robert K; Fortuno, Edgardo S; Brasfield, Alicia S; Yam, Cathy S; Newlon, Lindsay A; Kollmann, Tobias R; Miller, Samuel I; Wilson, Christopher B

    2012-01-01

    Although lipopolysaccharide (LPS) stimulation through the Toll-like receptor (TLR)-4/MD-2 receptor complex activates host defense against Gram-negative bacterial pathogens, how species-specific differences in LPS recognition impact host defense remains undefined. Herein, we establish how temperature dependent shifts in the lipid A of Yersinia pestis LPS that differentially impact recognition by mouse versus human TLR4/MD-2 dictate infection susceptibility. When grown at 37°C, Y. pestis LPS is hypo-acylated and less stimulatory to human compared with murine TLR4/MD-2. By contrast, when grown at reduced temperatures, Y. pestis LPS is more acylated, and stimulates cells equally via human and mouse TLR4/MD-2. To investigate how these temperature dependent shifts in LPS impact infection susceptibility, transgenic mice expressing human rather than mouse TLR4/MD-2 were generated. We found the increased susceptibility to Y. pestis for "humanized" TLR4/MD-2 mice directly paralleled blunted inflammatory cytokine production in response to stimulation with purified LPS. By contrast, for other Gram-negative pathogens with highly acylated lipid A including Salmonella enterica or Escherichia coli, infection susceptibility and the response after stimulation with LPS were indistinguishable between mice expressing human or mouse TLR4/MD-2. Thus, Y. pestis exploits temperature-dependent shifts in LPS acylation to selectively evade recognition by human TLR4/MD-2 uncovered with "humanized" TLR4/MD-2 transgenic mice.

  9. Computer Simulations of Lipid Bilayers and Proteins

    DEFF Research Database (Denmark)

    Sonne, Jacob

    2006-01-01

    The importance of computer simulations in lipid bilayer research has become more prominent for the last couple of decades and as computers get even faster, simulations will play an increasingly important part of understanding the processes that take place in and across cell membranes. This thesis...... entitled Computer simulations of lipid bilayers and proteins describes two molecular dynamics (MD) simulation studies of pure lipid bilayers as well as a study of a transmembrane protein embedded in a lipid bilayer matrix. Below follows a brief overview of the thesis. Chapter 1. This chapter is a short...... in the succeeding chapters is presented. Details on system setups, simulation parameters and other technicalities can be found in the relevant chapters. Chapter 3, DPPC lipid parameters: The quality of MD simulations is intimately dependent on the empirical potential energy function and its parameters, i...

  10. Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Yuan-Ping, E-mail: pang@mayo.edu

    2014-09-26

    Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.

  11. Alaska, Gulf spills share similarities

    International Nuclear Information System (INIS)

    Usher, D.

    1991-01-01

    The accidental Exxon Valdez oil spill in Alaska and the deliberate dumping of crude oil into the Persian Gulf as a tactic of war contain both glaring differences and surprising similarities. Public reaction and public response was much greater to the Exxon Valdez spill in pristine Prince William Sound than to the war-related tragedy in the Persian Gulf. More than 12,000 workers helped in the Alaskan cleanup; only 350 have been involved in Kuwait. But in both instances, environmental damages appear to be less than anticipated. Natures highly effective self-cleansing action is primarily responsible for minimizing the damages. One positive action growing out of the two incidents is increased international cooperation and participation in oil-spill clean-up efforts. In 1990, in the aftermath of the Exxon Valdez spill, 94 nations signed an international accord on cooperation in future spills. The spills can be historic environmental landmarks leading to creation of more sophisticated response systems worldwide

  12. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  13. Reactive molecular dynamic simulations on the gas separation performance of porous graphene membrane.

    Science.gov (United States)

    Esfandiarpoor, Somaye; Fazli, Mostafa; Ganji, Masoud Darvish

    2017-11-29

    The separation of gases molecules with similar diameter and shape is an important area of research. For example, the major challenge to set up sweeping carbon dioxide capture and storage (CCS) in power plants is the energy requisite to separate the CO 2 from flue gas. Porous graphene has been proposed as superior material for highly selective membranes for gas separation. Here we design some models of porous graphene with different sizes and shape as well as employ double layers porous graphene for efficient CO 2 /H 2 separation. The selectivity and permeability of gas molecules through various nanopores were investigated by using the reactive molecular dynamics simulation which considers the bond forming/breaking mechanism for all atoms. Furthermore, it uses a geometry-dependent charge calculation scheme that accounts appropriately for polarization effect which can play an important role in interacting systems. It was found that H-modified porous graphene membrane with pore diameter (short side) of about 3.75 Å has excellent selectivity for CO 2 /H 2 separation. The mechanism of gas penetration through the sub-nanometer pore was presented for the first time. The accuracy of MD simulation results validated by valuable DFT method. The present findings show that reactive MD simulation can propose an economical means of separating gases mixture.

  14. Investigation of arc repressor DNA-binding specificity by comparative molecular dynamics simulations.

    Science.gov (United States)

    Song, Wei; Guo, Jun-Tao

    2015-01-01

    Transcription factors regulate gene expression through binding to specific DNA sequences. How transcription factors achieve high binding specificity is still not well understood. In this paper, we investigated the role of protein flexibility in protein-DNA-binding specificity by comparative molecular dynamics (MD) simulations. Protein flexibility has been considered as a key factor in molecular recognition, which is intrinsically a dynamic process involving fine structural fitting between binding components. In this study, we performed comparative MD simulations on wild-type and F10V mutant P22 Arc repressor in both free and complex conformations. The F10V mutant has lower DNA-binding specificity though both the bound and unbound main-chain structures between the wild-type and F10V mutant Arc are highly similar. We found that the DNA-binding motif of wild-type Arc is structurally more flexible than the F10V mutant in the unbound state, especially for the six DNA base-contacting residues in each dimer. We demonstrated that the flexible side chains of wild-type Arc lead to a higher DNA-binding specificity through forming more hydrogen bonds with DNA bases upon binding. Our simulations also showed a possible conformational selection mechanism for Arc-DNA binding. These results indicate the important roles of protein flexibility and dynamic properties in protein-DNA-binding specificity.

  15. MdATG18a overexpression improves tolerance to nitrogen deficiency and regulates anthocyanin accumulation through increased autophagy in transgenic apple.

    Science.gov (United States)

    Sun, Xun; Jia, Xin; Huo, Liuqing; Che, Runmin; Gong, Xiaoqing; Wang, Ping; Ma, Fengwang

    2018-02-01

    Nitrogen (N) availability is an essential factor for plant growth. Recycling and remobilization of N have strong impacts on crop yield and quality under N deficiency. Autophagy is a critical nutrient-recycling process that facilitates remobilization under starvation. We previously showed that an important AuTophaGy (ATG) protein from apple, MdATG18a, has a positive role in drought tolerance. In this study, we explored its biological role in response to low-N. Overexpression of MdATG18a in both Arabidopsis and apple improved tolerance to N-depletion and caused a greater accumulation of anthocyanin. The increased anthocyanin concentration in transgenic apple was possibly due to up-regulating flavonoid biosynthetic and regulatory genes (MdCHI, MdCHS, MdANS, MdPAL, MdUFGT, and MdMYB1) and higher soluble sugars concentration. MdATG18a overexpression enhanced starch degradation with up-regulating amylase gene (MdAM1) and up-regulated sugar metabolism related genes (MdSS1, MdHXKs, MdFK1, and MdNINVs). Furthermore, MdATG18a functioned in nitrate uptake and assimilation by up-regulating nitrate reductase MdNIA2 and 3 high-affinity nitrate transporters MdNRT2.1/2.4/2.5. MdATG18a overexpression also elevated other important MdATG genes expression and autophagosomes formation under N-depletion, which play key contributions to above changes. Together, these results demonstrate that overexpression of MdATG18a enhances tolerance to N-deficiencies and plays positive roles in anthocyanin biosynthesis through greater autophagic activity. © 2017 John Wiley & Sons Ltd.

  16. Docking, thermodynamics and molecular dynamics (MD) studies of a non-canonical protease inhibitor, MP-4, from Mucuna pruriens.

    Science.gov (United States)

    Kumar, Ashish; Kaur, Harmeet; Jain, Abha; Nair, Deepak T; Salunke, Dinakar M

    2018-01-12

    Sequence and structural homology suggests that MP-4 protein from Mucuna pruriens belongs to Kunitz-type protease inhibitor family. However, biochemical assays showed that this protein is a poor inhibitor of trypsin. To understand the basis of observed poor inhibition, thermodynamics and molecular dynamics (MD) simulation studies on binding of MP-4 to trypsin were carried out. Molecular dynamics simulations revealed that temperature influences the spectrum of conformations adopted by the loop regions in the MP-4 structure. At an optimal temperature, MP-4 achieves maximal binding while above and below the optimum temperature, its functional activity is hampered due to unfavourable flexibility and relative rigidity, respectively. The low activity at normal temperature is due to the widening of the conformational spectrum of the Reactive Site Loop (RSL) that reduces the probability of formation of stabilizing contacts with trypsin. The unique sequence of the RSL enhances flexibility at ambient temperature and thus reduces its ability to inhibit trypsin. This study shows that temperature influences the function of a protein through modulation in the structure of functional domain of the protein. Modulation of function through appearance of new sequences that are more sensitive to temperature may be a general strategy for evolution of new proteins.

  17. 76 FR 20008 - Notice of Temporary Concession Contract for Assateague Island National Seashore, MD

    Science.gov (United States)

    2011-04-11

    ... pre-packaged food and beverage. This action is necessary to avoid interruption of visitor services... DEPARTMENT OF THE INTERIOR National Park Service [NPS-WASO-CONC-0111-6544; 2410-OYC] Notice of Temporary Concession Contract for Assateague Island National Seashore, MD AGENCY: National Park Service...

  18. Property values, parks, and crime: a hedonic analysis in Baltimore, MD

    Science.gov (United States)

    Austin Troy; J. Morgan Grove

    2008-01-01

    While urban parks are generally considered to be a positive amenity, past research suggests that some parks are perceived as a neighborhood liability. Using hedonic analysis of property data in Baltimore, MD, we attempted to determine whether crime rate mediates how parks are valued by the housing market. Transacted price was regressed against park proximity, area-...

  19. 77 FR 42179 - Safety Zone; Fireworks Display, Potomac River, Charles County, Newburg, MD

    Science.gov (United States)

    2012-07-18

    ...]30[sec] W, located at Newburg in Charles County, Maryland (NAD 1983). The temporary safety zone will... 1625-AA00 Safety Zone; Fireworks Display, Potomac River, Charles County, Newburg, MD AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard will establish a safety zone upon...

  20. 75 FR 18778 - Safety Zone; Ocean City Air Show 2010, Atlantic Ocean, Ocean City, MD

    Science.gov (United States)

    2010-04-13

    ...-AA00 Safety Zone; Ocean City Air Show 2010, Atlantic Ocean, Ocean City, MD AGENCY: Coast Guard, DHS... zone on the Atlantic Ocean in the vicinity of Ocean City, Maryland to support the Ocean City Air Show. This action is intended to restrict vessel traffic movement on the Atlantic Ocean to protect mariners...

  1. 75 FR 50878 - Airworthiness Directives; McDonnell Douglas Corporation Model MD-90-30 Airplanes

    Science.gov (United States)

    2010-08-18

    ... Airworthiness Directives; McDonnell Douglas Corporation Model MD- 90-30 Airplanes AGENCY: Federal Aviation... McDonnell Douglas Corporation: Amendment 39-16388. Docket No. FAA-2010-0433; Directorate Identifier 2009-NM..., 2010. Affected ADs (b) None. Applicability (c) This AD applies to McDonnell Douglas Corporation Model...

  2. 75 FR 68245 - Airworthiness Directives; McDonnell Douglas Corporation Model MD-90-30 Airplanes

    Science.gov (United States)

    2010-11-05

    ...-1043; Directorate Identifier 2010-NM-200-AD] RIN 2120-AA64 Airworthiness Directives; McDonnell Douglas... McDonnell Douglas Model MD-90-30 airplanes. This proposed AD would require installing new fire handle... airworthiness directive (AD): McDonnell Douglas Corporation: Docket No. FAA-2010-1043; Directorate Identifier...

  3. 75 FR 38056 - Airworthiness Directives; McDonnell Douglas Corporation Model MD-90-30 Airplanes

    Science.gov (United States)

    2010-07-01

    ...-0645; Directorate Identifier 2009-NM-200-AD] RIN 2120-AA64 Airworthiness Directives; McDonnell Douglas..., September 9, 2008), for certain McDonnell Douglas Corporation Model MD-90-30 airplanes. That AD requires a... fasteners in the aft mount support fitting of the left and right engines on 29 McDonnell Douglas Corporation...

  4. 75 FR 21528 - Airworthiness Directives; McDonnell Douglas Corporation Model MD-90-30 Airplanes

    Science.gov (United States)

    2010-04-26

    ...-0433; Directorate Identifier 2009-NM-117-AD] RIN 2120-AA64 Airworthiness Directives; McDonnell Douglas... main landing gear (MLG) during gear extension, damaging the hydraulic system on McDonnell Douglas.... The retract cylinder support fittings for the MLG on McDonnell Douglas Model MD-80 series airplanes...

  5. 75 FR 36577 - Airworthiness Directives; McDonnell Douglas Corporation Model MD-90-30 Airplanes

    Science.gov (United States)

    2010-06-28

    ... Airworthiness Directives; McDonnell Douglas Corporation Model MD- 90-30 Airplanes AGENCY: Federal Aviation... Douglas Corporation: Docket No. FAA-2010-0554; Directorate Identifier 2010-NM-082-AD. Comments Due Date (a... supersedes AD 2009-07-04, Amendment 39-15863. Applicability (c) This AD applies to McDonnell Douglas...

  6. 75 FR 80742 - Airworthiness Directives; McDonnell Douglas Corporation Model MD-90-30 Airplanes

    Science.gov (United States)

    2010-12-23

    ...-1202; Directorate Identifier 2010-NM-167-AD] RIN 2120-AA64 Airworthiness Directives; McDonnell Douglas... amends Sec. 39.13 by adding the following new airworthiness directive (AD): McDonnell Douglas Corporation... Douglas Corporation Model MD-90-30 airplanes, certificated in any category. Subject (d) Joint Aircraft...

  7. 75 FR 66653 - Airworthiness Directives; McDonnell Douglas Corporation Model MD-90-30 Airplanes

    Science.gov (United States)

    2010-10-29

    ... Airworthiness Directives; McDonnell Douglas Corporation Model MD- 90-30 Airplanes AGENCY: Federal Aviation...-15667 (73 FR 52203, September 9, 2008), and adding the following new AD: 2010-22-04 McDonnell Douglas... supersedes AD 2008-18-10, Amendment 39-15667. Applicability (c) This AD applies to McDonnell Douglas...

  8. 75 FR 51333 - Madison Square Federal Savings Bank, Baltimore, MD; Approval of Conversion Application

    Science.gov (United States)

    2010-08-19

    ... DEPARTMENT OF THE TREASURY Office of Thrift Supervision [AC-49: OTS Nos. 08156 and H4736] Madison Square Federal Savings Bank, Baltimore, MD; Approval of Conversion Application Notice is hereby given that on August 12, 2010, the Office of Thrift Supervision approved the application of Madison Square...

  9. 75 FR 24774 - Fairmount Bank, Baltimore, MD; Approval of Conversion Application

    Science.gov (United States)

    2010-05-05

    ... DEPARTMENT OF THE TREASURY Office of Thrift Supervision [AC-36 OTS Nos. 08193 and H4677] Fairmount Bank, Baltimore, MD; Approval of Conversion Application Notice is hereby given that on April 15, 2010, the Office of Thrift Supervision approved the application of Fairmount Bank, Baltimore, Maryland, to...

  10. 75 FR 31511 - Ideal Federal Savings Bank, Baltimore, MD; Approval of Conversion Application

    Science.gov (United States)

    2010-06-03

    ... DEPARTMENT OF THE TREASURY Office of Thrift Supervision [AC-46: OTS No. 08283] Ideal Federal Savings Bank, Baltimore, MD; Approval of Conversion Application Notice is hereby given that on May 24, 2010, the Office of Thrift Supervision approved the application of Ideal Federal Savings Bank...

  11. 77 FR 68149 - Karen Paul Holley, M.D.; Decision and Order

    Science.gov (United States)

    2012-11-15

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 12-51] Karen Paul Holley, M.D... revoke the DEA Certificate of Registration (COR), Number BH8988339, of Karen Paul Holley, M.D....D., 74 FR 17528, 174529 (2009); John B. Freitas, D.O., 74 FR 17524, 17525 (2009); Roger A. Rodriguez...

  12. 76 FR 20034 - Calvin Ramsey, M.D.; Revocation of Registration

    Science.gov (United States)

    2011-04-11

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 10-25] Calvin Ramsey, M.D.; Revocation of Registration On December 18, 2009, the Deputy Assistant Administrator, Office of Diversion... constitutional right to appointed counsel in a proceeding under 21 U.S.C. 824(a). See Goldberg v. Kelly, 397 U.S...

  13. 76 FR 9407 - Fraternity Federal Savings & Loan Association, Baltimore, MD; Approval of Conversion Application

    Science.gov (United States)

    2011-02-17

    ... DEPARTMENT OF THE TREASURY Office of Thrift Supervision [AC-58 OTS No. 01292 and H 4762] Fraternity Federal Savings & Loan Association, Baltimore, MD; Approval of Conversion Application Notice is hereby given that on February 10, 2011, the Office of Thrift Supervision approved the application of...

  14. 75 FR 49956 - Dewey C. Mackay, M.D.; Revocation of Registration

    Science.gov (United States)

    2010-08-16

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 09-28] Dewey C. Mackay, M.D.; Revocation of Registration On February 26, 2009, I, the Deputy Administrator of the Drug Enforcement Administration (DEA), issued an Order to Show Cause and Immediate Suspension of Registration to Dewey C. MacKay...

  15. 76 FR 65118 - Drawbridge Operation Regulation; Bear Creek, Sparrows Point, MD

    Science.gov (United States)

    2011-10-20

    ...-AA09 Drawbridge Operation Regulation; Bear Creek, Sparrows Point, MD AGENCY: Coast Guard, DHS. ACTION... regulation. The Baltimore County Revenue Authority (Dundalk Avenue) highway toll drawbridge across Bear Creek... applicable or necessary. Basis and Purpose The drawbridge across Bear Creek, mile 1.5 was removed and...

  16. Going Concern Opinions and Management's Forward Looking Disclosures: Evidence from the MD&A

    NARCIS (Netherlands)

    Enev, M.; Geiger, Marshall; Gold, A.H.; Wallage, P.

    In this study we examine the relationship between the auditor’s going concern opinion and management’s forward-looking disclosures in the Management’s Discussion and Analysis (MD&A) section of 10-K filings. The research objective is two-fold and addresses whether the presence of a going concern

  17. 77 FR 35054 - Donald Brooks Reece II, M.D.; Dismissal of Proceeding

    Science.gov (United States)

    2012-06-12

    ..., M.D. (Respondent), of Morehead City, N.C. The Order proposed the revocation of Respondent's DEA... pleading entitled: ``Notice To The Administrator Regarding State Authority,'' with attachments. Therein..., at 3. This Order was effective on December 8, 2011. Id., Attachment 5, at 6. Upon review of the...

  18. 75 FR 18056 - Safety Zone; Fireworks Display, Patuxent River, Solomons Island Harbor, MD

    Science.gov (United States)

    2010-04-09

    ... the event, and enhancing public and maritime safety. Basis and Purpose Fireworks displays are... promote public and maritime safety during a fireworks display, and to protect mariners transiting the area...-AA00 Safety Zone; Fireworks Display, Patuxent River, Solomons Island Harbor, MD AGENCY: Coast Guard...

  19. MD#2183: Calibration of the IR6 B2 diamond BLMs

    CERN Document Server

    Valette, Matthieu; Lindstrom, Bjorn Hans Filip

    2018-01-01

    In case of an asynchronous beam dump with a fully filled LHC machine, causing ~40 bunches to impact on the movable dump protection absorber (TCDQ), it is expected that all standard ionisation chamber Beam Loss Monitors (IC BLM) around the LHC dumping region in IR6 will be saturated. Diamond Beam Loss Monitors (dBLM) were therefore installed next to the TCDQ downstream of the extraction kickers. These detectors allow resolving losses at a nanosecond timescale and with a dynamic range of several orders of magnitude; thus, allowing to derive the number of nominal bunches impacting the TCDQ. After a first series of calibrations using asynchronous beam dump tests, an experiment was conducted during MD#1182 to demonstrate the possibility of resolving a nominal bunch hitting the TCDQ. During this first MD only the Beam 1 dBLM was calibrated appropriately, a second calibration MD was therefore performed in 2017 for the B2 system. Results from this MD and conclusions regarding dBLM saturation with a top energy nominal...

  20. 76 FR 71369 - Robert G. Crummie, M.D.; Decision and Order

    Science.gov (United States)

    2011-11-17

    ... agencies to perform meaningless tasks. See Layfe Robert Anthony, M.D., 67 FR 35582 (DEA 2002); Michael G.... Kirk v. Mullen, 749 F.2d 297 (6th Cir. 1984); Puerto Rico Aqueduct and Sewer Auth. v. EPA, 35 F.3d 600...

  1. The draft genome of MD-2 pineapple using hybrid error correction of long reads

    Science.gov (United States)

    Redwan, Raimi M.; Saidin, Akzam; Kumar, S. Vijay

    2016-01-01

    The introduction of the elite pineapple variety, MD-2, has caused a significant market shift in the pineapple industry. Better productivity, overall increased in fruit quality and taste, resilience to chilled storage and resistance to internal browning are among the key advantages of the MD-2 as compared with its previous predecessor, the Smooth Cayenne. Here, we present the genome sequence of the MD-2 pineapple (Ananas comosus (L.) Merr.) by using the hybrid sequencing technology from two highly reputable platforms, i.e. the PacBio long sequencing reads and the accurate Illumina short reads. Our draft genome achieved 99.6% genome coverage with 27,017 predicted protein-coding genes while 45.21% of the genome was identified as repetitive elements. Furthermore, differential expression of ripening RNASeq library of pineapple fruits revealed ethylene-related transcripts, believed to be involved in regulating the process of non-climacteric pineapple fruit ripening. The MD-2 pineapple draft genome serves as an example of how a complex heterozygous genome is amenable to whole genome sequencing by using a hybrid technology that is both economical and accurate. The genome will make genomic applications more feasible as a medium to understand complex biological processes specific to pineapple. PMID:27374615

  2. 78 FR 11142 - Connor Hayden Kraegel, 19917 Spurrier Avenue, Poolesville, MD 20837; Order Denying Export Privileges

    Science.gov (United States)

    2013-02-15

    ... DEPARTMENT OF COMMERCE Bureau of Industry and Security Connor Hayden Kraegel, 19917 Spurrier... Court, District of Maryland, Connor Hayden Kraegel (``Kraegel'') was convicted of violating Section 38... Hayden Kraegel, with a last known address at: 19917 Spurrier Avenue, Poolesville, MD 20837, and when...

  3. 75 FR 51945 - Safety Zone; Potomac River, St. Mary's River, St. Inigoes, MD

    Science.gov (United States)

    2010-08-24

    ...-AA00 Safety Zone; Potomac River, St. Mary's River, St. Inigoes, MD AGENCY: Coast Guard, DHS. ACTION... of the St. Mary's River, a tributary of the Potomac River. This action is necessary to provide for.... Navy helicopter located near St. Inigoes, Maryland. This safety zone is intended to protect the...

  4. Heat Flow Data Cruise MD72 RV Marion Dufresne over the Mascarene Ridge

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Data were gathered by the R/V Marion Dufresne in May and June of 1992 over the Mascarene Ridge in the Indian Ocean on cruise MD72/MASCAFLUX. Heat flow measurements...

  5. 75 FR 53574 - Safety Zone; Fireworks Displays, Potomac River, National Harbor, MD

    Science.gov (United States)

    2010-09-01

    ...-AA00 Safety Zone; Fireworks Displays, Potomac River, National Harbor, MD AGENCY: Coast Guard, DHS... safety of life on navigable waters during five fireworks displays launched from a discharge barge located... necessary to protect persons and vessels against the hazards associated with a fireworks display on...

  6. 78 FR 68002 - Safety Zone for Fireworks Display, Baltimore Harbor, Baltimore, MD

    Science.gov (United States)

    2013-11-13

    ... 1625-AA00 Safety Zone for Fireworks Display, Baltimore Harbor, Baltimore, MD AGENCY: Coast Guard, DHS... safety of life on navigable waters during a fireworks display launched from a barge located in Baltimore... rule involves a fireworks display associated with a New Year's Eve event that will take place in...

  7. 77 FR 11434 - Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD

    Science.gov (United States)

    2012-02-27

    ...-AA00 Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD AGENCY: Coast Guard, DHS... intended route immediately prior to, during, and following the scheduled towing evolution, vessel traffic... made to the maritime community via marine information broadcasts so mariners may adjust their plans...

  8. Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

    Science.gov (United States)

    Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash; hide

    2002-01-01

    A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.

  9. InforMD: a new initiative to raise public awareness about breast density.

    Science.gov (United States)

    Hugo, Honor J; Zysk, Aneta; Dasari, Pallave; Britt, Kara; Hopper, John L; Stone, Jennifer; Thompson, Erik W; Ingman, Wendy V

    2018-01-01

    On a mammogram, breast density (also known as mammographic density) is shown as white and bright regions and is associated with reduced sensitivity in cancer detection and increased breast cancer risk. However, many Australian women are unaware of the significance of breast density as it is not routinely reported or discussed. In order to address this lack of knowledge, Australian breast cancer researchers with expertise in mammographic density formed the InforMD alliance (INformation FORum on Mammographic Density) in 2016. The alliance is working to raise awareness of breast density with the goal of improving breast cancer diagnosis and health outcomes for women. The InforMD website (www.InforMD.org.au) was launched in October 2016, coinciding with a major nationwide public awareness campaign by the alliance during breast cancer awareness month. The website contains unbiased, accurate, updated information on breast density. The website also provides summaries of major research articles in layperson language, recent news items related to breast density, links to relevant information for health professionals, events, and feature articles. Members of the public and health professionals can also subscribe for news updates. The interactive online Forum section facilitates discussion between health professionals, scientists and members of the public. To increase online traffic to the website, Facebook (www.facebook.com/BeInforMD) and Twitter (https://twitter.com/BeInforMD_) pages were launched in December 2016. Since its launch, InforMD has generated considerable interest. The public awareness campaign reached over 7 million Australians through a combination of newspaper, TV, radio, and online news. The website has attracted 13,058 unique visitors and 30,353 page views (data as of 19/12/2017). Breast cancer researchers have a significant role to play in disseminating information to the public on breast density. A combination of mainstream and social media, together with

  10. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

    Directory of Open Access Journals (Sweden)

    Lauren Boldon

    2015-02-01

    Full Text Available In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS experiments, molecular dynamics (MD simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

  11. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

    Science.gov (United States)

    Boldon, Lauren; Laliberte, Fallon; Liu, Li

    2015-01-01

    In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

  12. Nature preservation acceptance model applied to tanker oil spill simulations

    DEFF Research Database (Denmark)

    Friis-Hansen, Peter; Ditlevsen, Ove Dalager

    2003-01-01

    is exemplified by a study of oil spills due to simulated tanker collisions in the Danish straits. It is found that the distribution of the oil spill volume per spill is well represented by an exponential distribution both in Oeresund and in Great Belt. When applied in the Poisson model, a risk profile reasonably...... acceptance criterion for the pollution of the environment. This NPWI acceptance criterion is applied to the oil spill example....... be defined in a similar way as the so-called Life Quality Index defined by Nathwani et al [Nathwani JS, Lind NC, Padey MD. Affordable safety by choice: the life quality method. Institute for Risk Research, University of Waterloo; Waterloo (Ontario, Canada):1997], and can be used to quantify the risk...

  13. Lessons Learned for Online Health Community Moderator Roles: A Mixed-Methods Study of Moderators Resigning From WebMD Communities

    Science.gov (United States)

    Marmor, Rebecca; Jiang, Xiaoqian

    2016-01-01

    Background Online health community (OHC) moderators help facilitate conversations and provide information to members. However, the necessity of the moderator in helping members achieve goals by providing the support they need remains unclear, with some prior research suggesting that moderation is unnecessary or even harmful for close-knit OHCs. Similarly, members’ perceptions of moderator roles are underexplored. Starting January of 2013, WebMD moderators stopped working for WebMD communities. This event provided an opportunity for us to study the perceived role of moderators in OHCs. Objective We examine the OHC members’ perception on OHC moderators by studying their reactions toward the departure of moderators in their communities. We also analyzed the relative posting activity on OHCs before and after the departure of moderators from the communities among all members and those who discussed moderators’ departures. Methods We applied a mixed-methods approach to study the posts of all 55 moderated WebMD communities by querying the terms relating to discussions surrounding moderators’ disappearance from the WebMD community. We performed open and axial coding and affinity diagramming to thematically analyze patients’ reactions to the disappeared moderators. The number of posts and poster groups (members and moderators) were analyzed over time to understand posting patterns around moderators’ departure. Results Of 821 posts retrieved under 95 threads, a total of 166 open codes were generated. The codes were then grouped into 2 main themes with 6 total subthemes. First, patients attempted to understand why moderators had left and what could be done to fill the void left by the missing moderators. During these discussions, the posts revealed that patients believed that moderators played critical roles in the communities by making the communities vibrant and healthy, finding solutions, and giving medical information. Some patients felt personally attached

  14. 固流耦合相似模拟材料研制及深部突水模拟试验%DEVELOPMENT APPLICATION OF SOLID-FLUID COUPLING SIMILAR MATERIAL FOR FLOOR STRATA AND SIMULATION TEST OF WATER- INRUSH IN DEEP MINING

    Institute of Scientific and Technical Information of China (English)

    孙文斌; 张士川; 李杨杨; 路畅

    2015-01-01

    模拟深部开采底板岩层的裂隙演化特征是深入探讨煤层开采底板突水规律和演化机制研究的关键,为开展深部开采高水压底板突水通道形成的模型试验,基于固流耦合相似理论,以固体材料研究为基础,研制了新型的适用于深井条件下的相似材料,提出适应该材料渗透系数的测量方法,得到不同配比对材料力学性质的影响规律,将该材料应用于底板突水模拟试验,揭示相似材料的破坏特征和深部底板突水通道的演化特征,即受采动影响开切眼处裂隙发育迅速而且程度较高,解释了此处突水概率大易发生突水危险,对解决实际工程问题具有一定的指导意义。%The simulation of floor rock fracture evolution characteristics in deep mining is the key of research on laws and evolution mechanism of water-inrush. In order to launch the model test on emergence ofwater-inrush channel in deep mining floor under high water pressure,based on the similarity theory for solid-fluid coupling and the study of solid materials,a new similar material for solid-fluid coupling was developed. This material is suitable for conditions of deep mining. The measuring method for the permeability coefficient of this material was put forward. The influence law that diverse ratios affected mechanical properties of materials was concluded. The material was applied to the simulation test of water-inrush in floor,which revealed failure characteristics of similar materials and evolution characteristics of water-inrush channel in floor. Fracture developed rapidly and with higher degree affected by mining in open-off cut. This explained the greater probability of water inrush,this place is prone to result in water inrush risk. The method has some practical meaning for coal mining engineering.

  15. Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications.

    Science.gov (United States)

    Stockner, Thomas; Mullen, Anna; MacMillan, Fraser

    2015-10-01

    ABC transporters are primary active transporters found in all kingdoms of life. Human multidrug resistance transporter ABCB1, or P-glycoprotein, has an extremely broad substrate spectrum and confers resistance against chemotherapy drug treatment in cancer cells. The bacterial ABC transporter MsbA is a lipid A flippase and a homolog to the human ABCB1 transporter, with which it partially shares its substrate spectrum. Crystal structures of MsbA and ABCB1 have been solved in multiple conformations, providing a glimpse into the possible conformational changes the transporter could be going through during the transport cycle. Crystal structures are inherently static, while a dynamic picture of the transporter in motion is needed for a complete understanding of transporter function. Molecular dynamics (MD) simulations and electron paramagnetic resonance (EPR) spectroscopy can provide structural information on ABC transporters, but the strength of these two methods lies in the potential to characterise the dynamic regime of these transporters. Information from the two methods is quite complementary. MD simulations provide an all atom dynamic picture of the time evolution of the molecular system, though with a narrow time window. EPR spectroscopy can probe structural, environmental and dynamic properties of the transporter in several time regimes, but only through the attachment sites of an exogenous spin label. In this review the synergistic effects that can be achieved by combining the two methods are highlighted, and a brief methodological background is also presented. © 2015 Authors; published by Portland Press Limited.

  16. JST Thesaurus Headwords and Synonyms: Md [MeCab user dictionary for science technology term[Archive

    Lifescience Database Archive (English)

    Full Text Available MeCab user dictionary for science technology term Md 名詞 一般 * * * * メンデレビウム メンデレビウム メンデレビューム Thesaurus2015 200906022783221535 C CA03 UNKNOWN_1 Md

  17. DMPD: Innate recognition of lipopolysaccharide by Toll-like receptor 4-MD-2. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 15051069 Innate recognition of lipopolysaccharide by Toll-like receptor 4-MD-2. Miy...ake K. Trends Microbiol. 2004 Apr;12(4):186-92. (.png) (.svg) (.html) (.csml) Show Innate recognition of lip...opolysaccharide by Toll-like receptor 4-MD-2. PubmedID 15051069 Title Innate recognition of lipopolysacchari

  18. 33 CFR 334.155 - Severn River, Naval Station Annapolis, Small Boat Basin, Annapolis, MD; naval restricted area.

    Science.gov (United States)

    2010-07-01

    ... Annapolis, Small Boat Basin, Annapolis, MD; naval restricted area. 334.155 Section 334.155 Navigation and... RESTRICTED AREA REGULATIONS § 334.155 Severn River, Naval Station Annapolis, Small Boat Basin, Annapolis, MD; naval restricted area. (a) The area. The waters within the Naval Station Annapolis small boat basin and...

  19. Usefulness of multidetector-row computed tomography (MD-CT) for diagnosis and evaluation of cardiovascular anomalies in infants

    International Nuclear Information System (INIS)

    Kani, Hiroyuki; Narabayashi, Isamu; Tanikake, Masato; Matsuki, Mitsuru; Uesugi, Yasuo

    2005-01-01

    We examined the effectiveness of multidetector-row CT (MD-CT) in the diagnosis and evaluation of cardiovascular anomalies in infants. MD-CT was performed 34 times on 21 patients with cardiovascular anomalies. We performed three evaluations: 1) The assessment of the specificity of MD-CT in detecting the morphological features of cardiovascular anomalies. 2) The diameters of aortae with coronary artery (CoA), and the diameters of pulmonary artery, measured by using MD-CT were compared with those by angiography. 3) The amount of exposure to radiation was measured. 1) MD-CT can detect CoA, pulmonary arteriovenous anomalies among extracardiac anomalies in all the patients. The diagnostic accuracy for intracardiac anomalies was poor as only six of the 15 anomalies could be accurately diagnosed. 2) The diameters of aortae and pulmonary artery obtained using MD-CT showed a good correlation with those obtained using arteriography (r=0.97, 0.95). 3) The average dose-length product was 269.2 mGy·cm. And the average effective dose was 5.1 mSv. MD-CT is not suitable for the evaluation of intracardiac anomalies, but is extremely effective in the evaluation of extracardiac major vascular anomalies. On the basis of the amount of information and noninvasive nature, MD-CT should be used first before angiography. (author)

  20. The Convergence of Business and Medicine: A Study of MD/MBA Programs in the United States

    Science.gov (United States)

    Keogh, Timothy J.; Martin, William Marty

    2011-01-01

    The purpose of this paper is to identify the convergence of business and medical education and describe the curricula of MD/MBA (Medical Doctor/Master of Business Administration) programs in the US. The focus of this study is to provide a guide to dual MD/MBA programs for physicians, aspiring physicians, policy makers and healthcare organizations.…

  1. Glass polymorphism in glycerol–water mixtures: I. A computer simulation study

    Science.gov (United States)

    Jahn, David A.; Wong, Jessina; Bachler, Johannes; Loerting, Thomas

    2016-01-01

    We perform out-of-equilibrium molecular dynamics (MD) simulations of water–glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA–HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ g = 0–13% and find that, for the present mixture models and rates, the LDA–HDA transformation is detectable up to χ g ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ g ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ g > 5%. We present an analysis of the molecular-level changes underlying the LDA–HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA–HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA–HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the

  2. Glass polymorphism in glycerol-water mixtures: I. A computer simulation study.

    Science.gov (United States)

    Jahn, David A; Wong, Jessina; Bachler, Johannes; Loerting, Thomas; Giovambattista, Nicolas

    2016-04-28

    We perform out-of-equilibrium molecular dynamics (MD) simulations of water-glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA-HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ(g) = 0-13% and find that, for the present mixture models and rates, the LDA-HDA transformation is detectable up to χ(g) ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ(g) ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ(g) > 5%. We present an analysis of the molecular-level changes underlying the LDA-HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA-HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA-HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the effects that

  3. Assessing the allelotypic effect of two aminocyclopropane carboxylic acid synthase-encoding genes MdACS1 and MdACS3a on fruit ethylene production and softening in Malus

    Science.gov (United States)

    Dougherty, Laura; Zhu, Yuandi; Xu, Kenong

    2016-01-01

    Phytohormone ethylene largely determines apple fruit shelf life and storability. Previous studies demonstrated that MdACS1 and MdACS3a, which encode 1-aminocyclopropane-1-carboxylic acid synthases (ACS), are crucial in apple fruit ethylene production. MdACS1 is well-known to be intimately involved in the climacteric ethylene burst in fruit ripening, while MdACS3a has been regarded a main regulator for ethylene production transition from system 1 (during fruit development) to system 2 (during fruit ripening). However, MdACS3a was also shown to have limited roles in initiating the ripening process lately. To better assess their roles, fruit ethylene production and softening were evaluated at five time points during a 20-day post-harvest period in 97 Malus accessions and in 34 progeny from 2 controlled crosses. Allelotyping was accomplished using an existing marker (ACS1) for MdACS1 and two markers (CAPS866 and CAPS870) developed here to specifically detect the two null alleles (ACS3a-G289V and Mdacs3a) of MdACS3a. In total, 952 Malus accessions were allelotyped with the three markers. The major findings included: The effect of MdACS1 was significant on fruit ethylene production and softening while that of MdACS3a was less detectable; allele MdACS1–2 was significantly associated with low ethylene and slow softening; under the same background of the MdACS1 allelotypes, null allele Mdacs3a (not ACS3a-G289V) could confer a significant delay of ethylene peak; alleles MdACS1–2 and Mdacs3a (excluding ACS3a-G289V) were highly enriched in M. domestica and M. hybrid when compared with those in M. sieversii. These findings are of practical implications in developing apples of low and delayed ethylene profiles by utilizing the beneficial alleles MdACS1-2 and Mdacs3a. PMID:27231553

  4. Structure and Interface Properties of Nanophase Ceramics: Multimillion Particle Molecular-Dynamics Simulations on Parallel Computer

    National Research Council Canada - National Science Library

    Kalia, Rajiv

    1997-01-01

    Large-scale molecular-dynamics (MD) simulations were performed to investigate: (1) sintering process, structural correlations, and mechanical behavior including dynamic fracture in microporous and nanophase Si3N4...

  5. Thermodynamic and Mechanical Properties of Epon 862 With Curing Agent Detda by Molecular Simulation

    National Research Council Canada - National Science Library

    Tack, Jeremy L

    2006-01-01

    Fully atomistic molecular dynamics (MD) simulations were used to predict the properties of EPON 862 cross-linked with curing agent DETDA, a potentially useful epoxy resin for future applications of nanocomposites...

  6. Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques.

    Science.gov (United States)

    Rajendiran, Nivedita; Durrant, Jacob D

    2018-05-05

    Molecular dynamics (MD) simulations provide critical insights into many biological mechanisms. Programs such as VMD, Chimera, and PyMOL can produce impressive simulation visualizations, but they lack many advanced rendering algorithms common in the film and video-game industries. In contrast, the modeling program Blender includes such algorithms but cannot import MD-simulation data. MD trajectories often require many gigabytes of memory/disk space, complicating Blender import. We present Pyrite, a Blender plugin that overcomes these limitations. Pyrite allows researchers to visualize MD simulations within Blender, with full access to Blender's cutting-edge rendering techniques. We expect Pyrite-generated images to appeal to students and non-specialists alike. A copy of the plugin is available at http://durrantlab.com/pyrite/, released under the terms of the GNU General Public License Version 3. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  7. Computer Simulation of Strain Engineering and Photonics Semiconducting Nanostructure on Parallel Architectures

    National Research Council Canada - National Science Library

    Nakano, Aiichiro

    2000-01-01

    ...; and dielectric properties of high permittivity TiO2 for ultrathin gate dielectric films. Scalable software infrastructure has been developed to enable multiscale simulations of nanoelectronic devices using MD and quantum mechanical...

  8. Fluctuation Solution Theory Properties from Molecular Simulation

    DEFF Research Database (Denmark)

    Abildskov, Jens; Wedberg, R.; O’Connell, John P.

    2013-01-01

    The thermodynamic properties obtained in the Fluctuation Solution Theory are based on spatial integrals of molecular TCFs between component pairs in the mixture. Molecular simulation, via either MD or MC calculations, can yield these correlation functions for model inter- and intramolecular...

  9. Development of similarity theory for control systems

    Science.gov (United States)

    Myshlyaev, L. P.; Evtushenko, V. F.; Ivushkin, K. A.; Makarov, G. V.

    2018-05-01

    The area of effective application of the traditional similarity theory and the need necessity of its development for systems are discussed. The main statements underlying the similarity theory of control systems are given. The conditions for the similarity of control systems and the need for similarity control control are formulated. Methods and algorithms for estimating and similarity control of control systems and the results of research of control systems based on their similarity are presented. The similarity control of systems includes the current evaluation of the degree of similarity of control systems and the development of actions controlling similarity, and the corresponding targeted change in the state of any element of control systems.

  10. MD1831: Single Bunch Instabilities with Q" and Non-Linear Corrections

    CERN Document Server

    Carver, Lee Robert; De Maria, Riccardo; Li, Kevin Shing Bruce; Amorim, David; Biancacci, Nicolo; Buffat, Xavier; Maclean, Ewen Hamish; Metral, Elias; Lasocha, Kacper; Lefevre, Thibaut; Levens, Tom; Salvant, Benoit; CERN. Geneva. ATS Department

    2017-01-01

    During MD1751, it was observed that both a full single beam and 964 non-colliding bunches in Beam 1 (B1) and Beam 2 (B2) were both stable at the End of Squeeze (EOS) for 0A in the Landau Octupoles. At ß* = 40cm there is also a significant Q" arising from the lattice, as well as uncorrected non-linearities in the Insertion Regions (IRs). Each of these effects could be capable of fully stabilising the beam. This MD made first use of a Q" knob through variation of the Main Sextupoles (MS) by stabilising a single bunch at Flat Top, before showing at EOS that the non-linearities were the main contributors to the beam stability.

  11. MD-portal: Highly Effective Website for Nuclear Materials Information Management

    International Nuclear Information System (INIS)

    Kil, Soyeon; Lee, Gyeonggeun; Kwon, Junhyun

    2014-01-01

    A web-based system is widespread in not only everyday activities but also business fields. In past years, the systematic information of various properties of materials usually has been provided as tabulated documents; however it recently has been provided as web-based DB. There are many websites providing material properties information, representative examples include MatWeb from the United States, Granta MI from England and MatNavi from Japan. In 2003, the nuclear materials division in KAERI established a website about nuclear materials property DB, called MatDB. To inherit it, a website called MD-portal has been recently set up to release degradation information and various properties of nuclear materials. In this presentation, the structure and characteristics of MD-portal will be mentioned, and comments on its application will be given

  12. Discovering and Developing Successful Cardiovascular Therapeutics: A Conversation With James N. Topper, MD, PhD.

    Science.gov (United States)

    Topper, James N; Rutherford, John D

    2016-11-15

    Dr James (also known as Jamie) N. Topper, MD, PhD, serves as Managing General Partner at Frazier Healthcare Partners, where he leads the Life Science Venture practice. In 2011, and 2016, he was named to the Midas List of leading venture capitalists, and, in 2013, he was recognized by Forbes as one of the top 10 healthcare investors. He has >25 years of experience working with entrepreneurs to found and build successful therapeutics-focused companies. Dr Topper holds a BS from the University of Michigan. He received an MD and PhD (in biophysics) from Stanford University School of Medicine. He completed postgraduate training in internal medicine and cardiovascular disease at the Brigham and Women's Hospital in Boston and is board certified in both disciplines. © 2016 American Heart Association, Inc.

  13. MD-CTS: An integrated terminology reference of clinical and translational medicine

    Directory of Open Access Journals (Sweden)

    Will Ray

    2016-01-01

    Full Text Available New vocabularies are rapidly evolving in the literature relative to the practice of clinical medicine and translational research. To provide integrated access to new terms, we developed a mobile and desktop online reference—Marshfield Dictionary of Clinical and Translational Science (MD-CTS. It is the first public resource that comprehensively integrates Wiktionary (word definition, BioPortal (ontology, Wiki (image reference, and Medline abstract (word usage information. MD-CTS is accessible at http://spellchecker.mfldclin.edu/. The website provides a broadened capacity for the wider clinical and translational science community to keep pace with newly emerging scientific vocabulary. An initial evaluation using 63 randomly selected biomedical words suggests that online references generally provided better coverage (73%-95% than paper-based dictionaries (57–71%.

  14. A virtual observatory for photoionized nebulae: the Mexican Million Models database (3MdB).

    Science.gov (United States)

    Morisset, C.; Delgado-Inglada, G.; Flores-Fajardo, N.

    2015-04-01

    Photoionization models obtained with numerical codes are widely used to study the physics of the interstellar medium (planetary nebulae, HII regions, etc). Grids of models are performed to understand the effects of the different parameters used to describe the regions on the observables (mainly emission line intensities). Most of the time, only a small part of the computed results of such grids are published, and they are sometimes hard to obtain in a user-friendly format. We present here the Mexican Million Models dataBase (3MdB), an effort to resolve both of these issues in the form of a database of photoionization models, easily accessible through the MySQL protocol, and containing a lot of useful outputs from the models, such as the intensities of 178 emission lines, the ionic fractions of all the ions, etc. Some examples of the use of the 3MdB are also presented.

  15. LHC MD 652: Coupled-Bunch Instability with Smaller Emittance (all HOMs)

    CERN Document Server

    AUTHOR|(CDS)2081238; Timko, Helga; CERN. Geneva. ATS Department

    2017-01-01

    The aim of the MD was to measure the coupled-bunch stability from all HOM impedances, with a reduced longitudinal emittance in order to explore the HL-LHC conditions. The acceleration ramp was performed with the nominal beams of 2016, but a reduced target bunch length and RF voltage. With this reduced emittance, the beam remained close but above the single-bunch stability threshold. No coupled-bunch oscillations were observed, so we can conclude that the stability threshold for coupled-bunch instability is not lower than the single-bunch threshold. An interesting observation in the MD was the long-lasting injection oscillations, whose traces can still be seen at arrival to flat top; in agreement with observations in earlier MDs. The measurements took place between 28th October 20:00 and 29th October 05:10.

  16. Why should biochemistry students be introduced to molecular dynamics simulations--and how can we introduce them?

    Science.gov (United States)

    Elmore, Donald E

    2016-01-01

    Molecular dynamics (MD) simulations play an increasingly important role in many aspects of biochemical research but are often not part of the biochemistry curricula at the undergraduate level. This article discusses the pedagogical value of exposing students to MD simulations and provides information to help instructors consider what software and hardware resources are necessary to successfully introduce these simulations into their courses. In addition, a brief review of the MD-based activities in this issue and other sources are provided. © 2016 The International Union of Biochemistry and Molecular Biology.

  17. β∗ levelling using the LHC Lumi Server (MD 2427)

    CERN Document Server

    Hostettler, Michi; Fuchsberger, Kajetan; Gabriel, Mathieu; Hemelsoet, Georges-Henry; Hruska, Marek; Jacquet, Delphine; Wenninger, Jorg; CERN. Geneva. ATS Department

    2018-01-01

    Luminosity levelling by β∗ is the baseline scenario for HL-LHC and will possibly be used in 2018 LHC operation. In this MD, we commissioned a novel controls approach to β∗ levelling using improved LSA trims and automatic orchestration. Compared to the regular squeeze using sequences, this approach is aimed to be minimally invasive to LHC operation in Stable Beams. Using this tool, we demonstrated the feasibility of β∗ levelling between 1 m and 30 cm.

  18. Prevalence of mood disorders and utility of the PRIME-MD in patients undergoing radiation therapy

    International Nuclear Information System (INIS)

    Leopold, Kenneth A.; Ahles, Tim A.; Walch, Susan; Amdur, Robert J.; Mott, Leila A.; Wiegand-Packard, Linda; Oxman, Thomas E.

    1998-01-01

    Purpose: To validate a short, structured interview procedure that allows practicing oncologists to quickly and reliably identify mood disorders in their patients, and to estimate the prevalence and types of mood disorders in a radiation therapy patient setting, noting relationships between mood disorders and patient characteristics. Methods: Consecutive, eligible adult patients from the practices of two radiation oncologists were administered the Primary Care Evaluation of Mental Disorders (PRIME-MD) by the treating physician. A subset of these patients was also evaluated with the SCID, administered by trained mental health care personnel. Agreement between the two instruments was examined using the kappa statistic. Prevalence of mood disorders was determined from the PRIME-MD. The significance of relationships between patient characteristics and mood disorders was examined by chi-square and ANOVA analysis, and subsequently by multivariate logistic regression analysis. Results: One hundred twenty-two patients were studied. Fifty-three of these were administered the SCID. Agreement between the two instruments was very good (kappa = 0.70). A diagnosis of a depressive or anxiety disorder by the PRIME-MD was made in 59 of the 122 patients (48%, 95% confidence interval = 39%, 58%). Multivariate analysis showed that a diagnosis of a depressive mood disorder was significantly related to pain intensity and prior history of depression. Conclusion: We have demonstrated the validity and feasibility of the PRIME-MD administered by oncologists in making diagnoses of mood disorders. The prevalence of mood disorders in our set of patients undergoing a course of RT was nearly 50%. Future studies should describe the natural history of these disorders, and determine optimal intervention strategies

  19. MD 2408: Study of Schottky Monitors for Q' Measurement at Injection

    CERN Document Server

    Tydecks, Tobias; Levens, Tom; Wendt, Manfred; Wenninger, Jorg; CERN. Geneva. ATS Department

    2018-01-01

    The Schottky monitors installed at the LHC enable the detection of Schottky noise of the two circulating proton / ion beams. From Schottky noise, beam parameters like tune, chromaticity, and relative emittance, can be extracted in a non-destructive and purely parasitic method of measurement. The primary goal of this MD was to study the Schottky monitors capability to reliably and accurately determine the beam chromaticities at injection energy. Furthermore, the possibility to track the beam emittance has been investigated.

  20. A comparative study of Message Digest 5(MD5) and SHA256 algorithm

    Science.gov (United States)

    Rachmawati, D.; Tarigan, J. T.; Ginting, A. B. C.

    2018-03-01

    The document is a collection of written or printed data containing information. The more rapid advancement of technology, the integrity of a document should be kept. Because of the nature of an open document means the document contents can be read and modified by many parties so that the integrity of the information as a content of the document is not preserved. To maintain the integrity of the data, it needs to create a mechanism which is called a digital signature. A digital signature is a specific code which is generated from the function of producing a digital signature. One of the algorithms that used to create the digital signature is a hash function. There are many hash functions. Two of them are message digest 5 (MD5) and SHA256. Those both algorithms certainly have its advantages and disadvantages of each. The purpose of this research is to determine the algorithm which is better. The parameters which used to compare that two algorithms are the running time and complexity. The research results obtained from the complexity of the Algorithms MD5 and SHA256 is the same, i.e., ⊖ (N), but regarding the speed is obtained that MD5 is better compared to SHA256.

  1. Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors.

    Science.gov (United States)

    Martinez-Rosell, Gerard; Harvey, Matt J; De Fabritiis, Gianni

    2018-03-26

    Fragment-based drug discovery (FBDD) has become a mainstream approach in drug design because it allows the reduction of the chemical space and screening libraries while identifying fragments with high protein-ligand efficiency interactions that can later be grown into drug-like leads. In this work, we leverage high-throughput molecular dynamics (MD) simulations to screen a library of 129 fragments for a total of 5.85 ms against the CXCL12 monomer, a chemokine involved in inflammation and diseases such as cancer. Our in silico binding assay was able to recover binding poses, affinities, and kinetics for the selected library and was able to predict 8 mM-affinity fragments with ligand efficiencies higher than 0.3. All of the fragment hits present a similar chemical structure, with a hydrophobic core and a positively charged group, and bind to either sY7 or H1S68 pockets, where they share pharmacophoric properties with experimentally resolved natural binders. This work presents a large-scale screening assay using an exclusive combination of thousands of short MD adaptive simulations analyzed with a Markov state model (MSM) framework.

  2. Simulations of simple linoleic acid-containing lipid membranes and models for the soybean plasma membranes.

    Science.gov (United States)

    Zhuang, Xiaohong; Ou, Anna; Klauda, Jeffery B

    2017-06-07

    The all-atom CHARMM36 lipid force field (C36FF) has been tested with saturated, monounsaturated, and polyunsaturated lipids; however, it has not been validated against the 18:2 linoleoyl lipids with an unsaturated sn-1 chain. The linoleoyl lipids are common in plants and the main component of the soybean membrane. The lipid composition of soybean plasma membranes has been thoroughly characterized with experimental studies. However, there is comparatively less work done with computational modeling. Our molecular dynamics (MD) simulation results show that the pure linoleoyl lipids, 1-stearoyl-2-linoleoyl-sn-glycero-3-phosphocholine (18:0/18:2) and 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (di-18:2), agree very well with the experiments, which demonstrates the accuracy of the C36FF for the computational study of soybean membranes. Based on the experimental composition, the soybean hypocotyl and root plasma membrane models are developed with each containing seven or eight types of linoleoyl phospholipids and two types of sterols (sitosterol and stigmasterol). MD simulations are performed to characterize soybean membranes, and the hydrogen bonds and clustering results demonstrate that the lipids prefer to interact with the lipids of the same/similar tail unsaturation. All the results suggest that these two soybean membrane models can be used as a basis for further research in soybean and higher plant membranes involving membrane-associated proteins.

  3. Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations.

    Science.gov (United States)

    Zhang, Yuxin; Huang, Xiaoqin; Han, Keli; Zheng, Fang; Zhan, Chang-Guo

    2016-11-25

    The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profile of the CocE)-(+)-cocaine binding process in comparison with that of the corresponding CocE-(-)-cocaine binding process. According to the MD simulations, the equilibrium CocE-(+)-cocaine binding mode is similar to the CocE-(-)-cocaine binding mode. However, based on the simulated free energy profiles, a significant free energy barrier (∼5 kcal/mol) exists in the CocE-(+)-cocaine binding process whereas no obvious free energy barrier exists in the CocE-(-)-cocaine binding process, although the free energy barrier of ∼5 kcal/mol is not high enough to really slow down the CocE-(+)-cocaine binding process. In addition, the obtained free energy profiles also demonstrate that (+)-cocaine and (-)-cocaine have very close binding free energies with CocE, with a negligible difference (∼0.2 kcal/mol), which is qualitatively consistent with the nearly same experimental K M values of the CocE enzyme for (+)-cocaine and (-)-cocaine. The consistency between the computational results and available experimental data suggests that the mechanistic insights obtained from this study are reasonable. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  4. Marriage Matters: Spousal Similarity in Life Satisfaction

    OpenAIRE

    Ulrich Schimmack; Richard Lucas

    2006-01-01

    Examined the concurrent and cross-lagged spousal similarity in life satisfaction over a 21-year period. Analyses were based on married couples (N = 847) in the German Socio-Economic Panel (SOEP). Concurrent spousal similarity was considerably higher than one-year retest similarity, revealing spousal similarity in the variable component of life satisfac-tion. Spousal similarity systematically decreased with length of retest interval, revealing simi-larity in the changing component of life sati...

  5. Diffusion in Liquids : Equilibrium Molecular Simulations and Predictive Engineering Models

    NARCIS (Netherlands)

    Liu, X.

    2013-01-01

    The aim of this thesis is to study multicomponent diffusion in liquids using Molecular Dynamics (MD) simulations. Diffusion plays an important role in mass transport processes. In binary systems, mass transfer processes have been studied extensively using both experiments and molecular simulations.

  6. An assessment of communication skills of the MD/MS students of institute of medicine in Nepal

    Directory of Open Access Journals (Sweden)

    Jagdish Prasad Agrawal

    2013-09-01

    Full Text Available Introduction The main objective of this study was to assess the level of interpersonal communication skills of MD/MS resident doctors and to provide recommendations for the future. Methods Descriptive, cross sectional, qualitative and quantitative research design was used. 7- point Likert scale (0 to 6 MAAS-Global scoring instrument was used. The subjects of the research were the MD/MS residents from various departments of Maharajgunj Medical Campus (MMC of Institute of Medicine, Maharajgunj, Kathmandu. Out of 162 MD/MS residents, only 30 (18.5% MD/MS residents were selected for the sample size for the study from 1st, 2nd and 3rd year. One MD/MS resident was required four video recording to conduct four interviews with patients coming to the outpatient department. Results There was high degree of positive correlation between Information sharing and Management (r=0.746 whereas weak negative correlation on clarification and diagnosis (r=-0.011. Inter-rater correlation was established before hand and was satisfactory (p < 0.05. Conclusions This base line study of MD/MS residents shows that over all MD/MS residents are deficient in almost all the components of interpersonal communication skills. A communication skills training course in postgraduate medical education could improve the existing communication skills of the doctors in Nepal.

  7. Hybrid Pressure Retarded Osmosis−Membrane Distillation (PRO−MD) Process for Osmotic Power and Clean Water Generation

    KAUST Repository

    Han, Gang

    2015-05-20

    A novel pressure retarded osmosis−membrane distillation (PRO−MD) hybrid process has been experimentally conceived for sustainable production of renewable osmotic power and clean water from various waters. The proposed PRO−MD system may possess unique advantages of high water recovery rate, huge osmotic power generation, well controlled membrane fouling, and minimal environmental impacts. Experimental results show that the PRO−MD hybrid process is promising that not only can harvest osmotic energy from freshwater but also from wastewater. When employing a 2 M NaCl MD concentrate as the draw solution, ultrahigh power densities of 31.0 W/m2 and 9.3 W/m2 have been demonstrated by the PRO subsystem using deionized water and real wastewater brine as the feeds, respectively. Simultaneously, high purity potable water with a flux of 32.5−63.1 L/(m2.h) can be produced by the MD subsystem at 40−60 °C without any detrimental effects of fouling. The energy consumption in the MD subsystem might be further reduced by applying a heat exchanger in the hybrid system and using low-grade heat or solar energy to heat up the feed solution. The newly developed PRO−MD hybrid process would provide insightful guidelines for the exploration of alternative green technologies for renewable osmotic energy and clean water production.

  8. Structure of Cu64.5Zr35.5 metallic glass by reverse Monte Carlo simulations

    International Nuclear Information System (INIS)

    Fang, X. W.; Huang, Li; Wang, C. Z.; Ho, K. M.; Ding, Z. J.

    2014-01-01

    Reverse Monte Carlo simulations (RMC) have been widely used to generate three dimensional (3D) atomistic models for glass systems. To examine the reliability of the method for metallic glass, we use RMC to predict the atomic configurations of a “known” structure from molecular dynamics (MD) simulations, and then compare the structure obtained from the RMC with the target structure from MD. We show that when the structure factors and partial pair correlation functions from the MD simulations are used as inputs for RMC simulations, the 3D atomistic structure of the glass obtained from the RMC gives the short- and medium-range order in good agreement with those from the target structure by the MD simulation. These results suggest that 3D atomistic structure model of the metallic glass alloys can be reasonably well reproduced by RMC method with a proper choice of input constraints

  9. Equations of states for an ionic liquid under high pressure: A molecular dynamics simulation study

    International Nuclear Information System (INIS)

    Ribeiro, Mauro C.C.; Pádua, Agílio A.H.; Gomes, Margarida F.C.

    2014-01-01

    Highlights: • We compare different equation of states, EoS, for an ionic liquid under high pressure. • Molecular dynamics, MD, simulations have been used to evaluate the best EoS. • MD simulations show that a group contribution model can be extrapolated to P ∼ 1.0 GPa. • A perturbed hard-sphere EoS also fits the densities calculated by MD simulations. - Abstract: The high-pressure dependence of density given by empirical equation of states (EoS) for the ionic liquid 1-butyl-3-methylimidazolium trifluoromethanesulfonate (or triflate), [C 4 C 1 im][TfO], is compared with results obtained by molecular dynamics (MD) simulations. Two EoS proposed for [C 4 C 1 im][TfO] in the pressure range of tens of MPa, which give very different densities when extrapolated to pressures beyond the original experiments, are compared with a group contribution model (GCM). The MD simulations provide support that one of the empirical EoS and the GCM is valid in the pressure range of hundreds of MPa. As an alternative to these EoS that are based on modified Tait equations, it is shown that a perturbed hard-sphere EoS based on the Carnahan–Starling–van der Waals equation also fits the densities calculated by MD simulations of [C 4 C 1 im][TfO] up to ∼1.0 GPa

  10. Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations

    Science.gov (United States)

    2017-01-01

    We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics. The propeller loops sampled similar ensembles for all GQ topologies and for all force-field dihedral-potential variants. The outcomes of standard and RECT simulations were consistent and captured similar spectrum of loop conformations. However, the most common crystallographic loop conformation was very unstable with all force-field versions. Although the loss of canonical γ-trans state of the first propeller loop nucleotide could be related to the indispensable bsc0 α/γ dihedral potential, even supporting this particular dihedral by a bias was insufficient to populate the experimentally dominant loop conformation. In conclusion, while our simulations were capable of providing a reasonable albeit not converged sampling of the TTA propeller loop conformational space, the force-field description still remained far from satisfactory. PMID:28475322

  11. Structure and dynamics of hydrated Fe(II) and Fe(III) ions. Quantum mechanical and molecular mechanical simulations

    International Nuclear Information System (INIS)

    Remsungnen, T.

    2002-11-01

    Classical molecular dynamics (MD) and combined em ab initio quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations have been performed to investigate structural, dynamical and energetical properties of Fe(II), and Fe(III) transition metal ions in aqueous solution. In the QM/MM-MD simulations the ion and its first hydration sphere were treated at the Hartree-Fock ab initio quantum mechanical level, while ab initio generated pair plus three-body potentials were employed for the remaining system. For the classical MD simulation the pair plus three-body potential were employed for all ion-water interactions. The coordination number of the first hydration shell is 100 % of 6 in both cases. The number of waters in the second hydration shell obtained from classical simulations are 13.4 and 15.1 for Fe(II) and Fe(III), respectively, while QM/MM-MD gives the values of 12.4 and 13.4 for Fe(II) and Fe(III). The energies of hydration obtained from MD and QM/MM-MD for Fe(II) are 520 and 500 kcal/mol, and for Fe(III) 1160 and 1100 kcal/mol respectively. The mean residence times of water in the second shell obtained from QM/MM-MD are 24 and 48 ps for Fe(II) and Fe(III), respectively. In contrast to the data obtained from classical MD simulation, the QM/MM-MD values are all in good agreement with the experimental data available. These investigations and results clearly indicate that many-body effects are essential for the proper description of all properties of the aqueous solution of both Fe(II) and Fe(III) ions. (author)

  12. Development of simulation approach for two-dimensional chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface

    Science.gov (United States)

    Qin, Yuan; Yao, Man; Hao, Ce; Wan, Lijun; Wang, Yunhe; Chen, Ting; Wang, Dong; Wang, Xudong; Chen, Yonggang

    2017-09-01

    Two-dimensional (2D) chiral self-assembly system of 5-(benzyloxy)-isophthalic acid derivative/(S)-(+)-2-octanol/highly oriented pyrolytic graphite was studied. A combined density functional theory/molecular mechanics/molecular dynamics (DFT/MM/MD) approach for system of 2D chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface was thus proposed. Structural models of the chiral assembly were built on the basis of scanning tunneling microscopy (STM) images and simplified for DFT geometry optimization. Merck Molecular Force Field (MMFF) was singled out as the suitable force field by comparing the optimized configurations of MM and DFT. MM and MD simulations for hexagonal unit model which better represented the 2D assemble network were then preformed with MMFF. The adhesion energy, evolution of self-assembly process and characteristic parameters of hydrogen bond were obtained and analyzed. According to the above simulation, the stabilities of the clockwise and counterclockwise enantiomorphous networks were evaluated. The calculational results were supported by STM observations and the feasibility of the simulation method was confirmed by two other systems in the presence of chiral co-absorbers (R)-(-)-2-octanol and achiral co-absorbers 1-octanol. This theoretical simulation method assesses the stability trend of 2D enantiomorphous assemblies with atomic scale and can be applied to the similar hydrogen bond driven 2D chirality of molecular self-assembly system.

  13. A Molecular Dynamics (MD and Quantum Mechanics/Molecular Mechanics (QM/MM Study on Ornithine Cyclodeaminase (OCD: A Tale of Two Iminiums

    Directory of Open Access Journals (Sweden)

    James W. Gauld

    2012-10-01

    Full Text Available Ornithine cyclodeaminase (OCD is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD and a hybrid quantum mechanics/molecular mechanics (QM/MM method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2+ Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2+ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline.

  14. A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums

    Science.gov (United States)

    Ion, Bogdan F.; Bushnell, Eric A. C.; De Luna, Phil; Gauld, James W.

    2012-01-01

    Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2 + Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2 + intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline. PMID:23202934

  15. Event Shape Sorting: selecting events with similar evolution

    Directory of Open Access Journals (Sweden)

    Tomášik Boris

    2017-01-01

    Full Text Available We present novel method for the organisation of events. The method is based on comparing event-by-event histograms of a chosen quantity Q that is measured for each particle in every event. The events are organised in such a way that those with similar shape of the Q-histograms end-up placed close to each other. We apply the method on histograms of azimuthal angle of the produced hadrons in ultrarelativsitic nuclear collisions. By selecting events with similar azimuthal shape of their hadron distribution one chooses events which are likely that they underwent similar evolution from the initial state to the freeze-out. Such events can more easily be compared to theoretical simulations where all conditions can be controlled. We illustrate the method on data simulated by the AMPT model.

  16. On different forms of self similarity

    International Nuclear Information System (INIS)

    Aswathy, R.K.; Mathew, Sunil

    2016-01-01

    Fractal geometry is mainly based on the idea of self-similar forms. To be self-similar, a shape must able to be divided into parts that are smaller copies, which are more or less similar to the whole. There are different forms of self similarity in nature and mathematics. In this paper, some of the topological properties of super self similar sets are discussed. It is proved that in a complete metric space with two or more elements, the set of all non super self similar sets are dense in the set of all non-empty compact sub sets. It is also proved that the product of self similar sets are super self similar in product metric spaces and that the super self similarity is preserved under isometry. A characterization of super self similar sets using contracting sub self similarity is also presented. Some relevant counterexamples are provided. The concepts of exact super and sub self similarity are introduced and a necessary and sufficient condition for a set to be exact super self similar in terms of condensation iterated function systems (Condensation IFS’s) is obtained. A method to generate exact sub self similar sets using condensation IFS’s and the denseness of exact super self similar sets are also discussed.

  17. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    Energy Technology Data Exchange (ETDEWEB)

    Bylaska, Eric J., E-mail: Eric.Bylaska@pnnl.gov [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States); Weare, Jonathan Q., E-mail: weare@uchicago.edu [Department of Mathematics, University of Chicago, Chicago, Illinois 60637 (United States); Weare, John H., E-mail: jweare@ucsd.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 (United States)

    2013-08-21

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} − f(x{sub (i−1})]{sub i} {sub =1,M} = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up

  18. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.

    Science.gov (United States)

    Bylaska, Eric J; Weare, Jonathan Q; Weare, John H

    2013-08-21

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0[ellipsis (horizontal)]tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution/timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a

  19. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    International Nuclear Information System (INIS)

    Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

    2013-01-01

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t i (trajectory positions and velocities x i = (r i , v i )) to time t i+1 (x i+1 ) by x i+1 = f i (x i ), the dynamics problem spanning an interval from t 0 …t M can be transformed into a root finding problem, F(X) = [x i − f(x (i−1 )] i =1,M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H 2 O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a

  20. Hybrid Pressure Retarded Osmosis−Membrane Distillation (PRO−MD) Process for Osmotic Power and Clean Water Generation

    KAUST Repository

    Han, Gang; Zuo, Jian; Wan, Chunfeng; Chung, Neal Tai-Shung

    2015-01-01

    unique advantages of high water recovery rate, huge osmotic power generation, well controlled membrane fouling, and minimal environmental impacts. Experimental results show that the PRO−MD hybrid process is promising that not only can harvest osmotic

  1. Age at onset of first signs or symptoms predicts age at loss of ambulation in Duchenne and Becker Muscular Dystrophy: Data from the MD STARnet.

    Science.gov (United States)

    Ciafaloni, Emma; Kumar, Anil; Liu, Ke; Pandya, Shree; Westfield, Christina; Fox, Deborah J; Caspers Conway, Kristin M; Cunniff, Christopher; Mathews, Katherine; West, Nancy; Romitti, Paul A; McDermott, Michael P

    2016-01-01

    We investigated the prognostic utility of onset age at first signs and symptoms (SS) to predict onset age at loss of ambulation (LOA) for childhood-onset Duchenne and Becker Muscular Dystrophies (DBMD). Our cohort comprised male cases with DBMD ascertained by the population-based Muscular Dystrophy Surveillance, Tracking, and Research Network (MD STARnet). Adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards models for associations between onset ages of first SS and LOA. Covariates controlled for were corticosteroid use, family history of DBMD, birth year, race/ethnicity, and MD STARnet site. Onset age at first SS was considered as a continuous and as a categorical variable. A one-year increase in onset age at first SS was significantly associated with a 10% reduction in annual risk of LOA (HR = 0.90, CI = 0.87-0.94). Treating onset age at first SS as a categorical variable yielded a similar association (≥ 5 years: referent; ≥ 3 to Becker muscular dystrophies.

  2. A workshop on leadership for senior MD-PhD students.

    Science.gov (United States)

    Meador, Catherine B; Parang, Bobak; Musser, Melissa A; Haliyur, Rachana; Owens, David A; Dermody, Terence S

    2016-01-01

    Leadership skills are essential for a successful career as a physician-scientist, yet many MD-PhD training programs do not offer formal training in leadership. The Vanderbilt Medical Scientist Training Program (MSTP) previously established a 2-day leadership workshop that has been held biennially since 2006 for students in the first and second years of the graduate school portion of combined MD and PhD training (G1/G2 students). Workshop attendees have consistently rated this workshop as a highly effective experience. However, opportunities for structured training in leadership competencies during the subsequent 3-5 years of MD-PhD training are limited. Given the success of the G1/G2 leadership workshop and the need for continuity in this model of leadership training, we developed a half-day workshop for MSTP students in the clinical years of medical school (M3/M4 students) to foster continued training in leadership. Our workshop curriculum, based in part on original cases drafted by Vanderbilt MSTP students, provides concrete strategies to manage conflict and navigate leadership transitions in the physician-scientist career path. The curriculum emphasizes both short-term competencies, such as effective participation as a member of a clinical team, and long-term competencies, such as leadership of a research team, division, or department. Our inaugural senior leadership workshop, held in August, 2015, was judged by student participants to be well organized and highly relevant to leadership concepts and skills. It will be offered biennially in our training curriculum for M3 and M4 MSTP students.

  3. Pressure-induced transformations in glassy water: A computer simulation study using the TIP4P/2005 model

    Science.gov (United States)

    Wong, Jessina; Jahn, David A.; Giovambattista, Nicolas

    2015-08-01

    We study the pressure-induced transformations between low-density amorphous (LDA) and high-density amorphous (HDA) ice by performing out-of-equilibrium molecular dynamics (MD) simulations. We employ the TIP4P/2005 water model and show that this model reproduces qualitatively the LDA-HDA transformations observed experimentally. Specifically, the TIP4P/2005 model reproduces remarkably well the (i) structure (OO, OH, and HH radial distribution functions) and (ii) densities of LDA and HDA at P = 0.1 MPa and T = 80 K, as well as (iii) the qualitative behavior of ρ(P) during compression-induced LDA-to-HDA and decompression-induced HDA-to-LDA transformations. At the rates explored, the HDA-to-LDA transformation is less pronounced than in experiments. By studying the LDA-HDA transformations for a broad range of compression/decompression temperatures, we construct a "P-T phase diagram" for glassy water that is consistent with experiments and remarkably similar to that reported previously for ST2 water. This phase diagram is not inconsistent with the possibility of TIP4P/2005 water exhibiting a liquid-liquid phase transition at low temperatures. A comparison with previous MD simulation studies of SPC/E and ST2 water as well as experiments indicates that, overall, the TIP4P/2005 model performs better than the SPC/E and ST2 models. The effects of cooling and compression rates as well as aging on our MD simulations results are also discussed. The MD results are qualitatively robust under variations of cooling/compression rates (accessible in simulations) and are not affected by aging the hyperquenched glass for at least 1 μs. A byproduct of this work is the calculation of TIP4P/2005 water's diffusion coefficient D(T) at P = 0.1 MPa. It is found that, for T ≥ 210 K, D(T) ≈ (T - TMCT)-γ as predicted by mode coupling theory and in agreement with experiments. For TIP4P/2005 water, TMCT = 209 K and γ = 2.14, very close to the corresponding experimental values TMCT = 221 K

  4. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

    Science.gov (United States)

    Dixit, Surjit B; Mezei, Mihaly; Beveridge, David L

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the

  5. Design and implementation of an ASIP-based cryptography processor for AES, IDEA, and MD5

    OpenAIRE

    Karim Shahbazi; Mohammad Eshghi; Reza Faghih Mirzaee

    2017-01-01

    In this paper, a new 32-bit ASIP-based crypto processor for AES, IDEA, and MD5 is designed. The instruction-set consists of both general purpose and specific instructions for the above cryptographic algorithms. The proposed architecture has nine function units and two data buses. It has also two types of 32-bit instruction formats for executing Memory Reference (M.R.), Register Reference (R.R.), and Input/Output Reference (I/O R.) instructions. The maximum achieved frequency is 166.916 MHz. T...

  6. A study on virtual source position for electron beams from a Mevatron MD linear accelerator

    International Nuclear Information System (INIS)

    Ravindran, B.P.

    1999-01-01

    The virtual source position (VSP) for electron beams of energies 5, 7, 9 10, 12 and 14 MeV and for the applicators (cones) available in the department have been measured for a Mevatron MD class linear accelerator. Different methods of obtaining the virtual source position for electron beams have been investigated in the present study. The results obtained have been compared with those of other workers. It is observed that the VSP is very much machine dependent and needs to be measured for each linear accelerator. The effect of shielding on virtual source position for the type of applicators available in the department has also been investigated. (author)

  7. Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013

    Science.gov (United States)

    2014-01-01

    A conference entitled ‘Human microbiome science: Vision for the future’ was organized in Bethesda, MD from July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and aimed at providing a comprehensive overview of the state of microbiome research, but more importantly to identify and discuss gaps, challenges and opportunities in this nascent field. This report summarizes the presentations but also describes what is needed for human microbiome research to move forward and deliver medical translational applications.

  8. Large margin classification with indefinite similarities

    KAUST Repository

    Alabdulmohsin, Ibrahim; Cisse, Moustapha; Gao, Xin; Zhang, Xiangliang

    2016-01-01

    Classification with indefinite similarities has attracted attention in the machine learning community. This is partly due to the fact that many similarity functions that arise in practice are not symmetric positive semidefinite, i.e. the Mercer

  9. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji; Genton, Marc G.; Jun, Mikyoung

    2016-01-01

    extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi

  10. Personality similarity and life satisfaction in couples

    OpenAIRE

    Furler Katrin; Gomez Veronica; Grob Alexander

    2013-01-01

    The present study examined the association between personality similarity and life satisfaction in a large nationally representative sample of 1608 romantic couples. Similarity effects were computed for the Big Five personality traits as well as for personality profiles with global and differentiated indices of similarity. Results showed substantial actor and partner effects indicating that both partners' personality traits were related to both partners' life satisfaction. Personality similar...

  11. Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.

    Science.gov (United States)

    Frank, Martin

    2015-01-01

    Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).

  12. Multiscale simulation of water flow past a C540 fullerene

    DEFF Research Database (Denmark)

    Walther, Jens Honore; Praprotnik, Matej; Kotsalis, Evangelos M.

    2012-01-01

    We present a novel, three-dimensional, multiscale algorithm for simulations of water flow past a fullerene. We employ the Schwarz alternating overlapping domain method to couple molecular dynamics (MD) of liquid water around the C540 buckyball with a Lattice–Boltzmann (LB) description for the Nav......We present a novel, three-dimensional, multiscale algorithm for simulations of water flow past a fullerene. We employ the Schwarz alternating overlapping domain method to couple molecular dynamics (MD) of liquid water around the C540 buckyball with a Lattice–Boltzmann (LB) description...

  13. Water vapor permeabilities through polymers: diffusivities from experiments and simulations

    International Nuclear Information System (INIS)

    Seethamraju, Sindhu; Ramamurthy, Praveen Chandrashekarapura; Madras, Giridhar

    2014-01-01

    This study experimentally determines water vapor permeabilities, which are subsequently correlated with the diffusivities obtained from simulations. Molecular dynamics (MD) simulations were used for determining the diffusion of water vapor in various polymeric systems such as polyethylene, polypropylene, poly (vinyl alcohol), poly (vinyl acetate), poly (vinyl butyral), poly (vinylidene chloride), poly (vinyl chloride) and poly (methyl methacrylate). Cavity ring down spectroscopy (CRDS) based methodology has been used to determine the water vapor transmission rates. These values were then used to calculate the diffusion coefficients for water vapor through these polymers. A comparative analysis is provided for diffusivities calculated from CRDS and MD based results by correlating the free volumes. (paper)

  14. Scaling, Similarity, and the Fourth Paradigm for Hydrology

    Science.gov (United States)

    Peters-Lidard, Christa D.; Clark, Martyn; Samaniego, Luis; Verhoest, Niko E. C.; van Emmerik, Tim; Uijlenhoet, Remko; Achieng, Kevin; Franz, Trenton E.; Woods, Ross

    2017-01-01

    In this synthesis paper addressing hydrologic scaling and similarity, we posit that roadblocks in the search for universal laws of hydrology are hindered by our focus on computational simulation (the third paradigm), and assert that it is time for hydrology to embrace a fourth paradigm of data-intensive science. Advances in information-based hydrologic science, coupled with an explosion of hydrologic data and advances in parameter estimation and modelling, have laid the foundation for a data-driven framework for scrutinizing hydrological scaling and similarity hypotheses. We summarize important scaling and similarity concepts (hypotheses) that require testing, describe a mutual information framework for testing these hypotheses, describe boundary condition, state flux, and parameter data requirements across scales to support testing these hypotheses, and discuss some challenges to overcome while pursuing the fourth hydrological paradigm. We call upon the hydrologic sciences community to develop a focused effort towards adopting the fourth paradigm and apply this to outstanding challenges in scaling and similarity.

  15. Simple model of surface roughness for binary collision sputtering simulations

    Energy Technology Data Exchange (ETDEWEB)

    Lindsey, Sloan J. [Institute of Solid-State Electronics, TU Wien, Floragasse 7, A-1040 Wien (Austria); Hobler, Gerhard, E-mail: gerhard.hobler@tuwien.ac.at [Institute of Solid-State Electronics, TU Wien, Floragasse 7, A-1040 Wien (Austria); Maciążek, Dawid; Postawa, Zbigniew [Institute of Physics, Jagiellonian University, ul. Lojasiewicza 11, 30348 Kraków (Poland)

    2017-02-15

    Highlights: • A simple model of surface roughness is proposed. • Its key feature is a linearly varying target density at the surface. • The model can be used in 1D/2D/3D Monte Carlo binary collision simulations. • The model fits well experimental glancing incidence sputtering yield data. - Abstract: It has been shown that surface roughness can strongly influence the sputtering yield – especially at glancing incidence angles where the inclusion of surface roughness leads to an increase in sputtering yields. In this work, we propose a simple one-parameter model (the “density gradient model”) which imitates surface roughness effects. In the model, the target’s atomic density is assumed to vary linearly between the actual material density and zero. The layer width is the sole model parameter. The model has been implemented in the binary collision simulator IMSIL and has been evaluated against various geometric surface models for 5 keV Ga ions impinging an amorphous Si target. To aid the construction of a realistic rough surface topography, we have performed MD simulations of sequential 5 keV Ga impacts on an initially crystalline Si target. We show that our new model effectively reproduces the sputtering yield, with only minor variations in the energy and angular distributions of sputtered particles. The success of the density gradient model is attributed to a reduction of the reflection coefficient – leading to increased sputtering yields, similar in effect to surface roughness.

  16. Simple model of surface roughness for binary collision sputtering simulations

    International Nuclear Information System (INIS)

    Lindsey, Sloan J.; Hobler, Gerhard; Maciążek, Dawid; Postawa, Zbigniew

    2017-01-01

    Highlights: • A simple model of surface roughness is proposed. • Its key feature is a linearly varying target density at the surface. • The model can be used in 1D/2D/3D Monte Carlo binary collision simulations. • The model fits well experimental glancing incidence sputtering yield data. - Abstract: It has been shown that surface roughness can strongly influence the sputtering yield – especially at glancing incidence angles where the inclusion of surface roughness leads to an increase in sputtering yields. In this work, we propose a simple one-parameter model (the “density gradient model”) which imitates surface roughness effects. In the model, the target’s atomic density is assumed to vary linearly between the actual material density and zero. The layer width is the sole model parameter. The model has been implemented in the binary collision simulator IMSIL and has been evaluated against various geometric surface models for 5 keV Ga ions impinging an amorphous Si target. To aid the construction of a realistic rough surface topography, we have performed MD simulations of sequential 5 keV Ga impacts on an initially crystalline Si target. We show that our new model effectively reproduces the sputtering yield, with only minor variations in the energy and angular distributions of sputtered particles. The success of the density gradient model is attributed to a reduction of the reflection coefficient – leading to increased sputtering yields, similar in effect to surface roughness.

  17. Predicting Flory-Huggins χ from Simulations

    Science.gov (United States)

    Zhang, Wenlin; Gomez, Enrique D.; Milner, Scott T.

    2017-07-01

    We introduce a method, based on a novel thermodynamic integration scheme, to extract the Flory-Huggins χ parameter as small as 10-3k T for polymer blends from molecular dynamics (MD) simulations. We obtain χ for the archetypical coarse-grained model of nonpolar polymer blends: flexible bead-spring chains with different Lennard-Jones interactions between A and B monomers. Using these χ values and a lattice version of self-consistent field theory (SCFT), we predict the shape of planar interfaces for phase-separated binary blends. Our SCFT results agree with MD simulations, validating both the predicted χ values and our thermodynamic integration method. Combined with atomistic simulations, our method can be applied to predict χ for new polymers from their chemical structures.

  18. Scalable Atomistic Simulation Algorithms for Materials Research

    Directory of Open Access Journals (Sweden)

    Aiichiro Nakano

    2002-01-01

    Full Text Available A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD simulations and quantum-mechanical (QM calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.

  19. On similarity and scaling of the radiative transfer equation

    International Nuclear Information System (INIS)

    Mitrescu, C.; Stephens, G.L.

    2004-01-01

    The present paper shows how the well-known similarity and scaling concepts are properties of the radiative transfer equation and not specifically of the degree of anisotropy of the phase function. It is shown that the key assumption regarding the angular dependence of the radiative field is essential in determining both the value for the parameter used to scale the radiative transfer, as well as the number of streams used in calculating the radiances for various atmospheric problems. Simulations performed on realistic type of cirrus clouds, characterized by strongly anisotropic functions, demonstrates the superior computational advantage for accurately simulating radiances. A new approach for determining the scaling parameter is introduced

  20. Similar Mediterranean diet adherence but greater central adiposity is observed among Greek diaspora adolescents living in Istanbul, compared to Athens.

    Science.gov (United States)

    Grammatikopoulou, Maria G; Maraki, Maria I; Giannopoulou, Despoina; Poulimeneas, Dimitrios; Sidossis, Labros S; Tsigga, Maria

    2018-02-01

    The aim of this case-control study was to compare Mediterranean diet (MD) adherence and anthropometry between Greek diaspora adolescents living in Istanbul and Greek adolescents, inhabitants of Athens. A total of 206 adolescents (103 from each site), aged 10.0-19.0 years old, all of Greek origin, were recruited from schools in Athens and minority schools in Istanbul, for the present case-control study. Participants at each site were age and sex-matched. Anthropometric measurements were performed, and diet adherence was assessed with the KIDMED score. Breakfast skipping, decreased dairy and increased commercially baked good/pastries consumption for breakfast, fast-food intake and consumption of several sweets each day was more prevalent in Istanbul, but, on the other hand, students from Athens reported eating fewer fruit, vegetables and nuts. The adoption of unhealthy eating habits in each site was counterbalanced by a more 'healthy' dietary element, resulting in an overall similar MD adherence between both sites. Additionally, although weight status was indifferent between the two cities, higher rates of abdominal obesity were recorded in Istanbul, when the weight-to-height ratio was used for diagnosis. Differences in several domains of the KIDMED score were recorded among cities, possibly as results of food availability and prices. However, MD adherence and weight status appeared similar, indicating that the dietary transition and acculturation experienced by the remnants is actually very slow and minimal during the 93 years since population exchange.