Evaluation of peptide designing strategy against subunit reassociation in mucin 1: A steered molecular dynamics approach.

Directory of Open Access Journals (Sweden)

J Lesitha Jeeva Kumari

Full Text Available Subunit reassociation in mucin 1, a breast cancer tumor marker, is reported as one of the critical factors for its cytoplasmic activation. Inhibition of its heterodimeric association would therefore result in loss of its function and alter disease progression. The present study aimed at evaluating peptide inhibitor designing strategies that may serve as antagonist against this receptor-ligand alliance. Several peptides and their derivatives were designed based on native residues, subunit interface, hydrogen bonding and secondary structure. Docking studies with the peptides were carried on the receptor subunit and their binding affinities were evaluated using steered molecular dynamics simulation and umbrella sampling. Our results showed that among all the different classes of peptides evaluated, the receptor based peptide showed the highest binding affinity. This result was concurrent with the experimental observation that the receptor-ligand alliance in mucin 1 is highly specific. Our results also show that peptide ligand against this subunit association is only stabilized through native residue inter-protein interaction irrespective of the peptide structure, peptide length and number of hydrogen bonds. Consistency in binding affinity, pull force and free energy barrier was observed with only the receptor derived peptides which resulted in favorable interprotein interactions at the interface. Several observations were made and discussed which will eventually lead to designing efficient peptide inhibitors against mucin 1 heterodimeric subunit reassociation.

Improvement of motor inertia influence of electric power steering; Dendoshiki power steering no motor kansei no eikyo to hosho

Energy Technology Data Exchange (ETDEWEB)

Takehara, S; Sakamoto, K; Hanamoto, Y [Mazda Motor Corp., Hiroshima (Japan); Noritsugu, T [Okayama University, Okayama (Japan)

1997-10-01

Motor inertia of electric power steering affects not only steering characteristics but vehicle dynamics. We have investigated the influence of motor inertia and proposed a feedback strategy to compensate it. Weight of the test vehicle is 1100Kg and the steering system is pinion type electric power steering. By using simulation model and vehicle test, we have realized natural steering maneuvering and stable vehicle dynamics. 4 refs., 11 figs.

Influence of Road Excitation and Steering Wheel Input on Vehicle System Dynamic Responses

Directory of Open Access Journals (Sweden)

Zhen-Feng Wang

2017-06-01

Full Text Available Considering the importance of increasing driving safety, the study of safety is a popular and critical topic of research in the vehicle industry. Vehicle roll behavior with sudden steering input is a main source of untripped rollover. However, previous research has seldom considered road excitation and its coupled effect on vehicle lateral response when focusing on lateral and vertical dynamics. To address this issue, a novel method was used to evaluate effects of varying road level and steering wheel input on vehicle roll behavior. Then, a 9 degree of freedom (9-DOF full-car roll nonlinear model including vertical and lateral dynamics was developed to study vehicle roll dynamics with or without of road excitation. Based on a 6-DOF half-car roll model and 9-DOF full-car nonlinear model, relationship between three-dimensional (3-D road excitation and various steering wheel inputs on vehicle roll performance was studied. Finally, an E-Class (SUV level car model in CARSIM® was used, as a benchmark, with and without road input conditions. Both half-car and full-car models were analyzed under steering wheel inputs of 5°, 10° and 15°. Simulation results showed that the half-car model considering road input was found to have a maximum accuracy of 65%. Whereas, the full-car model had a minimum accuracy of 85%, which was significantly higher compared to the half-car model under the same scenario.

Influence of Road Excitation and Steering Wheel Input on Vehicle System Dynamic Responses

OpenAIRE

Zhen-Feng Wang; Ming-Ming Dong; Liang Gu; Jagat-Jyoti Rath; Ye-Chen Qin; Bin Bai

2017-01-01

Considering the importance of increasing driving safety, the study of safety is a popular and critical topic of research in the vehicle industry. Vehicle roll behavior with sudden steering input is a main source of untripped rollover. However, previous research has seldom considered road excitation and its coupled effect on vehicle lateral response when focusing on lateral and vertical dynamics. To address this issue, a novel method was used to evaluate effects of varying road level and steer...

Driver steering model for closed-loop steering function analysis

Science.gov (United States)

Bolia, Pratiksh; Weiskircher, Thomas; Müller, Steffen

2014-05-01

In this paper, a two level preview driver steering control model for the use in numerical vehicle dynamics simulation is introduced. The proposed model is composed of cascaded control loops: The outer loop is the path following layer based on potential field framework. The inner loop tries to capture the driver's physical behaviour. The proposed driver model allows easy implementation of different driving situations to simulate a wide range of different driver types, moods and vehicle types. The expediency of the proposed driver model is shown with the help of developed driver steering assist (DSA) function integrated with a conventional series production (Electric Power steering System with rack assist servo unit) system. With the help of the DSA assist function, the driver is prevented from over saturating the front tyre forces and loss of stability and controllability during cornering. The simulation results show different driver reactions caused by the change in the parameters or properties of the proposed driver model if the DSA assist function is activated. Thus, the proposed driver model is useful for the advanced driver steering and vehicle stability assist function evaluation in the early stage of vehicle dynamics handling and stability evaluation.

Networks: structure and action : steering in and steering by policy networks

NARCIS (Netherlands)

Dassen, A.

2010-01-01

This thesis explores the opportunities to build a structural policy network model that is rooted in social network theories. By making a distinction between a process of steering in networks, and a process of steering by networks, it addresses the effects of network structures on network dynamics as

DYNAMICS BASED CONTROL OF A SKID STEERING MOBILE ROBOT

Directory of Open Access Journals (Sweden)

Osama Elshazly

2016-06-01

Full Text Available In this paper, development of a reduced order, augmented dynamics-drive model that combines both the dynamics and drive subsystems of the skid steering mobile robot (SSMR is presented. A Linear Quadratic Regulator (LQR control algorithm with feed-forward compensation of the disturbances part included in the reduced order augmented dynamics-drive model is designed. The proposed controller has many advantages such as its simplicity in terms of design and implementation in comparison with complex nonlinear control schemes that are usually designed for this system. Moreover, the good performance is also provided by the controller for the SSMR comparable with a nonlinear controller based on the inverse dynamics which depends on the availability of an accurate model describing the system. Simulation results illustrate the effectiveness and enhancement provided by the proposed controller.

Steering and evasion assist

NARCIS (Netherlands)

Dang, T.; Desens, J.; Franke, U.; Gavrila, D.; Schäfers, L.; Ziegler, W.; Eskandarian, A.

2012-01-01

Steering and evasion assistance defines a new and future class of driver assistance systems to avoid an impending collision with other traffic participants. Dynamic and kinematic considerations reveal that an evasive steering maneuver has high potential for collision avoidance in many driving

Wireless traffic steering for green cellular networks

CERN Document Server

Zhang, Shan; Zhou, Sheng; Niu, Zhisheng; Shen, Xuemin (Sherman)

2016-01-01

This book introduces wireless traffic steering as a paradigm to realize green communication in multi-tier heterogeneous cellular networks. By matching network resources and dynamic mobile traffic demand, traffic steering helps to reduce on-grid power consumption with on-demand services provided. This book reviews existing solutions from the perspectives of energy consumption reduction and renewable energy harvesting. Specifically, it explains how traffic steering can improve energy efficiency through intelligent traffic-resource matching. Several promising traffic steering approaches for dynamic network planning and renewable energy demand-supply balancing are discussed. This book presents an energy-aware traffic steering method for networks with energy harvesting, which optimizes the traffic allocated to each cell based on the renewable energy status. Renewable energy demand-supply balancing is a key factor in energy dynamics, aimed at enhancing renewable energy sustainability to reduce on-grid energy consum...

Analysis of Vehicle Steering and Driving Bifurcation Characteristics

Directory of Open Access Journals (Sweden)

Xianbin Wang

2015-01-01

Full Text Available The typical method of vehicle steering bifurcation analysis is based on the nonlinear autonomous vehicle model deriving from the classic two degrees of freedom (2DOF linear vehicle model. This method usually neglects the driving effect on steering bifurcation characteristics. However, in the steering and driving combined conditions, the tyre under different driving conditions can provide different lateral force. The steering bifurcation mechanism without the driving effect is not able to fully reveal the vehicle steering and driving bifurcation characteristics. Aiming at the aforementioned problem, this paper analyzed the vehicle steering and driving bifurcation characteristics with the consideration of driving effect. Based on the 5DOF vehicle system dynamics model with the consideration of driving effect, the 7DOF autonomous system model was established. The vehicle steering and driving bifurcation dynamic characteristics were analyzed with different driving mode and driving torque. Taking the front-wheel-drive system as an example, the dynamic evolution process of steering and driving bifurcation was analyzed by phase space, system state variables, power spectral density, and Lyapunov index. The numerical recognition results of chaos were also provided. The research results show that the driving mode and driving torque have the obvious effect on steering and driving bifurcation characteristics.

Unbinding pathway energy of glyphosate from the EPSPs enzyme binding site characterized by Steered Molecular Dynamics and Potential of Mean Force.

Science.gov (United States)

Ferreira, Moacir F; Franca, Eduardo F; Leite, Fábio L

2017-03-01

The quantification of herbicides in the environment, like glyphosate, is extremely important to prevent contamination. Nanobiosensors stands out in the quantization process, because of the high selectivity, sensitivity and short response time of the method. In order to emulate the detection of glyphosate using a specific nanobiossensor through an Atomic Force Microscope (AFM), this work carried out Steered Molecular Dynamics simulations (SMD) in which the herbicide was unbinded from the active site of the enzyme 5- enolpyruvylshikimate 3 phosphate synthase (EPSPS) along three different directions.After the simulations, Potential of Mean Force calculations were carried, from a cumulant expansion of Jarzynski's equation to obtain the profile of free energy of interaction between the herbicide and the active site of the enzyme in the presence of shikimate-3 substrate phosphate (S3P). The set of values for external work, had a Gaussian distribution. The PMF values ranged according to the directions of the unbindong pahway of each simulation, displaying energy values of 10.7, 14.7 and 19.5KJmol -1 . The results provide a theoretical support in order to assist the construction of a specific nanobiossensor to quantify the glyphosate herbicide. Copyright © 2016 Elsevier Inc. All rights reserved.

Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics

International Nuclear Information System (INIS)

Villarreal, Oscar D.; Yu, Lili; Rodriguez, Roberto A.; Chen, Liao Y.

2017-01-01

Computing the ligand-protein binding affinity (or the Gibbs free energy) with chemical accuracy has long been a challenge for which many methods/approaches have been developed and refined with various successful applications. False positives and, even more harmful, false negatives have been and still are a common occurrence in practical applications. Inevitable in all approaches are the errors in the force field parameters we obtain from quantum mechanical computation and/or empirical fittings for the intra- and inter-molecular interactions. These errors propagate to the final results of the computed binding affinities even if we were able to perfectly implement the statistical mechanics of all the processes relevant to a given problem. And they are actually amplified to various degrees even in the mature, sophisticated computational approaches. In particular, the free energy perturbation (alchemical) approaches amplify the errors in the force field parameters because they rely on extracting the small differences between similarly large numbers. In this paper, we develop a hybrid steered molecular dynamics (hSMD) approach to the difficult binding problems of a ligand buried deep inside a protein. Sampling the transition along a physical (not alchemical) dissociation path of opening up the binding cavity- -pulling out the ligand- -closing back the cavity, we can avoid the problem of error amplifications by not relying on small differences between similar numbers. We tested this new form of hSMD on retinol inside cellular retinol-binding protein 1 and three cases of a ligand (a benzylacetate, a 2-nitrothiophene, and a benzene) inside a T4 lysozyme L99A/M102Q(H) double mutant. In all cases, we obtained binding free energies in close agreement with the experimentally measured values. This indicates that the force field parameters we employed are accurate and that hSMD (a brute force, unsophisticated approach) is free from the problem of error amplification suffered by

Performance and welfare of steers housed on concrete slatted floors at fixed and dynamic (allometric based) space allowances.

Science.gov (United States)

Keane, Michael P; McGee, Mark; O'Riordan, Edward G; Kelly, Alan K; Earley, Bernadette

2018-04-03

The objectives of the study were to determine whether allometric equations are suitable for estimating the space requirements of finishing beef cattle housed on concrete slatted floors (CSF) and to examine the effect of fixed and dynamic space allowances on the performance and welfare of these cattle. Continental crossbred steers [n = 120: mean initial live weight, 590 (SD 29.8) kg] were blocked by breed, weight, and age and assigned to 1 of 5 space allowance treatments (3 fixed and 2 dynamic) on CSF: 1) 2.0 m2 per animal, 2) 2.5 m2 per animal, 3) 3.0 m2 per animal, 4) Equation 1 (E1); y = 0.033w0.667, where y = m2 per animal and w = body weight, and 5) Equation 2 (E2); y = 0.048w0.667. The length of the feed face was 3.0 m for all treatments. Steers were offered grass silage and concentrates ad libitum. DMI was recorded weekly on a pen basis. Steers were weighed and dirt scored every 14 d. Blood samples were collected every 28 d, and analyzed for complete cell counts. Behavior was recorded using closed-circuit infrared cameras. Steers' hooves were inspected for lesions at the beginning of the study and post-slaughter. Slaughter weight and ADG were lowest, and feed conversion ratio (FCR) was poorest, for steers accommodated at 2.0 m2, and slaughter weight and ADG were greatest, and FCR was the best, for steers accommodated at E2 (P 0.05) to those accommodated at 2.0 m2 and both 3.0 m2 and E1, whereas steers accommodated at 3.0 m2 and E1 were intermediate (P > 0.05) to 2.5 m2 and E2. Carcass weight of steers housed at 2.0 m2 was lower (P < 0.05) than all other treatments. Steers housed at 2.5 m2 had lower carcass weights (P < 0.05) than those with accommodated at E1 and E2, whereas the carcass weight of steers accommodated at 3.0 m2 was intermediate. Carcass fat scores and hide weights were lower (P < 0.05) in steers accommodated at 2.0 m2 than those housed at E2 with other treatments being intermediate. The number of steers lying at any one time and the number of

Dynamic steering beams for efficient force measurement in optical manipulation

Institute of Scientific and Technical Information of China (English)

Xiaocong Yuan; Yuquan Zhang; Rui Cao; Xing Zhao; Jing Bu; Siwei Zhu

2011-01-01

@@ An efficient and inexpensive method that uses a glass plate mounted onto a motorized rotating stage as a beam-steering device for the generation of dynamic optical traps is reported.Force analysis reveals that there are drag and trapping forces imposed on the bead in the opposite directions, respectively, in a viscous medium.The trapped bead will be rotated following the beam's motion before it reaches the critical escape velocity when the drag force is equal to the optical trapping force.The equilibrium condition facilitates the experimental measurement of the drag force with potential extensions to the determination of the viscosity of the medium or the refractive index of the bead.The proposed technique can easily be integrated into conventional optical microscopic systems with minimum modifications.%An efficient and inexpensive method that uses a glass plate mounted onto a motorized rotating stage as a beam-steering device for the generation of dynamic optical traps is reported. Force analysis reveals that there are drag and trapping forces imposed on the bead in the opposite directions, respectively, in a viscous medium. The trapped bead will be rotated following the beam's motion before it reaches the critical escape velocity when the drag force is equal to the optical trapping force. The equilibrium condition facilitates the experimental measurement of the drag force with potential extensions to the determination of the viscosity of the medium or the refractive index of the bead. The proposed technique can easily be integrated into conventional optical microscopic systems with minimum modifications.

An investigation on motor-driven power steering-based crosswind disturbance compensation for the reduction of driver steering effort

Science.gov (United States)

Kim, Kyuwon; Kim, Boemjun; Go, Youngil; Park, Jaeyong; Park, Joonhong; Suh, Insoo; Yi, Kyongsu

2014-07-01

This paper describes a lateral disturbance compensation algorithm for an application to a motor-driven power steering (MDPS)-based driver assistant system. The lateral disturbance including wind force and lateral load transfer by bank angle reduces the driver's steering refinement and at the same time increases the possibility of an accident. A lateral disturbance compensation algorithm is designed to determine the motor overlay torque of an MDPS system for reducing the manoeuvreing effort of a human driver under lateral disturbance. Motor overlay torque for the compensation of driver's steering torque induced by the lateral disturbance consists of human torque feedback and feedforward torque. Vehicle-driver system dynamics have been investigated using a combined dynamic model which consists of a vehicle dynamic model, driver steering dynamic model and lateral disturbance model. The human torque feedback input has been designed via the investigation of the vehicle-driver system dynamics. Feedforward input torque is calculated to compensate additional tyre self-aligning torque from an estimated lateral disturbance. The proposed compensation algorithm has been implemented on a developed driver model which represents the driver's manoeuvreing characteristics under the lateral disturbance. The developed driver model has been validated with test data via a driving simulator in a crosswind condition. Human-in-the-loop simulations with a full-scale driving simulator on a virtual test track have been conducted to investigate the real-time performance of the proposed lateral disturbance compensation algorithm. It has been shown from simulation studies and human-in-the-loop simulation results that the driver's manoeuvreing effort and a lateral deviation of the vehicle under the lateral disturbance can be significantly reduced via the lateral disturbance compensation algorithm.

Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.

Directory of Open Access Journals (Sweden)

Joseph L Baker

2013-04-01

Full Text Available Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and transition to a force-induced conformation. However, the details of force-generation, and the atomic-level characteristics of the force-induced conformation, are unknown. Here, steered molecular dynamics (SMD simulation was used to exert a force in silico on an 18 subunit segment of GC-T4P to address questions regarding the nature of the interactions that lead to the extraordinary strength of bacterial pili. SMD simulations revealed that the buried pilin α1 domains maintain hydrophobic contacts with one another within the core of the filament, leading to GC-T4P's structural stability. At the filament surface, gaps between pilin globular head domains in both the native and pulled states provide water accessible routes between the external environment and the interior of the filament, allowing water to access the pilin α1 domains as reported for VC-T4P in deuterium exchange experiments. Results were also compared to the experimentally observed force-induced conformation. In particular, an exposed amino acid sequence in the experimentally stretched filament was also found to become exposed during the SMD simulations, suggesting that initial stages of the force induced transition are well captured. Furthermore, a second sequence was shown to be initially hidden in the native filament and became exposed upon

Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.

Science.gov (United States)

Baker, Joseph L; Biais, Nicolas; Tama, Florence

2013-04-01

Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P) from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and transition to a force-induced conformation. However, the details of force-generation, and the atomic-level characteristics of the force-induced conformation, are unknown. Here, steered molecular dynamics (SMD) simulation was used to exert a force in silico on an 18 subunit segment of GC-T4P to address questions regarding the nature of the interactions that lead to the extraordinary strength of bacterial pili. SMD simulations revealed that the buried pilin α1 domains maintain hydrophobic contacts with one another within the core of the filament, leading to GC-T4P's structural stability. At the filament surface, gaps between pilin globular head domains in both the native and pulled states provide water accessible routes between the external environment and the interior of the filament, allowing water to access the pilin α1 domains as reported for VC-T4P in deuterium exchange experiments. Results were also compared to the experimentally observed force-induced conformation. In particular, an exposed amino acid sequence in the experimentally stretched filament was also found to become exposed during the SMD simulations, suggesting that initial stages of the force induced transition are well captured. Furthermore, a second sequence was shown to be initially hidden in the native filament and became exposed upon stretching.

Genetic algorithm–based varying parameter linear quadratic regulator control for four-wheel independent steering vehicle

Directory of Open Access Journals (Sweden)

Linlin Gao

2015-11-01

Full Text Available From the perspective of vehicle dynamics, the four-wheel independent steering vehicle dynamics stability control method is studied, and a four-wheel independent steering varying parameter linear quadratic regulator control system is proposed with the help of expert control method. In the article, a four-wheel independent steering linear quadratic regulator controller for model following purpose is designed first. Then, by analyzing the four-wheel independent steering vehicle dynamic characteristics and the influence of linear quadratic regulator control parameters on control performance, a linear quadratic regulator control parameter adjustment strategy based on vehicle steering state is proposed to achieve the adaptive adjustment of linear quadratic regulator control parameters. In addition, to further improve the control performance, the proposed varying parameter linear quadratic regulator control system is optimized by genetic algorithm. Finally, simulation studies have been conducted by applying the proposed control system to the 8-degree-of-freedom four-wheel independent steering vehicle dynamics model. The simulation results indicate that the proposed control system has better performance and robustness and can effectively improve the stability and steering safety of the four-wheel independent steering vehicle.

Vehicle steering by side stick: optimising steering characteristics

NARCIS (Netherlands)

Zuurbier, J.; Hogema, J.H.; Brekelmans, J.A.W.J.

2000-01-01

This paper describes a study that was conducted to investigate the possibilities for optimizing task performance when driving a side stick-steered vehicle. Using steer-by-wire technology, a conventional steering system was mimicked, thus yielding the possibility to modify the steering

A Vehicle Haptic Steering by Wire System Based on High Gain GPI Observers

Directory of Open Access Journals (Sweden)

A. Rodriguez-Angeles

2014-01-01

Full Text Available A vehicle steering by wire (SBW haptic system based on high gain generalized proportional integral (GPI observers is introduced. The observers are considered for the estimation of dynamic perturbations that are present at the tire and steering wheel. To ensure efficient tracking between the commanded steering wheel angle and the tire orientation angle, the estimated perturbations are on line canceled. As to provide a haptic interface with the driver, the estimated dynamic effects at the steering rack are fed back to the steering wheel, yielding a master-slave haptic system with bilateral communication. For implementation purposes few sensors and minimum knowledge of the dynamic model are required, which is a major advantage compared to other approaches. Only position tracking errors are fed back, while all other signals are estimated by the high gain GPI observers. The scheme is robust to uncertainty on the input gain and cancels dynamic perturbation effects such as friction and aligning forces on the tire. Experimental results are presented on a prototype platform.

Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

Science.gov (United States)

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

2012-01-01

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases.

Directory of Open Access Journals (Sweden)

Ly Le

2010-09-01

Full Text Available Oseltamivir (Tamiflu is currently the frontline antiviral drug employed to fight the flu virus in infected individuals by inhibiting neuraminidase, a flu protein responsible for the release of newly synthesized virions. However, oseltamivir resistance has become a critical problem due to rapid mutation of the flu virus. Unfortunately, how mutations actually confer drug resistance is not well understood. In this study, we employ molecular dynamics (MD and steered molecular dynamics (SMD simulations, as well as graphics processing unit (GPU-accelerated electrostatic mapping, to uncover the mechanism behind point mutation induced oseltamivir-resistance in both H5N1 "avian" and H1N1pdm "swine" flu N1-subtype neuraminidases. The simulations reveal an electrostatic binding funnel that plays a key role in directing oseltamivir into and out of its binding site on N1 neuraminidase. The binding pathway for oseltamivir suggests how mutations disrupt drug binding and how new drugs may circumvent the resistance mechanisms.

A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules.

Science.gov (United States)

Mendieta-Moreno, Jesús I; Marcos-Alcalde, Iñigo; Trabada, Daniel G; Gómez-Puertas, Paulino; Ortega, José; Mendieta, Jesús

2015-01-01

Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabilities. Here, we present a detailed explanation of the Fireball method and Fireball/Amber implementation. We also discuss how this tool can be used to analyze reactions in biomolecules using steered molecular dynamics simulations. The potential of this approach is shown by the analysis of a reaction catalyzed by the enzyme triose-phosphate isomerase (TIM). The conformational space and energetic landscape for this reaction are analyzed without a priori assumptions about the protonation states of the different residues during the reaction. The results offer a detailed description of the reaction and reveal some new features of the catalytic mechanism. In particular, we find a new reaction mechanism that is characterized by the intramolecular proton transfer from O1 to O2 and the simultaneous proton transfer from Glu 165 to C2. Copyright © 2015 Elsevier Inc. All rights reserved.

Modelling the influence of sensory dynamics on linear and nonlinear driver steering control

Science.gov (United States)

Nash, C. J.; Cole, D. J.

2018-05-01

A recent review of the literature has indicated that sensory dynamics play an important role in the driver-vehicle steering task, motivating the design of a new driver model incorporating human sensory systems. This paper presents a full derivation of the linear driver model developed in previous work, and extends the model to control a vehicle with nonlinear tyres. Various nonlinear controllers and state estimators are compared with different approximations of the true system dynamics. The model simulation time is found to increase significantly with the complexity of the controller and state estimator. In general the more complex controllers perform best, although with certain vehicle and tyre models linearised controllers perform as well as a full nonlinear optimisation. Various extended Kalman filters give similar results, although the driver's sensory dynamics reduce control performance compared with full state feedback. The new model could be used to design vehicle systems which interact more naturally and safely with a human driver.

Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

Directory of Open Access Journals (Sweden)

Ji-Long Zhang

Full Text Available The research on the binding process of ligand to pyrazinamidase (PncA is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD simulation methods were performed to investigate the unbinding process of nicotinamide (NAM from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF based on the steered molecular dynamics (SMD simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

A concurrent multiscale micromorphic molecular dynamics

International Nuclear Information System (INIS)

Li, Shaofan; Tong, Qi

2015-01-01

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation

One-way EPR steering and genuine multipartite EPR steering

Science.gov (United States)

He, Qiongyi; Reid, Margaret D.

2012-11-01

We propose criteria and experimental strategies to realise the Einstein-Podolsky-Rosen (EPR) steering nonlocality. One-way steering can be obtained where there is asymmetry of thermal noise on each system. We also present EPR steering inequalities that act as signatures and suggest how to optimise EPR correlations in specific schemes so that the genuine multipartite EPR steering nonlocality (EPR paradox) can also possibly be realised. The results presented here also apply to the spatially separated macroscopic atomic ensembles.

Creation of quantum steering by interaction with a common bath

Science.gov (United States)

Sun, Zhe; Xu, Xiao-Qiang; Liu, Bo

2018-05-01

By applying the hierarchy equation method, we computationally study the creation of quantum steering in a two-qubit system interacting with a common bosonic bath. The calculation does not adopt conventional approximate approaches, such as the Born, Markov, rotating-wave, and other perturbative approximations. Three kinds of quantum steering, i.e., Einstein-Podolsky-Rosen steering (EPRS), temporal steering (TS), and spatiotemporal steering (STS), are considered. Since the initial state of the two qubits is chosen as a product state, there does not exist EPRS at the beginning. During the evolution, we find that STS as well as EPRS are generated at the same time. An inversion relationship between STS and TS is revealed. By varying the system-bath coupling strength from weak to ultrastrong regimes, we find the nonmonotonic dependence of STS, TS, and EPRS on the coupling strength. It is interesting to study the dynamics of the three kinds of quantum steering by using an exactly numerical method, which is not considered in previous researches.

Modelling and Simulation of a Hydrostatic Steering System for Agricultural Tractors

Directory of Open Access Journals (Sweden)

Barbara Zardin

2018-01-01

Full Text Available The steering system of a vehicle impacts on the vehicle performance, safety and on the driver’s comfort. Moreover, in off-road vehicles using hydrostatic steering systems, the energy dissipation also becomes a critical issue. These aspects push and motivate innovation, research and analysis in the field of agricultural tractors. This paper proposes the modelling and analysis of a hydrostatic steering system for an agricultural tractor to calculate the performance of the system and determine the influence of its main design parameters. The focus here is on the driver’s steering feel, which can improve the driver’s behavior reducing unnecessary steering corrections during the working conditions. The hydrostatic steering system is quite complex and involves a hydraulic circuit and a mechanical mechanism to transmit the steering to the vehicle tires. The detailed lumped parameters model here proposed allows to simulate the dynamic behavior of the steering system and to both enhance the understanding of the system and to improve the design through parameters sensitivity analysis.

Computing the blood brain barrier (BBB) diffusion coefficient: A molecular dynamics approach

Energy Technology Data Exchange (ETDEWEB)

Shamloo, Amir, E-mail: shamloo@sharif.edu; Pedram, Maysam Z.; Heidari, Hossein; Alasty, Aria, E-mail: aalasti@sharif.edu

2016-07-15

Various physical and biological aspects of the Blood Brain Barrier (BBB) structure still remain unfolded. Therefore, among the several mechanisms of drug delivery, only a few have succeeded in breaching this barrier, one of which is the use of Magnetic Nanoparticles (MNPs). However, a quantitative characterization of the BBB permeability is desirable to find an optimal magnetic force-field. In the present study, a molecular model of the BBB is introduced that precisely represents the interactions between MNPs and the membranes of Endothelial Cells (ECs) that form the BBB. Steered Molecular Dynamics (SMD) simulations of the BBB crossing phenomenon have been carried out. Mathematical modeling of the BBB as an input-output system has been considered from a system dynamics modeling viewpoint, enabling us to analyze the BBB behavior based on a robust model. From this model, the force profile required to overcome the barrier has been extracted for a single NP from the SMD simulations at a range of velocities. Using this data a transfer function model has been obtained and the diffusion coefficient is evaluated. This study is a novel approach to bridge the gap between nanoscale models and microscale models of the BBB. The characteristic diffusion coefficient has the nano-scale molecular effects inherent, furthermore reducing the computational costs of a nano-scale simulation model and enabling much more complex studies to be conducted. - Highlights: • Molecular dynamics simulation of crossing nano-particles through the BBB membrane at different velocities. • Recording the position of nano-particle and the membrane-NP interaction force profile. • Identification of a frequency domain model for the membrane. • Calculating the diffusion coefficient based on MD simulation and identified model. • Obtaining a relation between continuum medium and discrete medium.

Different dynamic behaviors of the dissociation and recombination reactions in a model calculation of polyethylene by first-principles steered molecular dynamics simulation

International Nuclear Information System (INIS)

Higuchi, Yuji; Ishikawa, Takeshi; Ozawa, Nobuki; Chazeau, Laurent; Cavaillé, Jean-Yves; Kubo, Momoji

2015-01-01

Highlights: • We study the different dynamics of dissociation and recombination processes. • Hydrogen at the chain ends collides each other in the recombination process. • Dissociation and recombination processes take different pathway. - Abstract: We investigate the different dynamics of the stress-induced dissociation and recombination reactions in a model of polyethylene by a first-principles molecular dynamics simulation at the B3LYP/6-31g(d) level. The dissociation under external forces acting on the chemical reaction site at 300 K follows the same pathway as the one calculated by the static first-principles method because it has a similar activation barrier to that of the static first-principles calculation. On the other hand, in the recombination process, thermal fluctuations causes collisions between hydrogen atoms at the chain ends. Furthermore, when external forces do not directly act on the chemical reaction site, two different dissociation processes are observed. On the other hand, recombination process is not observed due to rarely contact of the radical carbon. These results indicate that dissociation and recombination dynamics are very different, showing the importance of the dynamic calculation.

Research on Sliding Mode Control for Steer-by-Wire System in Forklift

Directory of Open Access Journals (Sweden)

Huang Jun-Jie

2017-01-01

Full Text Available Aiming at steering stability and wheel angle tracking of steer-by-wire (SBW three wheeled forklift, steering dynamic model and SBW system mathematical model of three wheeled forklift are established. A control strategy for the ideal transmission ratio is introduced based on this model, which ensures forklift steering gain invariant. A sliding mode controller can then be designed based on the bound information of uncertain system parameters, uncertain self-aligning torque, and external disturbances. The results of simulation show the control strategies above can effectively reduce the sideslip angle when the forklift is steering and improve the sensitivity and stability of the steering forklift; at the same time can effectively restrain the parameter perturbation of internal system and external disturbance, which improves the tracking performance of the wheel angle.

Molecular Dynamics Simulations Suggest Ligand’s Binding to Nicotinamidase/Pyrazinamidase

Science.gov (United States)

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

2012-01-01

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA’s activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM’s unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand’s binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs. PMID:22761821

A theoretical model of speed-dependent steering torque for rolling tyres

Science.gov (United States)

Wei, Yintao; Oertel, Christian; Liu, Yahui; Li, Xuebing

2016-04-01

It is well known that the tyre steering torque is highly dependent on the tyre rolling speed. In limited cases, i.e. parking manoeuvre, the steering torque approaches the maximum. With the increasing tyre speed, the steering torque decreased rapidly. Accurate modelling of the speed-dependent behaviour for the tyre steering torque is a key factor to calibrate the electric power steering (EPS) system and tune the handling performance of vehicles. However, no satisfactory theoretical model can be found in the existing literature to explain this phenomenon. This paper proposes a new theoretical framework to model this important tyre behaviour, which includes three key factors: (1) tyre three-dimensional transient rolling kinematics with turn-slip; (2) dynamical force and moment generation; and (3) the mixed Lagrange-Euler method for contact deformation solving. A nonlinear finite-element code has been developed to implement the proposed approach. It can be found that the main mechanism for the speed-dependent steering torque is due to turn-slip-related kinematics. This paper provides a theory to explain the complex mechanism of the tyre steering torque generation, which helps to understand the speed-dependent tyre steering torque, tyre road feeling and EPS calibration.

Full drive-by-wire dynamic control for four-wheel-steer all-wheel-drive vehicles

Science.gov (United States)

Fahimi, Farbod

2013-03-01

Most of the controllers introduced for four-wheel-steer (4WS) vehicles are derived with the assumption that the longitudinal speed of the vehicle is constant. However, in real applications, the longitudinal speed varies, and the longitudinal, lateral, and yaw dynamics are coupled. In this paper, the longitudinal dynamics of the vehicle as well as its lateral and yaw motions are controlled simultaneously. This way, the effect of driving/braking forces of the tires on the lateral and yaw motions of the vehicle are automatically included in the control laws. To address the dynamic parameter uncertainty of the vehicle, a chatter-free variable structure controller is introduced. Elimination of chatter is achieved by introducing a dynamically adaptive boundary layer thickness. It is shown via simulations that the proposed control approach performs more robustly than the controllers developed based on dynamic models, in which longitudinal speed is assumed to be constant, and only lateral speed and yaw rate are used as system states. Furthermore, this approach supports all-wheel-drive vehicles. Front-wheel-drive or rear-wheel-drive vehicles are also supported as special cases of an all-wheel-drive vehicle.

Steering disturbance rejection using a physics-based neuromusculoskeletal driver model

Science.gov (United States)

Mehrabi, Naser; Sharif Razavian, Reza; McPhee, John

2015-10-01

The aim of this work is to develop a comprehensive yet practical driver model to be used in studying driver-vehicle interactions. Drivers interact with their vehicle and the road through the steering wheel. This interaction forms a closed-loop coupled human-machine system, which influences the driver's steering feel and control performance. A hierarchical approach is proposed here to capture the complexity of the driver's neuromuscular dynamics and the central nervous system in the coordination of the driver's upper extremity activities, especially in the presence of external disturbance. The proposed motor control framework has three layers: the first (or the path planning) plans a desired vehicle trajectory and the required steering angles to perform the desired trajectory; the second (or the musculoskeletal controller) actuates the musculoskeletal arm to rotate the steering wheel accordingly; and the final layer ensures the precision control and disturbance rejection of the motor control units. The physics-based driver model presented here can also provide insights into vehicle control in relaxed and tensed driving conditions, which are simulated by adjusting the driver model parameters such as cognition delay and muscle co-contraction dynamics.

Chaos vibration of pinion and rack steering trapezoidal mechanism containing two clearances

Science.gov (United States)

Wei, Daogao; Wang, Yu; Jiang, Tong; Zheng, Sifa; Zhao, Wenjing; Pan, Zhijie

2017-08-01

The multi-clearances of breaking type steering trapezoidal mechanism joints influences vehicle steering stability. Hence, to ascertain the influence of clearance value on steering stability, this paper takes the steering mechanism of a certain vehicle type as a prototype that can be simplified into a planar six-bar linkage, then establishes the system dynamic differential equations after considering the two clearances of tie rods and the steering knuckle arms. The influence of the clearance parameters on the movement stability of the steering mechanism is studied using a numerical computation method. Results show that when the two clearances are equal, the planar movement of the tie rods changes from period-doubling to chaos as the clearances increase. When the two clearances are 0.25 mm and 1.5 mm respectively, the planar movements of the two side tie rods come into chaos, causing the steering stability to deteriorate. Moreover, with the increase of clearances, turning moment fluctuates more intensively and the peak value increases.

Field test of wake steering at an offshore wind farm

Directory of Open Access Journals (Sweden)

P. Fleming

2017-05-01

Full Text Available In this paper, a field test of wake-steering control is presented. The field test is the result of a collaboration between the National Renewable Energy Laboratory (NREL and Envision Energy, a smart energy management company and turbine manufacturer. In the campaign, an array of turbines within an operating commercial offshore wind farm in China have the normal yaw controller modified to implement wake steering according to a yaw control strategy. The strategy was designed using NREL wind farm models, including a computational fluid dynamics model, Simulator fOr Wind Farm Applications (SOWFA, for understanding wake dynamics and an engineering model, FLOw Redirection and Induction in Steady State (FLORIS, for yaw control optimization. Results indicate that, within the certainty afforded by the data, the wake-steering controller was successful in increasing power capture, by amounts similar to those predicted from the models.

Steering Maps and Their Application to Dimension-Bounded Steering

Science.gov (United States)

Moroder, Tobias; Gittsovich, Oleg; Huber, Marcus; Uola, Roope; Gühne, Otfried

2016-03-01

The existence of quantum correlations that allow one party to steer the quantum state of another party is a counterintuitive quantum effect that was described at the beginning of the past century. Steering occurs if entanglement can be proven even though the description of the measurements on one party is not known, while the other side is characterized. We introduce the concept of steering maps, which allow us to unlock sophisticated techniques that were developed in regular entanglement detection and to use them for certifying steerability. As an application, we show that this allows us to go beyond even the canonical steering scenario; it enables a generalized dimension-bounded steering where one only assumes the Hilbert space dimension on the characterized side, with no description of the measurements. Surprisingly, this does not weaken the detection strength of very symmetric scenarios that have recently been carried out in experiments.

Dynamic Arc Fitting Path Follower for Skid-Steered Mobile Robots

Directory of Open Access Journals (Sweden)

Peter Lepej

2015-10-01

Full Text Available Many applications, such as surveillance, inspection or search and rescue operations, can be performed with autonomous robots. Our aim is a control of modular autonomous systems in rescue robotics. One of the basic problems with autonomous robotics is the execution part where the control commands (translation and rotational velocities are produced for mobile bases. Therefore we have focused on this area because there is only a small amount of available path following software for skid-steered mobile robots. Our goal was to develop a velocity controller that could be used for multiple skid-steered mobile bases. We considered differential drive mobile bases such as tracked skid-steering mobile bases. Our approach is based on an arc fitting algorithm, which takes into account the robot constraints and kinematical model. It produces a continuous trajectory where fitting to the given path is adapted based on given parameters. Moreover, we have included orientation angle compensation while the mobile robot is moving and ground inclination compensation. Our rescue robot is described, together with the simulation setup and algorithm implementation. We compared our algorithm to the Hector-based software and curvature velocity approach. The results for the proposed algorithm are shown for the simulation results and the experiment.

Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

International Nuclear Information System (INIS)

Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

1992-09-01

Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

Online optimized hysteresis-based steering feel model for steer-by-wire systems

Directory of Open Access Journals (Sweden)

Ahmet Kirli

2016-06-01

Full Text Available In rubber-wheeled road vehicles, the mechanical connection between steering wheel and front wheels provides steering-related feedback to the driver. The torque fed back to the driver through the steering linkages and steering wheel, which is called steering feel, helps the driver in controlling the vehicle. The torque feedback is reproduced via artificial methods in steer-by-wire systems due to the lack of mechanical connection. In this work, in order to minimize the physical workload and the lateral acceleration under the consideration of handling performance, optimization of a hysteresis-based steering feel has been studied. A 2-degree-of-freedom bicycle model based on the magic formula tire model has been used for simulations and hardware-in-the-loop experiments. A mathematical model is proposed in order to create an adaptive model-based optimization of the hysteresis parameters simultaneously while driving. A hardware-in-the-loop experimental setup has been used for the driving tests. The weave and the double-lane change tests have been performed with different drivers in order to demonstrate and quantify the optimization methods that are presented in this work.

On Optimizing Steering Performance of Multi-axle Vehicle Based on Driving Force Control

Directory of Open Access Journals (Sweden)

Wu Zhicheng

2017-01-01

Full Text Available The steering performance of multi-axle vehicle with independent driving system is affected by the distribution of the wheel driving force. A nonlinear vehicle dynamics model including magic formula tire model for describing 11 DoF four-axle vehicle with dual-front-axle-steering (DFAS system was presented. The influence of different driving force distribution scheme on the steering performance of the vehicle was analyzed. A control strategy for improving the steady response and transient response of the vehicle steering is proposed. The results show: For the steady response, setting different drive force for internal and external wheels according to the actual steering characteristics of the vehicle can effectively improve its steering characteristics; For the transient response, adopting the zero sideslip angle control strategy and using the PID control algorithm to control the driving force of the outside wheel of tear-two-axle, under angle step input, the vehicle sideslip angle can quickly stabilize to 0 and yaw rate also significantly decreases.

A new model to compute the desired steering torque for steer-by-wire vehicles and driving simulators

Science.gov (United States)

Fankem, Steve; Müller, Steffen

2014-05-01

This paper deals with the control of the hand wheel actuator in steer-by-wire (SbW) vehicles and driving simulators (DSs). A novel model for the computation of the desired steering torque is presented. The introduced steering torque computation does not only aim to generate a realistic steering feel, which means that the driver should not miss the basic steering functionality of a modern conventional steering system such as an electric power steering (EPS) or hydraulic power steering (HPS), and this in every driving situation. In addition, the modular structure of the steering torque computation combined with suitably selected tuning parameters has the objective to offer a high degree of customisability of the steering feel and thus to provide each driver with his preferred steering feel in a very intuitive manner. The task and the tuning of each module are firstly described. Then, the steering torque computation is parameterised such that the steering feel of a series EPS system is reproduced. For this purpose, experiments are conducted in a hardware-in-the-loop environment where a test EPS is mounted on a steering test bench coupled with a vehicle simulator and parameter identification techniques are applied. Subsequently, how appropriate the steering torque computation mimics the test EPS system is objectively evaluated with respect to criteria concerning the steering torque level and gradient, the feedback behaviour and the steering return ability. Finally, the intuitive tuning of the modular steering torque computation is demonstrated for deriving a sportier steering feel configuration.

On Electrohydraulic Pressure Control for Power Steering Applications : Active Steering for Road Vehicles

OpenAIRE

Dell'Amico, Alessandro

2016-01-01

This thesis deals with the Electrohydraulic Power Steering system for road vehicles, using electronic pressure control valves. With an ever increasing demand for safer vehicles and fewer traffic accidents, steering-related active safety functions are becoming more common in modern vehicles. Future road vehicles will also evolve towards autonomous vehicles, with several safety, environmental and financial benefits. A key component in realising such solutions is active steering. The power steer...

49 CFR 570.7 - Steering systems.

Science.gov (United States)

2010-10-01

... 49 Transportation 6 2010-10-01 2010-10-01 false Steering systems. 570.7 Section 570.7... Pounds or Less § 570.7 Steering systems. (a) System play. Lash or free play in the steering system shall... in the steering system. Table 1—Steering System Free Play Values Steering wheel diameter (inches...

The Optimal Steering Control System using Imperialist Competitive Algorithm on Vehicles with Steer-by-Wire System

Directory of Open Access Journals (Sweden)

F. Hunaini

2015-03-01

Full Text Available Steer-by-wire is the electrical steering systems on vehicles that are expected with the development of an optimal control system can improve the dynamic performance of the vehicle. This paper aims to optimize the control systems, namely Fuzzy Logic Control (FLC and the Proportional, Integral and Derivative (PID control on the vehicle steering system using Imperialist Competitive Algorithm (ICA. The control systems are built in a cascade, FLC to suppress errors in the lateral motion and the PID control to minimize the error in the yaw motion of the vehicle. FLC is built has two inputs (error and delta error and single output. Each input and output consists of three Membership Function (MF in the form of a triangular for language term "zero" and two trapezoidal for language term "negative" and "positive". In order to work optimally, each MF optimized using ICA to get the position and width of the most appropriate. Likewise, in the PID control, the constant at each Proportional, Integral and Derivative control also optimized using ICA, so there are six parameters of the control system are simultaneously optimized by ICA. Simulations performed on vehicle models with 10 Degree Of Freedom (DOF, the plant input using the variables of steering that expressed in the desired trajectory, and the plant outputs are lateral and yaw motion. The simulation results showed that the FLC-PID control system optimized by using ICA can maintain the movement of vehicle according to the desired trajectory with lower error and higher speed limits than optimized with Particle Swarm Optimization (PSO.

MTS-MD of Biomolecules Steered with 3D-RISM-KH Mean Solvation Forces Accelerated with Generalized Solvation Force Extrapolation.

Science.gov (United States)

Omelyan, Igor; Kovalenko, Andriy

2015-04-14

We developed a generalized solvation force extrapolation (GSFE) approach to speed up multiple time step molecular dynamics (MTS-MD) of biomolecules steered with mean solvation forces obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). GSFE is based on a set of techniques including the non-Eckart-like transformation of coordinate space separately for each solute atom, extension of the force-coordinate pair basis set followed by selection of the best subset, balancing the normal equations by modified least-squares minimization of deviations, and incremental increase of outer time step in motion integration. Mean solvation forces acting on the biomolecule atoms in conformations at successive inner time steps are extrapolated using a relatively small number of best (closest) solute atomic coordinates and corresponding mean solvation forces obtained at previous outer time steps by converging the 3D-RISM-KH integral equations. The MTS-MD evolution steered with GSFE of 3D-RISM-KH mean solvation forces is efficiently stabilized with our optimized isokinetic Nosé-Hoover chain (OIN) thermostat. We validated the hybrid MTS-MD/OIN/GSFE/3D-RISM-KH integrator on solvated organic and biomolecules of different stiffness and complexity: asphaltene dimer in toluene solvent, hydrated alanine dipeptide, miniprotein 1L2Y, and protein G. The GSFE accuracy and the OIN efficiency allowed us to enlarge outer time steps up to huge values of 1-4 ps while accurately reproducing conformational properties. Quasidynamics steered with 3D-RISM-KH mean solvation forces achieves time scale compression of conformational changes coupled with solvent exchange, resulting in further significant acceleration of protein conformational sampling with respect to real time dynamics. Overall, this provided a 50- to 1000-fold effective speedup of conformational sampling for these systems, compared to conventional MD

Experimental verification of multidimensional quantum steering

Science.gov (United States)

Li, Che-Ming; Lo, Hsin-Pin; Chen, Liang-Yu; Yabushita, Atsushi

2018-03-01

Quantum steering enables one party to communicate with another remote party even if the sender is untrusted. Such characteristics of quantum systems not only provide direct applications to quantum information science, but are also conceptually important for distinguishing between quantum and classical resources. While concrete illustrations of steering have been shown in several experiments, quantum steering has not been certified for higher dimensional systems. Here, we introduce a simple method to experimentally certify two different kinds of quantum steering: Einstein-Podolsky-Rosen (EPR) steering and single-system (SS) steering (i.e., temporal steering), for dimensionality (d) up to d = 16. The former reveals the steerability among bipartite systems, whereas the latter manifests itself in single quantum objects. We use multidimensional steering witnesses to verify EPR steering of polarization-entangled pairs and SS steering of single photons. The ratios between the measured witnesses and the maximum values achieved by classical mimicries are observed to increase with d for both EPR and SS steering. The designed scenario offers a new method to study further the genuine multipartite steering of large dimensionality and potential uses in quantum information processing.

Molecular dynamics simulation study of the "stay or leave" problem for two magnesium ions in gene transcription.

Science.gov (United States)

Wu, Shaogui

2017-06-01

Two magnesium ions play important roles in nucleotide addition cycle (NAC) of gene transcription. However, at the end of each NAC, why does one ion stay in the active site while the other ion leaves with product pyrophosphate (PP i )? This problem still remains obscure. In this work, we studied the problem using all-atom molecular dynamics simulation combined with steered molecular dynamics and umbrella sampling simulation methods. Our simulations reveal that although both ions are located in the active site after chemistry, their detailed positions are not symmetrical, leading to their different forces from surrounding groups. One ion makes weaker contacts with PP i than the whole protein. Hence, PP i release is less likely to take it away. The other one forms tighter contacts with PP i relative to the protein. The formed (Mg 2+ -PP i ) 2- complex is found to break the contacts with surrounding protein residues one by one so as to dissociate from the active site. This effectively avoids the coexistence of two ions in the active site after PP i release and guarantees a reasonable Mg 2+ ion number in the active site for the next NAC. The observations from this work can provide valuable information for comprehensively understanding the molecular mechanism of transcription. Proteins 2017; 85:1002-1007. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Color molecular dynamics for dense matter

International Nuclear Information System (INIS)

Maruyama, Toshiki; Hatsuda, Tetsuo

2000-01-01

We propose a microscopic approach for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with meson exchange potentials between quarks, we construct nucleons and nuclear/quark matter. Dynamical transition between confinement and deconfinement phases are studied at high baryon density with this molecular dynamics simulation. (author)

Lattice dynamics and molecular dynamics simulation of complex materials

International Nuclear Information System (INIS)

Chaplot, S.L.

1997-01-01

In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

Molecular dynamics for irradiation driven chemistry

DEFF Research Database (Denmark)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-01-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

A Vehicle Steering Recognition System Based on Low-Cost Smartphone Sensors

Directory of Open Access Journals (Sweden)

Xinhua Liu

2017-03-01

Full Text Available Recognizing how a vehicle is steered and then alerting drivers in real time is of utmost importance to the vehicle and driver’s safety, since fatal accidents are often caused by dangerous vehicle maneuvers, such as rapid turns, fast lane-changes, etc. Existing solutions using video or in-vehicle sensors have been employed to identify dangerous vehicle maneuvers, but these methods are subject to the effects of the environmental elements or the hardware is very costly. In the mobile computing era, smartphones have become key tools to develop innovative mobile context-aware systems. In this paper, we present a recognition system for dangerous vehicle steering based on the low-cost sensors found in a smartphone: i.e., the gyroscope and the accelerometer. To identify vehicle steering maneuvers, we focus on the vehicle’s angular velocity, which is characterized by gyroscope data from a smartphone mounted in the vehicle. Three steering maneuvers including turns, lane-changes and U-turns are defined, and a vehicle angular velocity matching algorithm based on Fast Dynamic Time Warping (FastDTW is adopted to recognize the vehicle steering. The results of extensive experiments show that the average accuracy rate of the presented recognition reaches 95%, which implies that the proposed smartphone-based method is suitable for recognizing dangerous vehicle steering maneuvers.

Study on control schemes of flexible steering system of a multi-axle all-wheel-steering robot

Directory of Open Access Journals (Sweden)

Pingxia Zhang

2016-05-01

Full Text Available It is well known that a multi-axle wheeled robot possesses larger load capability and also higher drive performance. However, its steering flexibility is degraded due to the large number of wheels. In order to solve this problem, in this article, we proposed three control schemes based on the center of rotation or the steering angles of both the first- and last-axle wheels. To release these control schemes, steering mode selection and also the left wheel’s steering angle in a specific axle are added approaching a practical application. Thereafter, the remaining wheels’ steering angles can be calculated with the Ackerman steering theorem. In order to verify the control effects, a five-axle all-wheel-steering wheeled robot has been developed with the Bluetooth wireless monitor system. Based on the newly designed robot, validation experiments are carried out, such as lateral movement, situ rotation, and multi-mode steering within a narrow space. The results indicate that the proposed design in this article can ensure a more flexible and faster movement within a narrow space. It shows large potential in obstacle avoidance compared with the conventional partial-wheel steering mode.

Steering smog prediction

NARCIS (Netherlands)

R. van Liere (Robert); J.J. van Wijk (Jack)

1997-01-01

textabstractThe use of computational steering for smog prediction is described. This application is representative for many underlying issues found in steering high performance applications: high computing times, large data sets, and many different input parameters. After a short description of the

Substructured multibody molecular dynamics.

Energy Technology Data Exchange (ETDEWEB)

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

2006-11-01

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Optimization of steering elements in the RIA driver linac

International Nuclear Information System (INIS)

Lessner, E. S.; Aseev, V. S.; Ostroumov, P. N.; Physics

2005-01-01

The driver linac of the projected RIA facility is a versatile accelerator, a 1.4-GV, CW superconducting (SC) linac designed to simultaneously accelerate several heavy-ion charge states, providing beams from proton to uranium at 400 MeV/u at power levels at a minimum of 100 kW and up to 400 kW for most beams. Acceleration of multiple-charge-state uranium beams places stringent requirements on the linac design. A steering algorithm was derived that fulfilled the driver's real estate requirements, such as placement of steering dipole coils on SC solenoids and of beam position monitors outside cryostats, and beam-dynamics requirements, such as coupling effects induced by the focusing solenoids. The algorithm has been fully integrated into the tracking code TRACK and it is used to study and optimize the number and position of steering elements that minimize the multiple-beam centroid oscillations and preserve the beam emittance under misalignments of accelerating and transverse focusing elements in the driver linac

A Frictionless Steering Mechanism for the Front Steering ECCD ITER Upper Port Launcher

International Nuclear Information System (INIS)

Chavan, R; Henderson, M A; Sanchez, F

2005-01-01

A FS launcher is being designed for the ITER upper port, which offers enhanced physics performance over the RS launcher. A two mirror system is used to decouple the focusing and steering aspects of the launcher and provide a relatively small beam waist ( 1.6 m from the steering mirror). The resulting NTM stabilization efficiency (maximum CD density divided by the local bootstrap current >1.6) is above marginal for the q = 2 and 3/2 rational flux surfaces of the relevant ITER equilibria (scenarios 2, 3a and 5) and a factor of ∼3 relative to an equivalent RS launcher. The performance of the FS launcher strongly depends on the reliability of the steering mechanism, which is used to rotate the plasma facing steering mirror. CRPP has designed a frictionless steering mechanism assembled in a compact cartridge capable of up to ±10 deg. rotation (corresponding to a poloidal steering range of up to ±20 deg. for the microwave beam around a fixed axis of rotation) that offers a high operation reliability despite the close proximity to the thermal and neutron flux coming from the ITER plasma

ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

Science.gov (United States)

Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

2010-04-15

We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. 2009 Wiley Periodicals, Inc.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

Science.gov (United States)

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-01

In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

Approximation of quantum observables by molecular dynamics simulations

KAUST Repository

Sandberg, Mattias

2016-01-06

In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

Steering handbook

CERN Document Server

Pfeffer, Peter

2017-01-01

This edited volume presents basic principles as well as advanced concepts of the computational modeling of steering systems. Moreover, the book includes the components and functionalities of modern steering system, which are presented comprehensively and in a practical way. The book is written by more than 15 leading experts from the automotive industry and its components suppliers. The target audience primarily comprises practicing engineers, developers, researchers as well as graduate students who want to specialize in this field.

Polymer friction Molecular Dynamics

DEFF Research Database (Denmark)

Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

46 CFR 182.610 - Main steering gear.

Science.gov (United States)

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Main steering gear. 182.610 Section 182.610 Shipping...) MACHINERY INSTALLATION Steering Systems § 182.610 Main steering gear. (a) A vessel must be provided with a main steering gear that is: (1) Of adequate strength and capable of steering the vessel at all service...

Next generation extended Lagrangian first principles molecular dynamics.

Science.gov (United States)

Niklasson, Anders M N

2017-08-07

Extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] is formulated for general Hohenberg-Kohn density-functional theory and compared with the extended Lagrangian framework of first principles molecular dynamics by Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)]. It is shown how extended Lagrangian Born-Oppenheimer molecular dynamics overcomes several shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while improving or maintaining important features of Car-Parrinello simulations. The accuracy of the electronic degrees of freedom in extended Lagrangian Born-Oppenheimer molecular dynamics, with respect to the exact Born-Oppenheimer solution, is of second-order in the size of the integration time step and of fourth order in the potential energy surface. Improved stability over recent formulations of extended Lagrangian Born-Oppenheimer molecular dynamics is achieved by generalizing the theory to finite temperature ensembles, using fractional occupation numbers in the calculation of the inner-product kernel of the extended harmonic oscillator that appears as a preconditioner in the electronic equations of motion. Material systems that normally exhibit slow self-consistent field convergence can be simulated using integration time steps of the same order as in direct Born-Oppenheimer molecular dynamics, but without the requirement of an iterative, non-linear electronic ground-state optimization prior to the force evaluations and without a systematic drift in the total energy. In combination with proposed low-rank and on the fly updates of the kernel, this formulation provides an efficient and general framework for quantum-based Born-Oppenheimer molecular dynamics simulations.

Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

Directory of Open Access Journals (Sweden)

Lin Lin

2013-12-01

Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

Quantum steering in cascaded four-wave mixing processes.

Science.gov (United States)

Wang, Li; Lv, Shuchao; Jing, Jietai

2017-07-24

Quantum steering is used to describe the "spooky action-at-a-distance" nonlocality raised in the Einstein-Podolsky-Rosen (EPR) paradox, which is important for understanding entanglement distribution and constructing quantum networks. Here, in this paper, we study an experimentally feasible scheme for generating quantum steering based on cascaded four-wave-mixing (FWM) processes in hot rubidium (Rb) vapor. Quantum steering, including bipartite steering and genuine tripartite steering among the output light fields, is theoretically analyzed. We find the corresponding gain regions in which the bipartite and tripartite steering exist. The results of bipartite steering can be used to establish a hierarchical steering model in which one beam can steer the other two beams in the whole gain region; however, the other two beams cannot steer the first beam simultaneously. Moreover, the other two beams cannot steer with each other in the whole gain region. More importantly, we investigate the gain dependence of the existence of the genuine tripartite steering and we find that the genuine tripartite steering exists in most of the whole gain region in the ideal case. Also we discuss the effect of losses on the genuine tripartite steering. Our results pave the way to experimental demonstration of quantum steering in cascaded FWM process.

A Molecular Dynamics Study of Lunasin | Singh | South African ...

African Journals Online (AJOL)

A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

MATHEMATICAL MODELING OF WORKING PROCESS IN HYDRAULIC DRIVE OF SPECIFICALLY HEAVY-DUTY TRUCK STEERING

Directory of Open Access Journals (Sweden)

E. M. Zabolotsky

2006-01-01

Full Text Available The paper provides an analysis that shows application of pump-controlled steering hydraulic drives. Dynamic model of steering hydraulic drive of open-cast BelAZ-75131 dump truck developed at BNTU and also mathematical models for circuit consisting of a metering pump and a turning cylinder and a flow amplifier and a turning cylinder with due account of compressibility and resistance of service drain line. It is noted that on the basis of the given methodology a multi-variant dynamic calculation has been carried out, drive dynamics has been analyzed at various design and component parameters of a metering pump and a flow amplifier, rational values of these parameters has been selected for design development. The paper also gives an algorithm scheme for the solution of the derived equation systems.

Multiobjective optimization of a steering linkage

Energy Technology Data Exchange (ETDEWEB)

Sleesonsom, S.; Bureerat, S. [Sustainable and Infrastructure Research and Development Center, Dept. of Mechanical Engineering, Faculty of Engineering, Khon Kaen University, Khon Kaen (Thailand)

2016-08-15

In this paper, multi-objective optimization of a rack-and-pinion steering linkage is proposed. This steering linkage is a common mechanism used in small cars with three advantages as it is simple to construct, economical to manufacture, and compact and easy to operate. In the previous works, many researchers tried to minimize a steering error but minimization of a turning radius is somewhat ignored. As a result, a multi-objective optimization problem is assigned to simultaneously minimize a steering error and a turning radius. The design variables are linkage dimensions. The design problem is solved by the hybrid of multi-objective population-based incremental learning and differential evolution with various constraint handling schemes. The new design strategy leads to effective design of rack-and-pinion steering linkages satisfying both steering error and turning radius criteria.

Multiobjective optimization of a steering linkage

International Nuclear Information System (INIS)

Sleesonsom, S.; Bureerat, S.

2016-01-01

In this paper, multi-objective optimization of a rack-and-pinion steering linkage is proposed. This steering linkage is a common mechanism used in small cars with three advantages as it is simple to construct, economical to manufacture, and compact and easy to operate. In the previous works, many researchers tried to minimize a steering error but minimization of a turning radius is somewhat ignored. As a result, a multi-objective optimization problem is assigned to simultaneously minimize a steering error and a turning radius. The design variables are linkage dimensions. The design problem is solved by the hybrid of multi-objective population-based incremental learning and differential evolution with various constraint handling schemes. The new design strategy leads to effective design of rack-and-pinion steering linkages satisfying both steering error and turning radius criteria

Equation of state of dense plasmas: Orbital-free molecular dynamics as the limit of quantum molecular dynamics for high-Z elements

Energy Technology Data Exchange (ETDEWEB)

Danel, J.-F.; Blottiau, P.; Kazandjian, L.; Piron, R.; Torrent, M. [CEA, DAM, DIF, 91297 Arpajon (France)

2014-10-15

The applicability of quantum molecular dynamics to the calculation of the equation of state of a dense plasma is limited at high temperature by computational cost. Orbital-free molecular dynamics, based on a semiclassical approximation and possibly on a gradient correction, is a simulation method available at high temperature. For a high-Z element such as lutetium, we examine how orbital-free molecular dynamics applied to the equation of state of a dense plasma can be regarded as the limit of quantum molecular dynamics at high temperature. For the normal mass density and twice the normal mass density, we show that the pressures calculated with the quantum approach converge monotonically towards those calculated with the orbital-free approach; we observe a faster convergence when the orbital-free approach includes the gradient correction. We propose a method to obtain an equation of state reproducing quantum molecular dynamics results up to high temperatures where this approach cannot be directly implemented. With the results already obtained for low-Z plasmas, the present study opens the way for reproducing the quantum molecular dynamics pressure for all elements up to high temperatures.

Subfemtosecond electron dynamics of H{sub 2} in strong fields or the quest for the molecular clock

Energy Technology Data Exchange (ETDEWEB)

Staudte, A.

2005-07-01

In this work we have studied experimentally and theoretically hydrogen and deuterium molecules in strong laser fields. We wanted to demonstrate that control of dynamical processes on the time scale below a single laser cycle (2.7 fs) can be achieved even without using attosecond pulses just by employing the advanced experimental technique COLTRIMS. In order to do this, we have pursued two goals: 1. To examine, whether laser steered electron wavepackets can be used for laser induced electron diffraction (LIED) on molecules. 2. To demonstrate, that the double ionization of H{sub 2} can be followed with sub laser cycle temporal resolution (the molecular clock). Laser induced electron diffraction needs linearly polarized light since its mechanism relies on rescattering of the ionized electron in the molecular potential. With rescattering occurring within a few hundred attoseconds, LIED is really a process of attosecond physics. In principle, two extreme scattering geometries are possible for a homonuclear diatomic molecule like H{sub 2}: the perpendicular geometry, which corresponds to the classical double slit experiment where the electron microbunch is steered transversely to the molecular axis, and the tangential geometry with the electron moving parallel to the molecular axis. Experimental restrictions prevented us to investigate the perpendicular geometry. The molecular clock, on the other hand, employs circularly polarized light to map the absolute phase of the laser electric field onto the spatial direction of the electron momentum. Thereby, a full laser cycle is mapped onto 360 in momentum space. Thus, different electron ejection angles in the laboratory frame correspond to different ejection times. Together with the correlated kinetic energy release of the Coulomb exploding molecules an unambiguous clock running from 0-8 fs with a few 100 as resolution can be envisioned. In direct relation to this experiment, we studied the influence of the long range

Steering wave packet dynamics and population transfer between electronic states of the Na2 molecule by femtosecond laser pulses

International Nuclear Information System (INIS)

Yuan Kaijun; Sun Zhigang; Cong Shulin; Wang Senming; Yu Jie; Lou Nanquan

2005-01-01

An approach used for steering the wave packet dynamics and the population transfer between electronic states of the Na 2 molecule by a pair of femtosecond laser pulses is demonstrated. Four controlling schemes, i.e., four different combinations of time delays (intuitive and counterintuitive sequences) and frequency detunings (positive and negative detunings), are discussed in detail. The light-induced potentials are used to describe the wave packet dynamics and population transfer. The numerical results show that the wave packet excited by femtosecond laser pulses oscillates drastically on 2 1 Π g state with time. The efficiency of controlling population transfer from the X 1 Σ g + to2 1 Π g states of Na 2 is nearly 100% for the schemes of the counterintuitive sequence pulses with positive and negative detunings

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

Science.gov (United States)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

A predictive control framework for torque-based steering assistance to improve safety in highway driving

Science.gov (United States)

Ercan, Ziya; Carvalho, Ashwin; Tseng, H. Eric; Gökaşan, Metin; Borrelli, Francesco

2018-05-01

Haptic shared control framework opens up new perspectives on the design and implementation of the driver steering assistance systems which provide torque feedback to the driver in order to improve safety. While designing such a system, it is important to account for the human-machine interactions since the driver feels the feedback torque through the hand wheel. The controller should consider the driver's impact on the steering dynamics to achieve a better performance in terms of driver's acceptance and comfort. In this paper we present a predictive control framework which uses a model of driver-in-the-loop steering dynamics to optimise the torque intervention with respect to the driver's neuromuscular response. We first validate the system in simulations to compare the performance of the controller in nominal and model mismatch cases. Then we implement the controller in a test vehicle and perform experiments with a human driver. The results show the effectiveness of the proposed system in avoiding hazardous situations under different driver behaviours.

Fundamental X-mode electron cyclotron current drive using remote-steering symmetric direction antenna at larger steering angles

International Nuclear Information System (INIS)

Idei, H.; Hanada, K.; Zushi, H.; Sato, K.N.; Sakamoto, M.; Iyomasa, A.; Kawasaki, S.; Nakashima, H.; Higashijima, A.; Ohkubo, K.; Kubo, S.; Shimozuma, T.; Ito, S.; Hasegawa, M.; Nakamura, K.; Notake, T.; Hoshika, H.; Maezono, N.; Nishi, S.; Nakashima, K.

2005-01-01

A remote steering antenna has been newly developed for Electron Cyclotron Heating and Current Drive (ECH/ECCD) experiments on the TRIAM-1M tokamak. It is a first application of the remote steering antenna to the ECH/ECCD experiments under the conditions relevant to International Thermonuclear Experimental Reactor. Our launcher is a symmetric direction antenna with extended steering capability. The larger steering angles of 8-19 degrees are available, in addition to that near 0 degree. The output beam from the antenna is the well-defined Gaussian beam with a correct steering angle. The Gaussian content and the steering angle accuracy are 0.85 and -0.3 degrees, respectively. Antenna transmission efficiency in the high power test is evaluated as 0.95. The efficiencies at the low and high power tests are consistent with those in the calculation with higher-order modes. The difference between plasma currents increased at co- and counter-steering injections [+/-19 degrees] is clearly observed in the superposition to the Lower Hybrid Current Driven (LHCD) plasma of the fundamental X-mode injection. (author)

Thermally driven molecular linear motors - A molecular dynamics study

DEFF Research Database (Denmark)

Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

2009-01-01

We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...

Non-Mechanical Beam Steering in Free-Space Optical Communication Transceivers

Science.gov (United States)

Shortt, Kevin

Free-space optical communications systems are a rapidly growing field as they carry many of the advantages of traditional fibre-based communications systems without the added investment of installing complex infrastructure. Moreover, these systems are finding key niches in mobile platforms in order to take advantage of the increased bandwidth over traditional RF systems. Of course, the inevitable problem of tracking arises when dealing with mobile stations. To compound the problem in the case of communications to low Earth or geosynchronous orbits, FSOC systems typically operate with tightly confined beams over great distances often requiring pointing accuracies on the order of micro-radians or smaller. Mechanisms such as gimbal mounts and fine-steering mirrors are the usual candidates for platform stabilization, however, these clearly have substantial power requirements and inflate the mass of the system. Spatial light modulators (also known as optical phased arrays), on the other hand, offer a suitable alternative for beam-pointing stabilization. Some of the advantages of spatial light modulators over fine-steering mirrors include programmable multiple simultaneous beams, dynamic focus/defocus and moderate to excellent optical power handling capability. This thesis serves as an investigation into the implementation of spatial light modulators as a replacement for traditional fine-steering mirrors in the fine-pointing subsystem. In particular, pointing accuracy and scanning ability will be highlighted as performance metrics in the context of a variety of communication scenarios. Keywords: Free-space optical communications, beam steering, fine-steering mirror, spatial light modulator, optical phased array.

GMTIFS: the adaptive optics beam steering mirror for the GMT integral-field spectrograph

Science.gov (United States)

Davies, J.; Bloxham, G.; Boz, R.; Bundy, D.; Espeland, B.; Fordham, B.; Hart, J.; Herrald, N.; Nielsen, J.; Sharp, R.; Vaccarella, A.; Vest, C.; Young, P. J.

2016-07-01

To achieve the high adaptive optics sky coverage necessary to allow the GMT Integral-Field Spectrograph (GMTIFS) to access key scientific targets, the on-instrument adaptive-optics wavefront-sensing (OIWFS) system must patrol the full 180 arcsecond diameter guide field passed to the instrument. The OIWFS uses a diffraction limited guide star as the fundamental pointing reference for the instrument. During an observation the offset between the science target and the guide star will change due to sources such as flexure, differential refraction and non-sidereal tracking rates. GMTIFS uses a beam steering mirror to set the initial offset between science target and guide star and also to correct for changes in offset. In order to reduce image motion from beam steering errors to those comparable to the AO system in the most stringent case, the beam steering mirror is set a requirement of less than 1 milliarcsecond RMS. This corresponds to a dynamic range for both actuators and sensors of better than 1/180,000. The GMTIFS beam steering mirror uses piezo-walk actuators and a combination of eddy current sensors and interferometric sensors to achieve this dynamic range and control. While the sensors are rated for cryogenic operation, the actuators are not. We report on the results of prototype testing of single actuators, with the sensors, on the bench and in a cryogenic environment. Specific failures of the system are explained and suspected reasons for them. A modified test jig is used to investigate the option of heating the actuator and we report the improved results. In addition to individual component testing, we built and tested a complete beam steering mirror assembly. Testing was conducted with a point source microscope, however controlling environmental conditions to less than 1 micron was challenging. The assembly testing investigated acquisition accuracy and if there was any un-sensed hysteresis in the system. Finally we present the revised beam steering mirror

Development of a Computational Steering Framework for High Performance Computing Environments on Blue Gene/P Systems

KAUST Repository

Danani, Bob K.

2012-07-01

Computational steering has revolutionized the traditional workflow in high performance computing (HPC) applications. The standard workflow that consists of preparation of an application’s input, running of a simulation, and visualization of simulation results in a post-processing step is now transformed into a real-time interactive workflow that significantly reduces development and testing time. Computational steering provides the capability to direct or re-direct the progress of a simulation application at run-time. It allows modification of application-defined control parameters at run-time using various user-steering applications. In this project, we propose a computational steering framework for HPC environments that provides an innovative solution and easy-to-use platform, which allows users to connect and interact with running application(s) in real-time. This framework uses RealityGrid as the underlying steering library and adds several enhancements to the library to enable steering support for Blue Gene systems. Included in the scope of this project is the development of a scalable and efficient steering relay server that supports many-to-many connectivity between multiple steered applications and multiple steering clients. Steered applications can range from intermediate simulation and physical modeling applications to complex computational fluid dynamics (CFD) applications or advanced visualization applications. The Blue Gene supercomputer presents special challenges for remote access because the compute nodes reside on private networks. This thesis presents an implemented solution and demonstrates it on representative applications. Thorough implementation details and application enablement steps are also presented in this thesis to encourage direct usage of this framework.

Demand side management using profile steering

NARCIS (Netherlands)

Gerards, Marco Egbertus Theodorus; Toersche, Hermen; Hoogsteen, Gerwin; van der Klauw, Thijs; Hurink, Johann L.; Smit, Gerardus Johannes Maria

2015-01-01

Many Demand Side Management (DSM) approaches use energy prices as steering signals. This paper shows that such steering signals may result in power quality problems and high losses. As an alternative, this paper proposes to use desired (e.g., flat) power profiles as steering signals and presents an

Experimental temporal quantum steering

Czech Academy of Sciences Publication Activity Database

Bartkiewicz, K.; Černoch, Antonín; Lemr, K.; Miranowicz, A.; Nori, F.

2016-01-01

Roč. 6, Nov (2016), 1-8, č. článku 38076. ISSN 2045-2322 R&D Projects: GA ČR GAP205/12/0382 Institutional support: RVO:68378271 Keywords : temporal quantum steering * EPR steering Subject RIV: BH - Optics, Masers, Lasers Impact factor: 4.259, year: 2016

Introduction to Molecular Dynamics and Accelerated Molecular Dynamics

International Nuclear Information System (INIS)

Perez, Danny

2012-01-01

We first introduce classical molecular dynamics (MD) simulations. We discuss their main constituents - the interatomic potentials, the boundary conditions, and the integrators - and the discuss the various ensembles that can be sampled. We discuss the strengths and weaknesses of MD, specifically in terms of time and length-scales. We then move on to discuss accelerated MD (AMD) methods, techniques that were designed to circumvent the timescale limitations of MD for rare event systems. The different methods are introduced and examples of use given.

Design Optimization of Steering Mechanisms for Articulated Off-Road Vehicles Based on Genetic Algorithms

Directory of Open Access Journals (Sweden)

Chen Zhou

2018-02-01

Full Text Available Two cylinders arranged symmetrically on a frame have become a major form of steering mechanism for articulated off-road vehicles (AORVs. However, the differences of stroke and arm lead to pressure fluctuation, vibration noise, and a waste of torque. In this paper, the differences of stroke and arm are reduced based on a genetic algorithm (GA. First, the mathematical model of the steering mechanism is put forward. Then, the difference of stroke and arm are optimized using a GA. Finally, a FW50GLwheel loader is used as an example to demonstrate the proposed GA-based optimization method, and its effectiveness is verified by means of automatic dynamic analysis of mechanical systems (ADAMS. The stroke difference of the steering hydraulic cylinders was reduced by 92% and the arm difference reached a decrease of 78% through GA optimization, in comparison with unoptimized structures. The simulation result shows that the steering mechanism optimized by GA behaved better than by previous methods.

46 CFR 176.814 - Steering systems.

Science.gov (United States)

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Steering systems. 176.814 Section 176.814 Shipping COAST...) INSPECTION AND CERTIFICATION Material Inspections § 176.814 Steering systems. At each initial and subsequent inspection for certification the owner or managing operator shall be prepared to test the steering systems of...

DockingShop: A Tool for Interactive Molecular Docking

Energy Technology Data Exchange (ETDEWEB)

Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

2005-04-24

Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

Analysis and experimental kinematics of a skid-steering wheeled robot based on a laser scanner sensor.

Science.gov (United States)

Wang, Tianmiao; Wu, Yao; Liang, Jianhong; Han, Chenhao; Chen, Jiao; Zhao, Qiteng

2015-04-24

Skid-steering mobile robots are widely used because of their simple mechanism and robustness. However, due to the complex wheel-ground interactions and the kinematic constraints, it is a challenge to understand the kinematics and dynamics of such a robotic platform. In this paper, we develop an analysis and experimental kinematic scheme for a skid-steering wheeled vehicle based-on a laser scanner sensor. The kinematics model is established based on the boundedness of the instantaneous centers of rotation (ICR) of treads on the 2D motion plane. The kinematic parameters (the ICR coefficient , the path curvature variable and robot speed ), including the effect of vehicle dynamics, are introduced to describe the kinematics model. Then, an exact but costly dynamic model is used and the simulation of this model's stationary response for the vehicle shows a qualitative relationship for the specified parameters and . Moreover, the parameters of the kinematic model are determined based-on a laser scanner localization experimental analysis method with a skid-steering robotic platform, Pioneer P3-AT. The relationship between the ICR coefficient and two physical factors is studied, i.e., the radius of the path curvature and the robot speed . An empirical function-based relationship between the ICR coefficient of the robot and the path parameters is derived. To validate the obtained results, it is empirically demonstrated that the proposed kinematics model significantly improves the dead-reckoning performance of this skid-steering robot.

Beam Steering Devices Reduce Payload Weight

Science.gov (United States)

2012-01-01

Scientists have long been able to shift the direction of a laser beam, steering it toward a target, but often the strength and focus of the light is altered. For precision applications, where the quality of the beam cannot be compromised, scientists have typically turned to mechanical steering methods, redirecting the source of the beam by swinging the entire laser apparatus toward the target. Just as the mechanical methods used for turning cars has evolved into simpler, lighter, power steering methods, so has the means by which researchers can direct lasers. Some of the typical contraptions used to redirect lasers are large and bulky, relying on steering gimbals pivoted, rotating supports to shift the device toward its intended target. These devices, some as large and awkward as a piece of heavy luggage, are subject to the same issues confronted by mechanical parts: Components rub, wear out, and get stuck. The poor reliability and bulk not to mention the power requirements to run one of the machines have made mechanical beam steering components less than ideal for use in applications where weight, bulk, and maneuverability are prime concerns, such as on an unmanned aerial vehicle (UAV) or a microscope. The solution to developing reliable, lighter weight, nonmechanical steering methods to replace the hefty steering boxes was to think outside the box, and a NASA research partner did just that by developing a new beam steering method that bends and redirects the beam, as opposed to shifting the entire apparatus. The benefits include lower power requirements, a smaller footprint, reduced weight, and better control and flexibility in steering capabilities. Such benefits are realized without sacrificing aperture size, efficiency, or scanning range, and can be applied to myriad uses: propulsion systems, structures, radiation protection systems, and landing systems.

Current-driven dynamics in molecular-scale devices

International Nuclear Information System (INIS)

Seideman, Tamar

2003-01-01

We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)

Molecular Dynamics Studies of Nanofluidic Devices

DEFF Research Database (Denmark)

Zambrano Rodriguez, Harvey Alexander

of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

Adaptive Sliding Mode Control Method Based on Nonlinear Integral Sliding Surface for Agricultural Vehicle Steering Control

Directory of Open Access Journals (Sweden)

Taochang Li

2014-01-01

Full Text Available Automatic steering control is the key factor and essential condition in the realization of the automatic navigation control of agricultural vehicles. In order to get satisfactory steering control performance, an adaptive sliding mode control method based on a nonlinear integral sliding surface is proposed in this paper for agricultural vehicle steering control. First, the vehicle steering system is modeled as a second-order mathematic model; the system uncertainties and unmodeled dynamics as well as the external disturbances are regarded as the equivalent disturbances satisfying a certain boundary. Second, a transient process of the desired system response is constructed in each navigation control period. Based on the transient process, a nonlinear integral sliding surface is designed. Then the corresponding sliding mode control law is proposed to guarantee the fast response characteristics with no overshoot in the closed-loop steering control system. Meanwhile, the switching gain of sliding mode control is adaptively adjusted to alleviate the control input chattering by using the fuzzy control method. Finally, the effectiveness and the superiority of the proposed method are verified by a series of simulation and actual steering control experiments.

Operator space approach to steering inequality

International Nuclear Information System (INIS)

Yin, Zhi; Marciniak, Marcin; Horodecki, Michał

2015-01-01

In Junge and Palazuelos (2011 Commun. Math. Phys. 306 695–746) and Junge et al (2010 Commun. Math. Phys. 300 715–39) the operator space theory was applied to study bipartite Bell inequalities. The aim of the paper is to follow this line of research and use the operator space technique to analyze the steering scenario. We obtain a bipartite steering functional with unbounded largest violation of steering inequality, as well as constructing all ingredients explicitly. It turns out that the unbounded largest violation is obtained by a non maximally entangled state. Moreover, we focus on the bipartite dichotomic case where we construct a steering functional with unbounded largest violation of steering inequality. This phenomenon is different to the Bell scenario where only the bounded largest violation can be obtained by any bipartite dichotomic Bell functional. (paper)

Theoretical Concepts in Molecular Photodissociation Dynamics

DEFF Research Database (Denmark)

Henriksen, Niels Engholm

1995-01-01

This chapter contains sections titled: Introduction Quantum Dynamics of Molecular Photofragmentation The Total Reaction Probability Final Product Distributions Time-Independent Approach, Stationary Scattering States Gaussian Wave Packet Dynamics Wigner Phase Space Representation The Diatomic...

Driver behavior following an automatic steering intervention.

Science.gov (United States)

Fricke, Nicola; Griesche, Stefan; Schieben, Anna; Hesse, Tobias; Baumann, Martin

2015-10-01

The study investigated driver behavior toward an automatic steering intervention of a collision mitigation system. Forty participants were tested in a driving simulator and confronted with an inevitable collision. They performed a naïve drive and afterwards a repeated exposure in which they were told to hold the steering wheel loosely. In a third drive they experienced a false alarm situation. Data on driving behavior, i.e. steering and braking behavior as well as subjective data was assessed in the scenarios. Results showed that most participants held on to the steering wheel strongly or counter-steered during the system intervention during the first encounter. Moreover, subjective data collected after the first drive showed that the majority of drivers was not aware of the system intervention. Data from the repeated drive in which participants were instructed to hold the steering wheel loosely, led to significantly more participants holding the steering wheel loosely and thus complying with the instruction. This study seems to imply that without knowledge and information of the system about an upcoming intervention, the most prevalent driving behavior is a strong reaction with the steering wheel similar to an automatic steering reflex which decreases the system's effectiveness. Results of the second drive show some potential for countermeasures, such as informing drivers shortly before a system intervention in order to prevent inhibiting reactions. Copyright © 2015 Elsevier Ltd. All rights reserved.

First principles molecular dynamics without self-consistent field optimization

International Nuclear Information System (INIS)

Souvatzis, Petros; Niklasson, Anders M. N.

2014-01-01

We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations

Biogas production from steer manures in Vietnam

DEFF Research Database (Denmark)

Pham, Cuong H.; Saggar, Surinder; Vu, Cuong C.

2017-01-01

manures collected from two different experiments of steers fed diets containing feed supplements. BMP was 110.1 (NLkg-1 VS) for manure from steers receiving a control diet, significantly lower 79.0 (NL kg-1 VS) for manure from steers fed a diet containing 0.3% tannin (%DM), but then showed an increasing...... trend to 90.9 and 91.2 (NL kg-1 VS) for manures from steers receiving 0.4 and 0.5% tannin (%DM) supplements, respectively. Similarly, the CH4 production (NL kg-1 VS) of manure from steers was 174 for control, 142 for control supplemented concentrate (C), 143 for control added rice straw treated...

Molecular dynamics and diffusion a compilation

CERN Document Server

Fisher, David

2013-01-01

The molecular dynamics technique was developed in the 1960s as the outgrowth of attempts to model complicated systems by using either a) direct physical simulation or (following the great success of Monte Carlo methods) by b) using computer techniques. Computer simulation soon won out over clumsy physical simulation, and the ever-increasing speed and sophistication of computers has naturally made molecular dynamics simulation into a more and more successful technique. One of its most popular applications is the study of diffusion, and some experts now even claim that molecular dynamics simulation is, in the case of situations involving well-characterised elements and structures, more accurate than experimental measurement. The present double volume includes a compilation (over 600 items) of predicted solid-state diffusion data, for all of the major materials groups, dating back nearly four decades. The double volume also includes some original papers: "Determination of the Activation Energy for Formation and ...

Extended Lagrangian Excited State Molecular Dynamics.

Science.gov (United States)

Bjorgaard, J A; Sheppard, D; Tretiak, S; Niklasson, A M N

2018-02-13

An extended Lagrangian framework for excited state molecular dynamics (XL-ESMD) using time-dependent self-consistent field theory is proposed. The formulation is a generalization of the extended Lagrangian formulations for ground state Born-Oppenheimer molecular dynamics [Phys. Rev. Lett. 2008 100, 123004]. The theory is implemented, demonstrated, and evaluated using a time-dependent semiempirical model, though it should be generally applicable to ab initio theory. The simulations show enhanced energy stability and a significantly reduced computational cost associated with the iterative solutions of both the ground state and the electronically excited states. Relaxed convergence criteria can therefore be used both for the self-consistent ground state optimization and for the iterative subspace diagonalization of the random phase approximation matrix used to calculate the excited state transitions. The XL-ESMD approach is expected to enable numerically efficient excited state molecular dynamics for such methods as time-dependent Hartree-Fock (TD-HF), Configuration Interactions Singles (CIS), and time-dependent density functional theory (TD-DFT).

Submillisecond Elastic Recoil Reveals Molecular Origins of Fibrin Fiber Mechanics

Science.gov (United States)

Hudson, Nathan E.; Ding, Feng; Bucay, Igal; O’Brien, E. Timothy; Gorkun, Oleg V.; Superfine, Richard; Lord, Susan T.; Dokholyan, Nikolay V.; Falvo, Michael R.

2013-01-01

Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin’s elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin’s mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. PMID:23790375

Advances in molecular vibrations and collision dynamics molecular clusters

CERN Document Server

Bacic, Zatko

1998-01-01

This volume focuses on molecular clusters, bound by van der Waals interactions and hydrogen bonds. Twelve chapters review a wide range of recent theoretical and experimental advances in the areas of cluster vibrations, spectroscopy, and reaction dynamics. The authors are leading experts, who have made significant contributions to these topics.The first chapter describes exciting results and new insights in the solvent effects on the short-time photo fragmentation dynamics of small molecules, obtained by combining heteroclusters with femtosecond laser excitation. The second is on theoretical work on effects of single solvent (argon) atom on the photodissociation dynamics of the solute H2O molecule. The next two chapters cover experimental and theoretical aspects of the energetics and vibrations of small clusters. Chapter 5 describes diffusion quantum Monte Carlo calculations and non additive three-body potential terms in molecular clusters. The next six chapters deal with hydrogen-bonded clusters, refle...

Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

Indian Academy of Sciences (India)

Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

46 CFR 108.641 - Instructions for changing steering gear.

Science.gov (United States)

2010-10-01

... 46 Shipping 4 2010-10-01 2010-10-01 false Instructions for changing steering gear. 108.641 Section... steering gear. Instructions stating, in order, the different steps to be taken for changing to emergency and secondary steering gear must be posted in the steering gear room and at each secondary steering...

Non-adiabatic molecular dynamic simulations of opening reaction of molecular junctions

Czech Academy of Sciences Publication Activity Database

Zobač, Vladimír; Lewis, J.P.; Jelínek, Pavel

2016-01-01

Roč. 27, č. 28 (2016), 1-8, č. článku 285202. ISSN 0957-4484 R&D Projects: GA ČR(CZ) GA14-02079S Institutional support: RVO:68378271 Keywords : non-adiabatic molecular dynamics * molecular junctions * molecular switches * DFT Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.440, year: 2016

Three-bead steering microswimmers

Science.gov (United States)

Rizvi, Mohd Suhail; Farutin, Alexander; Misbah, Chaouqi

2018-02-01

The self-propelled microswimmers have recently attracted considerable attention as model systems for biological cell migration as well as artificial micromachines. A simple and well-studied microswimmer model consists of three identical spherical beads joined by two springs in a linear fashion with active oscillatory forces being applied on the beads to generate self-propulsion. We have extended this linear microswimmer configuration to a triangular geometry where the three beads are connected by three identical springs in an equilateral triangular manner. The active forces acting on each spring can lead to autonomous steering motion; i.e., allowing the swimmer to move along arbitrary paths. We explore the microswimmer dynamics analytically and pinpoint its rich character depending on the nature of the active forces. The microswimmers can translate along a straight trajectory, rotate at a fixed location, as well as perform a simultaneous translation and rotation resulting in complex curved trajectories. The sinusoidal active forces on the three springs of the microswimmer contain naturally four operating parameters which are more than required for the steering motion. We identify the minimal operating parameters which are essential for the motion of the microswimmer along any given arbitrary trajectory. Therefore, along with providing insights into the mechanics of the complex motion of the natural and artificial microswimmers, the triangular three-bead microswimmer can be utilized as a model for targeted drug delivery systems and autonomous underwater vehicles where intricate trajectories are involved.

A Time Modulated Printed Dipole Antenna Array for Beam Steering Application

Directory of Open Access Journals (Sweden)

Ruchi Gahley

2017-01-01

Full Text Available This paper presents time modulated beam steered antenna array without phase shifters. The beam steering is analyzed considering a two-element time modulated antenna array (TMAA of printed dipoles with microstrip via-hole balun. The proposed array resonates at the Industrial, Scientific, and Medical (ISM radio bands, 2.45 GHz and 5.8 GHz, and offers wide bandwidth inherited due to modified structure of ground plane. Array elements are excited by complex exponential excitation signal through broadband power divider and radio frequency (RF switches to achieve amplitude and phase variation without phase shifters. Differential Evolution algorithm is used to modify the time sequences of the RF switches connected to the antennas to generate radiation pattern with optimum dynamic efficiency by suppressing sideband radiations. Also switch-on time instant of RF switch connected to the subsequent element is modulated to steer the beam towards different directions. The proposed prototype is fabricated followed by parametric optimization. The fabrication results agree significantly well with simulated results.

Automated vehicle guidance using discrete reference markers. [road surface steering techniques

Science.gov (United States)

Johnston, A. R.; Assefi, T.; Lai, J. Y.

1979-01-01

Techniques for providing steering control for an automated vehicle using discrete reference markers fixed to the road surface are investigated analytically. Either optical or magnetic approaches can be used for the sensor, which generates a measurement of the lateral offset of the vehicle path at each marker to form the basic data for steering control. Possible mechanizations of sensor and controller are outlined. Techniques for handling certain anomalous conditions, such as a missing marker, or loss of acquisition, and special maneuvers, such as u-turns and switching, are briefly discussed. A general analysis of the vehicle dynamics and the discrete control system is presented using the state variable formulation. Noise in both the sensor measurement and in the steering servo are accounted for. An optimal controller is simulated on a general purpose computer, and the resulting plots of vehicle path are presented. Parameters representing a small multipassenger tram were selected, and the simulation runs show response to an erroneous sensor measurement and acquisition following large initial path errors.

Visualizing Energy on Target: Molecular Dynamics Simulations

Science.gov (United States)

2017-12-01

ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

Nonadiabatic electron wavepacket dynamics behind molecular autoionization

Science.gov (United States)

Matsuoka, Takahide; Takatsuka, Kazuo

2018-01-01

A theoretical method for real-time dynamics of nonadiabatic reorganization of electronic configurations in molecules is developed, with dual aim that the intramolecular electron dynamics can be probed by means of direct and/or indirect photoionizations and that the physical origins behind photoionization signals attained in the time domain can be identified in terms of the language of time-dependent quantum chemistry. In doing so, we first formulate and implement a new computational scheme for nonadiabatic electron dynamics associated with molecular ionization, which well fits in the general theory of nonadiabatic electron dynamics. In this method, the total nonadiabatic electron wavepackets are propagated in time directly with complex natural orbitals without referring to Hartree-Fock molecular orbitals, and the amount of electron flux from a molecular region leading to ionization is evaluated in terms of the relevant complex natural orbitals. In the second half of this paper, we apply the method to electron dynamics in the elementary processes consisting of the Auger decay to demonstrate the methodological significance. An illustrative example is taken from an Auger decay starting from the 2a1 orbital hole-state of H2O+. The roles of nuclear momentum (kinetic) couplings in electronic-state mixing during the decay process are analyzed in terms of complex natural orbitals, which are schematically represented in the conventional language of molecular symmetry of the Hartree-Fock orbitals.

Ultrafast molecular dynamics illuminated with synchrotron radiation

International Nuclear Information System (INIS)

Bozek, John D.; Miron, Catalin

2015-01-01

Highlights: • Ultrafast molecular dynamics probed with synchrotron radiation. • Core-excitation as probe of ultrafast dynamics through core-hole lifetime. • Review of experimental and theoretical methods in ultrafast dynamics using core-level excitation. - Abstract: Synchrotron radiation is a powerful tool for studying molecular dynamics in small molecules in spite of the absence of natural matching between the X-ray pulse duration and the time scale of nuclear motion. Promoting core level electrons to unoccupied molecular orbitals simultaneously initiates two ultrafast processes, nuclear dynamics on the potential energy surfaces of the highly excited neutral intermediate state of the molecule on the one hand and an ultrafast electronic decay of the intermediate excited state to a cationic final state, characterized by a core hole lifetime. The similar time scales of these processes enable core excited pump-probe-type experiments to be performed with long duration X-ray pulses from a synchrotron source. Recent results obtained at the PLIEADES beamline concerning ultrafast dissociation of core excited states and molecular potential energy curve mapping facilitated by changes in the geometry of the short-lived intermediate core excited state are reviewed. High brightness X-ray beams combined with state-of-the art electron and ion-electron coincidence spectrometers and highly sophisticated theoretical methods are required to conduct these experiments and to achieve a full understanding of the experimental results.

Rheology via nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Hoover, W.G.

1982-10-01

The equilibrium molecular dynamics formulated by Newton, Lagrange, and Hamilton has been modified in order to simulate rheologial molecular flows with fast computers. This modified Nonequilibrium Molecular Dynamics (NEMD) has been applied to fluid and solid deformations, under both homogeneous and shock conditions, as well as to the transport of heat. The irreversible heating associated with dissipation could be controlled by carrying out isothermal NEMD calculations. The new isothermal NEMD equations of motion are consistent with Gauss' 1829 Least-Constraint principle as well as certain microscopic equilibrium and nonequilibrium statistical formulations due to Gibbs and Boltzmann. Application of isothermal NEMD revealed high-frequency and high-strain-rate behavior for simple fluids which resembled the behavior of polymer solutions and melts at lower frequencies and strain rates. For solids NEMD produces plastic flows consistent with experimental observations at much lower strain rates. The new nonequilibrium methods also suggest novel formulations of thermodynamics in nonequilibrium systems and shed light on the failure of the Principle of Material Frame Indifference

First-principles molecular dynamics for metals

International Nuclear Information System (INIS)

Fernando, G.W.; Qian, G.; Weinert, M.; Davenport, J.W.

1989-01-01

A Car-Parrinello-type first-principles molecular-dynamics approach capable of treating the partial occupancy of electronic states that occurs at the Fermi level in a metal is presented. The algorithms used to study metals are both simple and computationally efficient. We also discuss the connection between ordinary electronic-structure calculations and molecular-dynamics simulations as well as the role of Brillouin-zone sampling. This extension should be useful not only for metallic solids but also for solids that become metals in their liquid and/or amorphous phases

Method of Controlling Steering of a Ground Vehicle

Science.gov (United States)

Dawson, Andrew D. (Inventor); Bluethmann, William J. (Inventor); Lee, Chunhao J. (Inventor); Vitale, Robert L. (Inventor); Guo, Raymond (Inventor); Atluri, Venkata Prasad (Inventor)

2016-01-01

A method of controlling steering of a vehicle through setting wheel angles of a plurality of modular electronic corner assemblies (eModules) is provided. The method includes receiving a driving mode selected from a mode selection menu. A position of a steering input device is determined in a master controller. A velocity of the vehicle is determined, in the master controller, when the determined position of the steering input device is near center. A drive mode request corresponding to the selected driving mode to the plurality of steering controllers is transmitted to the master controller. A required steering angle of each of the plurality of eModules is determined, in the master controller, as a function of the determined position of the steering input device, the determined velocity of the vehicle, and the selected first driving mode. The eModules are set to the respective determined steering angles.

How Dynamic Visualization Technology Can Support Molecular Reasoning

Science.gov (United States)

Levy, Dalit

2013-01-01

This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…

Physical adsorption and molecular dynamics

International Nuclear Information System (INIS)

Cohan, N.V.

1981-01-01

Some aspects of noble gases adsorption (except He) on graphite substracts are reviewed. Experimental results from this adsorption are analyzed and compared with molecular dynamics calculations. (L.C.) [pt

46 CFR 61.20-1 - Steering gear.

Science.gov (United States)

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false Steering gear. 61.20-1 Section 61.20-1 Shipping COAST... Periodic Tests of Machinery and Equipment § 61.20-1 Steering gear. (a) The marine inspector must inspect the steering gear at each inspection for certification for vessels whose Certificate of Inspections...

Thomas-Fermi molecular dynamics

International Nuclear Information System (INIS)

Clerouin, J.; Pollock, E.L.; Zerah, G.

1992-01-01

A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated

Molecular dynamics for dense matter

International Nuclear Information System (INIS)

Maruyama, Toshiki; Chiba, Satoshi; Watanabe, Gentaro

2012-01-01

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear “pasta”, i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid–gas phase transition is not plausible at lower temperatures. (author)

Molecular dynamics for dense matter

Science.gov (United States)

Maruyama, Toshiki; Watanabe, Gentaro; Chiba, Satoshi

2012-08-01

We review a molecular dynamics method for nucleon many-body systems called quantum molecular dynamics (QMD), and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to neutron star crusts, supernova cores, and heavy-ion collisions. A key advantage of QMD is that we can study dynamical processes of nucleon many-body systems without any assumptions about the nuclear structure. First, we focus on the inhomogeneous structures of low-density nuclear matter consisting not only of spherical nuclei but also of nuclear "pasta", i.e., rod-like and slab-like nuclei. We show that pasta phases can appear in the ground and equilibrium states of nuclear matter without assuming nuclear shape. Next, we show our simulation of compression of nuclear matter which corresponds to the collapsing stage of supernovae. With the increase in density, a crystalline solid of spherical nuclei changes to a triangular lattice of rods by connecting neighboring nuclei. Finally, we discuss fragment formation in expanding nuclear matter. Our results suggest that a generally accepted scenario based on the liquid-gas phase transition is not plausible at lower temperatures.

Relative entropy of steering: on its definition and properties

International Nuclear Information System (INIS)

Kaur, Eneet; Wilde, Mark M

2017-01-01

In Gallego and Aolita (2015 Phys. Rev . X 5 041008), the authors proposed a definition for the relative entropy of steering and showed that the resulting quantity is a convex steering monotone. Here we advocate for a different definition for relative entropy of steering, based on well grounded concerns coming from quantum Shannon theory. We prove that this modified relative entropy of steering is a convex steering monotone. Furthermore, we establish that it is uniformly continuous and faithful, in both cases giving quantitative bounds that should be useful in applications. We also consider a restricted relative entropy of steering which is relevant for the case in which the free operations in the resource theory of steering have a more restricted form (the restricted operations could be more relevant in practical scenarios). The restricted relative entropy of steering is convex, monotone with respect to these restricted operations, uniformly continuous, and faithful. (paper)

Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

Science.gov (United States)

Knoch, Fabian; Schäfer, Ken; Diezemann, Gregor; Speck, Thomas

2018-01-01

We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.

Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

Science.gov (United States)

2014-01-01

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

Robust two degree of freedom vehicle steering control satisfying mixed sensitivity constraint

OpenAIRE

Aksun-Güvenc, B.; Güvenc, L.; Odenthal, D.; Bünte, T.

2001-01-01

Robust steering control is used here for improving the yaw dynamics of a passenger car. A specific two degree of freedom control structure is adapted to the vehicle yaw dynamics problem and shown to robustly improve performance. The design study is based on six operating conditions for vehicle speed and the coefficient of friction between the tires and the road representing the operating domain of the vehicle. The relevant design specifications are formulated as attaining Hurwitz stability a...

Molecular dynamics with deterministic and stochastic numerical methods

CERN Document Server

Leimkuhler, Ben

2015-01-01

This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications.  Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method...

Automated beam steering using optimal control

Energy Technology Data Exchange (ETDEWEB)

Allen, C. K. (Christopher K.)

2004-01-01

We present a steering algorithm which, with the aid of a model, allows the user to specify beam behavior throughout a beamline, rather than just at specified beam position monitor (BPM) locations. The model is used primarily to compute the values of the beam phase vectors from BPM measurements, and to define cost functions that describe the steering objectives. The steering problem is formulated as constrained optimization problem; however, by applying optimal control theory we can reduce it to an unconstrained optimization whose dimension is the number of control signals.

Speed choice and steering behavior in curve driving

NARCIS (Netherlands)

Winsum, W. van; Godthelp, J.

1996-01-01

The relation between speed choice and steering performance during curve negotiation was studied in a driving simulator. The hypothesis was that curve radius and steering competence both affect steering error during curve driving, resulting in compensatory speed choice. In this, the control of safety

46 CFR 58.25-20 - Piping for steering gear.

Science.gov (United States)

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false Piping for steering gear. 58.25-20 Section 58.25-20... MACHINERY AND RELATED SYSTEMS Steering Gear § 58.25-20 Piping for steering gear. (a) Pressure piping must... the hydraulic system can be readily recharged from within the steering-gear compartment and must be...

Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics.

Science.gov (United States)

Hudson, Nathan E; Ding, Feng; Bucay, Igal; O'Brien, E Timothy; Gorkun, Oleg V; Superfine, Richard; Lord, Susan T; Dokholyan, Nikolay V; Falvo, Michael R

2013-06-18

Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin's elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin's mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Molecular ions, Rydberg spectroscopy and dynamics

International Nuclear Information System (INIS)

Jungen, Ch.

2015-01-01

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

Molecular ions, Rydberg spectroscopy and dynamics

Energy Technology Data Exchange (ETDEWEB)

Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

2015-01-22

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

Directory of Open Access Journals (Sweden)

Renata De Paris

2015-01-01

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

Improving Einstein–Podolsky–Rosen steering inequalities with state information

International Nuclear Information System (INIS)

Schneeloch, James; Broadbent, Curtis J.; Howell, John C.

2014-01-01

We discuss the relationship between entropic Einstein–Podolsky–Rosen (EPR)-steering inequalities and their underlying uncertainty relations along with the hypothesis that improved uncertainty relations lead to tighter EPR-steering inequalities. In particular, we discuss how using information about the state of a quantum system affects one's ability to witness EPR-steering. As an example, we consider the recent improvement to the entropic uncertainty relation between pairs of discrete observables (Berta et al., 2010 [10]). By considering the assumptions that enter into the development of a steering inequality, we derive correct steering inequalities from these improved uncertainty relations and find that they are identical to ones already developed (Schneeloch et al., 2013 [9]). In addition, we consider how one can use state information to improve our ability to witness EPR-steering, and develop a new continuous variable symmetric EPR-steering inequality as a result.

Steer-by-wire innovations and demonstrator

NARCIS (Netherlands)

Lupker, H.A.; Zuurbier, J.; Verschuren, R.M.A.F.; Jansen, S.T.H.; Willemsen, D.M.C.

2002-01-01

Arguments for 'by-wire' systems include production costs, packaging and traffic safety. Innovations concern both product and development process e.g. combined virtual engineering and Hardware-in-the-loop testing. Three Steer-by-wire systems are discussed: a steering system simulator used as a

Design and manufacturing of mechanical steering system for ...

African Journals Online (AJOL)

Design and manufacturing of mechanical steering system for parallel parking, zero turning radius, minimum turning radius with traditional turning. ... of the steering system are designed so as to meet all the configuration of steering system and to be well-matched to the power train, suspension system and body of the car.

Research on Performance of Wire-controlled Hydraulic Steering System Based on Four-wheel Steering

Science.gov (United States)

Tao, P.; Jin, X. H.

2018-05-01

In this paper, the steering stability and control strategy of forklift are put forward. Drive based on yawing moment distribution of rotary torque coordination control method, through analyzing the linear two degree of freedom model of forklift truck, forklift yawing angular velocity and mass center side-slip Angle of expectations, as the control target parameters system, using fuzzy controller output driving forklift steering the yawing moment, to drive rotary torque distribution, make the forklift truck to drive horizontal pendulum angular velocity and side-slip Angle tracking reference model very well. In this paper, the lateral stability control system were designed, the joint simulation in MATLAB/Simulink, the simulation results show that under the different partial load, the control system can effectively to control side forklift lateral stability, enhanced the forklift driving safety, for the side forklift steering stability study provides a theoretical basis.

A fermionic molecular dynamics technique to model nuclear matter

International Nuclear Information System (INIS)

Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

2009-01-01

Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

Dynamical photo-induced electronic properties of molecular junctions

Science.gov (United States)

Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

2018-03-01

Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.

Dynamical processes in atomic and molecular physics

CERN Document Server

Ogurtsov, Gennadi

2012-01-01

Atomic and molecular physics underlie a basis for our knowledge of fundamental processes in nature and technology and in such applications as solid state physics, chemistry and biology. In recent years, atomic and molecular physics has undergone a revolutionary change due to great achievements in computing and experimental techniques. As a result, it has become possible to obtain information both on atomic and molecular characteristics and on dynamics of atomic and molecular processes. This e-book highlights the present state of investigations in the field of atomic and molecular physics. Rece

46 CFR 167.65-25 - Steering gear tests.

Science.gov (United States)

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Steering gear tests. 167.65-25 Section 167.65-25... SHIPS Special Operating Requirements § 167.65-25 Steering gear tests. On all nautical school ships making voyages of more than 48 hours' duration, the entire steering gear, the whistle, the means of...

Theory and application of quantum molecular dynamics

CERN Document Server

Zeng Hui Zhang, John

1999-01-01

This book provides a detailed presentation of modern quantum theories for treating the reaction dynamics of small molecular systems. Its main focus is on the recent development of successful quantum dynamics theories and computational methods for studying the molecular reactive scattering process, with specific applications given in detail for a number of benchmark chemical reaction systems in the gas phase and the gas surface. In contrast to traditional books on collision in physics focusing on abstract theory for nonreactive scattering, this book deals with both the development and the appli

Dynamics and Thermodynamics of Molecular Machines

DEFF Research Database (Denmark)

Golubeva, Natalia

2014-01-01

to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

Quantum Steering Beyond Instrumental Causal Networks

Science.gov (United States)

Nery, R. V.; Taddei, M. M.; Chaves, R.; Aolita, L.

2018-04-01

We theoretically predict, and experimentally verify with entangled photons, that outcome communication is not enough for hidden-state models to reproduce quantum steering. Hidden-state models with outcome communication correspond, in turn, to the well-known instrumental processes of causal inference but in the one-sided device-independent scenario of one black-box measurement device and one well-characterized quantum apparatus. We introduce one-sided device-independent instrumental inequalities to test against these models, with the appealing feature of detecting entanglement even when communication of the black box's measurement outcome is allowed. We find that, remarkably, these inequalities can also be violated solely with steering, i.e., without outcome communication. In fact, an efficiently computable formal quantifier—the robustness of noninstrumentality—naturally arises, and we prove that steering alone is enough to maximize it. Our findings imply that quantum theory admits a stronger form of steering than known until now, with fundamental as well as practical potential implications.

Multiple time step integrators in ab initio molecular dynamics

International Nuclear Information System (INIS)

Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

2014-01-01

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

Dynamic signature of molecular association in methanol

International Nuclear Information System (INIS)

Bertrand, C. E.; Copley, J. R. D.; Faraone, A.; Self, J. L.

2016-01-01

Quasielastic neutron scattering measurements and molecular dynamics simulations were combined to investigate the collective dynamics of deuterated methanol, CD 3 OD. In the experimentally determined dynamic structure factor, a slow, non-Fickian mode was observed in addition to the standard density-fluctuation heat mode. The simulation results indicate that the slow dynamical process originates from the hydrogen bonding of methanol molecules. The qualitative behavior of this mode is similar to the previously observed α-relaxation in supercooled water [M. C. Bellissent-Funel et al., Phys. Rev. Lett. 85, 3644 (2000)] which also originates from the formation and dissolution of hydrogen-bonded associates (supramolecular clusters). In methanol, however, this mode is distinguishable well above the freezing transition. This finding indicates that an emergent slow mode is not unique to supercooled water, but may instead be a general feature of hydrogen-bonding liquids and associating molecular liquids.

Assessment of a Boat Fractured Steering Wheel

Directory of Open Access Journals (Sweden)

Vukelic Goran

2016-09-01

Full Text Available During regular use of the steering wheel mounted on a boat, two cracks emanating from a fastener hole were noticed which, consequently, caused final fracture of the wheel. To determine the behavior of a boat steering wheel with cracks present, assessment of a fractured wheel was performed. Torque moments of the fasteners were measured prior to removing the steering wheel from the boat. Visual and dye penetrant inspection followed along with the material detection. Besides using experimental procedures, assessment of the fractured wheel was performed using finite element analysis, i.e. stress intensity factor values were numerically determined. Variation of stress intensity factor with crack length is presented. Possible causes of crack occurrence are given and they include excessive values of fastener torque moments coupled with fretting between fastener and fastener hole that was poorly machined. Results obtained by this assessment can be taken for predicting fracture behavior of a cracked steering wheel and as a reference in the design, mounting and exploitation process of steering wheels improving that way their safety in transportation environment.

Molecular dynamics for fermions

International Nuclear Information System (INIS)

Feldmeier, H.; Schnack, J.

2000-02-01

The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)

Holographic memory using beam steering

Science.gov (United States)

Chao, Tien-Hsin (Inventor); Hanan, Jay C. (Inventor); Reyes, George F. (Inventor); Zhou, Hanying (Inventor)

2006-01-01

A method, apparatus, and system provide the ability for storing holograms at high speed. A single laser diode emits a collimated laser beam to both write to and read from a photorefractice crystal. One or more liquid crystal beam steering spatial light modulators (BSSLMs) or Micro-Electro-Mechanical Systems (MEMS) mirrors steer a reference beam, split from the collimated laser beam, at high speed to the photorefractive crystal.

Pattern recognition in molecular dynamics. [FORTRAN

Energy Technology Data Exchange (ETDEWEB)

Zurek, W H; Schieve, W C [Texas Univ., Austin (USA)

1977-07-01

An algorithm for the recognition of the formation of bound molecular states in the computer simulation of a dilute gas is presented. Applications to various related problems in physics and chemistry are pointed out. Data structure and decision processes are described. Performance of the FORTRAN program based on the algorithm in cooperation with the molecular dynamics program is described and the results are presented.

Steering Angle Function Algorithm of Morphing of Residential Area

Directory of Open Access Journals (Sweden)

XIE Tian

2015-07-01

Full Text Available A residential area feature morphing method based on steering angle function is presented. To residential area with the same representation under two different scales,transforming the representation of the residential area polygon from vector coordinates to steering angle function,then using the steering angle function to match,and finding out the similarity and the differences between the residential areas under different scale to get the steering angle function of the the residential areas under any middle scale,the final,transforming the middle scale steering angle function to vector coordinates form,and get the middle shape interpolation of the the residential area polygon.Experimental results show:the residential area morphing method by using steering angle function presented can realize the continuous multi-scale representation under the premise of keeping in shape for the residential area with the rectangular boundary features.

Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

Institute of Scientific and Technical Information of China (English)

Chengzhen Sun; Bofeng Bai

2017-01-01

Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

Classical and quantum molecular dynamics in NMR spectra

CERN Document Server

Szymański, Sławomir

2018-01-01

The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

Multiscale equation-free algorithms for molecular dynamics

Science.gov (United States)

Abi Mansour, Andrew

Molecular dynamics is a physics-based computational tool that has been widely employed to study the dynamics and structure of macromolecules and their assemblies at the atomic scale. However, the efficiency of molecular dynamics simulation is limited because of the broad spectrum of timescales involved. To overcome this limitation, an equation-free algorithm is presented for simulating these systems using a multiscale model cast in terms of atomistic and coarse-grained variables. Both variables are evolved in time in such a way that the cross-talk between short and long scales is preserved. In this way, the coarse-grained variables guide the evolution of the atom-resolved states, while the latter provide the Newtonian physics for the former. While the atomistic variables are evolved using short molecular dynamics runs, time advancement at the coarse-grained level is achieved with a scheme that uses information from past and future states of the system while accounting for both the stochastic and deterministic features of the coarse-grained dynamics. To complete the multiscale cycle, an atom-resolved state consistent with the updated coarse-grained variables is recovered using algorithms from mathematical optimization. This multiscale paradigm is extended to nanofluidics using concepts from hydrodynamics, and it is demonstrated for macromolecular and nanofluidic systems. A toolkit is developed for prototyping these algorithms, which are then implemented within the GROMACS simulation package and released as an open source multiscale simulator.

Scalable Molecular Dynamics for Large Biomolecular Systems

Directory of Open Access Journals (Sweden)

Robert K. Brunner

2000-01-01

Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

Science.gov (United States)

Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

2015-05-01

Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

46 CFR 196.37-33 - Instructions for changing steering gear.

Science.gov (United States)

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Instructions for changing steering gear. 196.37-33... steering gear. (a) Instructions in at least 1/2 inch letters and figures shall be posted in the steering engineroom, relating in order, the different steps to be taken in changing to the emergency steering gear...

46 CFR 58.25-10 - Main and auxiliary steering gear.

Science.gov (United States)

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false Main and auxiliary steering gear. 58.25-10 Section 58.25... AUXILIARY MACHINERY AND RELATED SYSTEMS Steering Gear § 58.25-10 Main and auxiliary steering gear. (a) Power-operated main and auxiliary steering gear must be separate systems that are independent throughout their...

Steering Your Mysterious Mind

DEFF Research Database (Denmark)

Prasad, Ramjee

Steering the Mysterious Mind, describes a unique, novel concept for a way to gain control of your mind. The five basic elements of human life, that is; Creativity, Content­ment, Confidence, Calmness, and Concentration (C5) have been introduced in my previous book Unlock Your Personalization. Posi....... Compare it with going to the gym where you work on the physical body. In the same way as with arms and legs, the mind is a mus­cle which you exercise through C5 practice. Steering the mind on your personal goal will help you to be creative....

Working paper on public steering of privately owned sports facilities

DEFF Research Database (Denmark)

Iversen, Evald Bundgård

This short paper discusses how municipalities can steer privately owned sports facilities. Firstly I analyse why steering of privately owned facilities is an interesting subject. Secondly I discuss what the advantages and drawbacks of using different approaches for steering sports facilities are........ Finally I discuss the methodological challenges of measuring activities in sports facilities – and take a closer look at the advantages and drawbacks of using manual and thermal techniques for registering activity.......This short paper discusses how municipalities can steer privately owned sports facilities. Firstly I analyse why steering of privately owned facilities is an interesting subject. Secondly I discuss what the advantages and drawbacks of using different approaches for steering sports facilities are...

Einstein-Podolsky-Rosen paradox and quantum steering in a three-mode optomechanical system

Science.gov (United States)

He, Qiongyi; Ficek, Zbigniew

2014-02-01

We study multipartite entanglement, the generation of Einstein-Podolsky-Rosen (EPR) states, and quantum steering in a three-mode optomechanical system composed of an atomic ensemble located inside a single-mode cavity with a movable mirror. The cavity mode is driven by a short laser pulse, has a nonlinear parametric-type interaction with the mirror and a linear beam-splitter-type interaction with the atomic ensemble. There is no direct interaction of the mirror with the atomic ensemble. A threshold effect for the dynamics of the system is found, above which the system works as an amplifier and below which as an attenuator of the output fields. The threshold is determined by the ratio of the coupling strengths of the cavity mode to the mirror and to the atomic ensemble. It is shown that above the threshold, the system effectively behaves as a two-mode system in which a perfect bipartite EPR state can be generated, while it is impossible below the threshold. Furthermore, a fully inseparable tripartite entanglement and even further a genuine tripartite entanglement can be produced above and below the threshold. In addition, we consider quantum steering and examine the monogamy relations that quantify the amount of bipartite steering that can be shared between different modes. It is found that the mirror is more capable for steering of entanglement than the cavity mode. The two-way steering is found between the mirror and the atomic ensemble despite the fact that they are not directly coupled to each other, while it is impossible between the output of cavity mode and the ensemble which are directly coupled to each other.

Molecular quantum dynamics. From theory to applications

International Nuclear Information System (INIS)

Gatti, Fabien

2014-01-01

An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible introduction. Although the

Molecular quantum dynamics. From theory to applications

Energy Technology Data Exchange (ETDEWEB)

Gatti, Fabien (ed.) [Montpellier 2 Univ. (France). Inst. Charles Gerhardt - CNRS 5253

2014-09-01

An educational and accessible introduction to the field of molecular quantum dynamics. Illustrates the importance of the topic for broad areas of science: from astrophysics and the physics of the atmosphere, over elementary processes in chemistry, to biological processes. Presents chosen examples of striking applications, highlighting success stories, summarized by the internationally renowned experts. Including a foreword by Lorenz Cederbaum (University Heidelberg, Germany). This book focuses on current applications of molecular quantum dynamics. Examples from all main subjects in the field, presented by the internationally renowned experts, illustrate the importance of the domain. Recent success in helping to understand experimental observations in fields like heterogeneous catalysis, photochemistry, reactive scattering, optical spectroscopy, or femto- and attosecond chemistry and spectroscopy underline that nuclear quantum mechanical effects affect many areas of chemical and physical research. In contrast to standard quantum chemistry calculations, where the nuclei are treated classically, molecular quantum dynamics can cover quantum mechanical effects in their motion. Many examples, ranging from fundamental to applied problems, are known today that are impacted by nuclear quantum mechanical effects, including phenomena like tunneling, zero point energy effects, or non-adiabatic transitions. Being important to correctly understand many observations in chemical, organic and biological systems, or for the understanding of molecular spectroscopy, the range of applications covered in this book comprises broad areas of science: from astrophysics and the physics and chemistry of the atmosphere, over elementary processes in chemistry, to biological processes (such as the first steps of photosynthesis or vision). Nevertheless, many researchers refrain from entering this domain. The book ''Molecular Quantum Dynamics'' offers them an accessible

How Insect Flight Steering Muscles Work

OpenAIRE

Walker, Simon M.; Schwyn, Daniel A.; Mokso, Rajmund; Wicklein, Martina; Müller, Tonya; Doube, Michael; Stampanoni, Marco; Krapp, Holger G.; Taylor, Graham K.

2014-01-01

Dipteran flies are amongst the smallest and most agile of flying animals. Their wings are driven indirectly by large power muscles, which cause cyclical deformations of the thorax that are amplified through the intricate wing hinge. Asymmetric flight manoeuvres are controlled by 13 pairs of steering muscles acting directly on the wing articulations. Collectively the steering muscles account for

Excited-state molecular photoionization dynamics

International Nuclear Information System (INIS)

Pratt, S.T.

1995-01-01

This review presents a survey of work using resonance-enhanced multiphoton ionization and double-resonance techniques to study excited-state photoionization dynamics in molecules. These techniques routinely provide detail and precision that are difficult to achieve in single-photon ionization from the ground state. The review not only emphasizes new aspects of photoionization revealed in the excited-state experiments but also shows how the excited-state techniques can provide textbook illustrations of some fundamental mechanisms in molecular photoionization dynamics. Most of the examples are confined to diatomic molecules. (author)

Symmetry of quantum molecular dynamics

International Nuclear Information System (INIS)

Burenin, A.V.

2002-01-01

The paper reviews the current state-of-art in describing quantum molecular dynamics based on symmetry principles alone. This qualitative approach is of particular interest as the only method currently available for a broad and topical class of problems in the internal dynamics of molecules. Besides, a molecule is a physical system whose collective internal motions are geometrically structured, and its perturbation theory description requires a symmetry analysis of this structure. The nature of the geometrical symmetry groups crucial for the closed formulation of the qualitative approach is discussed [ru

Molecular dynamics modeling of polymer flammability

International Nuclear Information System (INIS)

Nyden, M.R.; Brown, J.E.; Lomakin, S.M.

1992-01-01

Molecular dynamic simulations were used to identify factors which promote char formation during the thermal degradation of polymers. Computer movies based on these simulations, indicate that cross-linked model polymers tend to undergo further cross-linking when burned, eventually forming a high molecular weight, thermally stable char. This paper reports that the prediction was confirmed by char yield measurements made on γ and e - -irradiated polyethylene and chemically cross-linked poly(methyl methacrylate)

Observation of one-way Einstein-Podolsky-Rosen steering

Science.gov (United States)

Händchen, Vitus; Eberle, Tobias; Steinlechner, Sebastian; Samblowski, Aiko; Franz, Torsten; Werner, Reinhard F.; Schnabel, Roman

2012-09-01

The distinctive non-classical features of quantum physics were first discussed in the seminal paper by A. Einstein, B. Podolsky and N. Rosen (EPR) in 1935. In his immediate response, E. Schrödinger introduced the notion of entanglement, now seen as the essential resource in quantum information as well as in quantum metrology. Furthermore, he showed that at the core of the EPR argument is a phenomenon that he called steering. In contrast to entanglement and violations of Bell's inequalities, steering implies a direction between the parties involved. Recent theoretical works have precisely defined this property, but the question arose as to whether there are bipartite states showing steering only in one direction. Here, we present an experimental realization of two entangled Gaussian modes of light that in fact shows the steering effect in one direction but not in the other. The generated one-way steering gives a new insight into quantum physics and may open a new field of applications in quantum information.

Electron-nuclear dynamics of molecular systems

International Nuclear Information System (INIS)

Diz, A.; Oehrn, Y.

1994-01-01

The content of an ab initio time-dependent theory of quantum molecular dynamics of electrons and atomic nuclei is presented. Employing the time-dependent variational principle and a family of approximate state vectors yields a set of dynamical equations approximating the time-dependent Schroedinger equation. These equations govern the time evolution of the relevant state vector parameters as molecular orbital coefficients, nuclear positions, and momenta. This approach does not impose the Born-Oppenheimer approximation, does not use potential energy surfaces, and takes into account electron-nuclear coupling. Basic conservation laws are fully obeyed. The simplest model of the theory employs a single determinantal state for the electrons and classical nuclei and is implemented in the computer code ENDyne. Results from this ab-initio theory are reported for ion-atom and ion-molecule collisions

Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics.

Science.gov (United States)

Martínez, Enrique; Cawkwell, Marc J; Voter, Arthur F; Niklasson, Anders M N

2015-04-21

Extended Lagrangian Born-Oppenheimer molecular dynamics is developed and analyzed for applications in canonical (NVT) simulations. Three different approaches are considered: the Nosé and Andersen thermostats and Langevin dynamics. We have tested the temperature distribution under different conditions of self-consistent field (SCF) convergence and time step and compared the results to analytical predictions. We find that the simulations based on the extended Lagrangian Born-Oppenheimer framework provide accurate canonical distributions even under approximate SCF convergence, often requiring only a single diagonalization per time step, whereas regular Born-Oppenheimer formulations exhibit unphysical fluctuations unless a sufficiently high degree of convergence is reached at each time step. The thermostated extended Lagrangian framework thus offers an accurate approach to sample processes in the canonical ensemble at a fraction of the computational cost of regular Born-Oppenheimer molecular dynamics simulations.

Dynamics of molecular superrotors in an external magnetic field

Science.gov (United States)

Korobenko, Aleksey; Milner, Valery

2015-08-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin-rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.

Control of intravascular catheters using an array of active steering coils.

Science.gov (United States)

Gudino, N; Heilman, J A; Derakhshan, J J; Sunshine, J L; Duerk, J L; Griswold, M A

2011-07-01

To extend the concept of deflecting the tip of a catheter with the magnetic force created in an MRI system through the use of an array of independently controllable steering coils located in the catheter tip, and to present methods for visualization of the catheter and/or surrounding areas while the catheter is deflected. An array of steering coils made of 42-gauge wire was built over a 2.5 Fr (0.83 mm) fiber braided microcatheter. Two of the coils were 70 turn axial coils separated by 1 cm, and the third was a 15-turn square side coil that was 2 x 4 mm2. Each coil was driven independently by a pulse width modulation (PWM) current source controlled by a microprocessor that received commands from a MATLAB routine that dynamically set current amplitude and direction for each coil. The catheter was immersed in a water phantom containing 1% Gd-DTPA that was placed at the isocenter of a 1.5 T MRI scanner. Deflections of the catheter tip were measured from image-based data obtained with a real-time radio frequency (RF) spoiled gradient echo sequence (GRE). The small local magnetic fields generated by the steering coils were exploited to generate a hyperintense signal at the catheter tip by using a modified GRE sequence that did not include slice-select rewinding gradients. Imaging and excitation modes were implemented by synchronizing the excitation of the steering coil array with the scanner by ensuring that no current was driven through the coils during the data acquisition window; this allowed visualization of the surrounding tissue while not affecting the desired catheter position. Deflections as large as 2.5 cm were measured when exciting the steering coils sequentially with a 100 mA maximum current per coil. When exciting a single axial coil, the deflection was half this value with 30% higher current. A hyperintense catheter tip useful for catheter tracking was obtained by imaging with the modified GRE sequence. Clear visualization of the areas surrounding the

Refractive waveguide non-mechanical beam steering (NMBS) in the MWIR

Science.gov (United States)

Myers, Jason D.; Frantz, Jesse A.; Spillmann, Christopher M.; Bekele, Robel Y.; Kolacz, Jakub; Gotjen, Henry; Naciri, Jawad; Shaw, Brandon; Sanghera, Jas S.

2018-02-01

Beam steering is a crucial technology for a number of applications, including chemical sensing/mapping and light detection and ranging (LIDAR). Traditional beam steering approaches rely on mechanical movement, such as the realignment of mirrors in gimbal mounts. The mechanical approach to steering has several drawbacks, including large size, weight and power usage (SWAP), and frequent mechanical failures. Recently, alternative non-mechanical approaches have been proposed and developed, but these technologies do not meet the demanding requirements for many beam steering applications. Here, we highlight the development efforts into a particular non-mechanical beam steering (NMBS) approach, refractive waveguides, for application in the MWIR. These waveguides are based on an Ulrich-coupled slab waveguide with a liquid crystal (LC) top cladding; by selectively applying an electric field across the liquid crystal through a prismatic electrode, steering is achieved by creating refraction at prismatic interfaces as light propagates through the device. For applications in the MWIR, we describe a versatile waveguide architecture based on chalcogenide glasses that have a wide range of refractive indices, transmission windows, and dispersion properties. We have further developed robust shadow-masking methods to taper the subcladding layers in the coupling region. We have demonstrated devices with >10° of steering in the MWIR and a number of advantageous properties for beam steering applications, including low-power operation, compact size, and fast point-to-point steering.

Study on Roll Instability Mechanism and Stability Index of Articulated Steering Vehicles

Directory of Open Access Journals (Sweden)

Xuefei Li

2016-01-01

Full Text Available This study examines the roll instability mechanism and stability index of articulated steering vehicles (ASVs by taking wheel loaders as the research object. A seven-degree-of-freedom nonlinear dynamics model of the ASVs is built on the basis of multibody dynamics. A physical prototype model of an ASV is designed and manufactured to validate the dynamic model. Test results reasonably agree with the simulation results, which indicates that the established dynamic model can reasonably describe ASV movements. Detailed analysis of the rollover stability of the wheel loader is performed with the use of the established dynamic model. Analysis results show that rollover will occur when the roll angular velocity exceeds a critical threshold, which is affected by lateral acceleration and slope angle. On this basis, a dynamic stability index applicable to the ASVs is presented.

Optimization Under Uncertainty for Wake Steering Strategies: Preprint

Energy Technology Data Exchange (ETDEWEB)

Quick, Julian [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Annoni, Jennifer [National Renewable Energy Laboratory (NREL), Golden, CO (United States); King, Ryan N [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Dykes, Katherine L [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Fleming, Paul A [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Ning, Andrew [Brigham Young University

2017-05-01

Wind turbines in a wind power plant experience significant power losses because of aerodynamic interactions between turbines. One control strategy to reduce these losses is known as 'wake steering,' in which upstream turbines are yawed to direct wakes away from downstream turbines. Previous wake steering research has assumed perfect information, however, there can be significant uncertainty in many aspects of the problem, including wind inflow and various turbine measurements. Uncertainty has significant implications for performance of wake steering strategies. Consequently, the authors formulate and solve an optimization under uncertainty (OUU) problem for finding optimal wake steering strategies in the presence of yaw angle uncertainty. The OUU wake steering strategy is demonstrated on a two-turbine test case and on the utility-scale, offshore Princess Amalia Wind Farm. When we accounted for yaw angle uncertainty in the Princess Amalia Wind Farm case, inflow-direction-specific OUU solutions produced between 0% and 1.4% more power than the deterministically optimized steering strategies, resulting in an overall annual average improvement of 0.2%. More importantly, the deterministic optimization is expected to perform worse and with more downside risk than the OUU result when realistic uncertainty is taken into account. Additionally, the OUU solution produces fewer extreme yaw situations than the deterministic solution.

BEAMLINE-CONTROLLED STEERING OF SOURCE-POINT ANGLE AT THE ADVANCED PHOTON SOURCE

Energy Technology Data Exchange (ETDEWEB)

Emery, L.; Fystro, G.; Shang, H.; Smith, M.

2017-06-25

An EPICS-based steering software system has been implemented for beamline personnel to directly steer the angle of the synchrotron radiation sources at the Advanced Photon Source. A script running on a workstation monitors "start steering" beamline EPICS records, and effects a steering given by the value of the "angle request" EPICS record. The new system makes the steering process much faster than before, although the older steering protocols can still be used. The robustness features of the original steering remain. Feedback messages are provided to the beamlines and the accelerator operators. Underpinning this new steering protocol is the recent refinement of the global orbit feedback process whereby feedforward of dipole corrector set points and orbit set points are used to create a local steering bump in a rapid and seamless way.

Bulling among yearling feedlot steers.

Science.gov (United States)

Pierson, R E; Jensen, R; Braddy, P M; Horton, D P; Christie, R M

1976-09-01

In a survey to determine the cause of illness and deaths among yearling feedlot cattle, bulling was found to be one of the major problems. During the years 1971-1974, 54,913 (2.88%) steers became bullers and represented an annual loss of around +325,000. Some of the causes of bulling were found to be hormones, either as implants or in the feed. In 1974, from 1,988 necropsies, it was determined that 83 steers died from riding injuries.

Fault-tolerant Actuator System for Electrical Steering of Vehicles

DEFF Research Database (Denmark)

Sørensen, Jesper Sandberg; Blanke, Mogens

2006-01-01

is needed that meets this requirement. This paper studies the fault-tolerance properties of an electrical steering system. It presents a fault-tolerant architecture where a dedicated AC motor design used in conjunction with cheap voltage measurements can ensure detection of all relevant faults......Being critical to the safety of vehicles, the steering system is required to maintain the vehicles ability to steer until it is brought to halt, should a fault occur. With electrical steering becoming a cost-effective candidate for electrical powered vehicles, a fault-tolerant architecture...

Methodologies for steering clocks

Science.gov (United States)

Chadsey, Harold

1995-01-01

One of the concerns of the PTTI community is the coordination of one time scale with another. This is accomplished through steering one clock system to another, with a goal of a zero or constant offset in time and frequency. In order to attain this goal, rate differences are calculated and allowed for by the steering algorithm. This paper will present several of these different methods of determining rate differences. Ideally, any change in rate should not cause the offset to change sign (overshoot) by any amount, but certainly not by as much as its previous absolute value. The advantages and disadvantages of each depend on the user's situation.

Collective multipartite Einstein-Podolsky-Rosen steering: more secure optical networks.

Science.gov (United States)

Wang, Meng; Gong, Qihuang; He, Qiongyi

2014-12-01

Collective multipartite Einstein-Podolsky-Rosen (EPR) steering is a type of quantum correlation shared among N parties, where the EPR paradox of one party can only be realized by performing local measurements on all the remaining N-1 parties. We formalize the collective tripartite steering in terms of local hidden state model and give the steering inequalities that act as signatures and suggest how to optimize collective tripartite steering in specific optical schemes. The special entangled states with property of collective multipartite steering may have potential applications in ultra-secure multiuser communication networks where the issue of trust is critical.

Directional control-response compatibility of joystick steered shuttle cars.

Science.gov (United States)

Burgess-Limerick, Robin; Zupanc, Christine M; Wallis, Guy

2012-01-01

Shuttle cars are an unusual class of vehicle operated in underground coal mines, sometimes in close proximity to pedestrians and steering errors may have very serious consequences. A directional control-response incompatibility has previously been described in shuttle cars which are controlled using a steering wheel oriented perpendicular to the direction of travel. Some other shuttle car operators are seated perpendicular to the direction of travel and steer the car via a seat mounted joystick. A virtual simulation was utilised to determine whether the steering arrangement in these vehicles maintains directional control-response compatibility. Twenty-four participants were randomly assigned to either a condition corresponding to this design (consistent direction), or a condition in which the directional steering response was reversed while driving in-bye (visual field compatible). Significantly less accurate steering performance was exhibited by the consistent direction group during the in-bye trials only. Shuttle cars which provide the joystick steering mechanism described here require operators to accommodate alternating compatible and incompatible directional control-response relationships with each change of car direction. A virtual simulation of an underground coal shuttle car demonstrates that the design incorporates a directional control-response incompatibility when driving the vehicle in one direction. This design increases the probability of operator error, with potential adverse safety and productivity consequences.

Femtochemistry and femtobiology ultrafast dynamics in molecular science

CERN Document Server

Douhal, Abderrazzak

2002-01-01

This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

Research on Handling Stability of Steering-by-wire System

Directory of Open Access Journals (Sweden)

Yuan Ying

2017-01-01

Full Text Available The main function of steer-by-wire (SBW system are improving steering characteristics, security and stability of the vehicle. In this paper, the variable steering ratio of SBW system is analyzed, and the method of steering ratio based on fuzzy control and neural network are researched. In order to solve the actual working condition, the wheel angle may not reach the expected value, this paper establishes a twodegree-of-freedom (2-DOF vehicle model, and a Matlab/Simulink simulation model, in which a control strategy based on PID controller is put forward to control the front wheel steering angle. Simulation results show that proposed control strategy based on fuzzy neural network can effectively reduce lateral deviation and improve the handling stability and comfortability of the vehicle.

Molecular dynamics simulation of ribosome jam

KAUST Repository

Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

2011-01-01

We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

DEFF Research Database (Denmark)

Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

2010-01-01

We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...

Dynamics of molecular superrotors in an external magnetic field

International Nuclear Information System (INIS)

Korobenko, Aleksey; Milner, Valery

2015-01-01

We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation. (paper)

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

Science.gov (United States)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Kinetics from Replica Exchange Molecular Dynamics Simulations.

Science.gov (United States)

Stelzl, Lukas S; Hummer, Gerhard

2017-08-08

Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

DEFF Research Database (Denmark)

Papaleo, Elena

2015-01-01

that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

AceCloud: Molecular Dynamics Simulations in the Cloud.

Science.gov (United States)

Harvey, M J; De Fabritiis, G

2015-05-26

We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

46 CFR 182.620 - Auxiliary means of steering.

Science.gov (United States)

2010-10-01

... TONS) MACHINERY INSTALLATION Steering Systems § 182.620 Auxiliary means of steering. (a) Except as... personnel hazards during normal or heavy weather operation. (b) A suitable hand tiller may be acceptable as...

Observation of quantum-memory-assisted entropic uncertainty relation under open systems, and its steering

Science.gov (United States)

Chen, Peng-Fei; Sun, Wen-Yang; Ming, Fei; Huang, Ai-Jun; Wang, Dong; Ye, Liu

2018-01-01

Quantum objects are susceptible to noise from their surrounding environments, interaction with which inevitably gives rise to quantum decoherence or dissipation effects. In this work, we examine how different types of local noise under an open system affect entropic uncertainty relations for two incompatible measurements. Explicitly, we observe the dynamics of the entropic uncertainty in the presence of quantum memory under two canonical categories of noisy environments: unital (phase flip) and nonunital (amplitude damping). Our study shows that the measurement uncertainty exhibits a non-monotonic dynamical behavior—that is, the amount of the uncertainty will first inflate, and subsequently decrease, with the growth of decoherence strengths in the two channels. In contrast, the uncertainty decreases monotonically with the growth of the purity of the initial state shared in prior. In order to reduce the measurement uncertainty in noisy environments, we put forward a remarkably effective strategy to steer the magnitude of uncertainty by means of a local non-unitary operation (i.e. weak measurement) on the qubit of interest. It turns out that this non-unitary operation can greatly reduce the entropic uncertainty, upon tuning the operation strength. Our investigations might thereby offer an insight into the dynamics and steering of entropic uncertainty in open systems.

Molecular dynamics simulations of RNA motifs

Czech Academy of Sciences Publication Activity Database

Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

2002-01-01

Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

Monte Carlo-molecular dynamics simulations for two-dimensional magnets

International Nuclear Information System (INIS)

Kawabata, C.; takeuchi, M.; Bishop, A.R.

1985-01-01

A combined Monte Carlo-molecular dynamics simulation technique is used to study the dynamic structure factor on a square lattice for isotropic Heisenberg and planar classical ferromagnetic spin Hamiltonians

Molecular dynamics and Monte Carlo calculations in statistical mechanics

International Nuclear Information System (INIS)

Wood, W.W.; Erpenbeck, J.J.

1976-01-01

Monte Carlo and molecular dynamics calculations on statistical mechanical systems is reviewed giving some of the more significant recent developments. It is noted that the term molecular dynamics refers to the time-averaging technique for hard-core and square-well interactions and for continuous force-law interactions. Ergodic questions, methodology, quantum mechanical, Lorentz, and one-dimensional, hard-core, and square and triangular-well systems, short-range soft potentials, and other systems are included. 268 references

Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties

Czech Academy of Sciences Publication Activity Database

Fojtíková, J.; Kalvoda, L.; Sedlák, Petr

2015-01-01

Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf

Nanotribology investigations with classical molecular dynamics

NARCIS (Netherlands)

Solhjoo, Soheil

2017-01-01

This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

Retrospective Review of Pectoralis Major Ruptures in Rodeo Steer Wrestlers

Directory of Open Access Journals (Sweden)

Breda H. F. Lau

2013-01-01

Full Text Available Background. Pectoralis major tendon ruptures have been reported in the literature as occupational injuries, accidental injuries, and sporting activities. Few cases have been reported with respect to rodeo activities. Purpose. To describe a series of PM tendon ruptures in professional steer wrestlers. Study Design. Case series, level of evidence, 4. Methods. A retrospective analysis of PM ruptures in a steer wrestling cohort was performed. Injury data between 1992 and 2008 were reviewed using medical records from the University of Calgary Sport Medicine Center. Results. Nine cases of pectoralis major ruptures in professional steer wrestlers were identified. Injuries occurred during the throwing phase of the steer or while breaking a fall. All athletes reported unexpected or abnormal behavior of the steer that contributed to the mechanism of injury. Seven cases were surgically repaired, while two cases opted for nonsurgical intervention. Eight cases reported successful return to competition following the injury. Conclusion. Steer wrestlers represent a unique cohort of PM rupture case studies. Steer wrestling is a demanding sport that involves throwing maneuvers that may predispose the muscle to rupture. All cases demonstrated good functional outcomes regardless of surgical or non-surgical treatment.

Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu, H.G.; Muckerman, J.T.

2010-06-01

The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

Directory of Open Access Journals (Sweden)

Mingyuan Xu

2018-05-01

Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

Science.gov (United States)

Cawkwell, M J; Niklasson, Anders M N

2012-10-07

Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

Analyzing machupo virus-receptor binding by molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Austin G. Meyer

2014-02-01

Full Text Available In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein–protein interactions. However, many commonly used methods to predict these effects perform poorly in important test cases. In particular, the effects of multiple mutations, non alanine substitutions, and flexible loops are difficult to predict with available tools and protocols. We present here an existing method applied in a novel way to a new test case; we interrogate affinity differences resulting from mutations in a host–virus protein–protein interface. We use steered molecular dynamics (SMD to computationally pull the machupo virus (MACV spike glycoprotein (GP1 away from the human transferrin receptor (hTfR1. We then approximate affinity using the maximum applied force of separation and the area under the force-versus-distance curve. We find, even without the rigor and planning required for free energy calculations, that these quantities can provide novel biophysical insight into the GP1/hTfR1 interaction. First, with no prior knowledge of the system we can differentiate among wild type and mutant complexes. Moreover, we show that this simple SMD scheme correlates well with relative free energy differences computed via free energy perturbation. Second, although the static co-crystal structure shows two large hydrogen-bonding networks in the GP1/hTfR1 interface, our simulations indicate that one of them may not be important for tight binding. Third, one viral site known to be critical for infection may mark an important evolutionary suppressor site for infection-resistant hTfR1 mutants. Finally, our approach provides a framework to compare the effects of multiple mutations, individually and jointly, on protein–protein interactions.

Analyzing machupo virus-receptor binding by molecular dynamics simulations

Science.gov (United States)

Sawyer, Sara L.; Ellington, Andrew D.; Wilke, Claus O.

2014-01-01

In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein–protein interactions. However, many commonly used methods to predict these effects perform poorly in important test cases. In particular, the effects of multiple mutations, non alanine substitutions, and flexible loops are difficult to predict with available tools and protocols. We present here an existing method applied in a novel way to a new test case; we interrogate affinity differences resulting from mutations in a host–virus protein–protein interface. We use steered molecular dynamics (SMD) to computationally pull the machupo virus (MACV) spike glycoprotein (GP1) away from the human transferrin receptor (hTfR1). We then approximate affinity using the maximum applied force of separation and the area under the force-versus-distance curve. We find, even without the rigor and planning required for free energy calculations, that these quantities can provide novel biophysical insight into the GP1/hTfR1 interaction. First, with no prior knowledge of the system we can differentiate among wild type and mutant complexes. Moreover, we show that this simple SMD scheme correlates well with relative free energy differences computed via free energy perturbation. Second, although the static co-crystal structure shows two large hydrogen-bonding networks in the GP1/hTfR1 interface, our simulations indicate that one of them may not be important for tight binding. Third, one viral site known to be critical for infection may mark an important evolutionary suppressor site for infection-resistant hTfR1 mutants. Finally, our approach provides a framework to compare the effects of multiple mutations, individually and jointly, on protein–protein interactions. PMID:24624315

Modeling ramp compression experiments using large-scale molecular dynamics simulation.

Energy Technology Data Exchange (ETDEWEB)

Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

2011-10-01

Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

p53 DNA结合域与抗癌多肽的拉伸分子动力学研究%Steered Molecular Dynamics of an Anticancer Peptide Interacting With The p53 DNA-binding Domain

Institute of Scientific and Technical Information of China (English)

许先进; 苏计国; 陈慰祖; 王存新; CANNISTRARO Salvatore; BIZZARRI Anna-Rita

2014-01-01

The p28 peptide,derived from the blue copper protein azurin,is known to enhance the anticancer capabilities of the tumor suppressor p53 likely binding to its DNA-binding domain (DBD).The p28-p53 DBD complex has been investigated by steered molecular dynamics in order to characterize the unbinding process at atomic resolution.We found that the unbinding of the complex follows a candidate pathway with a well-defined detaching sequence between the partners.The analysis of the unbinding force and the calculation of the irreversible work done along several unbinding paths have allowed us to extract information on the energy landscape regulating the unbinding process.%研究发现,取自蓝铜蛋白azur的一段多肽p28能够进入癌细胞,结合到肿瘤抑制因子p53的DNA结合域上,进而增加p53的抗癌能力.本工作中,通过拉伸分子动力学方法,在原子尺度上研究了p28-p53 DBD复合物的解离过程.分析结果显示复合物的解离过程遵循着一定的分离顺序.对解离力的分析以及对沿着解离路径的不可逆做功的计算,使我们能够从复合物的能量地貌中提取有用的信息,而这些信息也决定了复合物的解离过程.

Electronic differential control of 2WD electric vehicle considering steering stability

Science.gov (United States)

Hua, Yiding; Jiang, Haobin; Geng, Guoqing

2017-03-01

Aiming at the steering wheel differential steering control technology of rear wheel independent driving electric wheel, considering the assisting effect of electronic differential control on vehicle steering, based on the high speed steering characteristic of electric wheel car, the electronic differential speed of auxiliary wheel steering is also studied. A yaw moment control strategy is applied to the vehicle at high speed. Based on the vehicle stability reference value, yaw rate is used to design the fuzzy controller to distribute the driving wheel torque. The simulation results show that the basic electronic differential speed function is realized based on the yaw moment control strategy, while the vehicle stability control is improved and the driving safety is enhanced. On the other hand, the torque control strategy can also assist steering of vehicle.

A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

KAUST Repository

Neumann, Philipp; Tchipev, Nikola

2012-01-01

We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm

Development of active rear steer actuator. Development of four wheel steer actuator for active safety; Active rear steer actuator no kaihatsu. Yobo anzen ni muketa 4WS actuator no kaihatsu

Energy Technology Data Exchange (ETDEWEB)

Yamanaka, T [Aisin Seiki Co. Ltd., Aichi (Japan)

1997-10-01

Recently, ecology, energy saving and safety have become important issues. And Active Safety is spotlighted in vehicle control area. Many researches and developments on four wheel steer system have been done to improve vehicle stability. We have developed the Active Rear Steer system with electromechanical Actuator, which is mass-productive, compact, and high response and durable. 10 figs., 5 tabs.

supplementation of energy and/or protein to steers grazing summer ...

African Journals Online (AJOL)

Some aspects of the effect of supplementary energy and/or protein, strategically ptovided to steers on summer veld, were investi gated. 40 Friesland steers in the age ... was posed whether the strategic provision of energy and or protein to steers grazing .... Definitions and abbreviotions was determined after cooling for 24 h ...

46 CFR 78.47-55 - Instructions for changing steering gear.

Science.gov (United States)

2010-10-01

... 46 Shipping 3 2010-10-01 2010-10-01 false Instructions for changing steering gear. 78.47-55... OPERATIONS Markings for Fire and Emergency Equipment, Etc. § 78.47-55 Instructions for changing steering gear..., relating in order, the different steps to be taken in changing to the emergency steering gear. Each clutch...

Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

KAUST Repository

Yoon, Seyoon; Monteiro, Paulo J.M.

2013-01-01

The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current

Genuine Multipartite Einstein-Podolsky-Rosen Steering

Science.gov (United States)

He, Q. Y.; Reid, M. D.

2013-12-01

We develop the concept of genuine N-partite Einstein-Podolsky-Rosen (EPR) steering. This nonlocality is the natural multipartite extension of the original EPR paradox. Useful properties emerge that are not guaranteed for genuine multipartite entangled states. In particular, there is a close link with the task of one-sided, device-independent quantum secret sharing. We derive inequalities to demonstrate multipartite EPR steering for Greenberger-Horne-Zeilinger and Gaussian continuous variable states in loophole-free scenarios.

Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

DEFF Research Database (Denmark)

Toxvaerd, Søren

2001-01-01

Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

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.

Invariant molecular-dynamics approach to structural phase transitions

International Nuclear Information System (INIS)

Wentzcovitch, R.M.

1991-01-01

Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

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

International Nuclear Information System (INIS)

Aradi, Balint; Frauenheim, Thomas

2015-01-01

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

Easy GROMACS: A Graphical User Interface for GROMACS Molecular Dynamics Simulation Package

Science.gov (United States)

Dizkirici, Ayten; Tekpinar, Mustafa

2015-03-01

GROMACS is a widely used molecular dynamics simulation package. Since it is a command driven program, it is difficult to use this program for molecular biologists, biochemists, new graduate students and undergraduate researchers who are interested in molecular dynamics simulations. To alleviate the problem for those researchers, we wrote a graphical user interface that simplifies protein preparation for a classical molecular dynamics simulation. Our program can work with various GROMACS versions and it can perform essential analyses of GROMACS trajectories as well as protein preparation. We named our open source program `Easy GROMACS'. Easy GROMACS can give researchers more time for scientific research instead of dealing with technical intricacies.

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

Science.gov (United States)

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

2015-07-14

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

NMR investigations of molecular dynamics

Science.gov (United States)

Palmer, Arthur

2011-03-01

NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

46 CFR 97.37-33 - Instructions for changing steering gear.

Science.gov (United States)

2010-10-01

... 46 Shipping 4 2010-10-01 2010-10-01 false Instructions for changing steering gear. 97.37-33... steering gear. (a) Instructions in at least 1/2 inch letters and figures shall be posted in the steering... gear. Each clutch, gear, wheel, lever, valve, or switch which is used during the changeover shall be...

Applications of EPR steering in quantum teleportation and NOON states

Science.gov (United States)

Zárate, Laura Rosales

2018-04-01

Einstein-Podolsky-Rosen (EPR) steering refers to the type of correlations described in the EPR paradox, where one observer seems to affect ("steer") the state of other observer by using local measurements. There have been several works regarding characterization and quantification of EPR steering. One characteristic of this non-local correlation is that it can be asymmetric, while entanglement is symmetric. This asymmetric property is relevant for potential applications of EPR steering to quantum information, in particular to quantum cryptography and quantum teleportation. This latter refers to the process where one observer sends an unknown quantum state to Bob, who is in a different location. They communicate by classical means. Here we will show that EPR steering is a necessary resource to obtain secure continuous variable teleportation. We will also consider NOON states, which is an example of an entangled state. For this state, we will present a steering signature. This contribution reviews the work derived in Refs. [1] and [2], which was presented as an invited talk in ELAF 2017.

Excitation dynamics and relaxation in a molecular heterodimer

International Nuclear Information System (INIS)

Balevičius, V.; Gelzinis, A.; Abramavicius, D.; Mančal, T.; Valkunas, L.

2012-01-01

Highlights: ► Dynamics of excitation within a heterogenous molecular dimer. ► Excited states can be swapped due to different reorganization energies of monomers. ► Conventional excitonic basis becomes renormalized due to interaction with the bath. ► Relaxation is independent of mutual positioning of monomeric excited states. -- Abstract: The exciton dynamics in a molecular heterodimer is studied as a function of differences in excitation and reorganization energies, asymmetry in transition dipole moments and excited state lifetimes. The heterodimer is composed of two molecules modeled as two-level systems coupled by the resonance interaction. The system-bath coupling is taken into account as a modulating factor of the molecular excitation energy gap, while the relaxation to the ground state is treated phenomenologically. Comparison of the description of the excitation dynamics modeled using either the Redfield equations (secular and full forms) or the Hierarchical quantum master equation (HQME) is demonstrated and discussed. Possible role of the dimer as an excitation quenching center in photosynthesis self-regulation is discussed. It is concluded that the system-bath interaction rather than the excitonic effect determines the excitation quenching ability of such a dimer.

The nonequilibrium molecular dynamics

International Nuclear Information System (INIS)

Hoover, W.G.

1992-03-01

MOLECULAR DYNAMICS has been generalized in order to simulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation, intense heat conduction, strong shockwaves simulation, and far-from-equilibrium phase transformations. Continuing advances in technique and in the modeling of interatomic forces, coupled with qualitative improvements in computer hardware, are enabling such simulations to approximate real-world microscale and nanoscale experiments

Reaction dynamics of molecular hydrogen on silicon surfaces

DEFF Research Database (Denmark)

Bratu, P.; Brenig, W.; Gross, A.

1996-01-01

of the preexponential factor by about one order of magnitude per lateral degree of freedom. Molecular vibrations have practically no effect on the adsorption/desorption dynamics itself, but lead to vibrational heating in desorption with a strong isotope effect. Ab initio calculations for the H-2 interaction...... between the two surfaces. These results indicate that tunneling, molecular vibrations, and the structural details of the surface play only a minor role for the adsorption dynamics. Instead, they appear to be governed by the localized H-Si bonding and Si-Si lattice vibrations. Theoretically, an effective......Experimental and theoretical results on the dynamics of dissociative adsorption and recombinative desorption of hydrogen on silicon are presented. Using optical second-harmonic generation, extremely small sticking probabilities in the range 10(-9)-10(-5) could be measured for H-2 and D-2 on Si(111...

Monogamy inequalities for the Einstein-Podolsky-Rosen paradox and quantum steering

Science.gov (United States)

Reid, M. D.

2013-12-01

Monogamy inequalities for the way bipartite Einstein-Podolsky-Rosen (EPR) steering can be distributed among N systems are derived. One set of inequalities is based on witnesses with two measurement settings, and may be used to demonstrate correlation of outcomes between two parties, that cannot be shared with more parties. It is shown that the monogamy for steering is directional. Two parties cannot independently demonstrate steering of a third system, using the same two-setting steering witness, but it is possible for one party to steer two independent systems. This result explains the monogamy of two-setting Bell inequality violations and the sensitivity of the continuous variable (CV) EPR criterion to losses on the steering party. We generalize to m settings. A second type of monogamy relation gives the quantitative amount of sharing possible, when the number of parties is less than or equal to m, and takes a form similar to the Coffman-Kundu-Wootters relation for entanglement. The results enable characterization of the tripartite steering for CV Gaussian systems and qubit Greenberger-Horne-Zeilinger and W states.

Evaluation of flexible endoscope steering using haptic guidance

NARCIS (Netherlands)

Reilink, Rob; Stramigioli, Stefano; Kappers, Astrid M L; Misra, Sarthak

Background: Steering the tip of a flexible endoscope relies on the physician's dexterity and experience. For complex flexible endoscopes, conventional controls may be inadequate. Methods: A steering method based on a multi-degree-of-freedom haptic device is presented. Haptic cues are generated based

Evaluation of flexible endoscope steering using haptic guidance

NARCIS (Netherlands)

Reilink, Rob; Stramigioli, Stefano; Kappers, Astrid M.L.; Misra, Sarthak

2011-01-01

Background - Steering the tip of a flexible endoscope relies on the physician’s dexterity and experience. For complex flexible endoscopes, conventional controls may be inadequate. Methods - A steering method based on a multi-degree-of-freedom haptic device is presented. Haptic cues are generated

State-to-state dynamics of molecular energy transfer

Energy Technology Data Exchange (ETDEWEB)

Gentry, W.R.; Giese, C.F. [Univ. of Minnesota, Minneapolis (United States)

1993-12-01

The goal of this research program is to elucidate the elementary dynamical mechanisms of vibrational and rotational energy transfer between molecules, at a quantum-state resolved level of detail. Molecular beam techniques are used to isolate individual molecular collisions, and to control the kinetic energy of collision. Lasers are used both to prepare specific quantum states prior to collision by stimulated-emission pumping (SEP), and to measure the distribution of quantum states in the collision products by laser-induced fluorescence (LIF). The results are interpreted in terms of dynamical models, which may be cast in a classical, semiclassical or quantum mechanical framework, as appropriate.

Line-shape theory and molecular dynamics in collision-induced light scattering

International Nuclear Information System (INIS)

Balucani, U.; Tognetti, V.; Vallauri, R.

1979-01-01

Molecular-dynamics studies in argon at 148 amagats are presented for gaining information on the dynamical properties responsible for the depolarized light scattering from simple fluids. The total and pair-correlation functions are computed within the simple dipole--induced-dipole model of polarizability anisotropy. The pair spectral shape is derived. These results are compared with a theoretical analysis based on a continued-fraction approach. The necessary frequency moments are calculated both in the low-density limit and taking into account first-order density corrections, and compared with the molecular-dynamics data. The agreement between the theoretical spectra and molecular-dynamics data shows the validity of the memory-function approach. The comparison with the real experimental results allows one to test the relevant physical contributions to the polarizability anisotropy

Coulomb interactions via local dynamics: a molecular-dynamics algorithm

International Nuclear Information System (INIS)

Pasichnyk, Igor; Duenweg, Burkhard

2004-01-01

We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

Altered steering strategies for goal-directed locomotion in stroke

Science.gov (United States)

2013-01-01

Background Individuals who have sustained a stroke can manifest altered locomotor steering behaviors when exposed to optic flows expanding from different locations. Whether these alterations persist in the presence of a visible goal and whether they can be explained by the presence of a perceptuo-motor disorder remain unknown. The purpose of this study was to compare stroke participants and healthy participants on their ability to control heading while exposed to changing optic flows and target locations. Methods Ten participants with stroke (55.6 ± 9.3 yrs) and ten healthy controls (57.0 ± 11.5 yrs) participated in a mouse-driven steering task (perceptuo-motor task) while seated and in a walking steering task. In the seated steering task, participants were instructed to head or ‘walk’ toward a target in the virtual environment by using a mouse while wearing a helmet-mounted display (HMD). In the walking task, participants performed a similar steering task in the same virtual environment while walking overground at their comfortable speed. For both experiments, the target and/or the focus of expansion (FOE) of the optic flow shifted to the side (±20°) or remained centered. The main outcome measure was net heading errors (NHE). Secondary outcomes included mediolateral displacement, horizontal head orientation, and onsets of heading and head reorientation. Results In the walking steering task, the presence of FOE shifts modulated the extent and timing of mediolateral displacement and head rotation changes, as well as NHE magnitudes. Participants overshot and undershot their net heading, respectively, in response to ipsilateral and contralateral FOE and target shifts. Stroke participants made larger NHEs, especially when the FOE was shifted towards the non-paretic side. In the seated steering task, similar NHEs were observed between stroke and healthy participants. Conclusions The findings highlight the fine coordination between rotational and

Demonstration of Multisetting One-Way Einstein-Podolsky-Rosen Steering in Two-Qubit Systems

Science.gov (United States)

Xiao, Ya; Ye, Xiang-Jun; Sun, Kai; Xu, Jin-Shi; Li, Chuan-Feng; Guo, Guang-Can

2017-04-01

Einstein-Podolsky-Rosen (EPR) steering describes the ability of one party to remotely affect another's state through local measurements. One of the most distinguishable properties of EPR steering is its asymmetric aspect. Steering can work in one direction but fail in the opposite direction. This type of one-way steering, which is different from the symmetry concepts of entanglement and Bell nonlocality, has garnered much interest. However, an experimental demonstration of genuine one-way EPR steering in the simplest scenario, i.e., one that employs two-qubit systems, is still lacking. In this Letter, we experimentally demonstrate one-way EPR steering with multimeasurement settings for a class of two-qubit states, which are still one-way steerable even with infinite settings. The steerability is quantified by the steering radius, which represents a necessary and sufficient steering criterion. The demonstrated one-way steering in the simplest bipartite quantum system is of fundamental interest and may provide potential applications in one-way quantum information tasks.

Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

DEFF Research Database (Denmark)

Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

2012-01-01

In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

Consideration on the dynamics of course-driver-vehicle system of four-wheel steering vehicles. annex. Static directional stability and approximation of general motion by chain of steady-state circular turns; 4WS sha no shinro-driver-jidoshakei no undo rikigaku ni kansuru ichikosatsu. Seiteki hoko anteisei oyobi teijoen senkai de tsunagu kinjisei no kento

Energy Technology Data Exchange (ETDEWEB)

Togo, K [Yomiuri Koto Institute of Science and Engineering, Tokyo (Japan); Kondo, M [Tokyo Institute of Technology, Tokyo (Japan)

1997-10-01

One of the authors intended before to understand the fundamentals of automobile steering emphasizing the importance of the driver`s forward view point. This idea was called Kondo`s hypothesis by several Professors and has been used and developed by many researchers in Japan. Using this thought, dynamical properties and steering of four-wheel steering vehicles, of which two points of the vehicle`s body can trace the designated course, are studied in this paper. Some numerical calculations have shown the tendency similar to the actual steering now used by a Japanese manufacturer. This idea would be useful in the automatic driving systems such as ITS. 4 refs., 3 tabs., 1 tab.

Study on a New Steering Mechanism for Point-the-Bit Rotary Steerable System

Directory of Open Access Journals (Sweden)

Yuanzhi Li

2014-02-01

Full Text Available This paper presents a novel steering mechanism embedded in a point-the-bit rotary steerable system (RSS for oilfield exploitation. The new steering mechanism adopts a set of universal joints to alleviate the high alternative strain on drilling mandrel and employs a specially designed planetary gear small tooth number difference (PGSTD to achieve directional steering. Its principle and characteristics are explained and examined through a series of analyses. First, the eccentric displacement vector of the offset point on the drilling mandrel is formulated and kinematic solutions are established. Next, structural design for the new steering mechanism is addressed. Then, procedures and program architectures for simulating offset state of the drilling mandrel and motion trajectory of the whole steering mechanism are presented. After that, steering motion simulations of the new steering mechanism for both 2D and 3D well trajectories are then performed by combining LabVIEW and SolidWorks. Finally, experiments on the steering motion control of the new steering mechanism prototype are carried out. The simulations and experiments reveal that the steering performance of the new steering mechanism is satisfied. The research can provide good guidance for further research and engineering application of the point-the-bit RSS.

Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

Science.gov (United States)

Hu, Hao; Liu, Haiyan

2013-05-30

Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.

Collision-model approach to steering of an open driven qubit

Science.gov (United States)

Beyer, Konstantin; Luoma, Kimmo; Strunz, Walter T.

2018-03-01

We investigate quantum steering of an open quantum system by measurements on its environment in the framework of collision models. As an example we consider a coherently driven qubit dissipatively coupled to a bath. We construct local nonadaptive and adaptive as well as nonlocal measurement scenarios specifying explicitly the measured observable on the environment. Our approach shows transparently how the conditional evolution of the open system depends on the type of the measurement scenario and the measured observables. These can then be optimized for steering. The nonlocal measurement scenario leads to maximal violation of the used steering inequality at zero temperature. Further, we investigate the robustness of the constructed scenarios against thermal noise. We find generally that steering becomes harder at higher temperatures. Surprisingly, the system can be steered even when bipartite entanglement between the system and individual subenvironments vanishes.

Revisiting path steering for 3D manipulation tasks

NARCIS (Netherlands)

L. Liu (Lei); J.-B. Martens; R. van Liere (Robert)

2011-01-01

htmlabstractThe law of path steering, as proposed by Accot and Zhai, describes a quantitative relationship between human temporal performance and the path spatial characteristics. The steering law is formulated as a continuous goal crossing task, in which a large number of goals are crossed along

Revisiting path steering for 3D manipulation tasks

NARCIS (Netherlands)

L. Liu (Lei); J.-B. Martens; R. van Liere (Robert)

2010-01-01

htmlabstractThe law of path steering, as proposed by Accot and Zhai, describes a quantitative relationship between human temporal performance and the path spatial characteristics. The steering law is formulated as a continuous goal crossing task, in which a large number of goals are crossed along

Growth, carcass characteristics, and profitability of organic versus conventional dairy beef steers.

Science.gov (United States)

Bjorklund, E A; Heins, B J; Dicostanzo, A; Chester-Jones, H

2014-03-01

Bull calves (n=49), born at the University of Minnesota West Central Research and Outreach Center (Morris) between March and May 2011, were used to compare growth measurements and profitability of conventional and organic dairy steers. Calves were assigned to 1 of 3 replicated groups at birth: conventional (CONV; n=16), organic (pasture and concentrate; ORG; n=16), or organic grass only (GRS; n=17), and analysis of variables was on a pen basis. Breed groups of calves were Holstein (HO; n=9); Holsteins (n=11) maintained at 1964 breed average level; crossbreds (n=19) including combinations of HO, Montbéliarde, and Swedish Red; and crossbreds (n=10) including combinations of HO, Jersey, Swedish Red, and Normande. The CONV steers were fed a diet of 80% concentrate and 20% forage. The ORG steers were fed a diet of organic corn, organic corn silage, and at least 30% of their diet consisted of organic pasture during the grazing season. The GRS steers grazed pasture during the grazing season and were fed high-quality hay or hay silage during the nongrazing season. Intakes of a total mixed ration were recorded daily with herd management software. A profit function was defined to include revenues and expenses for beef value, feed intake, pasture intake, health cost, and yardage. The GRS (358.6 kg) steers had lesser total gains from birth to slaughter than ORG (429.6 kg) and CONV (534.5 kg) steers. Furthermore, the GRS (0.61 kg/d) steers had lesser average daily gain from birth compared with ORG (0.81 kg/d) and CONV (1.1 kg/d) steers. The GRS and ORG steers had smaller rib eye area (49.5 and 65.8 cm(2), respectively) compared with CONV (75.4 cm(2)) steers. For profitability, GRS steers had 43% greater profit than CONV steers due to organic beef price premiums and lower feed costs. On the other hand, ORG steers had substantially less profit than CONV steers. The higher cost of production for the ORG steers is due to the extreme high value of organic corn. The results of the

Probing the conformational energetics of alkyl thiols on gold surfaces by means of a morphing/steering non-equilibrium tool.

Science.gov (United States)

Piserchia, Andrea; Zerbetto, Mirco; Frezzato, Diego

2015-03-28

In this work we show that a non-equilibrium statistical tool based on Jarzynski's equality (JE) can be applied to achieve a sufficiently accurate mapping of the torsion free energy, bond-by-bond, for an alkyl thiol ligand tethered to a gold surface and sensing the presence of the surrounding cluster of similar chains. The strength of our approach is the employment of a strategy to let grow the internal energetics of the whole system (namely, the "energy morphing" stage recently presented by us in J. Comput. Chem., 2014, 35, 1865-1881) before initiating the rotational steering, which yields accurate results in terms of statistical uncertainties and bias on the free energy profiles. The work is mainly methodological and illustrates the feasibility of this kind of inspection on nanoscale molecular clusters with conformational flexibility. The outcomes for the archetype of self-assembled-monolayers considered here, a regular pattern of 10-carbon alkyl thiols on an ideal gold surface, give information on the conformational mobility of the ligands. Notably, such information is unlikely to be obtained by means of standard equilibrium techniques or by conventional molecular dynamics simulations.

Ab initio molecular dynamics in a finite homogeneous electric field.

Science.gov (United States)

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

Autonomous Shepherding Behaviors of Multiple Target Steering Robots.

Science.gov (United States)

Lee, Wonki; Kim, DaeEun

2017-11-25

This paper presents a distributed coordination methodology for multi-robot systems, based on nearest-neighbor interactions. Among many interesting tasks that may be performed using swarm robots, we propose a biologically-inspired control law for a shepherding task, whereby a group of external agents drives another group of agents to a desired location. First, we generated sheep-like robots that act like a flock. We assume that each agent is capable of measuring the relative location and velocity to each of its neighbors within a limited sensing area. Then, we designed a control strategy for shepherd-like robots that have information regarding where to go and a steering ability to control the flock, according to the robots' position relative to the flock. We define several independent behavior rules; each agent calculates to what extent it will move by summarizing each rule. The flocking sheep agents detect the steering agents and try to avoid them; this tendency leads to movement of the flock. Each steering agent only needs to focus on guiding the nearest flocking agent to the desired location. Without centralized coordination, multiple steering agents produce an arc formation to control the flock effectively. In addition, we propose a new rule for collecting behavior, whereby a scattered flock or multiple flocks are consolidated. From simulation results with multiple robots, we show that each robot performs actions for the shepherding behavior, and only a few steering agents are needed to control the whole flock. The results are displayed in maps that trace the paths of the flock and steering robots. Performance is evaluated via time cost and path accuracy to demonstrate the effectiveness of this approach.

Autonomous Shepherding Behaviors of Multiple Target Steering Robots

Directory of Open Access Journals (Sweden)

Wonki Lee

2017-11-01

Full Text Available This paper presents a distributed coordination methodology for multi-robot systems, based on nearest-neighbor interactions. Among many interesting tasks that may be performed using swarm robots, we propose a biologically-inspired control law for a shepherding task, whereby a group of external agents drives another group of agents to a desired location. First, we generated sheep-like robots that act like a flock. We assume that each agent is capable of measuring the relative location and velocity to each of its neighbors within a limited sensing area. Then, we designed a control strategy for shepherd-like robots that have information regarding where to go and a steering ability to control the flock, according to the robots’ position relative to the flock. We define several independent behavior rules; each agent calculates to what extent it will move by summarizing each rule. The flocking sheep agents detect the steering agents and try to avoid them; this tendency leads to movement of the flock. Each steering agent only needs to focus on guiding the nearest flocking agent to the desired location. Without centralized coordination, multiple steering agents produce an arc formation to control the flock effectively. In addition, we propose a new rule for collecting behavior, whereby a scattered flock or multiple flocks are consolidated. From simulation results with multiple robots, we show that each robot performs actions for the shepherding behavior, and only a few steering agents are needed to control the whole flock. The results are displayed in maps that trace the paths of the flock and steering robots. Performance is evaluated via time cost and path accuracy to demonstrate the effectiveness of this approach.

Drowsy Driver Detection via Steering Wheel

Directory of Open Access Journals (Sweden)

Herlina ABDUL RAHIM

2010-09-01

Full Text Available The main purpose of this project is to produce a safety system especially for fatigue car driver so as to prevent from accidents. The statistic on road fatality shows that human error constitute of 64.84 % road accidents fatality and 17.4 % due to technical factors. These systems encompassed the approach of hand pressure applied on the steering wheel. The steering will be installed with pressure sensors. At the same time these sensors can be used to measure gripping force while driving.

Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Bresme, F.; Armstrong, J.

2014-01-01

We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation

Experimental EPR-steering using Bell-local states

Science.gov (United States)

Saunders, D. J.; Jones, S. J.; Wiseman, H. M.; Pryde, G. J.

2010-11-01

The concept of `steering' was introduced in 1935 by Schrödinger as a generalization of the EPR (Einstein-Podolsky-Rosen) paradox. It has recently been formalized as a quantum-information task with arbitrary bipartite states and measurements, for which the existence of entanglement is necessary but not sufficient. Previous experiments in this area have been restricted to an approach that followed the original EPR argument in considering only two different measurement settings per side. Here we demonstrate experimentally that EPR-steering occurs for mixed entangled states that are Bell local (that is, that cannot possibly demonstrate Bell non-locality). Unlike the case of Bell inequalities, increasing the number of measurement settings beyond two-we use up to six-significantly increases the robustness of the EPR-steering phenomenon to noise.

Fermionic molecular dynamics for colliding and decaying nuclei

International Nuclear Information System (INIS)

Feldmeier, H.; Schnack, J.

1993-11-01

Fermionic Molecular Dynamics models a system of fermions by means of a trial many-body state composed of an antisymmetrized product of single-particle states which are localized gaussians in coordinate and momentum space. The parameters specifying them are the analogue to the variables in classical molecular dynamics. The time-dependent variational principle yields the equations of motion which are solved for collisions of 12 C+ 12 C and deexcitations of 12 C. The collisions show a great variety of phenomena including explosion, sequential fragmentation and multifragmentation. The deexcitation for nuclei with E * /A ∼ 5MeV is dominated by particle evaporation on time scales of the order of 10 -20 s or longer. (orig.)

Optical spectra and lattice dynamics of molecular crystals

CERN Document Server

Zhizhin, GN

1995-01-01

The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

Operational experience with model-based steering in the SLC linac

International Nuclear Information System (INIS)

Thompson, K.A.; Himel, T.; Moore, S.; Sanchez-Chopitea, L.; Shoaee, H.

1989-03-01

Operational experience with model-driven steering in the linac of the Stanford Linear Collider is discussed. Important issues include two-beam steering, sensitivity of algorithms to faulty components, sources of disagreement with the model, and the effects of the finite resolution of beam position monitors. Methods developed to make the steering algorithms more robust in the presence of such complications are also presented. 5 refs., 1 fig

Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids

International Nuclear Information System (INIS)

De Leeuw, S.W.; Brakkee, M.J.D.

1990-01-01

Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs

Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

Energy Technology Data Exchange (ETDEWEB)

Lambert, F

2007-08-15

The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

Science.gov (United States)

Cooke, Ben; Schmidler, Scott C

2008-10-28

We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.

Orthonormal Wavelet Bases for Quantum Molecular Dynamics

International Nuclear Information System (INIS)

Tymczak, C.; Wang, X.

1997-01-01

We report on the use of compactly supported, orthonormal wavelet bases for quantum molecular-dynamics (Car-Parrinello) algorithms. A wavelet selection scheme is developed and tested for prototypical problems, such as the three-dimensional harmonic oscillator, the hydrogen atom, and the local density approximation to atomic and molecular systems. Our method shows systematic convergence with increased grid size, along with improvement on compression rates, thereby yielding an optimal grid for self-consistent electronic structure calculations. copyright 1997 The American Physical Society

Non-Adiabatic Molecular Dynamics Methods for Materials Discovery

Energy Technology Data Exchange (ETDEWEB)

Furche, Filipp [Univ. of California, Irvine, CA (United States); Parker, Shane M. [Univ. of California, Irvine, CA (United States); Muuronen, Mikko J. [Univ. of California, Irvine, CA (United States); Roy, Saswata [Univ. of California, Irvine, CA (United States)

2017-04-04

The flow of radiative energy in light-driven materials such as photosensitizer dyes or photocatalysts is governed by non-adiabatic transitions between electronic states and cannot be described within the Born-Oppenheimer approximation commonly used in electronic structure theory. The non-adiabatic molecular dynamics (NAMD) methods based on Tully surface hopping and time-dependent density functional theory developed in this project have greatly extended the range of molecular materials that can be tackled by NAMD simulations. New algorithms to compute molecular excited state and response properties efficiently were developed. Fundamental limitations of common non-linear response methods were discovered and characterized. Methods for accurate computations of vibronic spectra of materials such as black absorbers were developed and applied. It was shown that open-shell TDDFT methods capture bond breaking in NAMD simulations, a longstanding challenge for single-reference molecular dynamics simulations. The methods developed in this project were applied to study the photodissociation of acetaldehyde and revealed that non-adiabatic effects are experimentally observable in fragment kinetic energy distributions. Finally, the project enabled the first detailed NAMD simulations of photocatalytic water oxidation by titania nanoclusters, uncovering the mechanism of this fundamentally important reaction for fuel generation and storage.

Self-testing through EPR-steering

International Nuclear Information System (INIS)

Šupić, Ivan; Hoban, Matty J

2016-01-01

The verification of quantum devices is an important aspect of quantum information, especially with the emergence of more advanced experimental implementations of quantum computation and secure communication. Within this, the theory of device-independent robust self-testing via Bell tests has reached a level of maturity now that many quantum states and measurements can be verified without direct access to the quantum systems: interaction with the devices is solely classical. However, the requirements for this robust level of verification are daunting and require high levels of experimental accuracy. In this paper we discuss the possibility of self-testing where we only have direct access to one part of the quantum device. This motivates the study of self-testing via EPR-steering, an intermediate form of entanglement verification between full state tomography and Bell tests. Quantum non-locality implies EPR-steering so results in the former can apply in the latter, but we ask what advantages may be gleaned from the latter over the former given that one can do partial state tomography? We show that in the case of self-testing a maximally entangled two-qubit state, or ebit, EPR-steering allows for simpler analysis and better error tolerance than in the case of full device-independence. On the other hand, this improvement is only a constant improvement and (up to constants) is the best one can hope for. Finally, we indicate that the main advantage in self-testing based on EPR-steering could be in the case of self-testing multi-partite quantum states and measurements. For example, it may be easier to establish a tensor product structure for a particular party’s Hilbert space even if we do not have access to their part of the global quantum system. (paper)

Dynamic combinatorial libraries based on hydrogen-bonde molecular boxes

NARCIS (Netherlands)

Kerckhoffs, J.M.C.A.; Mateos timoneda, Miguel; Reinhoudt, David; Crego Calama, Mercedes

2007-01-01

This article describes two different types of dynamic combinatorial libraries of host and guest molecules. The first part of this article describes the encapsulation of alizarin trimer 2 a3 by dynamic mixtures of up to twenty different self-assembled molecular receptors together with the

Molecular dynamics for reactions of heterogeneous catalysis

NARCIS (Netherlands)

Jansen, A.P.J.; Brongersma, H.H.; Santen, van R.A.

1991-01-01

An overview is given of Molecular Dynamics, and numerical integration techniques, system initialization, boundary conditions, force representation, statistics, system size, and simulations duration are discussed. Examples from surface science are used to illustrate the pros and cons of the method.

Strong Einstein-Podolsky-Rosen steering with unconditional entangled states

Science.gov (United States)

Steinlechner, Sebastian; Bauchrowitz, Jöran; Eberle, Tobias; Schnabel, Roman

2013-02-01

In 1935 Schrödinger introduced the terms entanglement and steering in the context of the famous gedanken experiment discussed by Einstein, Podolsky, and Rosen (EPR). Here, we report on a sixfold increase of the observed EPR-steering effect with regard to previous experiments, as quantified by the Reid criterion. We achieved an unprecedented low conditional variance product of about 0.04<1, where 1 is the upper bound below which steering is demonstrated. The steering effect was observed on an unconditional two-mode-squeezed entangled state that contained a total vacuum state contribution of less than 8%, including detection imperfections. Together with the achieved high interference contrast between the entangled state and a bright coherent laser field, our state is compatible with efficient applications in high-power laser interferometers and fiber-based networks for entanglement distribution.

Molecular dynamics simulations on PGLa using NMR orientational constraints

Energy Technology Data Exchange (ETDEWEB)

Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

2015-11-15

NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

Molecular dynamics simulations

International Nuclear Information System (INIS)

Alder, B.J.

1985-07-01

The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs

A new algorithm for extended nonequilibrium molecular dynamics simulations of mixed flow

NARCIS (Netherlands)

Hunt, T.A.; Hunt, Thomas A.; Bernardi, Stefano; Todd, B.D.

2010-01-01

In this work, we develop a new algorithm for nonequilibrium molecular dynamics of fluids under planar mixed flow, a linear combination of planar elongational flow and planar Couette flow. To date, the only way of simulating mixed flow using nonequilibrium molecular dynamics techniques was to impose

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

NARCIS (Netherlands)

van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J

2012-01-01

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations

NARCIS (Netherlands)

van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.

2012-01-01

Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

Reaction dynamics in polyatomic molecular systems

Energy Technology Data Exchange (ETDEWEB)

Miller, W.H. [Lawrence Berkeley Laboratory, CA (United States)

1993-12-01

The goal of this program is the development of theoretical methods and models for describing the dynamics of chemical reactions, with specific interest for application to polyatomic molecular systems of special interest and relevance. There is interest in developing the most rigorous possible theoretical approaches and also in more approximate treatments that are more readily applicable to complex systems.

Energy conservation in molecular dynamics simulations of classical systems

DEFF Research Database (Denmark)

Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

2012-01-01

Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

Implementation of surface hopping molecular dynamics using semiempirical methods

International Nuclear Information System (INIS)

Fabiano, E.; Keal, T.W.; Thiel, W.

2008-01-01

A molecular dynamics driver and surface hopping algorithm for nonadiabatic dynamics has been implemented in a development version of the MNDO semiempirical electronic structure package. The required energies, gradients and nonadiabatic couplings are efficiently evaluated on the fly using semiempirical configuration interaction methods. The choice of algorithms for the time evolution of the nuclear motion and quantum amplitudes is discussed, and different schemes for the computation of nonadiabatic couplings are analysed. The importance of molecular orbital tracking and electronic state following is underlined in the context of configuration interaction calculations. The method is applied to three case studies (ethylene, methaniminium ion, and methanimine) using the orthogonalization corrected OM2 Hamiltonian. In all three cases decay times and dynamics paths similar to high-level ab initio results are obtained

Ab Initio molecular dynamics with excited electrons

NARCIS (Netherlands)

Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

1994-01-01

A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

Molecular dynamics coupled with a virtual system for effective conformational sampling.

Science.gov (United States)

Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

2018-07-15

An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

DEFF Research Database (Denmark)

Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

2007-01-01

The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...

Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

Science.gov (United States)

Shekhar, Adarsh

Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in

Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu H. G.; Muckerman, J.T.

2012-05-29

The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

The impact of force feedback level on steering performance

NARCIS (Netherlands)

Anand, S.; Terken, J.; Hogema, J.H.

2013-01-01

Steer-by-wire systems provide designers the ability to customize and personalize force feedback on the steering wheel, based on individual preferences. Earlier studies using subjective responses have shown that there are individual differences in preferences for force feedback. It has also been

Vehicle systems: coupled and interactive dynamics analysis

Science.gov (United States)

Vantsevich, Vladimir V.

2014-11-01

This article formulates a new direction in vehicle dynamics, described as coupled and interactive vehicle system dynamics. Formalised procedures and analysis of case studies are presented. An analytical consideration, which explains the physics of coupled system dynamics and its consequences for dynamics of a vehicle, is given for several sets of systems including: (i) driveline and suspension of a 6×6 truck, (ii) a brake mechanism and a limited slip differential of a drive axle and (iii) a 4×4 vehicle steering system and driveline system. The article introduces a formal procedure to turn coupled system dynamics into interactive dynamics of systems. A new research direction in interactive dynamics of an active steering and a hybrid-electric power transmitting unit is presented and analysed to control power distribution between the drive axles of a 4×4 vehicle. A control strategy integrates energy efficiency and lateral dynamics by decoupling dynamics of the two systems thus forming their interactive dynamics.

Molecular dynamics simulation of self-diffusion coefficients for liquid metals

International Nuclear Information System (INIS)

Ju Yuan-Yuan; Zhang Qing-Ming; Gong Zi-Zheng; Ji Guang-Fu

2013-01-01

The temperature-dependent coefficients of self-diffusion for liquid metals are simulated by molecular dynamics methods based on the embedded-atom-method (EAM) potential function. The simulated results show that a good inverse linear relation exists between the natural logarithm of self-diffusion coefficients and temperature, though the results in the literature vary somewhat, due to the employment of different potential functions. The estimated activation energy of liquid metals obtained by fitting the Arrhenius formula is close to the experimental data. The temperature-dependent shear-viscosities obtained from the Stokes—Einstein relation in conjunction with the results of molecular dynamics simulation are generally consistent with other values in the literature. (atomic and molecular physics)

Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Federica Chiappori

Full Text Available Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD modulate substrate recognition at the Substrate Binding Domain (SBD. Herein, a comparative analysis of an allosteric (Hsp70-DnaK and a non-allosteric structural homolog (Hsp110-Sse1 of the Hsp70 family is carried out through molecular dynamics simulations, starting from different conformations and ligand-states. Analysis of ligand-dependent modulation of internal fluctuations and local deformation patterns highlights the structural and dynamical changes occurring at residue level upon ATP-ADP exchange, which are connected to the conformational transition between closed and open structures. By identifying the dynamically responsive protein regions and specific cross-domain hydrogen-bonding patterns that differentiate Hsp70 from Hsp110 as a function of the nucleotide, we propose a molecular mechanism for the allosteric signal propagation of the ATP-encoded conformational signal.

Catalysis and communication in dynamic molecular networks

NARCIS (Netherlands)

Fanlo Virgos, Hugo

2015-01-01

The interactions of a Dynamic Combinatorial Library (DCL) of molecules with specific targets leads to composition changes of the library which can reveal potential guests and / or catalysts. In this thesis some chemical systems have been proposed to achieve a certain level of molecular complexity

Molecular dynamics study of atomic displacements in disordered solid alloys

Science.gov (United States)

Puzyrev, Yevgeniy S.

The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

EVALUATION OF A CONCEPTUAL VEHICLE STEERING SYSTEM FOR INDEPENDENT WHEEL CONTROL

Directory of Open Access Journals (Sweden)

Ryszard BUCHALIK

2017-03-01

Full Text Available This paper presents a brief description of an unconventional steering system involving electronic stability control and its influence on vehicle motion. The proposed configuration enables individual changes in steering angle for each single wheel, in contrast to the mechanical linkage solution. An analysis of vehicle behaviour during emergency braking on a heterogeneous surface is conducted, especially with regard to the undesirable rotation of the vehicle body. The benefits of using this active steering system, implemented in the steer-by-wire mode, are characterized, while the problems for further consideration and the potential benefits of such a solution are described.

Bridging the gap between molecular dynamics simulations and phase-field modelling: dynamics of a [NixZr1-x]liquid-Zrcrystal solidification front

International Nuclear Information System (INIS)

Danilov, Denis; Nestler, Britta; Guerdane, Mohammed; Teichler, Helmar

2009-01-01

Results are presented from phase-field modelling and molecular dynamics simulations concerning the relaxation dynamics in a finite-temperature two-phase crystal-liquid sample subjected to an abrupt temperature drop. Relaxation takes place by propagation of the solidification front under formation of a spatially varying concentration profile in the melt. The molecular dynamics simulations are carried out with an interatomic model appropriate for the NiZr alloy system and provide the thermophysical data required for setting up the phase-field simulations. Regarding the concentration profile and velocity of the solidification front, best agreement between the phase-field model and molecular dynamics simulation is obtained when increasing the apparent diffusion coefficients in the phase-field treatment by a factor of four against their molecular dynamics estimates.

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Science.gov (United States)

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

Robotic needle steering: design, modeling, planning, and image guidance

NARCIS (Netherlands)

Cowan, Noah J.; Goldberg, Ken; Chirikjian, Gregory S.; Fichtinger, Gabor; Alterovitz, Ron; Reed, Kyle B.; Kallem, Vinutha; Misra, Sarthak; Park, Wooram; Okamura, Allison M.; Rosen, Jacob; Hannaford, Blake; Satava, Richard M.

2010-01-01

This chapter describes how advances in needle design, modeling, planning, and image guidance make it possible to steer flexible needles from outside the body to reach specified anatomical targets not accessible using traditional needle insertion methods. Steering can be achieved using a variety of

Multiquantum well beam-steering device for laser satellite communication

Science.gov (United States)

Lahat, Roee; Levy, Itamar; Shlomi, Arnon

2002-01-01

With the increasing interest in laser satellite communications, new methods are sought to solve the existing problems of accurate and rapid laser beam deflection. Current solutions in the form of galvanometers or piezo fast steering mirrors with one or two degrees of freedom are bulky, power-consuming and slow. The Multi-Quantum Well (MQW) is a semiconductor device with unique potential to steer laser beams without any moving parts. We have conducted a preliminary evaluation of the potential application of the MQW as a laser beam-steering device for laser satellite communication, examining the performance of critical parameters for this type of communications.

Evolved Control of Natural Plants: Crossing the Reality Gap for User-Defined Steering of Growth and Motion

DEFF Research Database (Denmark)

Hofstadler, Daniel Nicolas; Wahby, Mostafa; Heinrich, Mary Katherine

2017-01-01

in response to the simple controller is captured by image processing, and a model of the plant tip dynamics is developed. The model is used in simulation to evolve a robot controller that steers the plant tip such that it follows a number of randomly generated target points. Finally, we test the simulation-evolved...

Laser Controlled Molecular Orientation Dynamics

International Nuclear Information System (INIS)

Atabek, O.

2004-01-01

Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation

Molecular potentials and relaxation dynamics

International Nuclear Information System (INIS)

Karo, A.M.

1981-01-01

The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. Recent calculations of the X 1 Σ + and a 3 Σ + states of LiH, NaH, KH, RbH, and CsH and the X 2 Σ + states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, higly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm -1 over most of the potential curves) with the difference curves being considerably more accurate. In the method of computer molecular dynamics, the force acting on each particle is the resultant of all interactions with other atoms in the neighborhood and is obtained as the derivative of an effective many-body potential. Exploiting the pseudopotential approach, in obtaining the appropriate potentials may be very fruitful in the future. In the molecular dynamics example considered here, the conventional sum-of-pairwise-interatomic-potentials (SPP) approximation is used with the potentials derived either from experimental spectroscopic data or from Hartree-Fock calculations. The problem is the collisional de-excitation of vibrationally excited molecular hydrogen at an Fe surface. The calculations have been carried out for an initial vibrotational state v = 8, J = 1 and a translational temperature corresponding to a gas temperature of 500 0 K. Different angles of approach and different initial random impact points on the surface have been selected. For any given collision with the wall, the molecule may pick up or lose vibrotatonal and translational energy

Molecular dynamics simulations of solutions at constant chemical potential

Science.gov (United States)

Perego, C.; Salvalaglio, M.; Parrinello, M.

2015-04-01

Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

The 2011 Dynamics of Molecular Collisions Conference

Energy Technology Data Exchange (ETDEWEB)

Nesbitt, David J. [JILA, NIST

2011-07-11

The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor

Reducing Digging Losses by Using Automated Steering to Plant and Invert Peanuts

Directory of Open Access Journals (Sweden)

George Vellidis

2014-07-01

Full Text Available GPS guidance of farm machinery has been increasingly adopted by farmers because of the perceived gains in efficiency that it provides. In the southeastern USA one of the reasons farmers adopt GPS guidance, and specifically automated steering (auto-steer, is that it can theoretically result in large yield gains when used to plant and invert peanuts—one of the region’s most important crops. The goal of our study was to quantify the yield benefit of using real time kinematic (RTK-based auto-steer to plant and invert peanuts under a variety of terrain conditions. Yield benefits result from reduced digging losses. The study was conducted for two consecutive years (2010 and 2011 on a private farm in Georgia, USA. When all data are grouped together, auto-steer outperformed conventional by 579 kg/ha in 2010 and 451 kg/ha in 2011. We also evaluated the performance of auto-steer under different curvature conditions using low, medium, and high curvature rows. The results showed that auto-steer outperformed conventional under all curvature by a minimum of 338 kg/ha. Finally, we evaluated passive implement guidance in combination with auto-steer and found that it holds tremendous potential for further reducing digging losses. In many cases, auto-steer will pay for itself within a year.

Molecular dynamics analysis of conformational change of paramyxovirus F protein during the initial steps of membrane fusion

International Nuclear Information System (INIS)

Martín-García, Fernando; Mendieta-Moreno, Jesús Ignacio; Mendieta, Jesús; Gómez-Puertas, Paulino

2012-01-01

Highlights: ► Initial conformational change of paramyxovirus F protein is caused only by mechanical forces. ► HRA region undergoes a structural change from a beta + alpha conformation to an extended coil and then to an all-alpha conformation. ► HRS domains of F protein form three single α-helices prior to generation of the coiled coil. -- Abstract: The fusion of paramyxovirus to the cell membrane is mediated by fusion protein (F protein) present in the virus envelope, which undergoes a dramatic conformational change during the process. Unlike hemagglutinin in orthomyxovirus, this change is not mediated by an alteration of environmental pH, and its cause remains unknown. Steered molecular dynamics analysis leads us to suggest that the conformational modification is mediated only by stretching mechanical forces once the transmembrane fusion peptide of the protein is anchored to the cell membrane. Such elongating forces will generate major secondary structure rearrangement in the heptad repeat A region of the F protein; from β-sheet conformation to an elongated coil and then spontaneously to an α-helix. In addition, it is proposed that the heptad repeat A region adopts a final three-helix coiled coil and that this structure appears after the formation of individual helices in each monomer.

Towards the molecular bases of polymerase dynamics

International Nuclear Information System (INIS)

Chela Flores, J.

1991-03-01

One aspect of the strong relationship that is known to exist between the processes of DNA replication and transcription is manifest in the coupling of the rates of movement of the replication fork (r f ) and RNA polymerase (r t ). We address two issues concerning the largely unexplored area of polymerase dynamics: (i) The validity of an approximate kinematic formula linking r f and r t suggested by experiments in which transcription is initiated in some prokaryotes with the antibiotic streptolydigin, and (ii) What are the molecular bases of the kinematic formula? An analysis of the available data suggests possible molecular bases for polymerase dynamics. In particular, we are led to a hypothesis: In active chromatin r t may depend on the length (λ t ) of the transcript of the primary messenger RNA (pre-mRNA). This new effect is subject to experimental verification. We discuss possible experiments that may be performed in order to test this prediction. (author). Refs, 6 tabs

Dynamical quenching of tunneling in molecular magnets

International Nuclear Information System (INIS)

José Santander, María; Nunez, Alvaro S.; Roldán-Molina, A.; Troncoso, Roberto E.

2015-01-01

It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation

Dynamical quenching of tunneling in molecular magnets

Energy Technology Data Exchange (ETDEWEB)

José Santander, María, E-mail: maria.jose.noemi@gmail.com [Recursos Educativos Quántica, Santiago (Chile); Departamento de Física, Universidad de Santiago de Chile and CEDENNA, Avda. Ecuador 3493, Santiago (Chile); Nunez, Alvaro S., E-mail: alnunez@dfi.uchile.cl [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Casilla 487-3, Santiago (Chile); Roldán-Molina, A. [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Avenida Universidad 330, Curauma, Valparaíso (Chile); Troncoso, Roberto E., E-mail: r.troncoso.c@gmail.com [Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Avda. Ecuador 3493, Santiago 9170124 (Chile); Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso (Chile)

2015-12-15

It is shown that a single molecular magnet placed in a rapidly oscillating magnetic field displays the phenomenon of quenching of tunneling processes. The results open a way to manipulate the quantum states of molecular magnets by means of radiation in the terahertz range. Our analysis separates the time evolution into slow and fast components thereby obtaining an effective theory for the slow dynamics. This effective theory presents quenching of the tunnel effect, in particular, stands out its difference with the so-called coherent destruction of tunneling. We support our prediction with numerical evidence based on an exact solution of Schrödinger's equation. - Highlights: • Single molecular magnets under rapidly oscillating magnetic fields is studied. • It is shown that this system displays the quenching of tunneling processes. • Our findings provide a control of quantum molecular magnets via terahertz radiation.

A stochastic phase-field model determined from molecular dynamics

KAUST Repository

von Schwerin, Erik

2010-03-17

The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

A stochastic phase-field model determined from molecular dynamics

KAUST Repository

von Schwerin, Erik; Szepessy, Anders

2010-01-01

The dynamics of dendritic growth of a crystal in an undercooled melt is determined by macroscopic diffusion-convection of heat and by capillary forces acting on the nanometer scale of the solid-liquid interface width. Its modelling is useful for instance in processing techniques based on casting. The phase-field method is widely used to study evolution of such microstructural phase transformations on a continuum level; it couples the energy equation to a phenomenological Allen-Cahn/Ginzburg-Landau equation modelling the dynamics of an order parameter determining the solid and liquid phases, including also stochastic fluctuations to obtain the qualitatively correct result of dendritic side branching. This work presents a method to determine stochastic phase-field models from atomistic formulations by coarse-graining molecular dynamics. It has three steps: (1) a precise quantitative atomistic definition of the phase-field variable, based on the local potential energy; (2) derivation of its coarse-grained dynamics model, from microscopic Smoluchowski molecular dynamics (that is Brownian or over damped Langevin dynamics); and (3) numerical computation of the coarse-grained model functions. The coarse-grained model approximates Gibbs ensemble averages of the atomistic phase-field, by choosing coarse-grained drift and diffusion functions that minimize the approximation error of observables in this ensemble average. © EDP Sciences, SMAI, 2010.

Modeling of Driver Steering Operations in Lateral Wind Disturbances toward Driver Assistance System

Science.gov (United States)

Kurata, Yoshinori; Wada, Takahiro; Kamiji, Norimasa; Doi, Shun'ichi

Disturbances decrease vehicle stability and increase driver's mental and physical workload. Especially unexpected disturbances such as lateral winds have severe effect on vehicle stability and driver's workload. This study aims at building a driver model of steering operations in lateral wind toward developing effective driver assistance system. First, the relationship between the driver's lateral motion and its reactive quick steering behavior is investigated using driving simulator with lateral 1dof motion. In the experiments, four different wind patterns are displayed by the simulator. As the results, strong correlation was found between the driver's head lateral jerk by the lateral disturbance and the angular acceleration of the steering wheel. Then, we build a mathematical model of driver's steering model from lateral disturbance input to steering torque of the reactive quick feed-forward steering based on the experimental results. Finally, validity of the proposed model is shown by comparing the steering torque of experimental results and that of simulation results.

Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

Science.gov (United States)

Tsukanov, A. A.; Psakhie, S. G.

2017-12-01

The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.

Steering, Entanglement, Nonlocality, and the EPR Paradox

OpenAIRE

Wiseman, H. M.; Jones, S. J.; Doherty, A. C.

2006-01-01

The concept of steering was introduced by Schrodinger in 1935 as a generalization of the EPR paradox for arbitrary pure bipartite entangled states and arbitrary measurements by one party. Until now, it has never been rigorously defined, so it has not been known (for example) what mixed states are steerable (that is, can be used to exhibit steering). We provide an operational definition, from which we prove (by considering Werner states and Isotropic states) that steerable states are a strict ...

Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics

International Nuclear Information System (INIS)

Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.

2004-01-01

Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the 'Wannier gauge'. An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches

The use of molecular dynamics for the thermodynamic properties of simple and transition metals

International Nuclear Information System (INIS)

Straub, G.K.

1987-04-01

The technique of computer simulation of the molecular dynamics in metallic systems to calculate thermodynamic properties is discussed. The nature of a metal as determined by its electronic structure is used to determine the total adiabatic potential. The effective screened ion-ion interaction can then be used in a molecular dynamics simulation. The method for the construction of a molecular dynamics ensemble, its relation to the canonical ensemble, and the definition of thermodynamic functions from the Helmholtz free energy is given. The method for the analysis of the molecular dynamics results from quasiharmonic lattice dynamics and the decomposition in terms of harmonic and anharmonic contributions is given for solids. For fluid phase metals, procedures for calculating the thermodynamics and determining the constant of entropy are presented. The solid-fluid phase boundary as a function of pressure and temperature is determined using the results of molecular dynamics. Throughout, examples and results for metallic sodium are used. The treatment of the transition metal electronic d-states in terms of an effective pair-wise interaction is also discussed and the phonon dispersion curves of Al, Ni, and Cu are calculated

Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene

Energy Technology Data Exchange (ETDEWEB)

Cawkwell, M. J., E-mail: cawkwell@lanl.gov; Niklasson, Anders M. N. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Dattelbaum, Dana M. [Weapons Experiments Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2015-02-14

The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene.

Science.gov (United States)

Cawkwell, M J; Niklasson, Anders M N; Dattelbaum, Dana M

2015-02-14

The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.

A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS

NARCIS (Netherlands)

AHLSTROM, P; BERENDSEN, HJC

1993-01-01

Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)

Correlations and symmetry of interactions influence collective dynamics of molecular motors

International Nuclear Information System (INIS)

Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B

2015-01-01

Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)

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.)

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.)

Power-Production Diagnostic Tools for Low-Density Wind Farms with Applications to Wake Steering

Science.gov (United States)

Takle, E. S.; Herzmann, D.; Rajewski, D. A.; Lundquist, J. K.; Rhodes, M. E.

2016-12-01

Hansen (2011) provided guidelines for wind farm wake analysis with applications to "high density" wind farms (where average distance between turbines is less than ten times rotor diameter). For "low-density" (average distance greater than fifteen times rotor diameter) wind farms, or sections of wind farms we demonstrate simpler sorting and visualization tools that reveal wake interactions and opportunities for wind farm power prediction and wake steering. SCADA data from a segment of a large mid-continent wind farm, together with surface flux measurements and lidar data are subjected to analysis and visualization of wake interactions. A time-history animated visualization of a plan view of power level of individual turbines provides a quick analysis of wake interaction dynamics. Yaw-based sectoral histograms of enhancement/decline of wind speed and power from wind farm reference levels reveals angular width of wake interactions and identifies the turbine(s) responsible for the power reduction. Concurrent surface flux measurements within the wind farm allowed us to evaluate stability influence on wake loss. A one-season climatology is used to identify high-priority candidates for wake steering based on estimated power recovery. Typical clearing prices on the day-ahead market are used to estimate the added value of wake steering. Current research is exploring options for identifying candidate locations for wind farm "build-in" in existing low-density wind farms.

Molecular Dynamics Simulations of a Linear Nanomotor Driven by Thermophoretic Forces

DEFF Research Database (Denmark)

Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

Molecular Dynamics of a Linear Nanomotor Driven by Thermophoresis Harvey A. Zambrano1, Jens H. Walther1,2 and Richard L. Jaffe3 1Department of Mechanical Engineering, Fluid Mechanics, Technical University of Denmark, DK-2800 Lyngby, Denmark; 2Computational Science and Engineering Laboratory, ETH...... future molecular machines a complete understanding of the friction forces involved on the transport process at the molecular level have to be addressed.18 In this work we perform Molecular Dynamics (MD) simulations using the MD package FASTTUBE19 to study a molecular linear motor consisting of coaxial...... the valence forces within the CNT using Morse, harmonic angle and torsion potentials.19We include a nonbonded carbon-carbon Lennard-Jones potential to describe the vdW interaction between the carbon atoms within the double wall portion of the system. We equilibrate the system at 300K for 0.1 ns, by coupling...

Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

Science.gov (United States)

Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

2017-08-22

A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

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

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

Energy Technology Data Exchange (ETDEWEB)

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

2013-12-21

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

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

International Nuclear Information System (INIS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-01-01

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

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

Science.gov (United States)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

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

Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M

Directory of Open Access Journals (Sweden)

Pradeepkiran JA

2015-03-01

24934545 and ZINC72319544 – that showed high binding affinity among 2,829 drug analogs that bind with key active-site residues; these residues are considered for protein-ligand binding and unbinding pathways via steered molecular dynamics simulations. Arg215 in the model plays an important role in the stability of the protein-ligand complex via a hydrogen bonding interaction by aromatic-π contacts, and the ADMET (absorption, distribution, metabolism, and excretion analysis of best leads indicate nontoxic in nature with good potential for drug development. Keywords: brucellosis, rho proteins, transcription inhibitors, SMD simulations, ADMET analysis, therapeutics 

STEER Coastal Use Mapping Project

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The Coastal Use Mapping Project is designed to collect critical information on human activities in and near the St. Thomas East End Reserves (STEER). The project...

Design of a Path-Tracking Steering Controller for Autonomous Vehicles

Directory of Open Access Journals (Sweden)

Chuanyang Sun

2018-06-01

Full Text Available This paper presents a linearization method for the vehicle and tire models under the model predictive control (MPC scheme, and proposes a linear model-based MPC path-tracking steering controller for autonomous vehicles. The steering controller is designed to minimize lateral path-tracking deviation at high speeds. The vehicle model is linearized by a sequence of supposed steering angles, which are obtained by assuming the vehicle can reach the desired path at the end of the MPC prediction horizon and stay in a steady-state condition. The lateral force of the front tire is directly used as the control input of the model, and the rear tire’s lateral force is linearized by an equivalent cornering stiffness. The course-direction deviation, which is the angle between the velocity vector and the path heading, is chosen as a control reference state. The linearization model is validated through the simulation, and the results show high prediction accuracy even in regions of large steering angle. This steering controller is tested through simulations on the CarSim-Simulink platform (R2013b, MathWorks, Natick, MA, USA, showing the improved performance of the present controller at high speeds.

The Impact of Analog and Bang-Bang Steering Gear Control on Ship's Fuel Economy

DEFF Research Database (Denmark)

Nørtoft Thomsen, J. C.; Blanke, Mogens; Reid, R. E.

1982-01-01

it is found to be at least equally important regarding steering performance and fuel economy. The paper presents a comprehensive survey of steering gear principles commonly used, including relevant details of three analog steering gear servo principles, which have outperformed conventional designs. Control......The latest years have shown considerable efforts towards improving steering generated propulsion losses of ships by the introduction of various sophisticated control algorithms in the autopilots. However, little previous attention has been given to the steering gear control loop, although...

Shapiro like steps reveals molecular nanomagnets’ spin dynamics

International Nuclear Information System (INIS)

Abdollahipour, Babak; Abouie, Jahanfar; Ebrahimi, Navid

2015-01-01

We present an accurate way to detect spin dynamics of a nutating molecular nanomagnet by inserting it in a tunnel Josephson junction and studying the current voltage (I-V) characteristic. The spin nutation of the molecular nanomagnet is generated by applying two circularly polarized magnetic fields. We demonstrate that modulation of the Josephson current by the nutation of the molecular nanomagnet’s spin appears as a stepwise structure like Shapiro steps in the I-V characteristic of the junction. Width and heights of these Shapiro-like steps are determined by two parameters of the spin nutation, frequency and amplitude of the nutation, which are simply tuned by the applied magnetic fields

Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

DEFF Research Database (Denmark)

Solov'yov, Ilia A.; Korol, Andrei V.; Solov'yov, Andrey V.

-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science...... of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational...... practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational...

Violation of Continuous-Variable Einstein-Podolsky-Rosen Steering with Discrete Measurements

Science.gov (United States)

Schneeloch, James; Dixon, P. Ben; Howland, Gregory A.; Broadbent, Curtis J.; Howell, John C.

2013-03-01

In this Letter, we derive an entropic Einstein-Podolsky-Rosen (EPR) steering inequality for continuous-variable systems using only experimentally measured discrete probability distributions and details of the measurement apparatus. We use this inequality to witness EPR steering between the positions and momenta of photon pairs generated in spontaneous parametric down-conversion. We examine the asymmetry between parties in this inequality, and show that this asymmetry can be used to reduce the technical requirements of experimental setups intended to demonstrate the EPR paradox. Furthermore, we develop a more stringent steering inequality that is symmetric between parties, and use it to show that the down-converted photon pairs also exhibit symmetric EPR steering.

Extended Lagrangian formulation of charge-constrained tight-binding molecular dynamics.

Science.gov (United States)

Cawkwell, M J; Coe, J D; Yadav, S K; Liu, X-Y; Niklasson, A M N

2015-06-09

The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [Niklasson, Phys. Rev. Lett., 2008, 100, 123004] has been applied to a tight-binding model under the constraint of local charge neutrality to yield microcanonical trajectories with both precise, long-term energy conservation and a reduced number of self-consistent field optimizations at each time step. The extended Lagrangian molecular dynamics formalism restores time reversal symmetry in the propagation of the electronic degrees of freedom, and it enables the efficient and accurate self-consistent optimization of the chemical potential and atomwise potential energy shifts in the on-site elements of the tight-binding Hamiltonian that are required when enforcing local charge neutrality. These capabilities are illustrated with microcanonical molecular dynamics simulations of a small metallic cluster using an sd-valent tight-binding model for titanium. The effects of weak dissipation on the propagation of the auxiliary degrees of freedom for the chemical potential and on-site Hamiltonian matrix elements that is used to counteract the accumulation of numerical noise during trajectories was also investigated.

Electron-nuclear corellations for photoinduced dynamics in molecular dimers

Science.gov (United States)

Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

2003-03-01

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

Vectorization, parallelization and implementation of Quantum molecular dynamics codes (QQQF, MONTEV)

Energy Technology Data Exchange (ETDEWEB)

Kato, Kaori [High Energy Accelerator Research Organization, Tsukuba, Ibaraki (Japan); Kunugi, Tomoaki; Kotake, Susumu; Shibahara, Masahiko

1998-03-01

This report describes parallelization, vectorization and implementation for two simulation codes, Quantum molecular dynamics simulation code QQQF and Photon montecalro molecular dynamics simulation code MONTEV, that have been developed for the analysis of the thermalization of photon energies in the molecule or materials. QQQF has been vectorized and parallelized on Fujitsu VPP and has been implemented from VPP to Intel Paragon XP/S and parallelized. MONTEV has been implemented from VPP to Paragon and parallelized. (author)

The Front Steering Launcher Design for the ITER ECRH Upper Port

International Nuclear Information System (INIS)

Henderson, M A; Chavan, R; Heidinger, R; Nikkola, P; Ramponi, G; Saibene, G; Sanchez, F; Sauter, O; Serikov, A; Zohm, H

2005-01-01

The ECRH ITER upper port antenna's role is to stabilize the neoclassical tearing mode (NTM) on either the q = 2 or 3/2 rational flux surfaces, which requires a narrow current deposition profile (j CD ) over a wide range along the resonance surfaces. The width of j CD should be equivalent to the marginal island width to fully stabilise the NTM. Two antenna concepts are under consideration for the upper port launcher: front steering (FS) and remote steering (RS). The FS launcher decouples the steering and focusing aspects using a two mirror system (one focusing and one steering), achieving a wider steering range and higher current density for NTM stabilisation than required by ITER, offering a threefold increase in NTM stabilization efficiency over the RS launcher. The improved physics performance has motivated the further design study of the FS launcher aiming toward a build to print launcher. The present design is compatible with ≥2.0 MW CW operation and 8 beams per port plug. A frictionless backlashfree system is envisioned for the steering mechanism. An overview of the launcher design, the calculated physics performance and the possibility of using the upper port launcher for extended physics applications (beyond NTM stabilisation) are discussed

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

Science.gov (United States)

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

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

DYNAMIC SURFACE BOUNDARY-CONDITIONS - A SIMPLE BOUNDARY MODEL FOR MOLECULAR-DYNAMICS SIMULATIONS

NARCIS (Netherlands)

JUFFER, AH; BERENDSEN, HJC

1993-01-01

A simple model for the treatment of boundaries in molecular dynamics simulations is presented. The method involves the positioning of boundary atoms on a surface that surrounds a system of interest. The boundary atoms interact with the inner region and represent the effect of atoms outside the

An automatic beam steering system for the NSLS X-17T beam line using closed orbit feedback

International Nuclear Information System (INIS)

Nawrocky, R.J.; Ma, Li; Rarback, H.M.; Singh, O.V.; Yu, L.H.

1987-01-01

Initial observations of motion of the undulator radiation in the NSLS X-17T beam line clearly indicated that the beam had to be stabilized in both directions to be usable for the planned soft x-ray imaging experiments. The low frequency spectra of beam motion contained peaks in the range from dc to 60 Hz and at higher frequencies. A beam steering system employing closed orbit feedback has been designed and installed to stabilize the beam in both planes. In each plane of motion, beam position is measured with a beam position detector and a correction signal is fed back to a local four magnet orbit bump to dynamically control the angle of the radiation at the source. This paper describes the design and performance of the beam steering system

Molecular dynamics simulations and quantum chemical calculations ...

African Journals Online (AJOL)

Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

NARCIS (Netherlands)

Periole, Xavier; Vendruscolo, Michele; Mark, Alan E.

2007-01-01

A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which

Droplet spreading driven by van der Waals force: a molecular dynamics study

KAUST Repository

Wu, Congmin

2010-07-07

The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t) ∼ √t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid. © 2010 IOP Publishing Ltd.

Molecular dynamics simulations indicate that deoxyhemoglobin, oxyhemoglobin, carboxyhemoglobin, and glycated hemoglobin under compression and shear exhibit an anisotropic mechanical behavior.

Science.gov (United States)

Yesudasan, Sumith; Wang, Xianqiao; Averett, Rodney D

2018-05-01

We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior; however, this study investigates the mechanical behavior of hemoglobin, a major constituent of red blood cells, using steered molecular dynamics (SMD) simulations to obtain anisotropic mechanical behavior under compression and shear loading conditions. Four different configurations of hemoglobin molecules were considered: deoxyhemoglobin (deoxyHb), oxyhemoglobin (HbO 2 ), carboxyhemoglobin (HbCO), and glycated hemoglobin (HbA 1C ). The SMD simulations were performed on the hemoglobin variants to estimate their unidirectional stiffness and shear stiffness. Although hemoglobin is structurally denoted as a globular protein due to its spherical shape and secondary structure, our simulation results show a significant variation in the mechanical strength in different directions (anisotropy) and also a strength variation among the four different hemoglobin configurations studied. The glycated hemoglobin molecule possesses an overall higher compressive mechanical stiffness and shear stiffness when compared to deoxyhemoglobin, oxyhemoglobin, and carboxyhemoglobin molecules. Further results from the models indicate that the hemoglobin structures studied possess a soft outer shell and a stiff core based on stiffness.

Longitudinal shifts in bacterial diversity and fermentation pattern in the rumen of steers grazing wheat pasture.

Science.gov (United States)

Pitta, D W; Pinchak, W E; Dowd, S; Dorton, K; Yoon, I; Min, B R; Fulford, J D; Wickersham, T A; Malinowski, D P

2014-12-01

Grazing steers on winter wheat forage is routinely practiced in the Southern Great Plains of the US. Here, we investigated the dynamics in bacterial populations of both solid and liquid ruminal fractions of steers grazing on maturing wheat forage of changing nutritive quality. The relationship between bacterial diversity and fermentation parameters in the liquid fraction was also investigated. During the first 28 days, the wheat was in a vegetative phase with a relatively high crude protein content (CP; 21%), which led to the incidence of mild cases of frothy bloat among steers. Rumen samples were collected on days 14, 28, 56 and 76, separated into solid and liquid fractions and analyzed for bacterial diversity using 16S pyrotag technology. The predominant phyla identified were Bacteroidetes (59-77%) and Firmicutes (20-33%) across both ruminal fractions. Very few differences were observed in the rumen bacterial communities within solid and liquid fractions on day 14. However, by day 28, the relatively high CP content complemented a distinct bacterial and chemical composition of the rumen fluid that was characterized by a higher ratio (4:1) of Bacteroidetes:Firmicutes and a corresponding lower acetate:propionate (3:1) ratio. Further, a greater accumulation of biofilm (mucopolysaccharide complex) on day 28 was strongly associated with the abundance of Firmicutes lineages such as Clostridium, Ruminococcus, Oscillospira and Moryella (Prumen microbiome and their association with fermentation activity in the rumen of steers during the vegetative (bloat-prone) and reproductive stages of wheat forage. Copyright © 2014 Elsevier Ltd. All rights reserved.

Feed efficiency differences and reranking in beef steers fed grower and finisher diets.

Science.gov (United States)

Durunna, O N; Mujibi, F D N; Goonewardene, L; Okine, E K; Basarab, J A; Wang, Z; Moore, S S

2011-01-01

This 3-yr study used 490 steers to determine whether feedlot steers changed their feed efficiency (FE) ranking when fed a grower diet, then a finisher diet. The steers were crossbreds and were between 5 to 7 mo of age. There were 2 feeding periods each year. Within each year, approximately 90 steers had their diet switched from a grower to a finisher diet (feed-swap group), whereas another 90 steers were fed either the grower (grower-fed group) or the finisher (finisher-fed group) diet throughout the feeding trial. Each feeding test lasted for a minimum of 10 wk, and all steers were fed ad libitum. Individual animal feed intakes were collected using the GrowSafe feeding system, and BW were measured every 2 wk. Residual feed intake (RFI), G:F, and Kleiber ratio (KR) were computed at the end of each feeding period. For each measure of efficiency, animals were classified as low, medium, or high based on 0.5 SD from the mean. The majority of steers did not maintain the previous efficiency class in the second period. Approximately 58, 51, and 51% of steers in the feed-swap group, finisher-fed group, and the grower-fed group, respectively, changed their RFI measure by 0.5 SD. A low rank correlation occurred in all test groups but was less in the feed-swap group. Spearman rank correlations between the 2 feeding periods in the feed-swap group were 0.33, 0.20, and 0.31 for RFI, G:F, and KR, respectively. Classifications based on G:F and KR showed that a greater number of steers (P 0.05) between the proportions of individuals that changed or maintained their FE class. In the groups without a feed-swap, there was no difference (P > 0.05) in the proportion of steers that changed or maintained the same FE class for all FE measures. Our results suggest that diet type and feeding period affect the FE ranking in beef steers. A feedlot diet is ideal for evaluating the FE potential of steers for feedlot profitability; however, we suggest that tests involving less dense diets should

Molecular dynamics simulations of melting behavior of alkane as phase change materials slurry

International Nuclear Information System (INIS)

Rao Zhonghao; Wang Shuangfeng; Wu Maochun; Zhang Yanlai; Li Fuhuo

2012-01-01

Highlights: ► The melting behavior of phase change materials slurry was investigated by molecular dynamics simulation method. ► Four different PCM slurry systems including pure water and water/n-nonadecane composite were constructed. ► Amorphous structure and periodic boundary conditions were used in the molecular dynamics simulations. ► The simulated melting temperatures are very close to the published experimental values. - Abstract: The alkane based phase change materials slurry, with high latent heat storage capacity, is effective to enhance the heat transfer rate of traditional fluid. In this paper, the melting behavior of composite phase change materials slurry which consists of n-nonadecane and water was investigated by using molecular dynamics simulation. Four different systems including pure water and water/n-nonadecane composite were constructed with amorphous structure and periodic boundary conditions. The results showed that the simulated density and melting temperature were very close to the published experimental values. Mixing the n-nonadecane into water decreased the mobility but increased the energy storage capacity of composite systems. To describe the melting behavior of alkane based phase change materials slurry on molecular or atomic scale, molecular dynamics simulation is an effective method.

Magnetic nanoparticles in fluid environment: combining molecular dynamics and Lattice-Boltzmann

Energy Technology Data Exchange (ETDEWEB)

Melenev, Petr, E-mail: melenev@icmm.ru [Ural Federal University, 4, Turgeneva str., 620000 Ekaterinburg (Russian Federation); Institute of Continuous Media Mechanics, 1, Koroleva str., 614013 Perm (Russian Federation)

2017-06-01

Hydrodynamic interactions between magnetic nanoparticles suspended in the Newtonian liquid are accounted for using a combination of the lattice Boltzmann method and molecular dynamics simulations. Nanoparticle is modelled by the system of molecular dynamics material points (which form structure resembles raspberry) coupled to the lattice Boltzmann fluid. The hydrodynamic coupling between the colloids is studied by simulations of the thermo-induced rotational diffusion of two raspberry objects. It was found that for the considered range of model parameters the approaching of the raspberries leads to slight retard of the relaxation process. The presence of the weak magnetic dipolar interaction between the objects leads to modest decrease of the relaxation time and the extent of the acceleration of the diffusion is intensified along with magnetic forces. - Highlights: • The combination of molecular dynamics and lattice Boltzmann method is utilized for the reveal of the role of hydrodynamic interaction in rotational dynamics of colloid particles. • The verification of the model parameters is done based on the comparison with the results of Langevin dynamics. • For the task of free rotational diffusion of the pair of colloid particles the influence of the hydrodynamic interactions on the relaxation time is examined in the case of nonmagnetic particles and at the presence of weak dipolar interaction.

Microsecond atomic-scale molecular dynamics simulations of polyimides

NARCIS (Netherlands)

Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.

2013-01-01

We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long

Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms

Directory of Open Access Journals (Sweden)

Dirk-Sören Lühmann

2015-08-01

Full Text Available In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated π electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated π system of the artificial benzene molecule.

Moving contact lines: linking molecular dynamics and continuum-scale modelling.

Science.gov (United States)

Smith, Edward R; Theodorakis, Panagiotis E; Craster, Richard V; Matar, Omar K

2018-05-04

Despite decades of research, the modelling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily-life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide the link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which govern the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modelling, and highlight the opportunities for future developments in this area.

Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

Science.gov (United States)

Li, Jianwei; Nowak, Piotr; Otto, Sijbren

2013-06-26

Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.

Estimation of flow stress of radiation induced F/M steels using molecular dynamics and discrete dislocation dynamics approach

International Nuclear Information System (INIS)

More, Ameya; Dutta, B.K.; Durgaprasad, P.V.; Arya, A.K.

2012-01-01

Fe-Cr based Ferritic/Martensitic (F/M) steels are the candidate structural materials for future fusion reactors. In this work, a multi-scale approach comprising atomistic Molecular Dynamics (MD) simulations and Discrete Dislocation Dynamics (DDD) simulations are used to model the effect of irradiation dose on the flow stress of F/M steels. At the atomic scale, molecular dynamics simulations are used to study the dislocation interaction with irradiation induced defects, i.e. voids and He bubbles. Whereas, the DDD simulations are used to estimate the change in flow stress of the material as a result of irradiation hardening. (author)

Molecular dynamics studies of superionic conductors

International Nuclear Information System (INIS)

Rahman, A.; Vashishta, P.

1983-01-01

Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables

Nonequilibrium molecular dynamics theory, algorithms and applications

CERN Document Server

Todd, Billy D

2017-01-01

Written by two specialists with over twenty-five years of experience in the field, this valuable text presents a wide range of topics within the growing field of nonequilibrium molecular dynamics (NEMD). It introduces theories which are fundamental to the field - namely, nonequilibrium statistical mechanics and nonequilibrium thermodynamics - and provides state-of-the-art algorithms and advice for designing reliable NEMD code, as well as examining applications for both atomic and molecular fluids. It discusses homogenous and inhomogenous flows and pays considerable attention to highly confined fluids, such as nanofluidics. In addition to statistical mechanics and thermodynamics, the book covers the themes of temperature and thermodynamic fluxes and their computation, the theory and algorithms for homogenous shear and elongational flows, response theory and its applications, heat and mass transport algorithms, applications in molecular rheology, highly confined fluids (nanofluidics), the phenomenon of slip and...

Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles

NARCIS (Netherlands)

Marrink, SJ; Mark, AE

2003-01-01

Here, we use coarse grained molecular dynamics (MD) simulations to study the spontaneous aggregation of dipalmitoylphosphatidylcholine (DPPC) lipids into small unilamellar vesicles. We show that the aggregation process occurs on a nanosecond time scale, with bicelles and cuplike vesicles formed at

Test of Einstein-Podolsky-Rosen steering based on the all-versus-nothing proof.

Science.gov (United States)

Wu, Chunfeng; Chen, Jing-Ling; Ye, Xiang-Jun; Su, Hong-Yi; Deng, Dong-Ling; Wang, Zhenghan; Oh, C H

2014-03-06

In comparison with entanglement and Bell nonlocality, Einstein-Podolsky-Rosen steering is a newly emerged research topic and in its incipient stage. Although Einstein-Podolsky-Rosen steering has been explored via violations of steering inequalities both theoretically and experimentally, the known inequalities in the literatures are far from well-developed. As a result, it is not yet possible to observe Einstein-Podolsky-Rosen steering for some steerable mixed states. Recently, a simple approach was presented to identify Einstein-Podolsky-Rosen steering based on all-versus-nothing argument, offering a strong condition to witness the steerability of a family of two-qubit (pure or mixed) entangled states. In this work, we show that the all-versus-nothing proof of Einstein-Podolsky-Rosen steering can be tested by measuring the projective probabilities. Through the bound of probabilities imposed by local-hidden-state model, the proposed test shows that steering can be detected by the all-versus-nothing argument experimentally even in the presence of imprecision and errors. Our test can be implemented in many physical systems and we discuss the possible realizations of our scheme with non-Abelian anyons and trapped ions.

Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations

NARCIS (Netherlands)

Baoukina, Svetlana; Monticelli, Luca; Marrink, Siewert J.; Tieleman, D. Peter

2007-01-01

We calculated the pressure-area isotherm of a dipalmitoyl-phosphatidylcholine (DPPC) lipid monolayer from molecular dynamics simulations using a coarse-grained molecular model. We characterized the monolayer structure, geometry, and phases directly from the simulations and compared the calculated

Quantum molecular dynamics study of the Su-Schrieffer-Heeger model

NARCIS (Netherlands)

Michielsen, Kristel; Raedt, Hans De

A quantum molecular dynamics technique is presented to compute the static and dynamic properties of a system of fermions coupled to classical degrees of freedom. The method is employed to investigate the properties of the Su-Schrieffer-Heeger model, an electron-phonon model which is often used to

A comparative molecular dynamics study of diffusion of n-decane ...

Indian Academy of Sciences (India)

Administrator

Abstract. Molecular dynamics simulations are reported on the structure and dynamics of n-decane and. 3-methylpentane in zeolite NaY. We have calculated several properties such as the center of mass-center of mass rdf, the end-end distance distribution, bond angle distribution and dihedral angle distribution. We.

Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation

National Research Council Canada - National Science Library

Johnston, K

1998-01-01

.... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...

Friction in Carborane-Based Molecular Rotors Driven by Gas Flow or Electric Field: Classical Molecular Dynamics

Czech Academy of Sciences Publication Activity Database

Prokop, Alexandr; Vacek, Jaroslav; Michl, Josef

2012-01-01

Roč. 6, č. 3 (2012), s. 1901-1914 ISSN 1936-0851 R&D Projects: GA ČR GA203/09/1802; GA MŠk ME09020 Institutional research plan: CEZ:AV0Z40550506 Keywords : molecular rotors * molecular dynamics * potential energy barriers * friction * intramolecular vibrational redistribution Subject RIV: CC - Organic Chemistry Impact factor: 12.062, year: 2012

Novel Microstrip Patch Antennas with Frequency Agility, Polarization Reconfigurability, Dual Null Steering Capability and Phased Array Antenna with Beam Steering Performance

Science.gov (United States)

Babakhani, Behrouz

Nowadays the wireless communication technology is playing an important role in our daily life. People use wireless devices not only as a conventional communication device but also as tracking and navigation tool, web browsing tool, data storage and transfer tool and so for many other reasons. Based on the user demand, wireless communication engineers try to accommodate as many as possible wireless systems and applications in a single device and therefore, creates a multifunctional device. Antenna, as an integral part of any wireless communication systems, should also be evolved and adjusted with development of wireless transceiver systems. Therefore multifunctional antennas have been introduced to support and enhance the functionality on modern wireless systems. The main focus and contribution of this thesis is design of novel multifunctional microstrip antennas with frequency agility, polarization reconfigurablity, dual null steering capability and phased array antenna with beam steering performance. In this thesis, first, a wide bandwidth(1.10 GHz to 1.60 GHz) right-handed circularly polarized (RHCP) directional antenna for global positioning system (GPS) satellite receive application has been introduced which covers all the GPS bands starting from L1 to L5. This design consists of two crossed bow-tie dipole antennas fed with sequentially phase rotated feed network backed with an artificial high impedance surface (HIS) structure to generate high gain directional radiation patterns. This design shows good CP gain and axial ratio (AR) and wide beamwidth performance. Although this design has good radiation quality, the size and the weight can be reduced as future study. In the second design, a frequency agile antenna was developed which also covers the L-band (L1 to L5) satellite communication frequencies. This frequency agile antenna was designed and realized by new implementation of varactor diodes in the geometry of a circular patch antenna. Beside wide frequency

Design of Model-based Controller with Disturbance Estimation in Steer-by-wire System

Directory of Open Access Journals (Sweden)

Jung Sanghun

2018-01-01

Full Text Available The steer-by-wire system is a next generation steering control technology that has been actively studied because it has many advantages such as fast response, space efficiency due to removal of redundant mechanical elements, and high connectivity with vehicle chassis control, such as active steering. Steer-by-wire system has disturbance composed of tire friction torque and self-aligning torque. These disturbances vary widely due to the weight or friction coefficient change. Therefore, disturbance compensation logic is strongly required to obtain desired performance. This paper proposes model-based controller with disturbance compensation to achieve the robust control performance. Targeted steer-by-wire system is identified through the experiment and system identification method. Moreover, model-based controller is designed using the identified plant model. Disturbance of targeted steer-by-wire is estimated using disturbance observer(DOB, and compensate the estimated disturbance into control input. Experiment of various scenarios are conducted to validate the robust performance of proposed model-based controller.

Classical molecular dynamics simulations of fusion and fragmentation in fullerene-fullerene collisions

International Nuclear Information System (INIS)

Verkhovtsev, A.; Korol, A.V.; Solovyov, A.V.

2017-01-01

We present the results of classical molecular dynamics simulations of collision-induced fusion and fragmentation of C 60 fullerenes, performed by means of the MBN Explorer software package. The simulations provide information on structural differences of the fused compound depending on kinematics of the collision process. The analysis of fragmentation dynamics at different initial conditions shows that the size distributions of produced molecular fragments are peaked for dimers, which is in agreement with a well-established mechanism of C 60 fragmentation via preferential C 2 emission. Atomic trajectories of the colliding particles are analyzed and different fragmentation patterns are observed and discussed. On the basis of the performed simulations, characteristic time of C 2 emission is estimated as a function of collision energy. The results are compared with experimental time-of-flight distributions of molecular fragments and with earlier theoretical studies. Considering the widely explored case study of C 60 -C 60 collisions, we demonstrate broad capabilities of the MBN Explorer software, which can be utilized for studying collisions of a broad variety of nano-scale and bio-molecular systems by means of classical molecular dynamics. (authors)

Balancing an accurate representation of the molecular surface in generalized Born formalisms with integrator stability in molecular dynamics simulations

Czech Academy of Sciences Publication Activity Database

Chocholoušová, Jana; Feig, M.

2006-01-01

Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006

Demonstration of Einstein-Podolsky-Rosen steering with enhanced subchannel discrimination

Science.gov (United States)

Sun, Kai; Ye, Xiang-Jun; Xiao, Ya; Xu, Xiao-Ye; Wu, Yu-Chun; Xu, Jin-Shi; Chen, Jing-Ling; Li, Chuan-Feng; Guo, Guang-Can

2018-03-01

Einstein-Podolsky-Rosen (EPR) steering describes a quantum nonlocal phenomenon in which one party can nonlocally affect the other's state through local measurements. It reveals an additional concept of quantum non-locality, which stands between quantum entanglement and Bell nonlocality. Recently, a quantum information task named as subchannel discrimination (SD) provides a necessary and sufficient characterization of EPR steering. The success probability of SD using steerable states is higher than using any unsteerable states, even when they are entangled. However, the detailed construction of such subchannels and the experimental realization of the corresponding task are still technologically challenging. In this work, we designed a feasible collection of subchannels for a quantum channel and experimentally demonstrated the corresponding SD task where the probabilities of correct discrimination are clearly enhanced by exploiting steerable states. Our results provide a concrete example to operationally demonstrate EPR steering and shine a new light on the potential application of EPR steering.

Atomic and Molecular Dynamics on and in Superfluid Helium Nanodroplets

Science.gov (United States)

Lehmann, Kevin K.

2003-03-01

Studies of intramolecular and intermolecular dynamics is at the core of Molecular Spectroscopic research several decades. Gas phase, particularly molecular beam, studies have greatly illuminated these processes in isolated molecules, bimolecular collisions, or small covalent and van der Waals complexes. Parallel to this effort have been studies in condensed phases, but there has unfortunately been little intellectual contact between these. The recent development of Helium Nanodropet Isolation Spectroscopy is providing an intellectual bridge between gas phase and condensed phase spectroscopy. While droplets of 10,000 He atoms are effectively a condensed phase, their low temperature ( 0.4 K) and ultralow heat capacities combined with their superfluid state make them an almost ideal matrix in which to study both molecular dynamics, including solute induced relaxations. The nsec times scales for many of the relaxation events, orders of magnitude slower than in classical liquids, results in spectra with unprecedented resolution for the liquid state. In this talk, studies of the Princeton group will be highlighted, with particular emphasis on those for which a combination of theory and experiment have combined to reveal dynamics in this unique Quantum Fluid.

Stochastic stability of four-wheel-steering system

International Nuclear Information System (INIS)

Huang Dongwei; Wang Hongli; Zhu Zhiwen; Feng Zhang

2007-01-01

A four-wheel-steering system subjected to white noise excitations was reduced to a two-degree-of-freedom quasi-non-integrable-Hamiltonian system. Subsequently we obtained an one-dimensional Ito stochastic differential equation for the averaged Hamiltonian of the system by using the stochastic averaging method for quasi-non-integrable-Hamiltonian systems. Thus, the stochastic stability of four-wheel-steering system was analyzed by analyzing the sample behaviors of the averaged Hamiltonian at the boundary H = 0 and calculating its Lyapunov exponent. An example given at the end demonstrated that the conclusion obtained is of considerable significance

Accelerating convergence of molecular dynamics-based structural relaxation

DEFF Research Database (Denmark)

Christensen, Asbjørn

2005-01-01

We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...

Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...

Indian Academy of Sciences (India)

Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...

DyNet: visualization and analysis of dynamic molecular interaction networks.

Science.gov (United States)

Goenawan, Ivan H; Bryan, Kenneth; Lynn, David J

2016-09-01

: The ability to experimentally determine molecular interactions on an almost proteome-wide scale under different conditions is enabling researchers to move from static to dynamic network analysis, uncovering new insights into how interaction networks are physically rewired in response to different stimuli and in disease. Dynamic interaction data presents a special challenge in network biology. Here, we present DyNet, a Cytoscape application that provides a range of functionalities for the visualization, real-time synchronization and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the most 'rewired' nodes across many network states. DyNet is available at the Cytoscape (3.2+) App Store (http://apps.cytoscape.org/apps/dynet). david.lynn@sahmri.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

Science.gov (United States)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-10-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.

Synthesis of Steered Flat-top Beam Pattern Using Evolutionary Algorithm

Directory of Open Access Journals (Sweden)

D. Mandal

2016-12-01

Full Text Available In this paper a pattern synthesis method based on Evolutionary Algorithm is presented. A Flat-top beam pattern has been generated from a concentric ring array of isotropic elements by finding out the optimum set of elements amplitudes and phases using Differential Evolution algorithm. The said pattern is generated in three predefined azimuth planes instate of a single phi plane and also verified for a range of azimuth plane for the same optimum excitations. The main beam is steered to an elevation angle of 30 degree with lower peak SLL and ripple. Dynamic range ratio (DRR is also being improved by eliminating the weakly excited array elements, which simplify the design complexity of feed networks.

Vehicle dynamics theory and application

CERN Document Server

Jazar, Reza N

2014-01-01

This textbook is appropriate for senior undergraduate and first year graduate students in mechanical and automotive engineering. The contents in this book are presented at a theoretical-practical level. It explains vehicle dynamics concepts in detail, concentrating on their practical use. Related theorems and formal proofs are provided, as are real-life applications. Students, researchers and practicing engineers alike will appreciate the user-friendly presentation of a wealth of topics, most notably steering, handling, ride, and related components. This book also: Illustrates all key concepts with examples Includes exercises for each chapter Covers front, rear, and four wheel steering systems, as well as the advantages and disadvantages of different steering schemes Includes an emphasis on design throughout the text, which provides a practical, hands-on approach

A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

KAUST Repository

Neumann, Philipp

2012-06-01

We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.

Molecular electron recollision dynamics in intense circularly polarized laser pulses

Science.gov (United States)

Bandrauk, André D.; Yuan, Kai-Jun

2018-04-01

Extreme UV and x-ray table top light sources based on high-order harmonic generation (HHG) are focused now on circular polarization for the generation of circularly polarized attosecond pulses as new tools for controlling electron dynamics, such as charge transfer and migration and the generation of attosecond quantum electron currents for ultrafast magneto-optics. A fundamental electron dynamical process in HHG is laser induced electron recollision with the parent ion, well established theoretically and experimentally for linear polarization. We discuss molecular electron recollision dynamics in circular polarization by theoretical analysis and numerical simulation. The control of the polarization of HHG with circularly polarized ionizing pulses is examined and it is shown that bichromatic circularly polarized pulses enhance recollision dynamics, rendering HHG more efficient, especially in molecules because of their nonspherical symmetry. The polarization of the harmonics is found to be dependent on the compatibility of the rotational symmetry of the net electric field created by combinations of bichromatic circularly polarized pulses with the dynamical symmetry of molecules. We show how the field and molecule symmetry influences the electron recollision trajectories by a time-frequency analysis of harmonics. The results, in principle, offer new unique controllable tools in the study of attosecond molecular electron dynamics.

Ultra-compact laser beam steering device using holographically formed two dimensional photonic crystal.

Science.gov (United States)

Dou, Xinyuan; Chen, Xiaonan; Chen, Maggie Yihong; Wang, Alan Xiaolong; Jiang, Wei; Chen, Ray T

2010-03-01

In this paper, we report the theoretical study of polymer-based photonic crystals for laser beam steering which is based on the superprism effect as well as the experiment fabrication of the two dimensional photonic crystals for the laser beam steering. Superprism effect, the principle for beam steering, was separately studied in details through EFC (Equifrequency Contour) analysis. Polymer based photonic crystals were fabricated through double exposure holographic interference method using SU8-2007. The experiment results showed a beam steering angle of 10 degree for 30 nm wavelength variation.

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Vijaykumar, Adithya, E-mail: vijaykumar@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands); van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Bolhuis, Peter G. [van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam (Netherlands); Rein ten Wolde, Pieter, E-mail: p.t.wolde@amolf.nl [FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam (Netherlands)

2015-12-07

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

International Nuclear Information System (INIS)

Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter

2015-01-01

In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level

Human Skin Barrier Structure and Function Analyzed by Cryo-EM and Molecular Dynamics Simulation.

Science.gov (United States)

Lundborg, Magnus; Narangifard, Ali; Wennberg, Christian L; Lindahl, Erik; Daneholt, Bertil; Norlén, Lars

2018-04-24

In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems. Copyright © 2018. Published by Elsevier Inc.

Loophole-free Einstein-Podolsky-Rosen experiment via quantum steering

International Nuclear Information System (INIS)

Wittmann, Bernhard; Ramelow, Sven; Zeilinger, Anton; Steinlechner, Fabian; Langford, Nathan K; Ursin, Rupert; Brunner, Nicolas; Wiseman, Howard M

2012-01-01

Tests of the predictions of quantum mechanics for entangled systems have provided increasing evidence against local realistic theories. However, there remains the crucial challenge of simultaneously closing all major loopholes—the locality, freedom-of-choice and detection loopholes—in a single experiment. An important sub-class of local realistic theories can be tested with the concept of ‘steering’. The term ‘steering’ was introduced by Schrödinger in 1935 for the fact that entanglement would seem to allow an experimenter to remotely steer the state of a distant system as in the Einstein-Podolsky-Rosen (EPR) argument. Einstein called this ‘spooky action at a distance’. EPR-steering has recently been rigorously formulated as a quantum information task opening it up to new experimental tests. Here, we present the first loophole-free demonstration of EPR-steering by violating three-setting quadratic steering inequality, tested with polarization-entangled photons shared between two distant laboratories. Our experiment demonstrates this effect while simultaneously closing all loopholes: both the locality loophole and a specific form of the freedom-of-choice loophole are closed by having a large separation of the parties and using fast quantum random number generators, and the fair-sampling loophole is closed by having high overall detection efficiency. Thereby, we exclude—for the first time loophole-free—an important class of local realistic theories considered by EPR. Besides its foundational importance, loophole-free steering also allows the distribution of quantum entanglement secure event in the presence of an untrusted party. (paper)

Loophole-free Einstein-Podolsky-Rosen experiment via quantum steering

Science.gov (United States)

Wittmann, Bernhard; Ramelow, Sven; Steinlechner, Fabian; Langford, Nathan K.; Brunner, Nicolas; Wiseman, Howard M.; Ursin, Rupert; Zeilinger, Anton

2012-05-01

Tests of the predictions of quantum mechanics for entangled systems have provided increasing evidence against local realistic theories. However, there remains the crucial challenge of simultaneously closing all major loopholes—the locality, freedom-of-choice and detection loopholes—in a single experiment. An important sub-class of local realistic theories can be tested with the concept of ‘steering’. The term ‘steering’ was introduced by Schrödinger in 1935 for the fact that entanglement would seem to allow an experimenter to remotely steer the state of a distant system as in the Einstein-Podolsky-Rosen (EPR) argument. Einstein called this ‘spooky action at a distance’. EPR-steering has recently been rigorously formulated as a quantum information task opening it up to new experimental tests. Here, we present the first loophole-free demonstration of EPR-steering by violating three-setting quadratic steering inequality, tested with polarization-entangled photons shared between two distant laboratories. Our experiment demonstrates this effect while simultaneously closing all loopholes: both the locality loophole and a specific form of the freedom-of-choice loophole are closed by having a large separation of the parties and using fast quantum random number generators, and the fair-sampling loophole is closed by having high overall detection efficiency. Thereby, we exclude—for the first time loophole-free—an important class of local realistic theories considered by EPR. Besides its foundational importance, loophole-free steering also allows the distribution of quantum entanglement secure event in the presence of an untrusted party.

Computational challenges of large-scale, long-time, first-principles molecular dynamics

International Nuclear Information System (INIS)

Kent, P R C

2008-01-01

Plane wave density functional calculations have traditionally been able to use the largest available supercomputing resources. We analyze the scalability of modern projector-augmented wave implementations to identify the challenges in performing molecular dynamics calculations of large systems containing many thousands of electrons. Benchmark calculations on the Cray XT4 demonstrate that global linear-algebra operations are the primary reason for limited parallel scalability. Plane-wave related operations can be made sufficiently scalable. Improving parallel linear-algebra performance is an essential step to reaching longer timescales in future large-scale molecular dynamics calculations

Molecular dynamics study of silver

International Nuclear Information System (INIS)

Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.

1995-03-01

We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs

Nonlinear dynamics of zigzag molecular chains (in Russian)

DEFF Research Database (Denmark)

Savin, A. V.; Manevitsch, L. I.; Christiansen, Peter Leth

1999-01-01

models (two-dimensional alpha-spiral, polyethylene transzigzag backbone, and the zigzag chain of hydrogen bonds) shows that the zigzag structure essentially limits the soliton dynamics to finite, relatively narrow, supersonic soliton velocity intervals and may also result in that several acoustic soliton......Nonlinear, collective, soliton type excitations in zigzag molecular chains are analyzed. It is shown that the nonlinear dynamics of a chain dramatically changes in passing from the one-dimensional linear chain to the more realistic planar zigzag model-due, in particular, to the geometry...

Stability of molecular dynamics simulations of classical systems

DEFF Research Database (Denmark)

Toxværd, Søren

2012-01-01

The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...

Crystal structure and pair potentials: A molecular-dynamics study

Energy Technology Data Exchange (ETDEWEB)

Parrinello, M.; Rahman, A.

1980-10-06

With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

Molecular dynamics simulations and free energy profile of ...

Indian Academy of Sciences (India)

aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.

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...

Plastic dislocation motion via nonequilibrium molecular and continuum dynamics

International Nuclear Information System (INIS)

Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.

1980-01-01

The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition

Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

DEFF Research Database (Denmark)

Euro, Liliya; Haapanen, Outi; Róg, Tomasz

2017-01-01

of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...

Enhancing protein adsorption simulations by using accelerated molecular dynamics.

Directory of Open Access Journals (Sweden)

Christian Mücksch

Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.

Molecular Dynamics: New Frontier in Personalized Medicine.

Science.gov (United States)

Sneha, P; Doss, C George Priya

2016-01-01

The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.

Dissipation induced asymmetric steering of distant atomic ensembles

Science.gov (United States)

Cheng, Guangling; Tan, Huatang; Chen, Aixi

2018-04-01

The asymmetric steering effects of separated atomic ensembles denoted by the effective bosonic modes have been explored by the means of quantum reservoir engineering in the setting of the cascaded cavities, in each of which an atomic ensemble is involved. It is shown that the steady-state asymmetric steering of the mesoscopic objects is unconditionally achieved via the dissipation of the cavities, by which the nonlocal interaction occurs between two atomic ensembles, and the direction of steering could be easily controlled through variation of certain tunable system parameters. One advantage of the present scheme is that it could be rather robust against parameter fluctuations, and does not require the accurate control of evolution time and the original state of the system. Furthermore, the double-channel Raman transitions between the long-lived atomic ground states are used and the atomic ensembles act as the quantum network nodes, which makes our scheme insensitive to the collective spontaneous emission of atoms.

Einstein-Podolsky-Rosen-steering swapping between two Gaussian multipartite entangled states

Science.gov (United States)

Wang, Meihong; Qin, Zhongzhong; Wang, Yu; Su, Xiaolong

2017-08-01

Multipartite Einstein-Podolsky-Rosen (EPR) steering is a useful quantum resource for quantum communication in quantum networks. It has potential applications in secure quantum communication, such as one-sided device-independent quantum key distribution and quantum secret sharing. By distributing optical modes of a multipartite entangled state to space-separated quantum nodes, a local quantum network can be established. Based on the existing multipartite EPR steering in a local quantum network, secure quantum communication protocol can be accomplished. In this manuscript, we present swapping schemes for EPR steering between two space-separated Gaussian multipartite entangled states, which can be used to connect two space-separated quantum networks. Two swapping schemes, including the swapping between a tripartite Greenberger-Horne-Zeilinger (GHZ) entangled state and an EPR entangled state and that between two tripartite GHZ entangled states, are analyzed. Various types of EPR steering are presented after the swapping of two space-separated independent multipartite entanglement states without direct interaction, which can be used to implement quantum communication between two quantum networks. The presented schemes provide technical reference for more complicated quantum networks with EPR steering.

Sources of carbohydrates in the ingestive behavior of feedlot steers

Directory of Open Access Journals (Sweden)

Viviane Santos da Silva

2014-05-01

Full Text Available In this article we research the influence of different sources of carbohydrates (corn, soybean hulls or wheat bran upon the digestive behavior of 24 confined castrated steers with an initial average age and weight of 20 months and 330 kg born from the cross between Charolais and Nellore. The diet was composed of 40% sorghum silage and 60% concentrate. The time spent on total ruminating (an average of 454.6 min/day was not influenced by the source of carbohydrate. The animals from the wheat bran treatment spent less time idle (718 min in relation to those on the corn and soybean hulls treatments, which did not differ between themselves (an average of 792 min/day. The steers from the wheat bran treatment remained less time feeding (184 min/day compared with those fed the other treatments, whose average time of permanence in this activity was 214 minutes per day. The other studied variables did not present a significant difference between the treatments. Inclusion of wheat bran in the diet of the confined steers results in less spent time idle, while steers feeding on soybean hulls spend less time feeding. The use of corn, soybean hulls, or wheat bran in the diet of the confined steers does not affect the total cudding time.

Molecular dynamics based enhanced sampling of collective variables with very large time steps

Science.gov (United States)

Chen, Pei-Yang; Tuckerman, Mark E.

2018-01-01

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Molecular dynamics simulations of elasto-hydrodynamic lubrication and boundary lubrication for automotive tribology

International Nuclear Information System (INIS)

Washizu, Hitoshi; Sanda, Shuzo; Hyodo, Shi-aki; Ohmori, Toshihide; Nishino, Noriaki; Suzuki, Atsushi

2007-01-01

Friction control of machine elements on a molecular level is a challenging subject in vehicle technology. We describe the molecular dynamics studies of friction in two significant lubrication regimes. As a case of elastohydrodynamic lubrication, we introduce the mechanism of momentum transfer related to the molecular structure of the hydrocarbon fluids, phase transition of the fluids under high pressure, and a submicron thickness simulation of the oil film using a tera-flops computer. For boundary lubrication, the dynamic behavior of water molecules on hydrophilic and hydrophobic silicon surfaces under a shear condition is studied. The dynamic structure of the hydrogen bond network on the hydrophilic surface is related to the low friction of the diamond-like carbon containing silicon (DLC-Si) coating

Beam steering for circular switched parasitic arrays using a combinational approach

CSIR Research Space (South Africa)

Mofolo, ROM

2011-09-01

Full Text Available In this paper, the authors present a method of electronic beam steering for circular switched parasitic array (SPA) antennas. In circular SPA antennas, one achieves azimuth beam steering by open-circuiting and short-circuiting different parasitic...

comparative beef production from buli,s, steers and heifers under

African Journals Online (AJOL)

steers, although statistically significant, were much srnaller than differences obtained in the present study. Out of a maximum possible grading of 20 points, bulls obtained an average of 12,3 points (Grade I -) which is considerably lower than the grading points obtained by steers (16,3 = Prime) or by heifers (17,5 = Prime+).

Dynamic analysis of electron density in the course of the internal motion of molecular system

International Nuclear Information System (INIS)

Tachibana, A.; Hori, K.; Asai, Y.; Yamabe, T.

1984-01-01

The general dynamic aspect of electron density of a molecular system is studied on the basis of the general equation of the electron orbital which is formulated for the dynamic study of electronic motion. The newly defined electron orbital incorporates the dynamics of molecular vibration into the electronic structures. In this scheme, the change of electron distribution caused by excitation of vibrational state is defined as the ''dynamic electron transfer.'' The dynamic electron density is found to have the remarkable ''additive'' property. The time-dependent aspect of the dynamic electron redistribution is also analyzed on the basis of the ''coherent state.'' The new method relates the classical vibrational amplitude to the quantum number of the vibrational state. As a preliminary application of the present treatment, the dynamic electron densities of H 2 , HD, HT, HF, and HCl molecules are calculated by use of ab initio molecular orbital method

Design, Modeling And Control Of Steering And Braking For An Urban Electric Vehicle

OpenAIRE

Maciua, Dragos

1996-01-01

This report describes research which involved the design modification, modeling and control of automatic steering and braking systems for an urban electric vehicle. The vehicle is equipped with four-wheel independent drive, four-wheel independent braking and four-wheel steering. Control algorithms were developed for steering and braking. Simulation results show the feasibility of the algorithms.

Pick-up, transport and release of a molecular cargo using a small-molecule robotic arm

Science.gov (United States)

Kassem, Salma; Lee, Alan T. L.; Leigh, David A.; Markevicius, Augustinas; Solà, Jordi

2016-02-01

Modern-day factory assembly lines often feature robots that pick up, reposition and connect components in a programmed manner. The idea of manipulating molecular fragments in a similar way has to date only been explored using biological building blocks (specifically DNA). Here, we report on a wholly artificial small-molecule robotic arm capable of selectively transporting a molecular cargo in either direction between two spatially distinct, chemically similar, sites on a molecular platform. The arm picks up/releases a 3-mercaptopropanehydrazide cargo by formation/breakage of a disulfide bond, while dynamic hydrazone chemistry controls the cargo binding to the platform. Transport is controlled by selectively inducing conformational and configurational changes within an embedded hydrazone rotary switch that steers the robotic arm. In a three-stage operation, 79-85% of 3-mercaptopropanehydrazide molecules are transported in either (chosen) direction between the two platform sites, without the cargo at any time fully dissociating from the machine nor exchanging with other molecules in the bulk.

Avoiding Internal Capsule Stimulation With a New Eight-Channel Steering Deep Brain Stimulation Lead.

Science.gov (United States)

van Dijk, Kees J; Verhagen, Rens; Bour, Lo J; Heida, Ciska; Veltink, Peter H

2017-10-15

Novel deep brain stimulation (DBS) lead designs are currently entering the market, which are hypothesized to provide a way to steer the stimulation field away from neural populations responsible for side effects and towards populations responsible for beneficial effects. The objective of this study is to assess the performances of a new eight channel steering-DBS lead and compare this with a conventional cylindrical contact (CC) lead. The two leads were evaluated in a finite element electric field model combined with multicompartment neuron and axon models, representing the internal capsule (IC) fibers and subthalamic nucleus (STN) cells. We defined the optimal stimulation setting as the configuration that activated the highest percentage of STN cells, without activating any IC fibers. With this criterion, we compared monopolar stimulation using a single contact of the steering-DBS lead and CC lead, on three locations and four orientations of the lead. In addition, we performed a current steering test case by dividing the current over two contacts with the steering-DBS lead in its worst-case orientation. In most cases, the steering-DBS lead is able to stimulate a significantly higher percentage of STN cells compared to the CC lead using single contact stimulation or using a two contact current steering protocol when there is approximately a 1 mm displacement of the CC lead. The results also show that correct placement and orientation of the lead in the target remains an important aspect in achieving the optimal stimulation outcome. Currently, clinical trials are set up in Europe with a similar design as the steering-DBS lead. Our results illustrate the importance of the orientation of the new steering-DBS lead in avoiding side effects induced by stimulation of IC fibers. Therefore, in clinical trials sufficient attention should be paid to implanting the steering DBS-lead in the most effective orientation. © 2017 International Neuromodulation Society.

Molecular dynamic analysis of the structure of dendrimers

Energy Technology Data Exchange (ETDEWEB)

Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

2004-01-01

We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

Molecular dynamic analysis of the structure of dendrimers

International Nuclear Information System (INIS)

Canetta, E.; Maino, G.

2004-01-01

We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

Free energy from molecular dynamics with multiple constraints

NARCIS (Netherlands)

den Otter, Wouter K.; Briels, Willem J.

2000-01-01

In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to

Molecular Dynamics and Bioactivity of a Novel Mutated Human ...

African Journals Online (AJOL)

Keywords: Parathyroid hormone, Mutation prediction, Molecular dynamics, RANKL/OPG, UAMS-32P cell. Tropical .... PTH1R were used as MD simulation starting points. A full-atom ... Values of RMSD, Rg, and potential energy evaluation ...

Classical molecular dynamics simulation of nuclear fuels

International Nuclear Information System (INIS)

Devanathan, R.; Krack, M.; Bertolus, M.

2015-01-01

Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)

Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations

Directory of Open Access Journals (Sweden)

Cedrix J. Dongmo Foumthuim

2018-01-01

Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.

The chaos and order in nuclear molecular dynamics

International Nuclear Information System (INIS)

Srokowski, T.

1995-01-01

The subject of the presented report is role of chaos in scattering processes in the frame of molecular dynamics. In this model, it is assumed that scattering particles (nuclei) consist of not-interacted components as alpha particles or 12 C, 16 O and 20 Ne clusters. The results show such effects as dynamical in stabilities and fractal structure as well as compound nuclei decay and heavy-ion fusion. The goal of the report is to make the reader more familiar with the chaos model and its application to nuclear phenomena. 157 refs, 40 figs

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

Science.gov (United States)

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

1999-06-01

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

Can hydroxylamine be a more potent nucleophile for the reactivation of tabun-inhibited AChE than prototype oxime drugs? An answer derived from quantum chemical and steered molecular dynamics studies.

Science.gov (United States)

Lo, Rabindranath; Ganguly, Bishwajit

2014-07-29

Organophosphorus nerve agents are highly toxic compounds which strongly inhibit acetylcholinesterase (AChE) in the blood and in the central nervous system (CNS). Tabun is one of the highly toxic organophosphorus (OP) compounds and is resistant to many oxime drugs formulated for the reactivation of AChE. The reactivation mechanism of tabun-conjugated AChE with various drugs has been examined with density functional theory and ab initio quantum chemical calculations. The presence of a lone-pair located on the amidic group resists the nucleophilic attack at the phosphorus center of the tabun-conjugated AChE. We have shown that the newly designed drug candidate N-(pyridin-2-yl)hydroxylamine, at the MP2/6-31+G*//M05-2X/6-31G* level in the aqueous phase with the polarizable continuum solvation model (PCM), is more effective in reactivating the tabun-conjugated AChE than typical oxime drugs. The rate determining activation barrier with N-(pyridin-2-yl)hydroxylamine was found to be ∼1.7 kcal mol(-1), which is 7.2 kcal mol(-1) lower than the charged oxime trimedoxime (one of the most efficient reactivators in tabun poisonings). The greater nucleophilicity index (ω(-)) and higher CHelpG charge of pyridinylhydroxylamine compared to TMB4 support this observation. Furthermore, we have also examined the reactivation process of tabun-inhibited AChE with some other bis-quaternary oxime drug candidates such as methoxime (MMB4) and obidoxime. The docking analysis suggests that charged bis-quaternary pyridinium oximes have greater binding affinity inside the active-site gorge of AChE compared to the neutral pyridinylhydroxylamine. The peripheral ligand attached to the neutral pyridinylhydroxylamine enhanced the binding with the aromatic residues in the active-site gorge of AChE through effective π-π interactions. Steered molecular dynamics (SMD) simulations have also been performed with the charged oxime (TMB4) and the neutral hydroxylamine. From protein-drug interaction

Integrating atomistic molecular dynamics simulations, experiments and network analysis to study protein dynamics: strength in unity

Directory of Open Access Journals (Sweden)

Elena ePapaleo

2015-05-01

Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

Fermionic molecular dynamics for ground states and collisions of nuclei

International Nuclear Information System (INIS)

Feldmeier, H.; Bieler, K.; Schnack, J.

1994-08-01

The antisymmetric many-body trial state which describes a system of interacting fermions is parametrized in terms of localized wave packets. The equations of motion are derived from the time-dependent quantum variational principle. The resulting Fermionic Molecular Dynamics (FMD) equations include a wide range of semi-quantal to classical physics extending from deformed Hartree-Fock theory to Newtonian molecular dynamics. Conservation laws are discussed in connection with the choice of the trial state. The model is applied to heavy-ion collisions with which its basic features are illustrated. The results show a great variety of phenomena including deeply inelastic collisions, fusion, incomplete fusion, fragmentation, neck emission, promptly emitted nucleons and evaporation. (orig.)

Emission spectroscopic studies on dynamics of molecular excitation and dissociation by controlled electron impact

International Nuclear Information System (INIS)

Ogawa, Teiichiro

1986-01-01

Emission spectrum by controlled electron impact has been a successful technique for the investigation of molecular dynamics. (1) Molecular excitation. Aromatic molecules give an optical emission similar to fluorescence. However, as is shown by the vibrational structure and the electron energy dependence of benzene emission, its excitation process is not necessarily optical. Some aliphatic molecules also exhibit an emission band at the ultraviolet region. (2) Molecular dissociation. Analysis of the Doppler profile, the threshold energy, the excitation function and the isotope effect of the atomic emission produced in electron-molecule collisions has clarified the dynamics of the molecular dissociation. Especially the Doppler profile has given the translational energy distribution of the fragment atom, which is very useful to disclose the potential energy curve. Its angular dependence has recently found to allow determination of the symmetry of the intermediate excited state and the magnetic sublevel distribution of the fragment atom. These finding has revealed detailed state-to-state dynamics of the molecular dissociation. (author)

Effects of temperature and isotopic substitution on electron attachment dynamics of guanine–cytosine base pair: Ring-polymer and classical molecular dynamics simulations

International Nuclear Information System (INIS)

Minoshima, Yusuke; Seki, Yusuke; Takayanagi, Toshiyuki; Shiga, Motoyuki

2016-01-01

Highlights: • Dynamics of excess electron attachment to guanine–cytosine base pair. • Ring-polymer and classical molecular dynamics simulations are performed. • Temperature and isotope substitution effects are investigated. - Abstract: The dynamical process of electron attachment to a guanine–cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1 ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.

Effects of temperature and isotopic substitution on electron attachment dynamics of guanine–cytosine base pair: Ring-polymer and classical molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Minoshima, Yusuke; Seki, Yusuke [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Takayanagi, Toshiyuki, E-mail: tako@mail.saitama-u.ac.jp [Department of Chemistry, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570 (Japan); Shiga, Motoyuki [Center for Computational Science and E-Systems, Japan Atomic Energy Agency, 148-4, Kashiwanoha Campus, 178-4 Wakashiba, Kashiwa, Chiba 277-0871 (Japan)

2016-06-15

Highlights: • Dynamics of excess electron attachment to guanine–cytosine base pair. • Ring-polymer and classical molecular dynamics simulations are performed. • Temperature and isotope substitution effects are investigated. - Abstract: The dynamical process of electron attachment to a guanine–cytosine pair in the normal (h-GC) and deuterated (d-GC) forms has been studied theoretically by semiclassical ring-polymer molecular dynamics (RPMD) simulations using the empirical valence bond model. The initially formed dipole-bound anion is converted rapidly to the valence-bound anion within about 0.1 ps in both h-GC and d-GC. However, the subsequent proton transfer in h-GC occurs with a rate five times greater than the deuteron transfer in d-GC. The change of rates with isotopic substitution and temperature variation in the RPMD simulations are quantitatively and qualitatively different from those in the classical molecular dynamics (MD) simulations, demonstrating the importance of nuclear quantum effects on the dynamics of this system.

Molecular dynamics simulation of a chemical reaction

International Nuclear Information System (INIS)

Gorecki, J.; Gryko, J.

1988-06-01

Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs

Photocatalytic oxidation dynamics of acetone on TiO2: tight-binding quantum chemical molecular dynamics study

International Nuclear Information System (INIS)

Lv Chen; Wang Xiaojing; Agalya, Govindasamy; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira

2005-01-01

The clarification of the excited states dynamics on TiO 2 surface is important subject for the design of the highly active photocatalysts. In the present study, we applied our novel tight-binding quantum chemical molecular dynamics method to the investigation on the photocatalytic oxidation dynamics of acetone by photogenerated OH radicals on the hydrated anatase TiO 2 surface. The elucidated photocatalytic reaction mechanism strongly supports the previous experimental proposal and finally the effectiveness of our new approach for the clarification of the photocatalytic reaction dynamics employing the large simulation model was confirmed

Effects of slow-release urea on ruminal digesta characteristics and growth performance in beef steers

DEFF Research Database (Denmark)

Taylor-Edwards, C C; Hibbard, G; Kitts, S E

2009-01-01

Two experiments were conducted to evaluate the effects of slow urea (SRU) versus feed-grade urea on ruminal metabolite characteristics in steers and DMI, gain, and G:F in growing beef steers.......Two experiments were conducted to evaluate the effects of slow urea (SRU) versus feed-grade urea on ruminal metabolite characteristics in steers and DMI, gain, and G:F in growing beef steers....

ADHESION EFFECTS WITHIN THE HARD MATTER – SOFT MATTER INTERFACE: MOLECULAR DYNAMICS

Directory of Open Access Journals (Sweden)

Alexey Tsukanov

2016-12-01

Full Text Available In the present study three soft matter – hard matter systems consisting of different nanomaterials and organic molecules were studied using the steered molecular dynamics approach in order to reveal regularities in the formation of organic-inorganic hybrids and the stability of multimolecular complexes, as well as to analyze the energy aspects of adhesion between bio-molecules and layered ceramics. The combined process free energy estimation (COPFEE procedure was used for quantitative and qualitative assessment of the considered heterogeneous systems. Interaction of anionic and cationic amino acids with the surface of a [Mg4Al2(OH122+ 2Cl–] layered double hydroxide (LDH nanosheet was considered. In both cases, strong adhesion was observed despite the opposite signs of electric charge. The free energy of the aspartic amino acid anion, which has two deprotonated carboxylic groups, was determined to be –45 kJ/mol for adsorption on the LDH surface. For the cationic arginine, with only one carboxylic group and a positive net charge, the energy of adsorption was –26 kJ/mol, which is twice higher than that of chloride anion adsorption on the same cationic nanosheet. This fact clearly demonstrates the capability of “soft matter” species to adjust themselves and fit into the surface, minimizing energy of the system. The adsorption of protonated histamine, having no carboxylic groups, on a boehmite nanosheet is also energetically favorable, but the depth of free energy well is quite small at 3.6 kJ/mol. In the adsorbed state the protonated amino-group of histamine plays the role of proton donor, while the hydroxyl oxygens of the layered hydroxide have the role of proton acceptor, which is unusual. The obtained results represent a small step towards further understanding of the adhesion effects within the hard matter – soft matter contact zone.

Auditory orientation in crickets: Pattern recognition controls reactive steering

Science.gov (United States)

Poulet, James F. A.; Hedwig, Berthold

2005-10-01

Many groups of insects are specialists in exploiting sensory cues to locate food resources or conspecifics. To achieve orientation, bees and ants analyze the polarization pattern of the sky, male moths orient along the females' odor plume, and cicadas, grasshoppers, and crickets use acoustic signals to locate singing conspecifics. In comparison with olfactory and visual orientation, where learning is involved, auditory processing underlying orientation in insects appears to be more hardwired and genetically determined. In each of these examples, however, orientation requires a recognition process identifying the crucial sensory pattern to interact with a localization process directing the animal's locomotor activity. Here, we characterize this interaction. Using a sensitive trackball system, we show that, during cricket auditory behavior, the recognition process that is tuned toward the species-specific song pattern controls the amplitude of auditory evoked steering responses. Females perform small reactive steering movements toward any sound patterns. Hearing the male's calling song increases the gain of auditory steering within 2-5 s, and the animals even steer toward nonattractive sound patterns inserted into the speciesspecific pattern. This gain control mechanism in the auditory-to-motor pathway allows crickets to pursue species-specific sound patterns temporarily corrupted by environmental factors and may reflect the organization of recognition and localization networks in insects. localization | phonotaxis

Charge-dependent conformations and dynamics of pamam dendrimers revealed by neutron scattering and molecular dynamics

Science.gov (United States)

Wu, Bin

Neutron scattering and fully atomistic molecular dynamics (MD) are employed to investigate the structural and dynamical properties of polyamidoamine (PAMAM) dendrimers with ethylenediamine (EDA) core under various charge conditions. Regarding to the conformational characteristics, we focus on scrutinizing density profile evolution of PAMAM dendrimers as the molecular charge of dendrimer increases from neutral state to highly charged condition. It should be noted that within the context of small angle neutron scattering (SANS), the dendrimers are composed of hydrocarbon component (dry part) and the penetrating water molecules. Though there have been SANS experiments that studied the charge-dependent structural change of PAMAM dendrimers, their results were limited to the collective behavior of the aforementioned two parts. This study is devoted to deepen the understanding towards the structural responsiveness of intra-molecular polymeric and hydration parts separately through advanced contrast variation SANS data analysis scheme available recently and unravel the governing principles through coupling with MD simulations. Two kinds of acids, namely hydrochloric and sulfuric acids, are utilized to tune the pH condition and hence the molecular charge. As far as the dynamical properties, we target at understanding the underlying mechanism that leads to segmental dynamic enhancement observed from quasielstic neutron scattering (QENS) experiment previously. PAMAM dendrimers have a wealth of potential applications, such as drug delivery agency, energy harvesting medium, and light emitting diodes. More importantly, it is regarded as an ideal system to test many theoretical predictions since dendrimers conjugate both colloid-like globular shape and polymer-like flexible chains. This Ph.D. research addresses two main challenges in studying PAMAM dendrimers. Even though neutron scattering is an ideal tool to study this PAMAM dendrimer solution due to its matching temporal and

Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

International Nuclear Information System (INIS)

Hardy, David J.; Schulten, Klaus; Wolff, Matthew A.; Skeel, Robert D.; Xia, Jianlin

2016-01-01

The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle–mesh Ewald method falls short.

Analyzing the Molecular Kinetics of Water Spreading on Hydrophobic Surfaces via Molecular Dynamics Simulation.

Science.gov (United States)

Zhao, Lei; Cheng, Jiangtao

2017-09-07

In this paper, we report molecular kinetic analyses of water spreading on hydrophobic surfaces via molecular dynamics simulation. The hydrophobic surfaces are composed of amorphous polytetrafluoroethylene (PTFE) with a static contact angle of ~112.4° for water. On the basis of the molecular kinetic theory (MKT), the influences of both viscous damping and solid-liquid retarding were analyzed in evaluating contact line friction, which characterizes the frictional force on the contact line. The unit displacement length on PTFE was estimated to be ~0.621 nm and is ~4 times as long as the bond length of C-C backbone. The static friction coefficient was found to be ~[Formula: see text] Pa·s, which is on the same order of magnitude as the dynamic viscosity of water, and increases with the droplet size. A nondimensional number defined by the ratio of the standard deviation of wetting velocity to the characteristic wetting velocity was put forward to signify the strength of the inherent contact line fluctuation and unveil the mechanism of enhanced energy dissipation in nanoscale, whereas such effect would become insignificant in macroscale. Moreover, regarding a liquid droplet on hydrophobic or superhydrophobic surfaces, an approximate solution to the base radius development was derived by an asymptotic expansion approach.

Stereochemical errors and their implications for molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Freddolino Peter L

2011-05-01

Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.

In situ diffraction profile analysis during tensile deformation motivated by molecular dynamics

International Nuclear Information System (INIS)

Van Swygenhoven, H.; Budrovic, Z.; Derlet, P.M.; Froseth, A.G.; Van Petegem, S.

2005-01-01

Molecular dynamics simulations can provide insight into the slip mechanism at the atomic scale and suggest that in nanocrystalline metals dislocations are nucleated and absorbed by the grain boundaries. However, this technique is limited by very short simulation times. Using suggestions from molecular dynamics, we have developed a new in situ X-ray diffraction technique wherein the profile analysis of several Bragg diffraction peaks during tensile deformation is possible. Combining experiment and careful structural analysis the results confirm the suggestions from atomistic simulations

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

Science.gov (United States)

Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2017-03-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

A molecular dynamics algorithm for simulation of field theories in the canonical ensemble

International Nuclear Information System (INIS)

Kogut, J.B.; Sinclair, D.K.

1986-01-01

We add a single scalar degree of freedom (''demon'') to the microcanonical ensemble which converts its molecular dynamics into a simulation method for the canonical ensemble (euclidean path integral) of the underlying field theory. This generalization of the microcanonical molecular dynamics algorithm simulates the field theory at fixed coupling with a completely deterministic procedure. We discuss the finite size effects of the method, the equipartition theorem and ergodicity. The method is applied to the planar model in two dimensions and SU(3) lattice gauge theory with four species of light, dynamical quarks in four dimensions. The method is much less sensitive to its discrete time step than conventional Langevin equation simulations of the canonical ensemble. The method is a straightforward generalization of a procedure introduced by S. Nose for molecular physics. (orig.)

46 CFR 185.320 - Steering gear, controls, and communication system tests.

Science.gov (United States)

2010-10-01

... 46 Shipping 7 2010-10-01 2010-10-01 false Steering gear, controls, and communication system tests. 185.320 Section 185.320 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) SMALL PASSENGER VESSELS (UNDER 100 GROSS TONS) OPERATIONS Miscellaneous Operating Requirements § 185.320 Steering...

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.

Liquid-vapor coexistence by molecular dynamics simulation

International Nuclear Information System (INIS)

Baranyai, Andras; Cummings, Peter T.

2000-01-01

We present a simple and consistent molecular dynamics algorithm for determining the equilibrium properties of a bulk liquid and its coexisting vapor phase. The simulation follows the dynamics of the two systems simultaneously while maintaining the volume and the number of particles of the composite system fixed. The thermostat can constrain either the total energy or the temperature at a desired value. Division of the extensive properties between the two phases is governed by the difference of the corresponding intensive state variables. Particle numbers are continuous variables and vary only in virtual sense, i.e., the real sizes of the two systems are the same and do not change during the course of the simulation. Calculation of the chemical potential is separate from the dynamics; thus, one can replace the particle exchange step with other method if it improves the efficiency of the code. (c) 2000 American Institute of Physics