Theoretical determination of the ionization potential and the electron affinity of organic semiconductors

NASA Astrophysics Data System (ADS)

Yanagisawa, Susumu

2017-11-01

Ionization potential and electron affinity of organic semicondutors are important quantities, which are relevant to charge injection barriers. The electrostatic and dynamical contributions to the polarization energies for the injected charges in pentacene polymorphs were investigated. While the dynamical polarization induced narrowing of the energy gap, the electrostatic effect shifted up or down the frontier energy levels, which is sensitive to the molecular orientation at the surface.

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations.

PubMed

Sinko, William; de Oliveira, César Augusto F; Pierce, Levi C T; McCammon, J Andrew

2012-01-10

Molecular dynamics (MD) is one of the most common tools in computational chemistry. Recently, our group has employed accelerated molecular dynamics (aMD) to improve the conformational sampling over conventional molecular dynamics techniques. In the original aMD implementation, sampling is greatly improved by raising energy wells below a predefined energy level. Recently, our group presented an alternative aMD implementation where simulations are accelerated by lowering energy barriers of the potential energy surface. When coupled with thermodynamic integration simulations, this implementation showed very promising results. However, when applied to large systems, such as proteins, the simulation tends to be biased to high energy regions of the potential landscape. The reason for this behavior lies in the boost equation used since the highest energy barriers are dramatically more affected than the lower ones. To address this issue, in this work, we present a new boost equation that prevents oversampling of unfavorable high energy conformational states. The new boost potential provides not only better recovery of statistics throughout the simulation but also enhanced sampling of statistically relevant regions in explicit solvent MD simulations.

Energy Optimal Path Planning: Integrating Coastal Ocean Modelling with Optimal Control

NASA Astrophysics Data System (ADS)

Subramani, D. N.; Haley, P. J., Jr.; Lermusiaux, P. F. J.

2016-02-01

A stochastic optimization methodology is formulated for computing energy-optimal paths from among time-optimal paths of autonomous vehicles navigating in a dynamic flow field. To set up the energy optimization, the relative vehicle speed and headings are considered to be stochastic, and new stochastic Dynamically Orthogonal (DO) level-set equations that govern their stochastic time-optimal reachability fronts are derived. Their solution provides the distribution of time-optimal reachability fronts and corresponding distribution of time-optimal paths. An optimization is then performed on the vehicle's energy-time joint distribution to select the energy-optimal paths for each arrival time, among all stochastic time-optimal paths for that arrival time. The accuracy and efficiency of the DO level-set equations for solving the governing stochastic level-set reachability fronts are quantitatively assessed, including comparisons with independent semi-analytical solutions. Energy-optimal missions are studied in wind-driven barotropic quasi-geostrophic double-gyre circulations, and in realistic data-assimilative re-analyses of multiscale coastal ocean flows. The latter re-analyses are obtained from multi-resolution 2-way nested primitive-equation simulations of tidal-to-mesoscale dynamics in the Middle Atlantic Bight and Shelbreak Front region. The effects of tidal currents, strong wind events, coastal jets, and shelfbreak fronts on the energy-optimal paths are illustrated and quantified. Results showcase the opportunities for longer-duration missions that intelligently utilize the ocean environment to save energy, rigorously integrating ocean forecasting with optimal control of autonomous vehicles.

Control of base-excited dynamical systems through piezoelectric energy harvesting absorber

NASA Astrophysics Data System (ADS)

Abdelmoula, H.; Dai, H. L.; Abdelkefi, A.; Wang, L.

2017-09-01

The spring-mass absorber usually offers a good control to dynamical systems under direct base excitations for a specific value of the excitation frequency. As the vibrational energy of a primary dynamical system is transferred to the absorber, it gets dissipated. In this study, this energy is no longer dissipated but converted to available electrical power by designing efficient energy harvesters. A novel design of a piezoelectric beam installed inside an elastically-mounted dynamical system undergoing base excitations is considered. A design is carried out in order to determine the properties and dimensions of the energy harvester with the constraint of simultaneously decreasing the oscillating amplitudes of the primary dynamical system and increasing the harvested power of the energy harvesting absorber. An analytical model for the coupled system is constructed using Euler-Lagrange principle and Galerkin discretization. Different strategies for controlling the primary structure displacement and enhancing the harvested power as functions of the electrical load resistance and thickness of the beam substrate are performed. The linear polynomial approximation of the system’s key parameters as a function of the beam’s substrate thickness is first carried out. Then, the gradient method is applied to determine the adequate values of the electrical load resistance and thickness of the substrate under the constraints of minimizing the amplitudes of the primary structure or maximizing the levels of the harvested power. After that, an iterative strategy is considered in order to simultaneously minimize the amplitudes of the primary structure and maximize the levels of the harvested power as functions of the thickness of the substrate and electrical load resistance. In addition to harmonic excitations, the coupled system subjected to a white noise is explored. Through this analysis, the load resistance and thickness of the substrate of the piezoelectric energy harvester are determined. It is shown that, in addition to efficiently control the oscillating amplitudes of the primary structure, broadband resonance regions can take place and hence high levels of the harvested power are obtained.

Accurate calculation of dynamic Stark shifts and depopulation rates of Rydberg energy levels induced by blackbody radiation. Hydrogen, helium, and alkali-metal atoms

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

Farley, J.W.; Wing, W.H.

1981-05-01

A highly excited (Rydberg) atom bathed in blackbody radiation is perturbed in two ways. A dynamic Stark shift is induced by the off-resonant components of the blackbody radiation. Additionally, electric-dipole transitions to other atomic energy levels are induced by the resonant components of the blackbody radiation. This depopulation effect shortens the Rydberg-state lifetime, thereby broadening the energy level. Calculations of these two effects in many states of hydrogen, helium, and the alkali-metal atoms Li, Na, K, Rb, and Cs are presented for T = 300 K. Contributions from the entire blackbody spectrum and from both discrete and continuous perturbing statesmore » are included. The accuracy is considerably greater than that of previous estimates.« less

Increasing the Lifetime of Mobile WSNs via Dynamic Optimization of Sensor Node Communication Activity

PubMed Central

Guimarães, Dayan Adionel; Sakai, Lucas Jun; Alberti, Antonio Marcos; de Souza, Rausley Adriano Amaral

2016-01-01

In this paper, a simple and flexible method for increasing the lifetime of fixed or mobile wireless sensor networks is proposed. Based on past residual energy information reported by the sensor nodes, the sink node or another central node dynamically optimizes the communication activity levels of the sensor nodes to save energy without sacrificing the data throughput. The activity levels are defined to represent portions of time or time-frequency slots in a frame, during which the sensor nodes are scheduled to communicate with the sink node to report sensory measurements. Besides node mobility, it is considered that sensors’ batteries may be recharged via a wireless power transmission or equivalent energy harvesting scheme, bringing to the optimization problem an even more dynamic character. We report large increased lifetimes over the non-optimized network and comparable or even larger lifetime improvements with respect to an idealized greedy algorithm that uses both the real-time channel state and the residual energy information. PMID:27657075

Increasing the Lifetime of Mobile WSNs via Dynamic Optimization of Sensor Node Communication Activity.

PubMed

Guimarães, Dayan Adionel; Sakai, Lucas Jun; Alberti, Antonio Marcos; de Souza, Rausley Adriano Amaral

2016-09-20

In this paper, a simple and flexible method for increasing the lifetime of fixed or mobile wireless sensor networks is proposed. Based on past residual energy information reported by the sensor nodes, the sink node or another central node dynamically optimizes the communication activity levels of the sensor nodes to save energy without sacrificing the data throughput. The activity levels are defined to represent portions of time or time-frequency slots in a frame, during which the sensor nodes are scheduled to communicate with the sink node to report sensory measurements. Besides node mobility, it is considered that sensors' batteries may be recharged via a wireless power transmission or equivalent energy harvesting scheme, bringing to the optimization problem an even more dynamic character. We report large increased lifetimes over the non-optimized network and comparable or even larger lifetime improvements with respect to an idealized greedy algorithm that uses both the real-time channel state and the residual energy information.

Nonlinear modeling, strength-based design, and testing of flexible piezoelectric energy harvesters under large dynamic loads for rotorcraft applications

NASA Astrophysics Data System (ADS)

Leadenham, Stephen; Erturk, Alper

2014-04-01

There has been growing interest in enabling wireless health and usage monitoring for rotorcraft applications, such as helicopter rotor systems. Large dynamic loads and acceleration fluctuations available in these environments make the implementation of vibration-based piezoelectric energy harvesters a very promising choice. However, such extreme loads transmitted to the harvester can also be detrimental to piezoelectric laminates and overall system reliability. Particularly flexible resonant cantilever configurations tuned to match the dominant excitation frequency can be subject to very large deformations and failure of brittle piezoelectric laminates due to excessive bending stresses at the root of the harvester. Design of resonant piezoelectric energy harvesters for use in these environments require nonlinear electroelastic dynamic modeling and strength-based analysis to maximize the power output while ensuring that the harvester is still functional. This paper presents a mathematical framework to design and analyze the dynamics of nonlinear flexible piezoelectric energy harvesters under large base acceleration levels. A strength-based limit is imposed to design the piezoelectric energy harvester with a proof mass while accounting for material, geometric, and dissipative nonlinearities, with a focus on two demonstrative case studies having the same linear fundamental resonance frequency but different overhang length and proof mass values. Experiments are conducted at different excitation levels for validation of the nonlinear design approach proposed in this work. The case studies in this work reveal that harvesters exhibiting similar behavior and power generation performance at low excitation levels (e.g. less than 0.1g) can have totally different strength-imposed performance limitations under high excitations (e.g. above 1g). Nonlinear modeling and strength-based design is necessary for such excitation levels especially when using resonant cantilevers with no geometric constraint.

Stochastic Energy Deployment System

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

2011-11-30

SEDS is an economy-wide energy model of the U.S. The model captures dynamics between supply, demand, and pricing of the major energy types consumed and produced within the U.S. These dynamics are captured by including: the effects of macroeconomics; the resources and costs of primary energy types such as oil, natural gas, coal, and biomass; the conversion of primary fuels into energy products like petroleum products, electricity, biofuels, and hydrogen; and lastly the end- use consumption attributable to residential and commercial buildings, light and heavy transportation, and industry. Projections from SEDS extend to the year 2050 by one-year time stepsmore » and are generally projected at the national level. SEDS differs from other economy-wide energy models in that it explicitly accounts for uncertainty in technology, markets, and policy. SEDS has been specifically developed to avoid the computational burden, and sometimes fruitless labor, that comes from modeling significantly low-level details. Instead, SEDS focuses on the major drivers within the energy economy and evaluates the impact of uncertainty around those drivers.« less

Relation between the Dynamics of Glassy Clusters and Characteristic Features of their Energy Landscape

NASA Astrophysics Data System (ADS)

De, Sandip; Schaefer, Bastian; Sadeghi, Ali; Sicher, Michael; Kanhere, D. G.; Goedecker, Stefan

2014-02-01

Based on a recently introduced metric for measuring distances between configurations, we introduce distance-energy (DE) plots to characterize the potential energy surface of clusters. Producing such plots is computationally feasible on the density functional level since it requires only a few hundred stable low energy configurations including the global minimum. By using standard criteria based on disconnectivity graphs and the dynamics of Lennard-Jones clusters, we show that the DE plots convey the necessary information about the character of the potential energy surface and allow us to distinguish between glassy and nonglassy systems. We then apply this analysis to real clusters at the density functional theory level and show that both glassy and nonglassy clusters can be found in simulations. It turns out that among our investigated clusters only those can be synthesized experimentally which exhibit a nonglassy landscape.

Cache Energy Optimization Techniques For Modern Processors

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

Mittal, Sparsh

2013-01-01

Modern multicore processors are employing large last-level caches, for example Intel's E7-8800 processor uses 24MB L3 cache. Further, with each CMOS technology generation, leakage energy has been dramatically increasing and hence, leakage energy is expected to become a major source of energy dissipation, especially in last-level caches (LLCs). The conventional schemes of cache energy saving either aim at saving dynamic energy or are based on properties specific to first-level caches, and thus these schemes have limited utility for last-level caches. Further, several other techniques require offline profiling or per-application tuning and hence are not suitable for product systems. In thismore » book, we present novel cache leakage energy saving schemes for single-core and multicore systems; desktop, QoS, real-time and server systems. Also, we present cache energy saving techniques for caches designed with both conventional SRAM devices and emerging non-volatile devices such as STT-RAM (spin-torque transfer RAM). We present software-controlled, hardware-assisted techniques which use dynamic cache reconfiguration to configure the cache to the most energy efficient configuration while keeping the performance loss bounded. To profile and test a large number of potential configurations, we utilize low-overhead, micro-architecture components, which can be easily integrated into modern processor chips. We adopt a system-wide approach to save energy to ensure that cache reconfiguration does not increase energy consumption of other components of the processor. We have compared our techniques with state-of-the-art techniques and have found that our techniques outperform them in terms of energy efficiency and other relevant metrics. The techniques presented in this book have important applications in improving energy-efficiency of higher-end embedded, desktop, QoS, real-time, server processors and multitasking systems. This book is intended to be a valuable guide for both newcomers and veterans in the field of cache power management. It will help graduate students, CAD tool developers and designers in understanding the need of energy efficiency in modern computing systems. Further, it will be useful for researchers in gaining insights into algorithms and techniques for micro-architectural and system-level energy optimization using dynamic cache reconfiguration. We sincerely believe that the ``food for thought'' presented in this book will inspire the readers to develop even better ideas for designing ``green'' processors of tomorrow.« less

Evaluation of energy absorbers for use in a roadside/median barrier.

DOT National Transportation Integrated Search

2014-02-01

Several types of elastomeric energy absorbers were evaluated for use in a Manual for Assessing Safety Hardware (MASH) : Test Level 4 (TL-4) energy-absorbing, urban roadside/median barrier. Twelve dynamic bogie tests were conducted on 60- : and 80-dur...

First-Principles Approach to Energy Level Alignment at Aqueous Semiconductor Interfaces

NASA Astrophysics Data System (ADS)

Hybertsen, Mark

2015-03-01

We have developed a first principles method to calculate the energy level alignment between semiconductor band edges and reference energy levels at aqueous interfaces. This alignment is fundamental to understand the electrochemical characteristics of any semiconductor electrode in general and the potential for photocatalytic activity in particular. For example, in the search for new photo-catalytic materials, viable candidates must demonstrate both efficient absorption of the solar spectrum and an appropriate alignment of the band edge levels in the semiconductor to the redox levels for the target reactions. In our approach, the interface-specific contribution to the electrostatic step across the interface is evaluated using density functional theory (DFT) based molecular dynamics to sample the physical interface structure and the corresponding change in the electrostatic potential at the interface. The reference electronic levels in the semiconductor and in the water are calculated using the GW approach, which naturally corrects for errors inherent in the use of Kohn-Sham energy eigenvalues to approximate the electronic excitation energies in each material. Taken together, our calculations provide the alignment of the semiconductor valence band edge to the centroid of the highest occupied 1b1 level in water. The known relationship of the 1b1 level to the normal hydrogen electrode completes the connection to electrochemical levels. We discuss specific results for GaN, ZnO, and TiO2. The effect of interface structural motifs, such as different degrees of water dissociation, and of dynamical characteristics, will be presented together with available experimental data. Work supported by the US Department of Energy, Office of Basic Energy Sciences under Contract No. DE-AC02-98CH10886.

From ab Initio Potential Energy Surfaces to State-Resolved Reactivities: X + H 2O ↔ HX + OH [X = F, Cl, and O( 3P)] Reactions

DOE PAGES

Li, Jun; Jiang, Bin; Song, Hongwei; ...

2015-04-17

Here, we survey the recent advances in theoretical understanding of quantum state resolved dynamics, using the title reactions as examples. It is shown that the progress was made possible by major developments in two areas. First, an accurate analytical representation of many high-level ab initio points over a large configuration space can now be made with high fidelity and the necessary permutation symmetry. The resulting full-dimensional global potential energy surfaces enable dynamical calculations using either quasi-classical trajectory or more importantly quantum mechanical methods. The second advance is the development of accurate and efficient quantum dynamical methods, which are necessary formore » providing a reliable treatment of quantum effects in reaction dynamics such as tunneling, resonances, and zero-point energy. The powerful combination of the two advances has allowed us to achieve a quantitatively accurate characterization of the reaction dynamics, which unveiled rich dynamical features such as steric steering, strong mode specificity, and bond selectivity. The dependence of reactivity on reactant modes can be rationalized by the recently proposed sudden vector projection model, which attributes the mode specificity and bond selectivity to the coupling of reactant modes with the reaction coordinate at the relevant transition state. The deeper insights provided by these theoretical studies have advanced our understanding of reaction dynamics to a new level.« less

Dynamical resource nexus assessments: from accounting to sustainability approaches

NASA Astrophysics Data System (ADS)

Salmoral, Gloria; Yan, Xiaoyu

2017-04-01

Continued economic development and population growth result in increasing pressures on natural resources, from local to international levels, for meeting societal demands on water, energy and food. To date there are a few tools that link models to identify the relationships and to account for flows of water, energy and food. However, these tools in general can offer only a static view often at national level and with annual temporal resolution. Moreover, they can only account flows but cannot consider the required amounts and conditions of the natural capital that supplies and maintains these flows. With the emerging nexus thinking, our research is currently focused on promoting dynamical environmental analyses beyond the conventional silo mentalities. Our study aims to show new advancements in existing tools (e.g., dynamical life cycle assessment) and develop novel environmental indicators relevant for the resource nexus assessment. We aim to provide a step forward when sustainability conditions and resilience thresholds are aligned with flows under production (e.g., food, water and energy), process level under analysis (e.g., local production, transport, manufacturing, final consumption, reuse, disposal) and existing biophysical local conditions. This approach would help to embrace and better characterise the spatiotemporal dynamics, complexity and existing links between and within the natural and societal systems, which are crucial to evaluate and promote more environmentally sustainable economic activities.

Chemical dynamics simulations of X- + CH3Y → XCH3 + Y- gas-phase S(N)2 nucleophilic substitution reactions. Nonstatistical dynamics and nontraditional reaction mechanisms.

PubMed

Manikandan, Paranjothy; Zhang, Jiaxu; Hase, William L

2012-03-29

Extensive classical chemical dynamics simulations of gas-phase X(-) + CH(3)Y → XCH(3) + Y(-) S(N)2 nucleophilic substitution reactions are reviewed and discussed and compared with experimental measurements and predictions of theoretical models. The primary emphasis is on reactions for which X and Y are halogen atoms. Both reactions with the traditional potential energy surface (PES), which include pre- and postreaction potential energy minima and a central barrier, and reactions with nontraditional PESs are considered. These S(N)2 reactions exhibit important nonstatistical atomic-level dynamics. The X(-) + CH(3)Y → X(-)---CH(3)Y association rate constant is less than the capture model as a result of inefficient energy transfer from X(-)+ CH(3)Y relative translation to CH(3)Y rotation and vibration. There is weak coupling between the low-frequency intermolecular modes of the X(-)---CH(3)Y complex and higher frequency CH(3)Y intramolecular modes, resulting in non-RRKM kinetics for X(-)---CH(3)Y unimolecular decomposition. Recrossings of the [X--CH(3)--Y](-) central barrier is important. As a result of the above dynamics, the relative translational energy and temperature dependencies of the S(N)2 rate constants are not accurately given by statistical theory. The nonstatistical dynamics results in nonstatistical partitioning of the available energy to XCH(3) +Y(-) reaction products. Besides the indirect, complex forming atomic-level mechanism for the S(N)2 reaction, direct mechanisms promoted by X(-) + CH(3)Y relative translational or CH(3)Y vibrational excitation are possible, e.g., the roundabout mechanism.

A topological classification of the Chaplygin systems in the dynamics of a rigid body in a fluid

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

Nikolaenko, S S

2014-02-28

The paper is concerned with the topological analysis of the Chaplygin integrable case in the dynamics of a rigid body in a fluid. A full list of the topological types of Chaplygin systems in their dependence on the energy level is compiled on the basis of the Fomenko-Zieschang theory. An effective description of the topology of the Liouville foliation in terms of natural coordinate variables is also presented, which opens a direct way to calculating topological invariants. It turns out that on all nonsingular energy levels Chaplygin systems are Liouville equivalent to the well-known Euler case in the dynamics of a rigid body withmore » fixed point. Bibliography: 23 titles.« less

Topological classification of the Goryachev integrable case in rigid body dynamics

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

Nikolaenko, S S

2016-01-31

A topological analysis of the Goryachev integrable case in rigid body dynamics is made on the basis of the Fomenko-Zieschang theory. The invariants (marked molecules) which are obtained give a complete description, from the standpoint of Liouville classification, of the systems of Goryachev type on various level sets of the energy. It turns out that on appropriate energy levels the Goryachev case is Liouville equivalent to many classical integrable systems and, in particular, the Joukowski, Clebsch, Sokolov and Kovalevskaya-Yehia cases in rigid body dynamics, as well as to some integrable billiards in plane domains bounded by confocal quadrics -- in othermore » words, the foliations given by the closures of generic solutions of these systems have the same structure. Bibliography: 15 titles.« less

Dynamics of coherent states in regular and chaotic regimes of the non-integrable Dicke model

NASA Astrophysics Data System (ADS)

Lerma-Hernández, S.; Chávez-Carlos, J.; Bastarrachea-Magnani, M. A.; López-del-Carpio, B.; Hirsch, J. G.

2018-04-01

The quantum dynamics of initial coherent states is studied in the Dicke model and correlated with the dynamics, regular or chaotic, of their classical limit. Analytical expressions for the survival probability, i.e. the probability of finding the system in its initial state at time t, are provided in the regular regions of the model. The results for regular regimes are compared with those of the chaotic ones. It is found that initial coherent states in regular regions have a much longer equilibration time than those located in chaotic regions. The properties of the distributions for the initial coherent states in the Hamiltonian eigenbasis are also studied. It is found that for regular states the components with no negligible contribution are organized in sequences of energy levels distributed according to Gaussian functions. In the case of chaotic coherent states, the energy components do not have a simple structure and the number of participating energy levels is larger than in the regular cases.

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

Mittal, Sparsh; Zhang, Zhao

With each CMOS technology generation, leakage energy consumption has been dramatically increasing and hence, managing leakage power consumption of large last-level caches (LLCs) has become a critical issue in modern processor design. In this paper, we present EnCache, a novel software-based technique which uses dynamic profiling-based cache reconfiguration for saving cache leakage energy. EnCache uses a simple hardware component called profiling cache, which dynamically predicts energy efficiency of an application for 32 possible cache configurations. Using these estimates, system software reconfigures the cache to the most energy efficient configuration. EnCache uses dynamic cache reconfiguration and hence, it does not requiremore » offline profiling or tuning the parameter for each application. Furthermore, EnCache optimizes directly for the overall memory subsystem (LLC and main memory) energy efficiency instead of the LLC energy efficiency alone. The experiments performed with an x86-64 simulator and workloads from SPEC2006 suite confirm that EnCache provides larger energy saving than a conventional energy saving scheme. For single core and dual-core system configurations, the average savings in memory subsystem energy over a shared baseline configuration are 30.0% and 27.3%, respectively.« less

Photoinduced Ultrafast Intramolecular Excited-State Energy Transfer in the Silylene-Bridged Biphenyl and Stilbene (SBS) System: A Nonadiabatic Dynamics Point of View.

PubMed

Wang, Jun; Huang, Jing; Du, Likai; Lan, Zhenggang

2015-07-09

The photoinduced intramolecular excited-state energy-transfer (EET) process in conjugated polymers has received a great deal of research interest because of its important role in the light harvesting and energy transport of organic photovoltaic materials in photoelectric devices. In this work, the silylene-bridged biphenyl and stilbene (SBS) system was chosen as a simplified model system to obtain physical insight into the photoinduced intramolecular energy transfer between the different building units of the SBS copolymer. In the SBS system, the vinylbiphenyl and vinylstilbene moieties serve as the donor (D) unit and the acceptor (A) unit, respectively. The ultrafast excited-state dynamics of the SBS system was investigated from the point of view of nonadiabatic dynamics with the surface-hopping method at the TDDFT level. The first two excited states (S1 and S2) are characterized by local excitations at the acceptor (vinylstilbene) and donor (vinylbiphenyl) units, respectively. Ultrafast S2-S1 decay is responsible for the intramolecular D-A excitonic energy transfer. The geometric distortion of the D moiety play an essential role in this EET process, whereas the A moiety remains unchanged during the nonadiabatic dynamics simulation. The present work provides a direct dynamical approach to understand the ultrafast intramolecular energy-transfer dynamics in SBS copolymers and other similar organic photovoltaic copolymers.

Applied Dynamic Analysis of the Global Economy (ADAGE)

EPA Science Inventory

ADAGE is a dynamic computable general equilibrium (CGE) model capable of examining many types of economic, energy, environmental, climate change mitigation, and trade policies at the international, national, U.S. regional, and U.S. state levels. To investigate proposed policy eff...

Photoionization dynamics of ammonia (B(1)E''): dependence on ionizing photon energy and initial vibrational level.

PubMed

Hockett, Paul; Staniforth, Michael; Reid, Katharine L

2010-10-28

In this article we present photoelectron spectra and angular distributions in which ion rotational states are resolved. This data enables the comparison of direct and threshold photoionization techniques. We also present angle-resolved photoelectron signals at different total energies, providing a method to scan the structure of the continuum in the near-threshold region. Finally, we have studied the influence of vibrational excitation on the photoionization dynamics.

Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces.

PubMed

Szabó, István; Czakó, Gábor

2017-11-30

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F - + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle and product internal energy distributions, and (h) significant leaving group effect in accord with experiments.

Relative Energy Shift of a Two-Level Atom in a Cylindrical Spacetime

NASA Astrophysics Data System (ADS)

Zhang, Jia-Lin

2012-11-01

We investigate the evolution dynamics of a two-level atom system interacting with the massless scalar field in a Cylindrical spacetime. We find that both the energy shifts of ground state and excited state can be separated into two parts due to the vacuum fluctuations. One is the corresponding energy shift for a rest atom in four-dimensional Minkowski space without spatial compactification, the other is just the modification of the spatial compactified periodic length. It will reveal that the influence of the presence of one spatial compactified dimension can not be neglected in Lamb shift as the relative energy level shift of an atom.

Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects

NASA Astrophysics Data System (ADS)

Alakent, Burak; Camurdan, Mehmet C.; Doruker, Pemra

2005-10-01

Time series analysis tools are employed on the principal modes obtained from the Cα trajectories from two independent molecular-dynamics simulations of α-amylase inhibitor (tendamistat). Fluctuations inside an energy minimum (intraminimum motions), transitions between minima (interminimum motions), and relaxations in different hierarchical energy levels are investigated and compared with those encountered in vacuum by using different sampling window sizes and intervals. The low-frequency low-indexed mode relationship, established in vacuum, is also encountered in water, which shows the reliability of the important dynamics information offered by principal components analysis in water. It has been shown that examining a short data collection period (100ps) may result in a high population of overdamped modes, while some of the low-frequency oscillations (<10cm-1) can be captured in water by using a longer data collection period (1200ps). Simultaneous analysis of short and long sampling window sizes gives the following picture of the effect of water on protein dynamics. Water makes the protein lose its memory: future conformations are less dependent on previous conformations due to the lowering of energy barriers in hierarchical levels of the energy landscape. In short-time dynamics (<10ps), damping factors extracted from time series model parameters are lowered. For tendamistat, the friction coefficient in the Langevin equation is found to be around 40-60cm-1 for the low-indexed modes, compatible with literature. The fact that water has increased the friction and that on the other hand has lubrication effect at first sight contradicts. However, this comes about because water enhances the transitions between minima and forces the protein to reduce its already inherent inability to maintain oscillations observed in vacuum. Some of the frequencies lower than 10cm-1 are found to be overdamped, while those higher than 20cm-1 are slightly increased. As for the long-time dynamics in water, it is found that random-walk motion is maintained for approximately 200ps (about five times of that in vacuum) in the low-indexed modes, showing the lowering of energy barriers between the higher-level minima.

Assessment of contribution of Australia's energy production to CO2 emissions and environmental degradation using statistical dynamic approach.

PubMed

Sarkodie, Samuel Asumadu; Strezov, Vladimir

2018-10-15

Energy production remains the major emitter of atmospheric emissions, thus, in accordance with Australia's Emissions Projections by 2030, this study analyzed the impact of Australia's energy portfolio on environmental degradation and CO 2 emissions using locally compiled data on disaggregate energy production, energy imports and exports spanning from 1974 to 2013. This study employed the fully modified ordinary least squares, dynamic ordinary least squares, and canonical cointegrating regression estimators; statistically inspired modification of partial least squares regression analysis with a subsequent sustainability sensitivity analysis. The validity of the environmental Kuznets curve hypothesis proposes a paradigm shift from energy-intensive and carbon-intensive industries to less-energy-intensive and green energy industries and its related services, leading to a structural change in the economy. Thus, decoupling energy services provide better interpretation of the role of the energy sector portfolio in environmental degradation and CO 2 emissions assessment. The sensitivity analysis revealed that nonrenewable energy production above 10% and energy imports above 5% will dampen the goals for the 2030 emission reduction target. Increasing the share of renewable energy penetration in the energy portfolio decreases the level of CO 2 emissions, while increasing the share of non-renewable energy sources in the energy mix increases the level of atmospheric emissions, thus increasing climate change and their impacts. Copyright © 2018 Elsevier B.V. All rights reserved.

Fission dynamics with microscopic level densities

NASA Astrophysics Data System (ADS)

Randrup, Jørgen; Ward, Daniel; Carlsson, Gillis; Døssing, Thomas; Möller, Peter; Åberg, Sven

2018-03-01

Working within the Langevin framework of nuclear shape dynamics, we study the dependence of the evolution on the degree of excitation. As the excitation energy of the fissioning system is increased, the pairing correlations and the shell effects diminish and the effective potential-energy surface becomes ever more liquid-drop like. This feature can be included in the treatment in a formally well-founded manner by using the local level densities as a basis for the shape evolution. This is particularly easy to understand and implement in the Metropolis treatment where the evolution is simulated by means of a random walk on the five-dimensional lattice of shapes for which the potential energy has been tabulated. Because the individual steps between two neighboring lattice sites are decided on the basis of the ratio of the statistical weights, what is needed is the ratio of the local level densities for those shapes, evaluated at the associated local excitation energies. For this purpose, we adapt a recently developed combinatorial method for calculating level densities which employs the same single-particle levels as those that were used for the calculation of the pairing and shell contributions to the macroscopic-microscopic deformation-energy surface. For each nucleus under consideration, the level density (for a fixed total angular momentum) is calculated microscopically for each of the over five million shapes given in the three-quadratic-surface parametrization. This novel treatment, which introduces no new parameters, is illustrated for the fission fragment mass distributions for selected uranium and plutonium cases.

Microsecond protein dynamics observed at the single-molecule level

NASA Astrophysics Data System (ADS)

Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

2015-07-01

How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape.

Microsecond protein dynamics observed at the single-molecule level

PubMed Central

Otosu, Takuhiro; Ishii, Kunihiko; Tahara, Tahei

2015-01-01

How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape. PMID:26151767

First-principles quantum dynamical theory for the dissociative chemisorption of H2O on rigid Cu(111)

PubMed Central

Zhang, Zhaojun; Liu, Tianhui; Fu, Bina; Yang, Xueming; Zhang, Dong H.

2016-01-01

Despite significant progress made in the past decades, it remains extremely challenging to investigate the dissociative chemisorption dynamics of molecular species on surfaces at a full-dimensional quantum mechanical level, in particular for polyatomic-surface reactions. Here we report, to the best of our knowledge, the first full-dimensional quantum dynamics study for the dissociative chemisorption of H2O on rigid Cu(111) with all the nine molecular degrees of freedom fully coupled, based on an accurate full-dimensional potential energy surface. The full-dimensional quantum mechanical reactivity provides the dynamics features with the highest accuracy, revealing that the excitations in vibrational modes of H2O are more efficacious than increasing the translational energy in promoting the reaction. The enhancement of the excitation in asymmetric stretch is the largest, but that of symmetric stretch becomes comparable at very low energies. The full-dimensional characterization also allows the investigation of the validity of previous reduced-dimensional and approximate dynamical models. PMID:27283908

Motion-mode energy method for vehicle dynamics analysis and control

NASA Astrophysics Data System (ADS)

Zhang, Nong; Wang, Lifu; Du, Haiping

2014-01-01

Vehicle motion and vibration control is a fundamental motivation for the development of advanced vehicle suspension systems. In a vehicle-fixed coordinate system, the relative motions of the vehicle between body and wheel can be classified into several dynamic stages based on energy intensity, and can be decomposed into sets of uncoupled motion-modes according to modal parameters. Vehicle motions are coupled, but motion-modes are orthogonal. By detecting and controlling the predominating vehicle motion-mode, the system cost and energy consumption of active suspensions could be reduced. A motion-mode energy method (MEM) is presented in this paper to quantify the energy contribution of each motion-mode to vehicle dynamics in real time. The control of motion-modes is prioritised according to the level of motion-mode energy. Simulation results on a 10 degree-of-freedom nonlinear full-car model with the magic-formula tyre model illustrate the effectiveness of the proposed MEM. The contribution of each motion-mode to the vehicle's dynamic behaviour is analysed under different excitation inputs from road irregularities, directional manoeuvres and braking. With the identified dominant motion-mode, novel cost-effective suspension systems, such as active reconfigurable hydraulically interconnected suspension, can possibly be used to control full-car motions with reduced energy consumption. Finally, discussion, conclusions and suggestions for future work are provided.

A Back-to-Front Derivation: The Equal Spacing of Quantum Levels Is a Proof of Simple Harmonic Oscillator Physics

ERIC Educational Resources Information Center

Andrews, David L.; Romero, Luciana C. Davila

2009-01-01

The dynamical behaviour of simple harmonic motion can be found in numerous natural phenomena. Within the quantum realm of atomic, molecular and optical systems, two main features are associated with harmonic oscillations: a finite ground-state energy and equally spaced quantum energy levels. Here it is shown that there is in fact a one-to-one…

Monitoring ATP dynamics in electrically active white matter tracts

PubMed Central

Trevisiol, Andrea; Saab, Aiman S; Winkler, Ulrike; Marx, Grit; Imamura, Hiromi; Möbius, Wiebke; Kusch, Kathrin; Nave, Klaus-Armin; Hirrlinger, Johannes

2017-01-01

In several neurodegenerative diseases and myelin disorders, the degeneration profiles of myelinated axons are compatible with underlying energy deficits. However, it is presently impossible to measure selectively axonal ATP levels in the electrically active nervous system. We combined transgenic expression of an ATP-sensor in neurons of mice with confocal FRET imaging and electrophysiological recordings of acutely isolated optic nerves. This allowed us to monitor dynamic changes and activity-dependent axonal ATP homeostasis at the cellular level and in real time. We find that changes in ATP levels correlate well with compound action potentials. However, this correlation is disrupted when metabolism of lactate is inhibited, suggesting that axonal glycolysis products are not sufficient to maintain mitochondrial energy metabolism of electrically active axons. The combined monitoring of cellular ATP and electrical activity is a novel tool to study neuronal and glial energy metabolism in normal physiology and in models of neurodegenerative disorders. DOI: http://dx.doi.org/10.7554/eLife.24241.001 PMID:28414271

Observation of Water-Protein Interaction Dynamics with Broadband Two-Dimensional Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

De Marco, Luigi; Haky, Andrew; Tokmakoff, Andrei

Two-dimensional infrared (2D IR) spectroscopy has proven itself an indispensable tool for studying molecular dynamics and intermolecular interactions on ultrafast timescales. Using a novel source of broadband mid-IR pulses, we have collected 2D IR spectra of protein films at varying levels of hydration. With 2D IR, we can directly observe coupling between water's motions and the protein's. Protein films provide us with the ability to discriminate hydration waters from bulk water and thus give us access to studying water dynamics along the protein backbone, fluctuations in the protein structure, and the interplay between the molecular dynamics of the two. We present two representative protein films: poly-L-proline (PLP) and hen egg-white lysozyme (HEWL). Having no N-H groups, PLP allows us to look at water dynamics without interference from resonant energy transfer between the protein N-H stretch and the water O-H stretch. We conclude that at low hydration levels water-protein interactions dominate, and the water's dynamics are tied to those of the protein. In HEWL films, we take advantage of the robust secondary structure to partially deuterate the film, allowing us to spectrally distinguish the protein core from the exterior. From this, we show that resonant energy transfer to water provides an effective means of dissipating excess energy within the protein, while maintaining the structure. These methods are general and can easily be extended to studying specific protein-water interactions.

Consequences of the dynamic triple peak impact factor in Traumatic Brain Injury as Measured with Numerical Simulation.

PubMed

von Holst, Hans; Li, Xiaogai

2013-01-01

There is a lack of knowledge about the direct neuromechanical consequences in traumatic brain injury (TBI) at the scene of accident. In this study we use a finite element model of the human head to study the dynamic response of the brain during the first milliseconds after the impact with velocities of 10, 6, and 2 meters/second (m/s), respectively. The numerical simulation was focused on the external kinetic energy transfer, intracranial pressure (ICP), strain energy density and first principal strain level, and their respective impacts to the brain tissue. We show that the oblique impacts of 10 and 6 m/s resulted in substantial high peaks for the ICP, strain energy density, and first principal strain levels, however, with different patterns and time frames. Also, the 2 m/s impact showed almost no increase in the above mentioned investigated parameters. More importantly, we show that there clearly exists a dynamic triple peak impact factor to the brain tissue immediately after the impact regardless of injury severity associated with different impact velocities. The dynamic triple peak impacts occurred in a sequential manner first showing strain energy density and ICP and then followed by first principal strain. This should open up a new dimension to better understand the complex mechanisms underlying TBI. Thus, it is suggested that the combination of the dynamic triple peak impacts to the brain tissue may interfere with the cerebral metabolism relative to the impact severity thereby having the potential to differentiate between severe and moderate TBI from mild TBI.

Dual-level direct dynamics studies for the hydrogen abstraction reaction of 1,1-difluoroethane with O( 3P)

NASA Astrophysics Data System (ADS)

Liu, Jing-yao; Li, Ze-sheng; Dai, Zhen-wen; Zhang, Gang; Sun, Chia-chung

2004-01-01

We present dual-level direct dynamics calculations for the CH 3CHF 2 + O( 3P) hydrogen abstraction reaction in a wide temperature range, based on canonical variational transition-state theory including small curvature tunneling corrections. For this reaction, three distinct transition states, one for α-abstraction and two for β-abstraction, have been located. The potential energy surface information is obtained at the MP2(full)/6-311G(d,p) level of theory, and higher-level single-point calculations for the stationary points are preformed at several levels, namely QCISD(T)/6-311+G(3df,3pd), G2, and G3 using the MP2 geometries, as well as at the G3//MP4SDQ/6-311G(d,p) level. The energy profiles are further refined with the interpolated single-point energies method at the G3//MP2(full)/6-311G(d,p) level. The total rate constants match the experimental data reasonable well in the measured temperature range 1110-1340 K. It is shown that at low temperature α-abstraction may be the major reaction channel, while β-abstraction will have more contribution to the whole reaction rate as the temperature increases.

Earthquake fracture energy inferred from kinematic rupture models on extended faults

USGS Publications Warehouse

Tinti, E.; Spudich, P.; Cocco, M.

2005-01-01

We estimate fracture energy on extended faults for several recent earthquakes by retrieving dynamic traction evolution at each point on the fault plane from slip history imaged by inverting ground motion waveforms. We define the breakdown work (Wb) as the excess of work over some minimum traction level achieved during slip. Wb is equivalent to "seismological" fracture energy (G) in previous investigations. Our numerical approach uses slip velocity as a boundary condition on the fault. We employ a three-dimensional finite difference algorithm to compute the dynamic traction evolution in the time domain during the earthquake rupture. We estimate Wb by calculating the scalar product between dynamic traction and slip velocity vectors. This approach does not require specifying a constitutive law and assuming dynamic traction to be collinear with slip velocity. If these vectors are not collinear, the inferred breakdown work depends on the initial traction level. We show that breakdown work depends on the square of slip. The spatial distribution of breakdown work in a single earthquake is strongly correlated with the slip distribution. Breakdown work density and its integral over the fault, breakdown energy, scale with seismic moment according to a power law (with exponent 0.59 and 1.18, respectively). Our estimates of breakdown work range between 4 ?? 105 and 2 ?? 107 J/m2 for earthquakes having moment magnitudes between 5.6 and 7.2. We also compare our inferred values with geologic surface energies. This comparison might suggest that breakdown work for large earthquakes goes primarily into heat production. Copyright 2005 by the American Geophysical Union.

Dynamic Energy Loss Characteristics in the Native Aortic Valve

NASA Astrophysics Data System (ADS)

Hwai Yap, Choon; Dasi, Laksmi P.; Yoganathan, Ajit P.

2009-11-01

Aortic Valve (AV) stenosis if untreated leads to heart failure. From a mechanics standpoint, heart failure implies failure to generate sufficient mechanical power to overcome energy losses in the circulation. Thus energy efficiency-based measures are direct measures of AV disease severity, which unfortunately is not used in current clinical measures of stenosis severity. We present an analysis of the dynamic rate of energy dissipation through the AV from direct high temporal resolution measurements of flow and pressure drop across the AV in a pulsatile left heart setup. Porcine AV was used and measurements at various conditions were acquired: varying stroke volumes; heart rates; and stenosis levels. Energy dissipation waveform has a distinctive pattern of being skewed towards late systole, attributed to the explosive growth of flow instabilities from adverse pressure gradient. Increasing heart rate and stroke volume increases energy dissipation, but does not alter the normalized shape of the dissipation temporal profile. Stenosis increases energy dissipation and also alters the normalized shape of dissipation waveform with significantly more losses during late acceleration phase. Since stenosis produces a departure from the signature dissipation waveform shape, dynamic energy dissipation analysis can be extended into a clinical tool for AV evaluation.

Beyond Group: Multiple Person Tracking via Minimal Topology-Energy-Variation.

PubMed

Gao, Shan; Ye, Qixiang; Xing, Junliang; Kuijper, Arjan; Han, Zhenjun; Jiao, Jianbin; Ji, Xiangyang

2017-12-01

Tracking multiple persons is a challenging task when persons move in groups and occlude each other. Existing group-based methods have extensively investigated how to make group division more accurately in a tracking-by-detection framework; however, few of them quantify the group dynamics from the perspective of targets' spatial topology or consider the group in a dynamic view. Inspired by the sociological properties of pedestrians, we propose a novel socio-topology model with a topology-energy function to factor the group dynamics of moving persons and groups. In this model, minimizing the topology-energy-variance in a two-level energy form is expected to produce smooth topology transitions, stable group tracking, and accurate target association. To search for the strong minimum in energy variation, we design the discrete group-tracklet jump moves embedded in the gradient descent method, which ensures that the moves reduce the energy variation of group and trajectory alternately in the varying topology dimension. Experimental results on both RGB and RGB-D data sets show the superiority of our proposed model for multiple person tracking in crowd scenes.

Direct dynamics simulation of dioxetane formation and decomposition via the singlet .O-O-CH2-CH2. biradical: Non-RRKM dynamics

NASA Astrophysics Data System (ADS)

Sun, Rui; Park, Kyoyeon; de Jong, Wibe A.; Lischka, Hans; Windus, Theresa L.; Hase, William L.

2012-07-01

Electronic structure calculations and direct chemical dynamics simulations are used to study the formation and decomposition of dioxetane on its ground state singlet potential energy surface. The stationary points for 1O2 + C2H4, the singlet .O-O-CH2-CH2. biradical, the transition state (TS) connecting this biradical with dioxetane, and the two transition states and gauche .O-CH2-CH2-O. biradical connecting dioxetane with the formaldehyde product molecules are investigated at different levels of electronic structure theory including UB3LYP, UMP2, MRMP2, and CASSCF and a range of basis sets. The UB3LYP/6-31G* method was found to give representative energies for the reactive system and was used as a model for the simulations. UB3LYP/6-31G* direct dynamics trajectories were initiated at the TS connecting the .O-O-CH2-CH2. biradical and dioxetane by sampling the TS's vibrational energy levels, and rotational and reaction coordinate energies, with Boltzmann distributions at 300, 1000, and 1500 K. This corresponds to the transition state theory model for trajectories that pass the TS. The trajectories were directed randomly towards both the biradical and dioxetane. A small fraction of the trajectories directed towards the biradical recrossed the TS and formed dioxetane. The remainder formed 1O2 + C2H4 and of these ˜ 40% went directly from the TS to 1O2 + C2H4 without getting trapped and forming an intermediate in the .O-O-CH2-CH2. biradical potential energy minimum, a non-statistical result. The dioxetane molecules which are formed dissociate to two formaldehyde molecules with a rate constant two orders of magnitude smaller than that predicted by Rice-Ramsperger-Kassel-Marcus theory. The reaction dynamics from dioxetane to the formaldehyde molecules do not follow the intrinsic reaction coordinate or involve trapping in the gauche .O-CH2-CH2-O. biradical potential energy minimum. Important non-statistical dynamics are exhibited for this reactive system.

Ab Initio Potential Energy Surfaces and Quantum Dynamics for Polyatomic Bimolecular Reactions.

PubMed

Fu, Bina; Zhang, Dong H

2018-05-08

There has been great progress in the development of potential energy surfaces (PESs) and quantum dynamics calculations in the gas phase. The establishment of a fitting procedure for highly accurate PESs and new developments in quantum reactive scattering on reliable PESs allow accurate characterization of reaction dynamics beyond triatomic systems. This review will give the recent development in our group in constructing ab initio PESs based on neural networks and the time-dependent wave packet calculations for bimolecular reactions beyond three atoms. Bimolecular reactions of current interest to the community, namely, OH + H 2 , H + H 2 O, OH + CO, H + CH 4 , and Cl + CH 4 , are focused on. Quantum mechanical characterization of these reactions uncovers interesting dynamical phenomena with an unprecedented level of sophistication and has greatly advanced our understanding of polyatomic reaction dynamics.

Using Dynamic Time Warping and Data Forensics to Examine Tradeoffs among Land-Energy-Water Networks Across the Conterminous United States

NASA Astrophysics Data System (ADS)

McManamay, R.; Allen, M. R.; Piburn, J.; Sanyal, J.; Stewart, R.; Bhaduri, B. L.

2017-12-01

Characterizing interdependencies among land-energy-water sectors, their vulnerabilities, and tipping points, is challenging, especially if all sectors are simultaneously considered. Because such holistic system behavior is uncertain, largely unmodeled, and in need of testable hypotheses of system drivers, these dynamics are conducive to exploratory analytics of spatiotemporal patterns, powered by tools, such as Dynamic Time Warping (DTW). Here, we conduct a retrospective analysis (1950 - 2010) of temporal trends in land use, energy use, and water use within US counties to identify commonalities in resource consumption and adaptation strategies to resource limitations. We combine existing and derived data from statistical downscaling to synthesize a temporally comprehensive land-energy-water dataset at the US county level and apply DTW and subsequent hierarchical clustering to examine similar temporal trends in resource typologies for land, energy, and water sectors. As expected, we observed tradeoffs among water uses (e.g., public supply vs irrigation) and land uses (e.g., urban vs ag). Strong associations between clusters amongst sectors reveal tight system interdependencies, whereas weak associations suggest unique behaviors and potential for human adaptations towards disruptive technologies and less resource-dependent population growth. Our framework is useful for exploring complex human-environmental system dynamics and generating hypotheses to guide subsequent energy-water-nexus research.

Dynamic impact of urbanization, economic growth, energy consumption, and trade openness on CO 2 emissions in Nigeria.

PubMed

Ali, Hamisu Sadi; Law, Siong Hook; Zannah, Talha Ibrahim

2016-06-01

The objective of this paper is to examine the dynamic impact of urbanization, economic growth, energy consumption, and trade openness on CO 2 emissions in Nigeria based on autoregressive distributed lags (ARDL) approach for the period of 1971-2011. The result shows that variables were cointegrated as null hypothesis was rejected at 1 % level of significance. The coefficients of long-run result reveal that urbanization does not have any significant impact on CO 2 emissions in Nigeria, economic growth, and energy consumption has a positive and significant impact on CO 2 emissions. However, trade openness has negative and significant impact on CO 2 emissions. Consumption of energy is among the main determinant of CO 2 emissions which is directly linked to the level of income. Despite the high level of urbanization in the country, consumption of energy still remains low due to lower income of the majority populace and this might be among the reasons why urbanization does not influence emissions of CO 2 in the country. Initiating more open economy policies will be welcoming in the Nigerian economy as the openness leads to the reduction of pollutants from the environment particularly CO 2 emissions which is the major gases that deteriorate physical environment.

Componentry for lower extremity prostheses.

PubMed

Friel, Karen

2005-09-01

Prosthetic components for both transtibial and transfemoral amputations are available for patients of every level of ambulation. Most current suspension systems, knees, foot/ankle assemblies, and shock absorbers use endoskeletal construction that emphasizes total contact and weight distribution between bony structures and soft tissues. Different components offer varying benefits to energy expenditure, activity level, balance, and proprioception. Less dynamic ambulators may use fixed-cadence knees and non-dynamic response feet; higher functioning walkers benefit from dynamic response feet and variable-cadence knees. In addition, specific considerations must be kept in mind when fitting a patient with peripheral vascular disease or diabetes.

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

Tamanini, Nicola; Wright, Matthew, E-mail: nicola.tamanini@cea.fr, E-mail: matthew.wright.13@ucl.ac.uk

We investigate the cosmological dynamics of the recently proposed extended chameleon models at both background and linear perturbation levels. Dynamical systems techniques are employed to fully characterize the evolution of the universe at the largest distances, while structure formation is analysed at sub-horizon scales within the quasi-static approximation. The late time dynamical transition from dark matter to dark energy domination can be well described by almost all extended chameleon models considered, with no deviations from ΛCDM results at both background and perturbation levels. The results obtained in this work confirm the cosmological viability of extended chameleons as alternative dark energymore » models.« less

Bivariate quadratic method in quantifying the differential capacitance and energy capacity of supercapacitors under high current operation

NASA Astrophysics Data System (ADS)

Goh, Chin-Teng; Cruden, Andrew

2014-11-01

Capacitance and resistance are the fundamental electrical parameters used to evaluate the electrical characteristics of a supercapacitor, namely the dynamic voltage response, energy capacity, state of charge and health condition. In the British Standards EN62391 and EN62576, the constant capacitance method can be further improved with a differential capacitance that more accurately describes the dynamic voltage response of supercapacitors. This paper presents a novel bivariate quadratic based method to model the dynamic voltage response of supercapacitors under high current charge-discharge cycling, and to enable the derivation of the differential capacitance and energy capacity directly from terminal measurements, i.e. voltage and current, rather than from multiple pulsed-current or excitation signal tests across different bias levels. The estimation results the author achieves are in close agreement with experimental measurements, within a relative error of 0.2%, at various high current levels (25-200 A), more accurate than the constant capacitance method (4-7%). The archival value of this paper is the introduction of an improved quantification method for the electrical characteristics of supercapacitors, and the disclosure of the distinct properties of supercapacitors: the nonlinear capacitance-voltage characteristic, capacitance variation between charging and discharging, and distribution of energy capacity across the operating voltage window.

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.

PubMed

Jorgensen, William L; Tirado-Rives, Julian

2005-05-10

An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.

General properties of quantum optical systems in a strong field limit

NASA Technical Reports Server (NTRS)

Chumakov, S. M.; Klimov, Andrei B.

1994-01-01

We investigate the dynamics of an arbitrary atomic system (n-level atoms or many n-level atoms) interacting with a resonant quantized mode of an em field. If the initial field state is a coherent state with a large photon number then the system dynamics possesses some general features, independently of the particular structure of the atomic system. Namely, trapping states, factorization of the wave function, collapses and revivals of the atomic energy oscillations are discussed.

Diffusion dynamics of the Li+ ion on a model surface of amorphous carbon: a direct molecular orbital dynamics study.

PubMed

Tachikawa, Hiroto; Shimizu, Akira

2005-07-14

Diffusion processes of the Li+ ion on a model surface of amorphous carbon (Li+C96H24 system) have been investigated by means of the direct molecular orbital (MO) dynamics method at the semiempirical AM1 level. The total energy and energy gradient on the full-dimensional AM1 potential energy surface were calculated at each time step in the dynamics calculation. The optimized structure, where Li+ is located in the center of the cluster, was used as the initial structure at time zero. The dynamics calculation was carried out in the temperature range 100-1000 K. The calculations showed that the Li+ ion vibrates around the equilibrium point below 200 K, while the Li+ ion moves on the surface above 250 K. At intermediate temperatures (300 K < T < 400 K), the ion moves on the surface and falls in the edge regions of the cluster. At higher temperatures (600 K < T), the Li+ ion transfers freely on the surface and edge regions. The diffusion pathway of the Li+ ion was discussed on the basis of theoretical results.

Species Richness Patterns and Water-Energy Dynamics in the Drylands of Northwest China

PubMed Central

Zerbe, Stefan; Abdusalih, Nurbay; Tang, Zhiyao; Ma, Ming; Yin, Linke; Mohammat, Anwar; Han, Wenxuan; Fang, Jingyun

2013-01-01

Dryland ecosystems are highly vulnerable to climatic and land-use changes, while the mechanisms underlying patterns of dryland species richness are still elusive. With distributions of 3637 native vascular plants, 154 mammals, and 425 birds in Xinjiang, China, we tested the water-energy dynamics hypothesis for species richness patterns in Central Asian drylands. Our results supported the water-energy dynamics hypothesis. We found that species richness of all three groups was a hump-shaped function of energy availability, but a linear function of water availability. We further found that water availability had stronger effects on plant richness, but weaker effects on vertebrate richness than energy availability. We conducted piecewise linear regressions to detect the breakpoints in the relationship between species richness and potential evapotranspiration which divided Xinjiang into low and high energy regions. The concordance between mammal and plant richness was stronger in high than in low energy regions, which was opposite to that between birds and plants. Plant richness had stronger effects than climate on mammal richness regardless of energy levels, but on bird richness only in high energy regions. The changes in the concordance between vertebrate and plant richness along the climatic gradient suggest that cautions are needed when using concordance between taxa in conservation planning. PMID:23840472

Species richness patterns and water-energy dynamics in the drylands of Northwest China.

PubMed

Li, Liping; Wang, Zhiheng; Zerbe, Stefan; Abdusalih, Nurbay; Tang, Zhiyao; Ma, Ming; Yin, Linke; Mohammat, Anwar; Han, Wenxuan; Fang, Jingyun

2013-01-01

Dryland ecosystems are highly vulnerable to climatic and land-use changes, while the mechanisms underlying patterns of dryland species richness are still elusive. With distributions of 3637 native vascular plants, 154 mammals, and 425 birds in Xinjiang, China, we tested the water-energy dynamics hypothesis for species richness patterns in Central Asian drylands. Our results supported the water-energy dynamics hypothesis. We found that species richness of all three groups was a hump-shaped function of energy availability, but a linear function of water availability. We further found that water availability had stronger effects on plant richness, but weaker effects on vertebrate richness than energy availability. We conducted piecewise linear regressions to detect the breakpoints in the relationship between species richness and potential evapotranspiration which divided Xinjiang into low and high energy regions. The concordance between mammal and plant richness was stronger in high than in low energy regions, which was opposite to that between birds and plants. Plant richness had stronger effects than climate on mammal richness regardless of energy levels, but on bird richness only in high energy regions. The changes in the concordance between vertebrate and plant richness along the climatic gradient suggest that cautions are needed when using concordance between taxa in conservation planning.

Dynamics of heat storage in evapotranspiration estimate

USDA-ARS?s Scientific Manuscript database

One of the widely discussed reasons for a lack of surface energy balance closure when using eddy covariance is neglect of storage term elements. Storage as related to the surface energy balance refers to all heat stored below the observation level of eddies. It represents the sum of several componen...

Consistent multiphase-field theory for interface driven multidomain dynamics

NASA Astrophysics Data System (ADS)

Tóth, Gyula I.; Pusztai, Tamás; Gránásy, László

2015-11-01

We present a multiphase-field theory for describing pattern formation in multidomain and/or multicomponent systems. The construction of the free energy functional and the dynamic equations is based on criteria that ensure mathematical and physical consistency. We first analyze previous multiphase-field theories and identify their advantageous and disadvantageous features. On the basis of this analysis, we introduce a way of constructing the free energy surface and derive a generalized multiphase description for arbitrary number of phases (or domains). The presented approach retains the variational formalism, reduces (or extends) naturally to lower (or higher) number of fields on the level of both the free energy functional and the dynamic equations, enables the use of arbitrary pairwise equilibrium interfacial properties, penalizes multiple junctions increasingly with the number of phases, ensures non-negative entropy production and the convergence of the dynamic solutions to the equilibrium solutions, and avoids the appearance of spurious phases on binary interfaces. The approach is tested for multicomponent phase separation and grain coarsening.

Exploring the Influence of Dynamic Disorder on Excitons in Solid Pentacene

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

Strong-field two-photon transition by phase shaping

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

Lee, Sangkyung; Lim, Jongseok; Ahn, Jaewook

2010-08-15

We demonstrate the ultrafast coherent control of a nonlinear two-photon absorption in a dynamically shifted energy level structure. We use a spectrotemporal laser-pulse shaping that is programed to preserve the resonant absorption condition during the intense laser-field interaction. Experiments carried out in the strong-field regime of two-photon absorption in the ground state of atomic cesium reveal that the analytically obtained offset and curvature of a laser spectrum compensate the effect of both static and dynamic energy shifts of the given light-atom interaction.

Calculation of the X-Ray emission K and L 2,3 bands of metallic magnesium and aluminum with allowance for multielectron effects

NASA Astrophysics Data System (ADS)

Ovcharenko, R. E.; Tupitsyn, I. I.; Savinov, E. P.; Voloshina, E. N.; Dedkov, Yu. S.; Shulakov, A. S.

2014-01-01

A procedure is proposed to calculate the shape of the characteristic X-ray emission bands of metals with allowance for multielectron effects. The effects of the dynamic screening of a core vacancy by conduction electrons and the Auger effect in the valence band are taken into account. The dynamic screening of a core vacancy, which is known to be called the MND (Mahan-Nozeieres-De Dominics) effect, is taken into account by an ab initio band calculation of crystals using the PAW (projected augmented waves) method. The Auger effect is taken into account by a semiempirical method using the approximation of a quadratic dependence of the level width in the valence band on the difference between the level energy and the Fermi energy. The proposed calculation procedure is used to describe the X-ray emission K and L 2,3 bands of metallic magnesium and aluminum crystals. The calculated spectra agree well with the experimental bands both near the Fermi level and in the low-energy part of the spectra in all cases.

Inherent Structure versus Geometric Metric for State Space Discretization

PubMed Central

Liu, Hanzhong; Li, Minghai; Fan, Jue; Huo, Shuanghong

2016-01-01

Inherent structure (IS) and geometry-based clustering methods are commonly used for analyzing molecular dynamics trajectories. ISs are obtained by minimizing the sampled conformations into local minima on potential/effective energy surface. The conformations that are minimized into the same energy basin belong to one cluster. We investigate the influence of the applications of these two methods of trajectory decomposition on our understanding of the thermodynamics and kinetics of alanine tetrapeptide. We find that at the micro cluster level, the IS approach and root-mean-square deviation (RMSD) based clustering method give totally different results. Depending on the local features of energy landscape, the conformations with close RMSDs can be minimized into different minima, while the conformations with large RMSDs could be minimized into the same basin. However, the relaxation timescales calculated based on the transition matrices built from the micro clusters are similar. The discrepancy at the micro cluster level leads to different macro clusters. Although the dynamic models established through both clustering methods are validated approximately Markovian, the IS approach seems to give a meaningful state space discretization at the macro cluster level. PMID:26915811

Research on System Coherence Evolution of Different Environmental Models

NASA Astrophysics Data System (ADS)

Zhang, Si-Qi; Lu, Jing-Bin; Li, Hong; Liu, Ji-Ping; Zhang, Xiao-Ru; Liu, Han; Liang, Yu; Ma, Ji; Liu, Xiao-Jing; Wu, Xiang-Yao

2018-04-01

In this paper, we have studied the evolution curve of two-level atomic system that the initial state is excited state. At the different of environmental reservoir models, which include the single Lorentzian, ideal photon band-gap, double Lorentzian and square Lorentzian reservoir, we researched the influence of these environmental reservoir models on the evolution of energy level population. At static no modulation, comparing the four environmental models, the atomic energy level population oscillation of square Lorentzian reservoir model is fastest, and the atomic system decoherence is slowest. Under dynamic modulation, comparing the photon band-gap model with the single Lorentzian reservoir model, no matter what form of dynamic modulation, the time of atoms decay to the ground state is longer for the photonic band-gap model. These conclusions make the idea of using the environmental change to modulate the coherent evolution of atomic system become true.

Effects of microsolvation on a SN2 reaction: indirect atomistic dynamics and weakened suppression of reactivity.

PubMed

Yang, Li; Liu, Xu; Zhang, Jiaxu; Xie, Jing

2017-04-12

Systematic studies of microsolvation in the gas phase have enriched our knowledge of solvent effects. Here, the dynamics of a prototype S N 2 reaction of a hydrated fluoride ion with methyl iodide is uncovered employing direct dynamics simulations that show strikingly distinct features from those determined for an unsolvated system. An indirect scattering is found to prevail, which occurs dominantly by forming hydrated F - (H 2 O)-HCH 2 I and F - (H 2 O)-CH 3 I pre-reaction complexes at low energies, but proceeds through their water-free counterparts at higher energies. This finding is in strong contrast to a general evolution from indirect to direct dynamics with enhancing energy for the unsolvated substitution reactions, and this discrepancy is understood by the substantial steric hindrance introduced by a water molecule. As established in experiments, solvation suppresses the reactivity, whereas we find that this depression is remarkably frustrated upon raising the energy given that collision-induced dehydration essentially diminishes the water block for reactive collisions. The present study sheds light on how solute-solvent interactions affect the underlying dynamics at a deeper atomic level, thereby promoting our understanding of the fundamental solvent effects on chemical reactions in solution.

Kinetic energy spectra, vertical resolution and dissipation in high-resolution atmospheric simulations.

NASA Astrophysics Data System (ADS)

Skamarock, W. C.

2017-12-01

We have performed week-long full-physics simulations with the MPAS global model at 15 km cell spacing using vertical mesh spacings of 800, 400, 200 and 100 meters in the mid-troposphere through the mid-stratosphere. We find that the horizontal kinetic energy spectra in the upper troposphere and stratosphere does not converge with increasing vertical resolution until we reach 200 meter level spacing. Examination of the solutions indicates that significant inertia-gravity waves are not vertically resolved at the lower vertical resolutions. Diagnostics from the simulations indicate that the primary kinetic energy dissipation results from the vertical mixing within the PBL parameterization and from the gravity-wave drag parameterization, with smaller but significant contributions from damping in the vertical transport scheme and from the horizontal filters in the dynamical core. Most of the kinetic energy dissipation in the free atmosphere occurs within breaking mid-latitude baroclinic waves. We will briefly review these results and their implications for atmospheric model configuration and for atmospheric dynamics, specifically that related to the dynamics associated with the mesoscale kinetic energy spectrum.

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations.

PubMed

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

2016-01-28

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

NASA Astrophysics Data System (ADS)

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

2016-01-01

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential energy distortions encountered in constrained ICMD simulations of peptide molecules.

Quantum dynamics in strong fluctuating fields

NASA Astrophysics Data System (ADS)

Goychuk, Igor; Hänggi, Peter

A large number of multifaceted quantum transport processes in molecular systems and physical nanosystems, such as e.g. nonadiabatic electron transfer in proteins, can be treated in terms of quantum relaxation processes which couple to one or several fluctuating environments. A thermal equilibrium environment can conveniently be modelled by a thermal bath of harmonic oscillators. An archetype situation provides a two-state dissipative quantum dynamics, commonly known under the label of a spin-boson dynamics. An interesting and nontrivial physical situation emerges, however, when the quantum dynamics evolves far away from thermal equilibrium. This occurs, for example, when a charge transferring medium possesses nonequilibrium degrees of freedom, or when a strong time-dependent control field is applied externally. Accordingly, certain parameters of underlying quantum subsystem acquire stochastic character. This may occur, for example, for the tunnelling coupling between the donor and acceptor states of the transferring electron, or for the corresponding energy difference between electronic states which assume via the coupling to the fluctuating environment an explicit stochastic or deterministic time-dependence. Here, we review the general theoretical framework which is based on the method of projector operators, yielding the quantum master equations for systems that are exposed to strong external fields. This allows one to investigate on a common basis, the influence of nonequilibrium fluctuations and periodic electrical fields on those already mentioned dynamics and related quantum transport processes. Most importantly, such strong fluctuating fields induce a whole variety of nonlinear and nonequilibrium phenomena. A characteristic feature of such dynamics is the absence of thermal (quantum) detailed balance.ContentsPAGE1. Introduction5262. Quantum dynamics in stochastic fields531 2.1. Stochastic Liouville equation531 2.2. Non-Markovian vs. Markovian discrete state fluctuations531 2.3. Averaging the quantum propagator533  2.3.1. Kubo oscillator535  2.3.2. Averaged dynamics of two-level quantum systems exposed to two-state stochastic fields537 2.4. Projection operator method: a primer5403. Two-state quantum dynamics in periodic fields542 3.1. Coherent destruction of tunnelling542 3.2. Driving-induced tunnelling oscillations (DITO)5434. Dissipative quantum dynamics in strong time-dependent fields544 4.1. General formalism544  4.1.1. Weak-coupling approximation545  4.1.2. Markovian approximation: Generalised Redfield Equations5475. Application I: Quantum relaxation in driven, dissipative two-level systems548 5.1. Decoupling approximation for fast fluctuating energy levels550  5.1.1. Control of quantum rates551  5.1.2. Stochastic cooling and inversion of level populations552  5.1.3. Emergence of an effective energy bias553 5.2. Quantum relaxation in strong periodic fields554 5.3. Approximation of time-dependent rates554 5.4. Exact averaging for dichotomous Markovian fluctuations5556. Application II: Driven electron transfer within a spin-boson description557 6.1. Curve-crossing problems with dissipation558 6.2. Weak system-bath coupling559 6.3. Beyond weak-coupling theory: Strong system-bath coupling563  6.3.1. Fast fluctuating energy levels565  6.3.2. Exact averaging over dichotomous fluctuations of the energy levels566  6.3.3. Electron transfer in fast oscillating periodic fields567  6.3.4. Dichotomously fluctuating tunnelling barrier5687. Quantum transport in dissipative tight-binding models subjected tostrong external fields569 7.1. Noise-induced absolute negative mobility571 7.2. Dissipative quantum rectifiers573 7.3. Limit of vanishing dissipation575 7.4. Case of harmonic mixing drive5758. Summary576Acknowledgements578References579

MCC level C formulation requirements. Shuttle TAEM targeting

NASA Technical Reports Server (NTRS)

Carman, G. L.; Montez, M. N.

1980-01-01

The level C requirements for the shuttle orbiter terminal area energy management (TAEM) guidance and flight control functions to be incorporated into the Mission Control Center entry profile planning processor are described. This processor is used for preentry evaluation of the entry through landing maneuvers, and includes a simplified three degree-of-freedom model of the body rotational dynamics that is necessary to account for the effects of attitude response on the trajectory dynamics. This simulation terminates at TAEM-autoland interface.

Double Trouble at High Density: Cross-Level Test of Resource-Related Adaptive Plasticity and Crowding-Related Fitness

PubMed Central

Gergs, André; Preuss, Thomas G.; Palmqvist, Annemette

2014-01-01

Population size is often regulated by negative feedback between population density and individual fitness. At high population densities, animals run into double trouble: they might concurrently suffer from overexploitation of resources and also from negative interference among individuals regardless of resource availability, referred to as crowding. Animals are able to adapt to resource shortages by exhibiting a repertoire of life history and physiological plasticities. In addition to resource-related plasticity, crowding might lead to reduced fitness, with consequences for individual life history. We explored how different mechanisms behind resource-related plasticity and crowding-related fitness act independently or together, using the water flea Daphnia magna as a case study. For testing hypotheses related to mechanisms of plasticity and crowding stress across different biological levels, we used an individual-based population model that is based on dynamic energy budget theory. Each of the hypotheses, represented by a sub-model, is based on specific assumptions on how the uptake and allocation of energy are altered under conditions of resource shortage or crowding. For cross-level testing of different hypotheses, we explored how well the sub-models fit individual level data and also how well they predict population dynamics under different conditions of resource availability. Only operating resource-related and crowding-related hypotheses together enabled accurate model predictions of D. magna population dynamics and size structure. Whereas this study showed that various mechanisms might play a role in the negative feedback between population density and individual life history, it also indicated that different density levels might instigate the onset of the different mechanisms. This study provides an example of how the integration of dynamic energy budget theory and individual-based modelling can facilitate the exploration of mechanisms behind the regulation of population size. Such understanding is important for assessment, management and the conservation of populations and thereby biodiversity in ecosystems. PMID:24626228

Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

NASA Astrophysics Data System (ADS)

Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

2016-05-01

The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

Collision dynamics of H+ + N2 at low energies based on time-dependent density-functional theory

NASA Astrophysics Data System (ADS)

Yu, W.; Zhang, Y.; Zhang, F. S.; Hutton, R.; Zou, Y.; Gao, C.-Z.; Wei, B.

2018-02-01

Using time-dependent density-functional theory at the level of local density approximation augmented by a self-interaction correction and coupled non-adiabatically to molecular dynamics, we study, from a theoretical perspective, scattering dynamics of the proton in collisions with the N2 molecule at 30 eV. Nine different collision configurations are employed to analyze the proton energy loss spectra, electron depletion, scattering angles and self-interaction effects. Our results agree qualitatively with the experimental data and previous theoretical calculations. The discrepancies are ascribed to the limitation of the theoretical models in use. We find that self-interaction effects can significantly influence the electron capture and the excited diatomic vibrational motion, which is in consistent with other calculations. In addition, it is found that the molecular structure can be readily retrieved from the proton energy loss spectra due to a significant momentum transfer in head-on collisions.

Energy harvesting from electrospun piezoelectric nanofibers for structural health monitoring of a cable-stayed bridge

NASA Astrophysics Data System (ADS)

Maruccio, Claudio; Quaranta, Giuseppe; De Lorenzis, Laura; Monti, Giorgio

2016-08-01

Wireless monitoring could greatly impact the fields of structural health assessment and infrastructure asset management. A common problem to be tackled in wireless networks is the electric power supply, which is typically provided by batteries replaced periodically. A promising remedy for this issue would be to harvest ambient energy. Within this framework, the present paper proposes to harvest ambient-induced vibrations of bridge structures using a new class of piezoelectric textiles. The considered case study is an existing cable-stayed bridge located in Italy along a high-speed road that connects Rome and Naples, for which a recent monitoring campaign has allowed to record the dynamic responses of deck and cables. Vibration measurements have been first elaborated to provide a comprehensive dynamic assessment of this infrastructure. In order to enhance the electric energy that can be converted from ambient vibrations, the considered energy harvester exploits a power generator built using arrays of electrospun piezoelectric nanofibers. A finite element analysis is performed to demonstrate that such power generator is able to provide higher energy levels from recorded dynamic loading time histories than a standard piezoelectric energy harvester. Its feasibility for bridge health monitoring applications is finally discussed.

Length-scale dependent mechanical properties of Al-Cu eutectic alloy: Molecular dynamics based model and its experimental verification

NASA Astrophysics Data System (ADS)

Tiwary, C. S.; Chakraborty, S.; Mahapatra, D. R.; Chattopadhyay, K.

2014-05-01

This paper attempts to gain an understanding of the effect of lamellar length scale on the mechanical properties of two-phase metal-intermetallic eutectic structure. We first develop a molecular dynamics model for the in-situ grown eutectic interface followed by a model of deformation of Al-Al2Cu lamellar eutectic. Leveraging the insights obtained from the simulation on the behaviour of dislocations at different length scales of the eutectic, we present and explain the experimental results on Al-Al2Cu eutectic with various different lamellar spacing. The physics behind the mechanism is further quantified with help of atomic level energy model for different length scale as well as different strain. An atomic level energy partitioning of the lamellae and the interface regions reveals that the energy of the lamellae core are accumulated more due to dislocations irrespective of the length-scale. Whereas the energy of the interface is accumulated more due to dislocations when the length-scale is smaller, but the trend is reversed when the length-scale is large beyond a critical size of about 80 nm.

Microstructure and Mechanical Properties of an Ultrasonic Spot Welded Aluminum Alloy: The Effect of Welding Energy

PubMed Central

Peng, He; Chen, Daolun; Jiang, Xianquan

2017-01-01

The aim of this study is to evaluate the microstructures, tensile lap shear strength, and fatigue resistance of 6022-T43 aluminum alloy joints welded via a solid-state welding technique–ultrasonic spot welding (USW)–at different energy levels. An ultra-fine necklace-like equiaxed grain structure is observed along the weld line due to the occurrence of dynamic crystallization, with smaller grain sizes at lower levels of welding energy. The tensile lap shear strength, failure energy, and critical stress intensity of the welded joints first increase, reach their maximum values, and then decrease with increasing welding energy. The tensile lap shear failure mode changes from interfacial fracture at lower energy levels, to nugget pull-out at intermediate optimal energy levels, and to transverse through-thickness (TTT) crack growth at higher energy levels. The fatigue life is longer for the joints welded at an energy of 1400 J than 2000 J at higher cyclic loading levels. The fatigue failure mode changes from nugget pull-out to TTT crack growth with decreasing cyclic loading for the joints welded at 1400 J, while TTT crack growth mode remains at all cyclic loading levels for the joints welded at 2000 J. Fatigue crack basically initiates from the nugget edge, and propagates with “river-flow” patterns and characteristic fatigue striations. PMID:28772809

Microstructure and Mechanical Properties of an Ultrasonic Spot Welded Aluminum Alloy: The Effect of Welding Energy.

PubMed

Peng, He; Chen, Daolun; Jiang, Xianquan

2017-04-25

The aim of this study is to evaluate the microstructures, tensile lap shear strength, and fatigue resistance of 6022-T43 aluminum alloy joints welded via a solid-state welding technique-ultrasonic spot welding (USW)-at different energy levels. An ultra-fine necklace-like equiaxed grain structure is observed along the weld line due to the occurrence of dynamic crystallization, with smaller grain sizes at lower levels of welding energy. The tensile lap shear strength, failure energy, and critical stress intensity of the welded joints first increase, reach their maximum values, and then decrease with increasing welding energy. The tensile lap shear failure mode changes from interfacial fracture at lower energy levels, to nugget pull-out at intermediate optimal energy levels, and to transverse through-thickness (TTT) crack growth at higher energy levels. The fatigue life is longer for the joints welded at an energy of 1400 J than 2000 J at higher cyclic loading levels. The fatigue failure mode changes from nugget pull-out to TTT crack growth with decreasing cyclic loading for the joints welded at 1400 J, while TTT crack growth mode remains at all cyclic loading levels for the joints welded at 2000 J. Fatigue crack basically initiates from the nugget edge, and propagates with "river-flow" patterns and characteristic fatigue striations.

A dynamical model of plasma turbulence in the solar wind

PubMed Central

Howes, G. G.

2015-01-01

A dynamical approach, rather than the usual statistical approach, is taken to explore the physical mechanisms underlying the nonlinear transfer of energy, the damping of the turbulent fluctuations, and the development of coherent structures in kinetic plasma turbulence. It is argued that the linear and nonlinear dynamics of Alfvén waves are responsible, at a very fundamental level, for some of the key qualitative features of plasma turbulence that distinguish it from hydrodynamic turbulence, including the anisotropic cascade of energy and the development of current sheets at small scales. The first dynamical model of kinetic turbulence in the weakly collisional solar wind plasma that combines self-consistently the physics of Alfvén waves with the development of small-scale current sheets is presented and its physical implications are discussed. This model leads to a simplified perspective on the nature of turbulence in a weakly collisional plasma: the nonlinear interactions responsible for the turbulent cascade of energy and the formation of current sheets are essentially fluid in nature, while the collisionless damping of the turbulent fluctuations and the energy injection by kinetic instabilities are essentially kinetic in nature. PMID:25848075

Method of electric powertrain matching for battery-powered electric cars

NASA Astrophysics Data System (ADS)

Ning, Guobao; Xiong, Lu; Zhang, Lijun; Yu, Zhuoping

2013-05-01

The current match method of electric powertrain still makes use of longitudinal dynamics, which can't realize maximum capacity for on-board energy storage unit and can't reach lowest equivalent fuel consumption as well. Another match method focuses on improving available space considering reasonable layout of vehicle to enlarge rated energy capacity for on-board energy storage unit, which can keep the longitudinal dynamics performance almost unchanged but can't reach lowest fuel consumption. Considering the characteristics of driving motor, method of electric powertrain matching utilizing conventional longitudinal dynamics for driving system and cut-and-try method for energy storage system is proposed for passenger cars converted from traditional ones. Through combining the utilization of vehicle space which contributes to the on-board energy amount, vehicle longitudinal performance requirements, vehicle equivalent fuel consumption level, passive safety requirements and maximum driving range requirement together, a comprehensive optimal match method of electric powertrain for battery-powered electric vehicle is raised. In simulation, the vehicle model and match method is built in Matlab/simulink, and the Environmental Protection Agency (EPA) Urban Dynamometer Driving Schedule (UDDS) is chosen as a test condition. The simulation results show that 2.62% of regenerative energy and 2% of energy storage efficiency are increased relative to the traditional method. The research conclusions provide theoretical and practical solutions for electric powertrain matching for modern battery-powered electric vehicles especially for those converted from traditional ones, and further enhance dynamics of electric vehicles.

Dynamical Evolution of an Effective Two-Level System with {\\mathscr{P}}{\\mathscr{T}} Symmetry

NASA Astrophysics Data System (ADS)

Du, Lei; Xu, Zhihao; Yin, Chuanhao; Guo, Liping

2018-05-01

We investigate the dynamics of parity- and time-reversal (PT ) symmetric two-energy-level atoms in the presence of two optical and a radio-frequency (rf) fields. The strength and relative phase of fields can drive the system from unbroken to broken PT symmetric regions. Compared with the Hermitian model, Rabi-type oscillation is still observed, and the oscillation characteristics are also adjusted by the strength and relative phase in the region of unbroken PT symmetry. At exception point (EP), the oscillation breaks down. To better understand the underlying properties we study the effective Bloch dynamics and find the emergence of the z components of the fixed points is the feature of the PT symmetry breaking and the projections in x-y plane can be controlled with high flexibility compared with the standard two-level system with PT symmetry. It helps to study the dynamic behavior of the complex PT symmetric model.

Energy-optimal path planning in the coastal ocean

NASA Astrophysics Data System (ADS)

Subramani, Deepak N.; Haley, Patrick J.; Lermusiaux, Pierre F. J.

2017-05-01

We integrate data-driven ocean modeling with the stochastic Dynamically Orthogonal (DO) level-set optimization methodology to compute and study energy-optimal paths, speeds, and headings for ocean vehicles in the Middle-Atlantic Bight (MAB) region. We hindcast the energy-optimal paths from among exact time-optimal paths for the period 28 August 2006 to 9 September 2006. To do so, we first obtain a data-assimilative multiscale reanalysis, combining ocean observations with implicit two-way nested multiresolution primitive-equation simulations of the tidal-to-mesoscale dynamics in the region. Second, we solve the reduced-order stochastic DO level-set partial differential equations (PDEs) to compute the joint probability of minimum arrival time, vehicle-speed time series, and total energy utilized. Third, for each arrival time, we select the vehicle-speed time series that minimize the total energy utilization from the marginal probability of vehicle-speed and total energy. The corresponding energy-optimal path and headings are obtained through the exact particle-backtracking equation. Theoretically, the present methodology is PDE-based and provides fundamental energy-optimal predictions without heuristics. Computationally, it is 3-4 orders of magnitude faster than direct Monte Carlo methods. For the missions considered, we analyze the effects of the regional tidal currents, strong wind events, coastal jets, shelfbreak front, and other local circulations on the energy-optimal paths. Results showcase the opportunities for vehicles that intelligently utilize the ocean environment to minimize energy usage, rigorously integrating ocean forecasting with optimal control of autonomous vehicles.

Dynamic and energetic characteristics of a bistable piezoelectric vibration energy harvester with an elastic magnifier

NASA Astrophysics Data System (ADS)

Wang, Guangqing; Liao, Wei-Hsin; Yang, Binqiang; Wang, Xuebao; Xu, Wentan; Li, Xiuling

2018-05-01

Bistable piezoelectric energy harvesters are being increasingly seen as an alternative to batteries in low-power devices. However, their energy harvesting characteristics are limited. To enhance these, we use a configuration including an elastic magnifier to amplify base excitation and provide sufficient kinetic energy to overcome potential well barriers, thus leading to large-amplitude bistable motion. We derive the distributed parameter mathematical model of this configuration by using Hamilton's principle. We then investigate the nonlinear dynamic behaviors and energetic characteristics and analyze the bifurcation for the equilibrium solution of the model. The simulations and experiments show high electromechanical responses and energy generation characteristics of the proposed system over a broad frequency band. The results suggest that, compared with a typical bistable piezoelectric energy harvester, the proposed energy harvester system with an elastic magnifier can provide higher output over a broader frequency band at lower excitation levels by adjusting the system's mass and stiffness ratios.

Energetic Particle Observations from Fengyun-2G Satellite

NASA Astrophysics Data System (ADS)

Wang, C.

2017-12-01

Observations of high energy electrons and protons with High Energy Particle Instrument(HEPI) carried on the Fengyun-2G( FY-2G )satellite are presented. The instrument consists of two sets detectors- high energy electrons detector which can measure 200keV to greater than 4MeV electrons with eleven channels, and high energy protons and heavy ions detector which mainly senses incident flux of solar protons with seven channels from 4MeV to 300 MeV. The observation results showed both of the detectors can reach an accurate response to various disturbances and can provide refined particles data. Comparison of particles dynamic observations of FY2G satellite with GOES series satellites appears that energetic particle fluxes can enter into a coherent level on some quasi-quiet conditions, great difference occur on disturbances times, which can be helpful for data assimilation of multi-satellite as well as further research in more complicated magnetosphere energy particle dynamics.

Linking Adverse Outcome Pathways to Dynamic Energy Budgets: A Conceptual Model

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

Murphy, Cheryl; Nisbet, Roger; Antczak, Philipp

Ecological risk assessment quantifies the likelihood of undesirable impacts of stressors, primarily at high levels of biological organization. Data used to inform ecological risk assessments come primarily from tests on individual organisms or from suborganismal studies, indicating a disconnect between primary data and protection goals. We know how to relate individual responses to population dynamics using individual-based models, and there are emerging ideas on how to make connections to ecosystem services. However, there is no established methodology to connect effects seen at higher levels of biological organization with suborganismal dynamics, despite progress made in identifying Adverse Outcome Pathways (AOPs) thatmore » link molecular initiating events to ecologically relevant key events. This chapter is a product of a working group at the National Center for Mathematical and Biological Synthesis (NIMBioS) that assessed the feasibility of using dynamic energy budget (DEB) models of individual organisms as a “pivot” connecting suborganismal processes to higher level ecological processes. AOP models quantify explicit molecular, cellular or organ-level processes, but do not offer a route to linking sub-organismal damage to adverse effects on individual growth, reproduction, and survival, which can be propagated to the population level through individual-based models. DEB models describe these processes, but use abstract variables with undetermined connections to suborganismal biology. We propose linking DEB and quantitative AOP models by interpreting AOP key events as measures of damage-inducing processes in a DEB model. Here, we present a conceptual model for linking AOPs to DEB models and review existing modeling tools available for both AOP and DEB.« less

Combined impacts of tidal energy extraction and sea level rise in the Gulf of Maine

NASA Astrophysics Data System (ADS)

Hashemi, M. R.; Kresning, B.

2016-12-01

The objective of this study was to assess the combined effects of SLR and tidal energy extraction on the dynamics of tides in the Gulf of Maine in both US and Canadian waters. The dynamics of tides in the Gulf of Maine is dominated by tidal resonance, which generates one of the largest tidal ranges in the world. Further, sea level rise (SLR) is affecting tidal circulations globally, and in the Gulf of Maine. A large tidal energy resource is available in the Gulf of Maine, particularly in the Bay of Fundy, and is expected to be harvested in the future. Currently, more than 6 projects are operational or under development in this region (in both US and Canadian waters). Understanding the far-field impacts of tidal-stream arrays is important for future development of tidal energy extraction. The impacts include possible changes in water elevation, which can potentially increase flooding in coastal areas. Further, SLR can affect tidal energy resources and the impacts of tidal energy extraction during the project lifetime - which is usually more than 25 years. A tidal model of the Gulf of Maine was developed using Regional Ocean Model System (ROMS) at one arcminute scale. An array of turbines were simulated in the model. After validation of the model at NOAA tidal gauge stations and NERACOOS buoys, several scenarios; including SLR scenario, and tidal extraction scenario, were examined. In particular, the results of a recent research was used to assess the impacts of SLR on the boundary of the model domain, which was neglected in previous studies. The results of the impacts of the tidal energy extraction with and without the SLR were presented, and compared with those from literature. This includes the decrease of tidal range and M2 amplitude in Minas Basin due to the 2.5 GW extraction scenario, and possible changes in Massachusetts coastal area. The impacts were compared with the level of uncertainty in the model. It was shown that the impact of SLR on the dynamics of tides is more than those from energy extraction assuming 2.5 GW extraction in Minas Passage.

Pseudo Asynchronous Level Crossing adc for ecg Signal Acquisition.

PubMed

Marisa, T; Niederhauser, T; Haeberlin, A; Wildhaber, R A; Vogel, R; Goette, J; Jacomet, M

2017-02-07

A new pseudo asynchronous level crossing analogue-to-digital converter (adc) architecture targeted for low-power, implantable, long-term biomedical sensing applications is presented. In contrast to most of the existing asynchronous level crossing adc designs, the proposed design has no digital-to-analogue converter (dac) and no continuous time comparators. Instead, the proposed architecture uses an analogue memory cell and dynamic comparators. The architecture retains the signal activity dependent sampling operation by generating events only when the input signal is changing. The architecture offers the advantages of smaller chip area, energy saving and fewer analogue system components. Beside lower energy consumption the use of dynamic comparators results in a more robust performance in noise conditions. Moreover, dynamic comparators make interfacing the asynchronous level crossing system to synchronous processing blocks simpler. The proposed adc was implemented in [Formula: see text] complementary metal-oxide-semiconductor (cmos) technology, the hardware occupies a chip area of 0.0372 mm 2 and operates from a supply voltage of [Formula: see text] to [Formula: see text]. The adc's power consumption is as low as 0.6 μW with signal bandwidth from [Formula: see text] to [Formula: see text] and achieves an equivalent number of bits (enob) of up to 8 bits.

Nuclear shape evolution based on microscopic level densities

DOE PAGES

Ward, D. E.; Carlsson, B. G.; Døssing, T.; ...

2017-02-27

Here, by combining microscopically calculated level densities with the Metropolis walk method, we develop a consistent framework for treating the energy and angular-momentum dependence of the nuclear shape evolution in the fission process. For each nucleus under consideration, the level density is calculated microscopically for each of more than five million shapes with a recently developed combinatorial method. The method employs the same single-particle levels as those used for the extraction of the pairing and shell contributions to the macroscopic-microscopic deformation-energy surface. Containing no new parameters, the treatment is suitable for elucidating the energy dependence of the dynamics of warmmore » nuclei on pairing and shell effects. It is illustrated for the fission fragment mass distribution for several uranium and plutonium isotopes of particular interest.« less

The multi-level perspective analysis: Indonesia geothermal energy transition study

NASA Astrophysics Data System (ADS)

Wisaksono, A.; Murphy, J.; Sharp, J. H.; Younger, P. L.

2018-01-01

The study adopts a multi-level perspective in technology transition to analyse how the transition process in the development of geothermal energy in Indonesia is able to compete against the incumbent fossil-fuelled energy sources. Three levels of multi-level perspective are socio-technical landscape (ST-landscape), socio-technical regime (ST-regime) and niche innovations in Indonesia geothermal development. The identification, mapping and analysis of the dynamic relationship between each level are the important pillars of the multi-level perspective framework. The analysis considers the set of rules, actors and controversies that may arise in the technological transition process. The identified geothermal resource risks are the basis of the emerging geothermal technological innovations in Indonesian geothermal. The analysis of this study reveals the transition pathway, which yields a forecast for the Indonesian geothermal technology transition in the form of scenarios and probable impacts.

A temperature dependent study on charge dynamics in organic molecular device: Effect of shallow traps on space charge limited behavior

NASA Astrophysics Data System (ADS)

Mukherjee, A. K.; Kavala, A. K.

2014-04-01

Shallow traps play a significant role in influencing charge dynamics through organic molecular thin films, such as pentacene. Sandwich cells of pentacene capped by gold electrodes are an excellent specimen to study the nature of underlying charge dynamics. In this paper, self-consistent numerical simulation of I-V characteristics is performed at various temperatures. The results have revealed negative value of Poole Frenkel coefficient. The location of trap energy level is found to be located at 0.24 eV above the highest occupied molecular orbit (HOMO) level of pentacene. Other physical parameters related to trap levels, such as density of states due to traps and effective carrier density due to traps, have also been estimated in this study.

Classical Trajectory Study of Collision Energy Transfer between Ne and C2H2 on a Full Dimensional Accurate Potential Energy Surface.

PubMed

Liu, Yang; Huang, Yin; Ma, Jianyi; Li, Jun

2018-02-15

Collision energy transfer plays an important role in gas phase reaction kinetics and relaxation of excited molecules. However, empirical treatments are generally adopted for the collisional energy transfer in the master equation based approach. In this work, classical trajectory approach is employed to investigate the collision energy transfer dynamics in the C 2 H 2 -Ne system. The entire potential energy surface is described as the sum of the C 2 H 2 potential and interaction potential between C 2 H 2 and Ne. It is highlighted that both parts of the entire potential are highly accurate. In particular, the interaction potential is fit to ∼41 300 configurations determined at the level of CCSD(T)-F12a/cc-pCVTZ-F12 with the counterpoise correction. Collision energy transfer dynamics are then carried out on this benchmark potential and the widely used Lennard-Jones and Buckingham interaction potentials. Energy transfers and related probability densities at different collisional energies are reported and discussed.

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale.

PubMed

McCarty, J; Clark, A J; Copperman, J; Guenza, M G

2014-05-28

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.

Energy Level Alignment at Aqueous GaN and ZnO Interfaces

NASA Astrophysics Data System (ADS)

Hybertsen, Mark S.; Kharche, Neerav; Muckerman, James T.

2014-03-01

Electronic energy level alignment at semiconductor-electrolyte interfaces is fundamental to electrochemical activity. Motivated in particular by the search for new materials that can be more efficient for photocatalysis, we develop a first principles method to calculate this alignment at aqueous interfaces and demonstrate it for the specific case of non-polar GaN and ZnO interfaces with water. In the first step, density functional theory (DFT) based molecular dynamics is used to sample the physical interface structure and to evaluate the electrostatic potential step at the interface. In the second step, the GW approach is used to evaluate the reference electronic energy level separately in the bulk semiconductor (valence band edge energy) and in bulk water (the 1b1 energy level), relative to the internal electrostatic energy reference. Use of the GW approach naturally corrects for errors inherent in the use of Kohn-Sham energy eigenvalues to approximate the electronic excitation energies in each material. With this predicted interface alignment, specific redox levels in water, with potentials known relative to the 1b1 level, can then be compared to the semiconductor band edge positions. Our results will be discussed in the context of experiments in which photoexcited GaN and ZnO drive the hydrogen evolution reaction. Research carried out at Brookhaven National Laboratory under Contract No. DE-AC02-98CH10886 with the U.S. Department of Energy.

Bi-Level Decision Making for Supporting Energy and Water Nexus

NASA Astrophysics Data System (ADS)

Zhang, X.; Vesselinov, V. V.

2016-12-01

The inseparable relationship between energy production and water resources has led to the emerging energy-water nexus concept, which provides a means for integrated management and decision making of these two critical resources. However, the energy-water nexus frequently involves decision makers with different and competing management objectives. Furthermore, there is a challenge that decision makers and stakeholders might be making decisions sequentially from a higher level to a lower level, instead of at the same decision level, whereby the objective of a decision maker at a higher level should be satisfied first. In this study, a bi-level decision model is advanced to handle such decision-making situations for managing the energy-water nexus. The work represents a unique contribution to developing an integrated decision-support framework/tool to quantify and analyze the tradeoffs between the two-level energy-water nexus decision makers. Here, plans for electricity generation, fuel supply, water supply, capacity expansion of the power plants and environmental impacts are optimized to provide effective decision support. The developed decision-support framework is implemented in Julia (a high-level, high-performance dynamic programming language for technical computing) and is a part of the MADS (Model Analyses & Decision Support) framework (http://mads.lanl.gov). To demonstrate the capabilities of the developed methodology, a series of analyses are performed for synthetic problems consistent with actual real-world energy-water nexus management problems.

Model of photoinduced structural change induced by THz pulse irradiation

NASA Astrophysics Data System (ADS)

Ishida, Kunio; Nasu, Keiichiro

Recently intense optical pulses with THz frequency have been obtained, and it is of interest to study the effect of irradiated THz pulses on electronic systems. We theoretically study the photoinduced cooperative dynamics triggered by irradiation of THz pulses. We employed a model of two-level localized electrons coupled with an optical phonon mode taking into account the nonadiabaticity of the electron dynamics, and solved the time-dependent Schrödinger equation numerically. We consider the cases in which the THz pulses create phonons near the surface of the system, and pursue the electronic transitions induced by the propagation of the phonons. We found that they are able to induce excited-state domain growth, and that the interference between them plays an important role in the growth dynamics. Hence, the domain growth is affected by the geometry of the surface of the system, which is different from the photoinduced structural change by visible/UV pulses. We also show that the nonadiabatic/adiabatic electronic transitions should be taken into account though the domain growth mainly proceeds on the ground-state potential energy surfaces(PESs). In other words, the energy level/structure of excited-state PESs are relevant to the domain-growth dynamics.

Structure and spectral features of H+(H2O)7: Eigen versus Zundel forms.

PubMed

Shin, Ilgyou; Park, Mina; Min, Seung Kyu; Lee, Eun Cheol; Suh, Seung Bum; Kim, Kwang S

2006-12-21

The two dimensional (2D) to three dimensional (3D) transition for the protonated water cluster has been controversial, in particular, for H(+)(H(2)O)(7). For H(+)(H(2)O)(7) the 3D structure is predicted to be lower in energy than the 2D structure at most levels of theory without zero-point energy (ZPE) correction. On the other hand, with ZPE correction it is predicted to be either 2D or 3D depending on the calculational levels. Although the ZPE correction favors the 3D structure at the level of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using the aug-cc-pVDZ basis set, the result based on the anharmonic zero-point vibrational energy correction favors the 2D structure. Therefore, the authors investigated the energies based on the complete basis set limit scheme (which we devised in an unbiased way) at the resolution of the identity approximation Moller-Plesset second order perturbation theory and CCSD(T) levels, and found that the 2D structure has the lowest energy for H(+)(H(2)O)(7) [though nearly isoenergetic to the 3D structure for D(+)(D(2)O)(7)]. This structure has the Zundel-type configuration, but it shows the quantum probabilistic distribution including some of the Eigen-type configuration. The vibrational spectra of MP2/aug-cc-pVDZ calculations and Car-Parrinello molecular dynamics simulations, taking into account the thermal and dynamic effects, show that the 2D Zundel-type form is in good agreement with experiments.

Structure and spectral features of H+(H2O)7: Eigen versus Zundel forms

NASA Astrophysics Data System (ADS)

Shin, Ilgyou; Park, Mina; Min, Seung Kyu; Lee, Eun Cheol; Suh, Seung Bum; Kim, Kwang S.

2006-12-01

The two dimensional (2D) to three dimensional (3D) transition for the protonated water cluster has been controversial, in particular, for H+(H2O)7. For H+(H2O)7 the 3D structure is predicted to be lower in energy than the 2D structure at most levels of theory without zero-point energy (ZPE) correction. On the other hand, with ZPE correction it is predicted to be either 2D or 3D depending on the calculational levels. Although the ZPE correction favors the 3D structure at the level of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using the aug-cc-pVDZ basis set, the result based on the anharmonic zero-point vibrational energy correction favors the 2D structure. Therefore, the authors investigated the energies based on the complete basis set limit scheme (which we devised in an unbiased way) at the resolution of the identity approximation Møller-Plesset second order perturbation theory and CCSD(T) levels, and found that the 2D structure has the lowest energy for H+(H2O)7 [though nearly isoenergetic to the 3D structure for D+(D2O)7]. This structure has the Zundel-type configuration, but it shows the quantum probabilistic distribution including some of the Eigen-type configuration. The vibrational spectra of MP2/aug-cc-pVDZ calculations and Car-Parrinello molecular dynamics simulations, taking into account the thermal and dynamic effects, show that the 2D Zundel-type form is in good agreement with experiments.

Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction

PubMed Central

2015-01-01

Metadynamics is an enhanced sampling method designed to flatten free energy surfaces uniformly. However, the highest-energy regions are often irrelevant to study and dangerous to explore because systems often change irreversibly in unforeseen ways in response to driving forces in these regions, spoiling the sampling. Introducing an on-the-fly domain restriction allows metadynamics to flatten only up to a specified energy level and no further, improving efficiency and safety while decreasing the pressure on practitioners to design collective variables that are robust to otherwise irrelevant high energy driving. This paper describes a new method that achieves this using sequential on-the-fly estimation of energy wells and redefinition of the metadynamics hill shape, termed metabasin metadynamics. The energy level may be defined a priori or relative to unknown barrier energies estimated on-the-fly. Altering only the hill ensures that the method is compatible with many other advances in metadynamics methodology. The hill shape has a natural interpretation in terms of multiscale dynamics, and the computational overhead in simulation is minimal when studying systems of any reasonable size, for instance proteins or other macromolecules. Three example applications show that the formula is accurate and robust to complex dynamics, making metadynamics significantly more forgiving with respect to CV quality and thus more feasible to apply to the most challenging biomolecular systems. PMID:26587809

Models of charge pair generation in organic solar cells.

PubMed

Few, Sheridan; Frost, Jarvist M; Nelson, Jenny

2015-01-28

Efficient charge pair generation is observed in many organic photovoltaic (OPV) heterojunctions, despite nominal electron-hole binding energies which greatly exceed the average thermal energy. Empirically, the efficiency of this process appears to be related to the choice of donor and acceptor materials, the resulting sequence of excited state energy levels and the structure of the interface. In order to establish a suitable physical model for the process, a range of different theoretical studies have addressed the nature and energies of the interfacial states, the energetic profile close to the heterojunction and the dynamics of excited state transitions. In this paper, we review recent developments underpinning the theory of charge pair generation and phenomena, focussing on electronic structure calculations, electrostatic models and approaches to excited state dynamics. We discuss the remaining challenges in achieving a predictive approach to charge generation efficiency.

Random walk numerical simulation for hopping transport at finite carrier concentrations: diffusion coefficient and transport energy concept.

PubMed

Gonzalez-Vazquez, J P; Anta, Juan A; Bisquert, Juan

2009-11-28

The random walk numerical simulation (RWNS) method is used to compute diffusion coefficients for hopping transport in a fully disordered medium at finite carrier concentrations. We use Miller-Abrahams jumping rates and an exponential distribution of energies to compute the hopping times in the random walk simulation. The computed diffusion coefficient shows an exponential dependence with respect to Fermi-level and Arrhenius behavior with respect to temperature. This result indicates that there is a well-defined transport level implicit to the system dynamics. To establish the origin of this transport level we construct histograms to monitor the energies of the most visited sites. In addition, we construct "corrected" histograms where backward moves are removed. Since these moves do not contribute to transport, these histograms provide a better estimation of the effective transport level energy. The analysis of this concept in connection with the Fermi-level dependence of the diffusion coefficient and the regime of interest for the functioning of dye-sensitised solar cells is thoroughly discussed.

New Possibilities of Substance Identification Based on THz Time Domain Spectroscopy Using a Cascade Mechanism of High Energy Level Excitation

PubMed Central

Trofimov, Vyacheslav A.; Varentsova, Svetlana A.; Zakharova, Irina G.; Zagursky, Dmitry Yu.

2017-01-01

Using an experiment with thin paper layers and computer simulation, we demonstrate the principal limitations of standard Time Domain Spectroscopy (TDS) based on using a broadband THz pulse for the detection and identification of a substance placed inside a disordered structure. We demonstrate the spectrum broadening of both transmitted and reflected pulses due to the cascade mechanism of the high energy level excitation considering, for example, a three-energy level medium. The pulse spectrum in the range of high frequencies remains undisturbed in the presence of a disordered structure. To avoid false absorption frequencies detection, we apply the spectral dynamics analysis method (SDA-method) together with certain integral correlation criteria (ICC). PMID:29186849

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

PubMed Central

2017-01-01

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

Shuttle program. MCC level C formulation requirements: Shuttle TAEM guidance and flight control

NASA Technical Reports Server (NTRS)

Carman, G. L.

1980-01-01

The Level C requirements for the shuttle orbiter terminal area energy management (TAEM) guidance and flight control functions to be incorporated into the Mission Control Center entry profile planning processor are defined. This processor will be used for preentry evaluation of the entry through landing maneuvers, and will include a simplified three degree-of-freedom model of the body rotational dynamics that is necessary to account for the effects of attitude response on the trajectory dynamics. This simulation terminates at TAEM-autoland interface.

Optimization of CW Fiber Lasers With Strong Nonlinear Cavity Dynamics

NASA Astrophysics Data System (ADS)

Shtyrina, O. V.; Efremov, S. A.; Yarutkina, I. A.; Skidin, A. S.; Fedoruk, M. P.

2018-04-01

In present work the equation for the saturated gain is derived from one-level gain equations describing the energy evolution inside the laser cavity. It is shown how to derive the parameters of the mathematical model from the experimental results. The numerically-estimated energy and spectrum of the signal are in good agreement with the experiment. Also, the optimization of the output energy is performed for a given set of model parameters.

Positrons vs electrons channeling in silicon crystal: energy levels, wave functions and quantum chaos manifestations

NASA Astrophysics Data System (ADS)

Shul'ga, N. F.; Syshchenko, V. V.; Tarnovsky, A. I.; Solovyev, I. I.; Isupov, A. Yu.

2018-01-01

The motion of fast electrons through the crystal during axial channeling could be regular and chaotic. The dynamical chaos in quantum systems manifests itself in both statistical properties of energy spectra and morphology of wave functions of the individual stationary states. In this report, we investigate the axial channeling of high and low energy electrons and positrons near [100] direction of a silicon crystal. This case is particularly interesting because of the fact that the chaotic motion domain occupies only a small part of the phase space for the channeling electrons whereas the motion of the channeling positrons is substantially chaotic for the almost all initial conditions. The energy levels of transverse motion, as well as the wave functions of the stationary states, have been computed numerically. The group theory methods had been used for classification of the computed eigenfunctions and identification of the non-degenerate and doubly degenerate energy levels. The channeling radiation spectrum for the low energy electrons has been also computed.

Inherent structure versus geometric metric for state space discretization.

PubMed

Liu, Hanzhong; Li, Minghai; Fan, Jue; Huo, Shuanghong

2016-05-30

Inherent structure (IS) and geometry-based clustering methods are commonly used for analyzing molecular dynamics trajectories. ISs are obtained by minimizing the sampled conformations into local minima on potential/effective energy surface. The conformations that are minimized into the same energy basin belong to one cluster. We investigate the influence of the applications of these two methods of trajectory decomposition on our understanding of the thermodynamics and kinetics of alanine tetrapeptide. We find that at the microcluster level, the IS approach and root-mean-square deviation (RMSD)-based clustering method give totally different results. Depending on the local features of energy landscape, the conformations with close RMSDs can be minimized into different minima, while the conformations with large RMSDs could be minimized into the same basin. However, the relaxation timescales calculated based on the transition matrices built from the microclusters are similar. The discrepancy at the microcluster level leads to different macroclusters. Although the dynamic models established through both clustering methods are validated approximately Markovian, the IS approach seems to give a meaningful state space discretization at the macrocluster level in terms of conformational features and kinetics. © 2016 Wiley Periodicals, Inc.

Dynamics of energy transfer from lycopene to bacteriochlorophyll in genetically-modified LH2 complexes of Rhodobacter sphaeroides.

PubMed

Hörvin Billsten, H; Herek, J L; Garcia-Asua, G; Hashøj, L; Polívka, T; Hunter, C N; Sundström, V

2002-03-26

LH2 complexes from Rb. sphaeroides were modified genetically so that lycopene, with 11 saturated double bonds, replaced the native carotenoids which contain 10 saturated double bonds. Tuning the S1 level of the carotenoid in LH2 in this way affected the dynamics of energy transfer within LH2, which were investigated using both steady-state and time-resolved techniques. The S1 energy of lycopene in n-hexane was determined to be approximately 12 500 +/- 150 cm(-1), by direct measurement of the S1-S2 transient absorption spectrum using a femtosecond IR-probing technique, thus placing an upper limit on the S1 energy of lycopene in the LH2 complex. Fluorescence emission and excitation spectra demonstrated that energy can be transferred from lycopene to the bacteriochlorophyll molecules within this LH2 complex. The energy-transfer dynamics within the mutant complex were compared to wild-type LH2 from Rb. sphaeroides containing the carotenoid spheroidene and from Rs. molischianum, in which lycopene is the native carotenoid. The results show that the overall efficiency for Crt --> B850 energy transfer is approximately 80% in lyco-LH2 and approximately 95% in WT-LH2 of Rb. sphaeroides. The difference in overall Crt --> BChl transfer efficiency of lyco-LH2 and WT-LH2 mainly relates to the low efficiency of the Crt S(1) --> BChl pathway for complexes containing lycopene, which was 20% in lyco-LH2. These results show that in an LH2 complex where the Crt S1 energy is sufficiently high to provide efficient spectral overlap with both B800 and B850 Q(y) states, energy transfer via the Crt S1 state occurs to both pigments. However, the introduction of lycopene into the Rb. sphaeroides LH2 complex lowers the S1 level of the carotenoid sufficiently to prevent efficient transfer of energy to the B800 Q(y) state, leaving only the Crt S1 --> B850 channel, strongly suggesting that Crt S1 --> BChl energy transfer is controlled by the relative Crt S1 and BChl Q(y) energies.

The Thick Level-Set model for dynamic fragmentation

DOE PAGES

Stershic, Andrew J.; Dolbow, John E.; Moës, Nicolas

2017-01-04

The Thick Level-Set (TLS) model is implemented to simulate brittle media undergoing dynamic fragmentation. This non-local model is discretized by the finite element method with damage represented as a continuous field over the domain. A level-set function defines the extent and severity of damage, and a length scale is introduced to limit the damage gradient. Numerical studies in one dimension demonstrate that the proposed method reproduces the rate-dependent energy dissipation and fragment length observations from analytical, numerical, and experimental approaches. In conclusion, additional studies emphasize the importance of appropriate bulk constitutive models and sufficient spatial resolution of the length scale.

Development and implementation of a dynamic TES dispatch control component in a PV-CSP techno-economic performance modelling tool

NASA Astrophysics Data System (ADS)

Hansson, Linus; Guédez, Rafael; Larchet, Kevin; Laumert, Bjorn

2017-06-01

The dispatchability offered by thermal energy storage (TES) in concentrated solar power (CSP) and solar hybrid plants based on such technology presents the most important difference compared to power generation based only on photovoltaics (PV). This has also been one reason for recent hybridization efforts of the two technologies and the creation of Power Purchase Agreement (PPA) payment schemes based on offering higher payment multiples during daily hours of higher (peak or priority) demand. Recent studies involving plant-level thermal energy storage control strategies are however to a large extent based on pre-determined approaches, thereby not taking into account the actual dynamics of thermal energy storage system operation. In this study, the implementation of a dynamic dispatch strategy in the form of a TRNSYS controller for hybrid PV-CSP plants in the power-plant modelling tool DYESOPT is presented. In doing this it was attempted to gauge the benefits of incorporating a day-ahead approach to dispatch control compared to a fully pre-determined approach determining hourly dispatch only once prior to annual simulation. By implementing a dynamic strategy, it was found possible to enhance technical and economic performance for CSP-only plants designed for peaking operation and featuring low values of the solar multiple. This was achieved by enhancing dispatch control, primarily by taking storage levels at the beginning of every simulation day into account. The sequential prediction of the TES level could therefore be improved, notably for evaluated plants without integrated PV, for which the predicted storage levels deviated less than when PV was present in the design. While also featuring dispatch performance gains, optimal plant configurations for hybrid PV-CSP was found to present a trade-off in economic performance in the form of an increase in break-even electricity price when using the dynamic strategy which was offset to some extent by a reduction in upfront investment cost. An increase in turbine starts for the implemented strategy however highlights that this is where further improvements can be made.

Development and application of dynamic hybrid multi-region inventory analysis for macro-level environmental policy analysis: a case study on climate policy in Taiwan.

PubMed

Chao, Chia-Wei; Heijungs, Reinout; Ma, Hwong-wen

2013-03-19

We develop a novel inventory method called Dynamic Hybrid Multi-Region Inventory analysis (DHMRI), which integrates the EEMRIOA and Integrated Hybrid LCA and applies time-dependent environmental intervention information for inventory analysis. Consequently, DHMRI is able to quantify the change in the environmental footprint caused by a specific policy while taking structural changes and technological dynamics into consideration. DHMRI is applied to assess the change in the total CO2 emissions associated with the total final demand caused by the climate policy in Taiwan to demonstrate the practicality of this novel method. The evaluation reveals that the implementation of mitigation measures included in the existing climate policy, such as an enhancement in energy efficiency, promotion of renewable energy, and limitation of the growth of energy-intensive industries, will lead to a 28% increase in the total CO2 emissions and that the main driver is the export-oriented electronics industry. Moreover, a major increase in the total emissions is predicted to occur in Southeast Asia and China. The observations from the case study reveal that DHMRI is capable of overcoming the limitations of existing assessment tools at macro-level evaluation of environmental policies.

Advanced secondary batteries: Their applications, technological status, market and opportunity

NASA Astrophysics Data System (ADS)

Yao, M.

1989-03-01

Program planning for advanced battery energy storage technology is supported within the NEMO Program. Specifically this study had focused on the review of advanced battery applications; the development and demonstration status of leading battery technologies; and potential marketing opportunity. Advanced secondary (or rechargeable) batteries have been under development for the past two decades in the U.S., Japan, and parts of Europe for potential applications in electric utilities and for electric vehicles. In the electric utility applications, the primary aim of a battery energy storage plant is to facilitate peak power load leveling and/or dynamic operations to minimize the overall power generation cost. In the application for peak power load leveling, the battery stores the off-peak base load energy and is discharged during the period of peak power demand. This allows a more efficient use of the base load generation capacity and reduces the need for conventional oil-fired or gas-fire peak power generation equipment. Batteries can facilitate dynamic operations because of their basic characteristics as an electrochemical device capable of instantaneous response to the changing load. Dynamic operating benefits results in cost savings of the overall power plant operation. Battery-powered electric vehicles facilitate conservation of petroleum fuel in the transportation sector, but more importantly, they reduce air pollution in the congested inner cities.

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

NASA Astrophysics Data System (ADS)

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp; Huy Pham, C.; Riera, Marc; Moberg, Daniel R.; Morales, Miguel A.; Knight, Chris; Götz, Andreas W.; Paesani, Francesco

2016-11-01

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulations as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.

Are shocks to renewable energy consumption permanent or temporary? Evidence from 54 developing and developed countries.

PubMed

Demir, Ender; Gozgor, Giray

2018-02-01

The renewable energy sources are considered as the important factor to decrease the level of carbon emissions and to promote the global green economy. Understanding the dynamics of renewable energy consumption, this paper analyzes whether there is a unit root in renewable energy consumption in 54 countries over the period 1971-2016. To this end, the unit root test of Narayan-Popp with two endogenous (unknown) breaks is implemented. The paper finds that renewable energy consumption series are stationary around a level and the time trend in 45 of 54 countries. In other words, renewable energy consumption follows a unit root process only in nine countries: Brazil, China, Colombia, India, Israel, Japan, the Netherlands, Spain, and Turkey. The evidence implies that renewable energy demand policies, which aimed to decrease the carbon emissions, will only have permanent effects in those nine countries.

Ultralow-power electronics for biomedical applications.

PubMed

Chandrakasan, Anantha P; Verma, Naveen; Daly, Denis C

2008-01-01

The electronics of a general biomedical device consist of energy delivery, analog-to-digital conversion, signal processing, and communication subsystems. Each of these blocks must be designed for minimum energy consumption. Specific design techniques, such as aggressive voltage scaling, dynamic power-performance management, and energy-efficient signaling, must be employed to adhere to the stringent energy constraint. The constraint itself is set by the energy source, so energy harvesting holds tremendous promise toward enabling sophisticated systems without straining user lifestyle. Further, once harvested, efficient delivery of the low-energy levels, as well as robust operation in the aggressive low-power modes, requires careful understanding and treatment of the specific design limitations that dominate this realm. We outline the performance and power constraints of biomedical devices, and present circuit techniques to achieve complete systems operating down to power levels of microwatts. In all cases, approaches that leverage advanced technology trends are emphasized.

Shape coexistence in the N = 19 neutron-rich nucleus 31Mg explored by β-γ spectroscopy of spin-polarized 31Na

NASA Astrophysics Data System (ADS)

Nishibata, H.; Shimoda, T.; Odahara, A.; Morimoto, S.; Kanaya, S.; Yagi, A.; Kanaoka, H.; Pearson, M. R.; Levy, C. D. P.; Kimura, M.

2017-04-01

The structure of excited states in the neutron-rich nucleus 31Mg, which is in the region of the ;island of inversion; associated with the neutron magic number N = 20, is studied by β-γ spectroscopy of spin-polarized 31Na. Among the 31Mg levels below the one neutron separation energy of 2.3 MeV, the spin values of all five positive-parity levels are unambiguously determined by observing the anisotropic β decay. Two rotational bands with Kπ = 1 /2+ and 1 /2- are proposed based on the spins and energies of the levels. Comparison on a level-by-level basis is performed between the experimental results and theoretical calculations by the antisymmetrized molecular dynamics (AMD) plus generator coordinate method (GCM). It is found that various nuclear structures coexist in the low excitation energy region in 31Mg.

Impact Testing and Simulation of a Sinusoid Foam Sandwich Energy Absorber

NASA Technical Reports Server (NTRS)

Jackson, Karen E.; Fasanella, Edwin L; Littell, Justin D.

2015-01-01

A sinusoidal-shaped foam sandwich energy absorber was developed and evaluated at NASA Langley Research Center through multi-level testing and simulation performed under the Transport Rotorcraft Airframe Crash Testbed (TRACT) research project. The energy absorber, designated the "sinusoid," consisted of hybrid carbon- Kevlar® plain weave fabric face sheets, two layers for each face sheet oriented at +/-45deg with respect to the vertical or crush direction, and a closed-cell ELFOAM(TradeMark) P200 polyisocyanurate (2.0-lb/ft3) foam core. The design goal for the energy absorber was to achieve an average floor-level acceleration of between 25- and 40-g during the full-scale crash test of a retrofitted CH-46E helicopter airframe, designated TRACT 2. Variations in the design were assessed through quasi-static and dynamic crush testing of component specimens. Once the design was finalized, a 5-ft-long subfloor beam was fabricated and retrofitted into a barrel section of a CH-46E helicopter. A vertical drop test of the barrel section was conducted onto concrete to evaluate the performance of the energy absorber prior to retrofit into TRACT 2. Finite element models were developed of all test articles and simulations were performed using LSDYNA ®, a commercial nonlinear explicit transient dynamic finite element code. Test analysis results are presented for the sinusoid foam sandwich energy absorber as comparisons of load-displacement and acceleration-time-history responses, as well as predicted and experimental structural deformations and progressive damage for each evaluation level (component testing through barrel section drop testing).

Landau-Zener-Stückelberg-Majorana interference in a 3D transmon driven by a chirped microwave

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

Gong, Ming; Department of Physics and Astronomy, University of Kansas, Lawrence, Kansas 66045; Zhou, Yu

2016-03-14

By driving a 3D transmon with microwave fields, we generate an effective avoided energy-level crossing. Then we chirp microwave frequency, which is equivalent to driving the system through the avoided energy-level crossing by sweeping the avoided crossing. A double-passage chirp produces Landau-Zener-Stückelberg-Majorana (LZSM) interference that agree well with the numerical results, especially with the initial state being an eigen-energy state in the center of an avoided level crossing. A time-resolved state tomography measurement is performed in the evolution of LZSM interference, showing an experimental evidence for the dynamical evolution of quantum state. Our method is fully applicable to other quantummore » systems that contain no intrinsic avoided level crossing, providing an alternative approach for quantum control and quantum simulation.« less

Urinary C-peptide levels in male bonobos (Pan paniscus) are related to party size and rank but not to mate competition.

PubMed

Surbeck, Martin; Deschner, Tobias; Behringer, Verena; Hohmann, Gottfried

2015-05-01

Within- and between-species variation in male mating strategies has been attributed to a multitude of factors including male competitive ability and the distribution of fertile females across space and time. Differences in energy balance across and within males allow for the identification of some of the trade-offs associated with certain social and mating strategies. Bonobos live in groups with a high degree of fission-fusion dynamics, there is co-dominance between the sexes and a linear dominance hierarchy among males. Males compete over access to females, breeding is aseasonal, and females exhibit sexual swellings over extended time periods. In this study we use urinary C-peptide (UCP) levels in male bonobos (Pan paniscus) obtained from 260 urine samples from a wild bonobo community, to quantify male energy balance during mate competition and levels of gregariousness in the species. Although high ranking males are more aggressive, spend more time in proximity to maximally tumescent females, and have higher mating frequencies, we found no indication that mate guarding or mate competition affected male energy balance. Our results showed a positive correlation between monthly mean UCP levels and mean party size. When traveling in large parties, high ranking males had higher UCP levels than those of the low ranking males. These results support the hypothesis that patterns of fission-fusion dynamics in bonobos are either linked to energy availability in the environment or to the energetic costs of foraging. The finding of a rank-bias in UCP levels in larger parties could also reflect an increase in contest competition among males over access to food. Copyright © 2015. Published by Elsevier Inc.

PHYSICAL EFFECTS OCCURRING DURING GENERATION AND AMPLIFICATION OF LASER RADIATION: Discharge energy balance in the nitrogen-containing active medium of an electron-beam-controlled CO laser

NASA Astrophysics Data System (ADS)

Dolinina, V. I.; Koterov, V. N.; Pyatakhin, Mikhail V.; Urin, B. M.

1989-02-01

Numerical methods were used to investigate theoretically the dynamics of the energy balance of a discharge in a CO-N2 mixture, taking into account the mutual influence of the distributions of the electron energy and of the populations of the molecules over the vibrational levels. It was shown that this influence plays a decisive part in substantially redistributing the pump energy between the vibrational levels of the CO and N2 molecules in favor of the N2 molecules. A stabilizing action of the nitrogen on the thermal regime of the CO laser-active medium was discovered and the range of optimal CO:N2 ratios was determined.

Embodying Markov blankets. Comment on "Answering Schrödinger's question: A free-energy formulation" by Maxwell James Désormeau Ramstead et al.

NASA Astrophysics Data System (ADS)

Pezzulo, Giovanni; Levin, Michael

2018-03-01

The free-energy principle (FEP) has been initially proposed as a theory of brain structure and function [1], but its scope is rapidly extending to explain biological phenomena at multiple levels of complexity, from simple life forms and their morphology [2] to complex societal and cultural dynamics [3].

Length-scale dependent mechanical properties of Al-Cu eutectic alloy: Molecular dynamics based model and its experimental verification

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

Tiwary, C. S., E-mail: cst.iisc@gmail.com; Chattopadhyay, K.; Chakraborty, S.

2014-05-28

This paper attempts to gain an understanding of the effect of lamellar length scale on the mechanical properties of two-phase metal-intermetallic eutectic structure. We first develop a molecular dynamics model for the in-situ grown eutectic interface followed by a model of deformation of Al-Al{sub 2}Cu lamellar eutectic. Leveraging the insights obtained from the simulation on the behaviour of dislocations at different length scales of the eutectic, we present and explain the experimental results on Al-Al{sub 2}Cu eutectic with various different lamellar spacing. The physics behind the mechanism is further quantified with help of atomic level energy model for different lengthmore » scale as well as different strain. An atomic level energy partitioning of the lamellae and the interface regions reveals that the energy of the lamellae core are accumulated more due to dislocations irrespective of the length-scale. Whereas the energy of the interface is accumulated more due to dislocations when the length-scale is smaller, but the trend is reversed when the length-scale is large beyond a critical size of about 80 nm.« less

Effect of temperature variations and thermal noise on the static and dynamic behavior of straintronics devices

NASA Astrophysics Data System (ADS)

Barangi, Mahmood; Mazumder, Pinaki

2015-11-01

A theoretical model quantifying the effect of temperature variations on the magnetic properties and static and dynamic behavior of the straintronics magnetic tunneling junction is presented. Four common magnetostrictive materials (Nickel, Cobalt, Terfenol-D, and Galfenol) are analyzed to determine their temperature sensitivity and to provide a comprehensive database for different applications. The variations of magnetic anisotropies are studied in detail for temperature levels up to the Curie temperature. The energy barrier of the free layer and the critical voltage required for flipping the magnetization vector are inspected as important metrics that dominate the energy requirements and noise immunity when the device is incorporated into large systems. To study the dynamic thermal noise, the effect of the Langevin thermal field on the free layer's magnetization vector is incorporated into the Landau-Lifshitz-Gilbert equation. The switching energy, flipping delay, write, and hold error probabilities are studied, which are important metrics for nonvolatile memories, an important application of the straintronics magnetic tunneling junctions.

Impact of wind generator infed on dynamic performance of a power system

NASA Astrophysics Data System (ADS)

Alam, Md. Ahsanul

Wind energy is one of the most prominent sources of electrical energy in the years to come. A tendency to increase the amount of electricity generation from wind turbine can be observed in many countries. One of the major concerns related to the high penetration level of the wind energy into the existing power grid is its influence on power system dynamic performance. In this thesis, the impact of wind generation system on power system dynamic performance is investigated through detailed dynamic modeling of the entire wind generator system considering all the relevant components. Nonlinear and linear models of a single machine as well as multimachine wind-AC system have been derived. For the dynamic model of integrated wind-AC system, a general transformation matrix is determined for the transformation of machine and network quantities to a common reference frame. Both time-domain and frequency domain analyses on single machine and multimachine systems have been carried out. The considered multimachine systems are---A 4 machine 12 bus system, and 10 machine 39 bus New England system. Through eigenvalue analysis, impact of asynchronous wind system on overall network damping has been quantified and modes responsible for the instability have been identified. Over with a number of simulation studies it is observed that for a induction generator based wind generation system, the fixed capacitor located at the generator terminal cannot normally cater for the reactive power demand during the transient disturbances like wind gust and fault on the system. For weak network connection, system instability may be initiated because of induction generator terminal voltage collapse under certain disturbance conditions. Incorporation of dynamic reactive power compensation scheme through either variable susceptance control or static compensator (STATCOM) is found to improve the dynamic performance significantly. Further improvement in transient profile has been brought in by supporting STATCOM with bulk energy storage devices. Two types of energy storage system (ESS) have been considered---battery energy storage system, and supercapacitor based energy storage system. A decoupled P -- Q control strategy has been implemented on STATCOM/ESS. It is observed that wind generators when supported by STATCOM/ESS can achieve significant withstand capability in the presence of grid fault of reasonable duration. It experiences almost negligible rotor speed variation, maintains constant terminal voltage, and resumes delivery of smoothed (almost transient free) power to the grid immediately after the fault is cleared. Keywords: Wind energy, induction generator, dynamic performance of wind generators, energy storage system, decoupled P -- Q control, multimachine system.

Influence of light-induced conical intersection on the photodissociation dynamics of D2(+) starting from individual vibrational levels.

PubMed

Halász, Gábor J; Csehi, András; Vibók, Ágnes; Cederbaum, Lorenz S

2014-12-26

Previous works have shown that dressing of diatomic molecules by standing or by running laser waves gives rise to the appearance of so-called light-induced conical intersections (LICIs). Because of the strong nonadiabatic couplings, the existence of such LICIs may significantly change the dynamical properties of a molecular system. In our former paper (J. Phys. Chem. A 2013, 117, 8528), the photodissociation dynamics of the D(2)(+) molecule were studied in the LICI framework starting the initial vibrational nuclear wave packet from the superposition of all the vibrational states initially produced by ionizing D(2). The present work complements our previous investigation by letting the initial nuclear wave packets start from different individual vibrational levels of D(2)(+), in particular, above the energy of the LICI. The kinetic energy release spectra, the total dissociation probabilities, and the angular distributions of the photofragments are calculated and discussed. An interesting phenomenon has been found in the spectra of the photofragments. Applying the light-induced adiabatic picture supported by LICI, explanations are given for the unexpected structure of the spectra.

Stochastic feeding dynamics arise from the need for information and energy.

PubMed

Scholz, Monika; Dinner, Aaron R; Levine, Erel; Biron, David

2017-08-29

Animals regulate their food intake in response to the available level of food. Recent observations of feeding dynamics in small animals showed feeding patterns of bursts and pauses, but their function is unknown. Here, we present a data-driven decision-theoretical model of feeding in Caenorhabditis elegans Our central assumption is that food intake serves a dual purpose: to gather information about the external food level and to ingest food when the conditions are good. The model recapitulates experimentally observed feeding patterns. It naturally implements trade-offs between speed versus accuracy and exploration versus exploitation in responding to a dynamic environment. We find that the model predicts three distinct regimes in responding to a dynamical environment, with a transition region where animals respond stochastically to periodic signals. This stochastic response accounts for previously unexplained experimental data.

Shot noise as a measure of the lifetime and energy splitting of Majorana bound states

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

Lü, Hai-Feng; Guo, Zhen; Ke, Sha-Sha

We propose a scheme to measure the lifetime and energy splitting of a pair of Majorana bound states at the ends of a superconducting nanowire by using the shot noise in a dynamical channel blockade system. A quantum dot is coupled to one end of the wire and connected with two electron reservoirs. It is found that a finite Majorana energy splitting tends to produce a super-Poissonian shot noise, while Majorana relaxation process relieves the dynamical channel blockade and suppresses the noise Fano factor. When the dot energy level locates in the middle of the gap of topological superconductor, themore » Fano factor is independent on Majorana lifetime and Majorana energy splitting is thus extracted. For a finite energy splitting, we could evaluate the Majorana relaxation rate from the suppression of Fano factor. Under a realistic condition, the expected resolution of Majorana energy splitting and its relaxation rate calculated from our model are about 1μeV and 0.01−1μeV, respectively.« less

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

Mittal, Sparsh; Zhang, Zhao; Vetter, Jeffrey S

Recent trends of CMOS scaling and use of large last level caches (LLCs) have led to significant increase in the leakage energy consumption of LLCs and hence, managing their energy consumption has become extremely important in modern processor design. The conventional cache energy saving techniques require offline profiling or provide only coarse granularity of cache allocation. We present FlexiWay, a cache energy saving technique which uses dynamic cache reconfiguration. FlexiWay logically divides the cache sets into multiple (e.g. 16) modules and dynamically turns off suitable and possibly different number of cache ways in each module. FlexiWay has very small implementationmore » overhead and it provides fine-grain cache allocation even with caches of typical associativity, e.g. an 8-way cache. Microarchitectural simulations have been performed using an x86-64 simulator and workloads from SPEC2006 suite. Also, FlexiWay has been compared with two conventional energy saving techniques. The results show that FlexiWay provides largest energy saving and incurs only small loss in performance. For single, dual and quad core systems, the average energy saving using FlexiWay are 26.2%, 25.7% and 22.4%, respectively.« less

Multi-Level Experimental and Analytical Evaluation of Two Composite Energy Absorbers

NASA Technical Reports Server (NTRS)

Jackson, Karen E.; Littell, Justin D.; Fasanella, Edwin L.; Annett, Martin S.; Seal, Michael D., II

2015-01-01

Two composite energy absorbers were developed and evaluated at NASA Langley Research Center through multi-level testing and simulation performed under the Transport Rotorcraft Airframe Crash Testbed (TRACT) research program. A conical-shaped energy absorber, designated the conusoid, was evaluated that consisted of four layers of hybrid carbon-Kevlar plain weave fabric oriented at [+45 deg/-45 deg/-45 deg/+45 deg] with respect to the vertical, or crush, direction. A sinusoidal-shaped energy absorber, designated the sinusoid, was developed that consisted of hybrid carbon-Kevlar plain weave fabric face sheets, two layers for each face sheet oriented at +/-45deg with respect to the vertical direction and a closed-cell ELFOAM P200 polyisocyanurate (2.0-lb/cu ft) foam core. The design goal for the energy absorbers was to achieve average floor-level accelerations of between 25- and 40-g during the full-scale crash test of a retrofitted CH-46E helicopter airframe, designated TRACT 2. Variations in both designs were assessed through dynamic crush testing of component specimens. Once the designs were finalized, subfloor beams of each configuration were fabricated and retrofitted into a barrel section of a CH-46E helicopter. A vertical drop test of the barrel section was conducted onto concrete to evaluate the performance of the energy absorbers prior to retrofit into TRACT 2. The retrofitted airframe was crash tested under combined forward and vertical velocity conditions onto soil, which is characterized as a sand/clay mixture. Finite element models were developed of all test articles and simulations were performed using LS-DYNA, a commercial nonlinear explicit transient dynamic finite element code. Test-analysis results are presented for each energy absorber as comparisons of time-history responses, as well as predicted and experimental structural deformations and progressive damage under impact loading for each evaluation level.

Single and double core-hole ion emission spectroscopy of transient neon plasmas produced by ultraintense x-ray laser pulses

NASA Astrophysics Data System (ADS)

Gao, Cheng; Zeng, Jiaolong; Yuan, Jianmin

2016-05-01

Single core-hole (SCH) and double core-hole (DCH) spectroscopy is investigated systematically for neon gas in the interaction with ultraintense x-ray pulses with photon energy from 937 eV to 2000 eV. A time-dependent rate equation, implemented in the detailed level accounting approximation, is utilized to study the dynamical evolution of the level population and emission properties of the laser-produced highly transient plasmas. The plasma density effects on level populations are demonstrated with an x-ray photon energy of 2000 eV. For laser photon energy in the range of 937 - 1360 eV, resonant absorptions (RA) of 1s-np (n> = 2) transitions play important roles in time evolution of the population and DCH emission spectroscopy. For x-ray photon energy larger than 1360 eV, no RA exist and transient plasmas show different features in the DCH spectroscopy.

Wind farm and solar park effects on plant–soil carbon cycling: uncertain impacts of changes in ground-level microclimate

PubMed Central

Armstrong, Alona; Waldron, Susan; Whitaker, Jeanette; Ostle, Nicholas J

2014-01-01

Global energy demand is increasing as greenhouse gas driven climate change progresses, making renewable energy sources critical to future sustainable power provision. Land-based wind and solar electricity generation technologies are rapidly expanding, yet our understanding of their operational effects on biological carbon cycling in hosting ecosystems is limited. Wind turbines and photovoltaic panels can significantly change local ground-level climate by a magnitude that could affect the fundamental plant–soil processes that govern carbon dynamics. We believe that understanding the possible effects of changes in ground-level microclimates on these phenomena is crucial to reducing uncertainty of the true renewable energy carbon cost and to maximize beneficial effects. In this Opinions article, we examine the potential for the microclimatic effects of these land-based renewable energy sources to alter plant–soil carbon cycling, hypothesize likely effects and identify critical knowledge gaps for future carbon research. PMID:24132939

Global solutions and finite time blow-up for fourth order nonlinear damped wave equation

NASA Astrophysics Data System (ADS)

Xu, Runzhang; Wang, Xingchang; Yang, Yanbing; Chen, Shaohua

2018-06-01

In this paper, we study the initial boundary value problem and global well-posedness for a class of fourth order wave equations with a nonlinear damping term and a nonlinear source term, which was introduced to describe the dynamics of a suspension bridge. The global existence, decay estimate, and blow-up of solution at both subcritical (E(0) < d) and critical (E(0) = d) initial energy levels are obtained. Moreover, we prove the blow-up in finite time of solution at the supercritical initial energy level (E(0) > 0).

Dynamical manifestations of quantum chaos

NASA Astrophysics Data System (ADS)

Torres Herrera, Eduardo Jonathan; Santos, Lea

2017-04-01

A main feature of a chaotic quantum system is a rigid spectrum, where the levels do not cross. Dynamical quantities, such as the von Neumann entanglement entropy, Shannon information entropy, and out-of-time correlators can differentiate the ergodic from the nonergodic phase in disordered interacting systems, but not level repulsion from level crossing in the delocalized phase of disordered and clean models. This is in contrast with the long-time evolution of the survival probability of the initial state. The onset of correlated energy levels is manifested by a drop, referred to as correlation hole, below the asymptotic value of the survival probability. The correlation hole is an unambiguous indicator of the presence of level repulsion. EJTH is grateful to VIEP, BUAP for financial support through the VIEP projects program.

Photodissociation dynamics of OClO

NASA Astrophysics Data System (ADS)

Davis, H. Floyd; Lee, Yuan T.

1996-11-01

Photofragment translational energy spectroscopy was used to study the dissociation dynamics of a range of electronically excited OClO(A 2A2) vibrational states. For all levels studied, corresponding to OClO(A 2A2←X 2B1) excitation wavelengths between 350 and 475 nm, the dominant product (≳96%) was ClO(2Π)+O(3P). We also observed production of Cl+O2 with a quantum yield of up to 3.9±0.8% near 404 nm, decreasing at longer and shorter wavelengths. The branching ratios between the two channels were dependent on the OClO(A 2A2) excited state vibrational mode. The Cl+O2 yield was enhanced slightly by exciting A 2A2 levels having symmetric stretching+bending, but diminished by as much as a factor of 10 for neighboring peaks associated with symmetric stretching+asymmetric stretching. Mode specificity was also observed in the vibrationally state resolved translational energy distributions for the dominant ClO(2Π)+O(3P) channel. The photochemical dynamics of OClO possesses two energy regimes with distinctly different dynamics observed for excitation energies above and below ˜3.1 eV (λ˜400 nm). At excitation energies below 3.1 eV (λ≳400 nm), nearly all energetically accessible ClO vibrational energy levels were populated, and the minor Cl+O2 channel was observed. Although at least 20% of the O2 product is formed in the ground (X 3Σ-g) state, most O2 is electronically excited (a 1Δg). At E<3.1 eV, both dissociation channels occur by an indirect mechanism involving two nearby excited states, 2A1 and 2B2. Long dissociation time scales and significant parent bending before dissociation led to nearly isotropic polarization angular distributions (β˜0). At excitation energies above 3.1 eV (λ<400 nm), the Cl+O2 yield began to decrease sharply, with this channel becoming negligible at λ<370 nm. At these higher excitation energies, the ClO product was formed with relatively little vibrational energy and a large fraction of the excess energy was channeled into ClO+O translational energy. The photofragment anisotropy parameter (β) also increased, implying shorter dissociation time scales. The sharp change in the disposal of excess energy into the ClO products, the decrease of Cl+O2 production, and more anisotropic product angular distributions at E≳3.1 eV signify the opening of a new ClO+O channel. From our experimental results and recent ab initio calculations, dissociation at wavelengths shorter than 380 nm to ClO+O proceeds via a direct mechanism on the optically prepared A 2A2 surface over a large potential energy barrier. From the ClO(2Π)+O(3P) translational energy distributions, D0(O-ClO) was found to be less than or equal to 59.0±0.2 kcal/mol.

Machine learning of accurate energy-conserving molecular force fields.

PubMed

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof T; Müller, Klaus-Robert

2017-05-01

Using conservation of energy-a fundamental property of closed classical and quantum mechanical systems-we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol -1 for energies and 1 kcal mol -1 Å̊ -1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

Monochromatic X-ray-induced thermal effect on four-reflection “nested” meV-monochromators: dynamical diffraction theory and finite-element analysis

NASA Astrophysics Data System (ADS)

Hu, Ling-Fei; Gao, Li-Dan; Li, Zhen-Jie; Wang, Shan-Feng; Sheng, Wei-Fan; Liu, Peng; Xu, Wei

2015-09-01

The high energy resolution monochromator (HRM) is widely used in inelastic scattering programs to detect phonons with energy resolution, down to the meV level. Although the large amount of heat from insertion devices can be reduced by a high heat-load monochromator, the unbalanced heat load on the inner pair of crystals in a nested HRM can affect its overall performance. Here, a theoretical analysis of the unbalanced heat load using dynamical diffraction theory and finite element analysis is presented. By utilizing the ray-tracing method, the performance of different HRM nesting configurations is simulated. It is suggested that the heat balance ratio, energy resolution, and overall spectral transmission efficiency are the figures of merit for evaluating the performance of nested HRMs. Although the present study is mainly focused on nested HRMs working at 57Fe nuclear resonant energy at 14.4 keV, it is feasible to extend this to other nested HRMs working at different energies.

Replica Exchange Gaussian Accelerated Molecular Dynamics: Improved Enhanced Sampling and Free Energy Calculation.

PubMed

Huang, Yu-Ming M; McCammon, J Andrew; Miao, Yinglong

2018-04-10

Through adding a harmonic boost potential to smooth the system potential energy surface, Gaussian accelerated molecular dynamics (GaMD) provides enhanced sampling and free energy calculation of biomolecules without the need of predefined reaction coordinates. This work continues to improve the acceleration power and energy reweighting of the GaMD by combining the GaMD with replica exchange algorithms. Two versions of replica exchange GaMD (rex-GaMD) are presented: force constant rex-GaMD and threshold energy rex-GaMD. During simulations of force constant rex-GaMD, the boost potential can be exchanged between replicas of different harmonic force constants with fixed threshold energy. However, the algorithm of threshold energy rex-GaMD tends to switch the threshold energy between lower and upper bounds for generating different levels of boost potential. Testing simulations on three model systems, including the alanine dipeptide, chignolin, and HIV protease, demonstrate that through continuous exchanges of the boost potential, the rex-GaMD simulations not only enhance the conformational transitions of the systems but also narrow down the distribution width of the applied boost potential for accurate energetic reweighting to recover biomolecular free energy profiles.

Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction

DOE PAGES

Dama, James F.; Hocky, Glen M.; Sun, Rui; ...

2015-11-03

Metadynamics is an enhanced sampling method designed to flatten free energy surfaces uniformly. However, the highest-energy regions are often irrelevant to study and dangerous to explore because systems often respond irreversibly in unforeseen ways in response to driving forces in these regions, spoiling the sampling. Introducing an on-the-fly domain restriction allows metadynamics to flatten only up to a specified energy level and no further, improving efficiency and safety while decreasing the pressure on practitioners to design collective variables that are robust to otherwise irrelevant high energy driving. Here this paper describes a new method that achieves this using sequential on-the-flymore » estimation of energy wells and redefinition of the metadynamics hill shape, termed metabasin metadynamics. The energy level may be defined a priori or relative to unknown barrier energies estimated on the fly. Altering only the hill ensures that the method is compatible with many other advances in metadynamics methodology. The hill shape has a natural interpretation in terms of multiscale dynamics and the computational overhead in simulation is minimal when studying systems of any reasonable size, for instance proteins or other macromolecules. Ultimately, three example applications show that the formula is accurate and robust to complex dynamics, making metadynamics significantly more forgiving with respect to CV quality and thus more feasible to apply to the most challenging biomolecular systems.« less

Perturbations for transient acceleration

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

Vargas, Cristofher Zuñiga; Zimdahl, Winfried; Hipólito-Ricaldi, Wiliam S., E-mail: win_unac@hotmail.com, E-mail: hipolito@ceunes.ufes.br, E-mail: winfried.zimdahl@pq.cnpq.br

2012-04-01

According to the standard ΛCDM model, the accelerated expansion of the Universe will go on forever. Motivated by recent observational results, we explore the possibility of a finite phase of acceleration which asymptotically approaches another period of decelerated expansion. Extending an earlier study on a corresponding homogeneous and isotropic dynamics, in which interactions between dark matter and dark energy are crucial, the present paper also investigates the dynamics of the matter perturbations both on the Newtonian and General Relativistic (GR) levels and quantifies the potential relevance of perturbations of the dark-energy component. In the background, the model is tested againstmore » the Supernova type Ia (SNIa) data of the Constitution set and on the perturbative level against growth rate data, among them those of the WiggleZ survey, and the data of the 2dFGRS project. Our results indicate that a transient phase of accelerated expansion is not excluded by current observations.« less

Theoretical study of optical pump process in solid gain medium based on four-energy-level model

NASA Astrophysics Data System (ADS)

Ma, Yongjun; Fan, Zhongwei; Zhang, Bin; Yu, Jin; Zhang, Hongbo

2018-04-01

A semiclassical algorithm is explored to a four-energy level model, aiming to find out the factors that affect the dynamics behavior during the pump process. The impacts of pump intensity Ω p , non-radiative transition rate γ 43 and decay rate of electric dipole δ 14 are discussed in detail. The calculation results show that large γ 43, small δ 14, and strong pumping Ω p are beneficial to the establishing of population inversion. Under strong pumping conditions, the entire pump process can be divided into four different phases, tentatively named far-from-equilibrium process, Rabi oscillation process, quasi dynamic equilibrium process and ‘equilibrium’ process. The Rabi oscillation can slow the pumping process and cause some instability. Moreover, the duration of the entire process is negatively related to Ω p and γ 43 whereas positively related to δ 14.

Pulsed photothermal interferometry for spectroscopic gas detection with hollow-core optical fibre

PubMed Central

Lin, Yuechuan; Jin, Wei; Yang, Fan; Ma, Jun; Wang, Chao; Ho, Hoi Lut; Liu, Yang

2016-01-01

Gas detection with hollow-core photonic bandgap fibre (HC-PBF) and pulsed photothermal (PT) interferometry spectroscopy are studied theoretically and experimentally. A theoretical model is developed and used to compute the gas-absorption-induced temperature and phase modulation in a HC-PBF filled with low-concentration of C2H2 in nitrogen. The PT phase modulation dynamics for different pulse duration, peak power and energy of pump beam are numerically modelled, which are supported by the experimental results obtained around the P(9) absorption line of C2H2 at 1530.371 nm. Thermal conduction is identified as the main process responsible for the phase modulation dynamics. For a constant peak pump power level, the phase modulation is found to increase with pulse duration up to ~1.2 μs, while it increases with decreasing pulse duration for a constant pulse energy. It is theoretically possible to achieve ppb level detection of C2H2 with ~1 m length HC-PBF and a pump beam with ~10 ns pulse duration and ~100 nJ pulse energy. PMID:28009011

Pulsed photothermal interferometry for spectroscopic gas detection with hollow-core optical fibre.

PubMed

Lin, Yuechuan; Jin, Wei; Yang, Fan; Ma, Jun; Wang, Chao; Ho, Hoi Lut; Liu, Yang

2016-12-23

Gas detection with hollow-core photonic bandgap fibre (HC-PBF) and pulsed photothermal (PT) interferometry spectroscopy are studied theoretically and experimentally. A theoretical model is developed and used to compute the gas-absorption-induced temperature and phase modulation in a HC-PBF filled with low-concentration of C 2 H 2 in nitrogen. The PT phase modulation dynamics for different pulse duration, peak power and energy of pump beam are numerically modelled, which are supported by the experimental results obtained around the P(9) absorption line of C 2 H 2 at 1530.371 nm. Thermal conduction is identified as the main process responsible for the phase modulation dynamics. For a constant peak pump power level, the phase modulation is found to increase with pulse duration up to ~1.2 μs, while it increases with decreasing pulse duration for a constant pulse energy. It is theoretically possible to achieve ppb level detection of C 2 H 2 with ~1 m length HC-PBF and a pump beam with ~10 ns pulse duration and ~100 nJ pulse energy.

Dynamic modeling of hybrid renewable energy systems for off-grid applications

NASA Astrophysics Data System (ADS)

Hasemeyer, Mark David

The volatile prices of fossil fuels and their contribution to global warming have caused many people to turn to renewable energy systems. Many developing communities are forced to use these systems as they are too far from electrical distribution. As a result, numerous software models have been developed to simulate hybrid renewable energy systems. However almost, if not all, implementations are static in design. A static design limits the ability of the model to account for changes over time. Dynamic modeling can be used to fill the gaps where other modeling techniques fall short. This modeling practice allows the user to account for the effects of technological and economic factors over time. These factors can include changes in energy demand, energy production, and income level. Dynamic modeling can be particularly useful for developing communities who are off-grid and developing at rapid rates. In this study, a dynamic model was used to evaluate a real world system. A non-governmental organization interested in improving their current infrastructure was selected. Five different scenarios were analyzed and compared in order to discover which factors the model is most sensitive to. In four of the scenarios, a new energy system was purchased in order to account for the opening of a restaurant that would be used as a source of local income generation. These scenarios were then compared to a base case in which a new system was not purchased, and the restaurant was not opened. Finally, the results were used to determine which variables had the greatest impact on the various outputs of the simulation.

Cavity hydration dynamics in cytochrome c oxidase and functional implications

PubMed Central

Son, Chang Yun; Cui, Qiang

2017-01-01

Cytochrome c oxidase (CcO) is a transmembrane protein that uses the free energy of O2 reduction to generate the proton concentration gradient across the membrane. The regulation of competitive proton transfer pathways has been established to be essential to the vectorial transport efficiency of CcO, yet the underlying mechanism at the molecular level remains lacking. Recent studies have highlighted the potential importance of hydration-level change in an internal cavity that connects the proton entrance channel, the site of O2 reduction, and the putative proton exit route. In this work, we use atomistic molecular dynamics simulations to investigate the energetics and timescales associated with the volume fluctuation and hydration-level change in this central cavity. Extensive unrestrained molecular dynamics simulations (accumulatively ∼4 μs) and free energy computations for different chemical states of CcO support a model in which the volume and hydration level of the cavity are regulated by the protonation state of a propionate group of heme a3 and, to a lesser degree, the redox state of heme a and protonation state of Glu286. Markov-state model analysis of ∼2-μs trajectories suggests that hydration-level change occurs on the timescale of 100–200 ns before the proton-loading site is protonated. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration-level change of the cavity can indeed be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport. PMID:28973914

Dynamics of drive systems for wind energy conversion

NASA Technical Reports Server (NTRS)

Martinez-Sanchez, M.

1978-01-01

Calculations are performed to determine the dynamic effects of mechanical power transmission from the nacelle of a horizontal axis wind machine to the ground or to an intermediate level. It is found that resonances are likely at 2 or 4/REV, but they occur at low power only, and seem easily correctable. Large reductions are found in the harmonic torque inputs to the generator at powers near rated.

A decentralised multi-agent approach to enhance the stability of smart microgrids with renewable energy

NASA Astrophysics Data System (ADS)

Rahman, M. S.; Pota, H. R.; Mahmud, M. A.; Hossain, M. J.

2016-05-01

This paper presents the impact of large penetration of wind power on the transient stability through a dynamic evaluation of the critical clearing times (CCTs) by using intelligent agent-based approach. A decentralised multi-agent-based framework is developed, where agents represent a number of physical device models to form a complex infrastructure for computation and communication. They enable the dynamic flow of information and energy for the interaction between the physical processes and their activities. These agents dynamically adapt online measurements and use the CCT information for relay coordination to improve the transient stability of power systems. Simulations are carried out on a smart microgrid system for faults at increasing wind power penetration levels and the improvement in transient stability using the proposed agent-based framework is demonstrated.

Potential energy surfaces and reaction dynamics of polyatomic molecules

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

Chang, Yan-Tyng

A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogenmore » atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.« less

A multi-stakeholder framework for sustainable energy behavior: A multidisciplinary systems study

NASA Astrophysics Data System (ADS)

Khansari, Nasrin

Growth of population and moving towards over-consumption and over-pollution are significant threats to the environment and therefore necessitate moving towards sustainability approaches. CO2 emissions are considered to be the main basis of the incredible increase in the earth's surface temperature in recent years. Most emissions result from human activities. Thus, developing a detailed framework representing the parameters affecting individuals' energy behaviors is required. This dissertation offers an integrated conceptual framework to increase the efficiency of energy systems under complex and uncertainty conditions, facilitate energy consumption problem solving, and support the development of capacities at the individual, social, and technical levels to improve managing energy consumptions in the future. This research presents a conceptual soft systems model to explore the process of individuals' energy behavior change based on socio-structural and techno-structural contexts. In addition, a comprehensive model based on systems dynamics principles is presented to address the issue of CO2 emissions related to the households' energy consumption behavior. The proposed systems dynamics model provides a broad overview of the key agents affecting energy consumption, including government/public sector, households, and power industry. The model is created based on the research in the literature discussing the causal relations between various variables. The proposed systems dynamics model is verified by simulating different scenarios. In this research a survey is designed and conducted to investigate the role of individual, social and technical behaviors in reducing energy consumption, energy costs and carbon footprints based on the energy use profile. In sum, this study investigates the process of energy behavior change based on socio-structural and techno-structural contexts.

Dual-wavelength photo-Hall effect spectroscopy of deep levels in high resistive CdZnTe with negative differential photoconductivity

NASA Astrophysics Data System (ADS)

Musiienko, A.; Grill, R.; Moravec, P.; Korcsmáros, G.; Rejhon, M.; Pekárek, J.; Elhadidy, H.; Šedivý, L.; Vasylchenko, I.

2018-04-01

Photo-Hall effect spectroscopy was used in the study of deep levels in high resistive CdZnTe. The monochromator excitation in the photon energy range 0.65-1.77 eV was complemented by a laser diode high-intensity excitation at selected photon energies. A single sample characterized by multiple unusual features like negative differential photoconductivity and anomalous depression of electron mobility was chosen for the detailed study involving measurements at both the steady and dynamic regimes. We revealed that the Hall mobility and photoconductivity can be both enhanced and suppressed by an additional illumination at certain photon energies. The anomalous mobility decrease was explained by an excitation of the inhomogeneously distributed deep level at the energy Ev + 1.0 eV, thus enhancing potential non-uniformities. The appearance of negative differential photoconductivity was interpreted by an intensified electron occupancy of that level by a direct valence band-to-level excitation. Modified Shockley-Read-Hall theory was used for fitting experimental results by a model comprising five deep levels. Properties of the deep levels and their impact on the device performance were deduced.

Cyclohexane isomerization. Unimolecular dynamics of the twist-boat intermediate.

PubMed

Kakhiani, Khatuna; Lourderaj, Upakarasamy; Hu, Wenfang; Birney, David; Hase, William L

2009-04-23

Direct dynamics simulations were performed at the HF/6-31G level of theory to investigate the intramolecular and unimolecuar dynamics of the twist-boat (TB) intermediate on the cyclohexane potential energy surface (PES). Additional calculations were performed at the MP2/aug-cc-pVDZ level of theory to further characterize the PES's stationary points. The trajectories were initiated at the C(1) and C(2) half-chair transition states (TSs) connecting a chair conformer with a TB intermediate, via an intrinsic reaction coordinate (IRC). Energy was added in accord with a microcanonical ensemble at the average energy for experiments at 263 K. Important nontransition state theory (TST), non-IRC, and non-RRKM dynamics were observed in the simulations. Trajectories initially directed toward the chair conformer had a high probability of recrossing the TS, with approximately 30% forming a TB intermediate instead of accessing the potential energy well for the conformer. The TB intermediate initially formed was not necessarily the one connected to the TS via the IRC. Of the trajectories initiated at the C(2) half-chair TS and initially directed toward the chair conformer, 35% formed a TB intermediate instead of the chair conformer. Also, of the trajectories forming a TB intermediate, only 16% formed the TB intermediate connected with the C(2) TS via the IRC. Up to eight consecutive TB --> TB isomerizations were followed, and non-RRKM behavior was observed in their dynamics. A TB can isomerize to two different TBs, one by a clockwise rotation of C-C-C-C dihedral angles and the other by a counterclockwise rotation. In contrast to RRKM theory, which predicts equivalent probabilities for these rotations, the trajectory dynamics show they are not equivalent and depend on whether the C(1) or C(2) half-chair TS is initially excited. Non-RRKM dynamics is also observed in the isomerization of the TB intermediates to the chair conformers. RRKM theory assumes equivalent probabilities for isomerizing to the two chair conformers. In contrast, for the first and following TB intermediate formed, there is a preference to isomerize to the chair conformer connected to the TS at which the trajectories were initiated. For the first TB intermediate formed, approximately 30% of the isomerization is to a chair conformer, but this fraction decreases for the later formed TB intermediates and becomes approximately 10% for the eighth consecutive TB intermediate formed.

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

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

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulationsmore » as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water. Published by AIP Publishing.« less

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice [How good is the MB-pol many-body potential for water?

DOE PAGES

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp; ...

2016-11-17

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. Here, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. We investigate several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure through classical molecular dynamics simulations as amore » function of temperature. Furthermore, the structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.« less

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice [How good is the MB-pol many-body potential for water?

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

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. Here, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. We investigate several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure through classical molecular dynamics simulations as amore » function of temperature. Furthermore, the structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.« less

Modification and optimization of the united-residue (UNRES) potential-energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins

PubMed Central

Liwo, Adam; Khalili, Mey; Czaplewski, Cezary; Kalinowski, Sebastian; Ołdziej, Stanisław; Wachucik, Katarzyna; Scheraga, Harold A.

2011-01-01

We report the modification and parameterization of the united-residue (UNRES) force field for energy-based protein-structure prediction and protein-folding simulations. We tested the approach on three training proteins separately: 1E0L (β), 1GAB (α), and 1E0G (α + β). Heretofore, the UNRES force field had been designed and parameterized to locate native-like structures of proteins as global minima of their effective potential-energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES, and applied it with success to simulate protein folding pathways. How ever, the force field turned out to be largely biased towards α-helical structures in canonical simulations because the conformational entropy had been neglected in the parameterization. We applied the hierarchical optimization method developed in our earlier work to optimize the force field, in which the conformational space of a training protein is divided into levels each corresponding to a certain degree of native-likeness. The levels are ordered according to increasing native-likeness; level 0 corresponds to structures with no native-like elements and the highest level corresponds to the fully native-like structures. The aim of optimization is to achieve the order of the free energies of levels, decreasing as their native-likeness increases. The procedure is iterative, and decoys of the training protein(s) generated with the energy-function parameters of the preceding iteration are used to optimize the force field in a current iteration. We applied the multiplexing replica exchange molecular dynamics (MREMD) method, recently implemented in UNRES, to generate decoys; with this modification, conformational entropy is taken into account. Moreover, we optimized the free-energy gaps between levels at temperatures corresponding to a predominance of folded or unfolded structures, as well as to structures at the putative folding-transition temperature, changing the sign of the gaps at the transition temperature. This enabled us to obtain force fields characterized by a single peak in the heat capacity at the transition temperature. Furthermore, we introduced temperature dependence to the UNRES force field; this is consistent with the fact that it is a free-energy and not a potential-energy function. PMID:17201450

A Distributed and Energy-Efficient Algorithm for Event K-Coverage in Underwater Sensor Networks

PubMed Central

Jiang, Peng; Xu, Yiming; Liu, Jun

2017-01-01

For event dynamic K-coverage algorithms, each management node selects its assistant node by using a greedy algorithm without considering the residual energy and situations in which a node is selected by several events. This approach affects network energy consumption and balance. Therefore, this study proposes a distributed and energy-efficient event K-coverage algorithm (DEEKA). After the network achieves 1-coverage, the nodes that detect the same event compete for the event management node with the number of candidate nodes and the average residual energy, as well as the distance to the event. Second, each management node estimates the probability of its neighbor nodes’ being selected by the event it manages with the distance level, the residual energy level, and the number of dynamic coverage event of these nodes. Third, each management node establishes an optimization model that uses expectation energy consumption and the residual energy variance of its neighbor nodes and detects the performance of the events it manages as targets. Finally, each management node uses a constrained non-dominated sorting genetic algorithm (NSGA-II) to obtain the Pareto set of the model and the best strategy via technique for order preference by similarity to an ideal solution (TOPSIS). The algorithm first considers the effect of harsh underwater environments on information collection and transmission. It also considers the residual energy of a node and a situation in which the node is selected by several other events. Simulation results show that, unlike the on-demand variable sensing K-coverage algorithm, DEEKA balances and reduces network energy consumption, thereby prolonging the network’s best service quality and lifetime. PMID:28106837

A Distributed and Energy-Efficient Algorithm for Event K-Coverage in Underwater Sensor Networks.

PubMed

Jiang, Peng; Xu, Yiming; Liu, Jun

2017-01-19

For event dynamic K-coverage algorithms, each management node selects its assistant node by using a greedy algorithm without considering the residual energy and situations in which a node is selected by several events. This approach affects network energy consumption and balance. Therefore, this study proposes a distributed and energy-efficient event K-coverage algorithm (DEEKA). After the network achieves 1-coverage, the nodes that detect the same event compete for the event management node with the number of candidate nodes and the average residual energy, as well as the distance to the event. Second, each management node estimates the probability of its neighbor nodes' being selected by the event it manages with the distance level, the residual energy level, and the number of dynamic coverage event of these nodes. Third, each management node establishes an optimization model that uses expectation energy consumption and the residual energy variance of its neighbor nodes and detects the performance of the events it manages as targets. Finally, each management node uses a constrained non-dominated sorting genetic algorithm (NSGA-II) to obtain the Pareto set of the model and the best strategy via technique for order preference by similarity to an ideal solution (TOPSIS). The algorithm first considers the effect of harsh underwater environments on information collection and transmission. It also considers the residual energy of a node and a situation in which the node is selected by several other events. Simulation results show that, unlike the on-demand variable sensing K-coverage algorithm, DEEKA balances and reduces network energy consumption, thereby prolonging the network's best service quality and lifetime.

Sustainability through Dynamic Energy Management - Continuum Magazine |

Science.gov Websites

NREL Sustainability through Dynamic Energy Management Sustainability through Dynamic Energy Management Integrating behavior change with advanced building systems is the new model in energy efficiency , it's necessary to integrate dynamic energy management with occupant behavior change. As plans were

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

PubMed

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ↔ Closed Transitions

PubMed Central

Beckstein, Oliver; Denning, Elizabeth J.; Perilla, Juan R.; Woolf, Thomas B.

2009-01-01

Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free energy calculations and our new dynamic importance sampling (DIMS) molecular dynamics (MD) method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular four ionic bonds are identified that open in a sequential, zipper-like fashion and thus dominate the free energy landscape of the transition. Transitions between the closed and open conformations only have to overcome moderate free energy barriers. Unexpectedly, the closed and open state encompass broad free energy basins that contain conformations differing in domain hinge motions by up to 40°. The significance of these extended states is discussed in relation to recent experimental FRET measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an “all-or-nothing” mechanism for the opening and closing of AdK. Our efficient DIMS-MD computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK. PMID:19751742

Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

PubMed Central

Li, Dechang; Liu, Ming S.; Ji, Baohua

2015-01-01

Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems. PMID:26244746

Equivalent circuit-level model of quantum cascade lasers with integrated hot-electron and hot-phonon effects

NASA Astrophysics Data System (ADS)

Yousefvand, H. R.

2017-12-01

We report a study of the effects of hot-electron and hot-phonon dynamics on the output characteristics of quantum cascade lasers (QCLs) using an equivalent circuit-level model. The model is developed from the energy balance equation to adopt the electron temperature in the active region levels, the heat transfer equation to include the lattice temperature, the nonequilibrium phonon rate to account for the hot phonon dynamics and simplified two-level rate equations to incorporate the carrier and photon dynamics in the active region. This technique simplifies the description of the electron-phonon interaction in QCLs far from the equilibrium condition. Using the presented model, the steady and transient responses of the QCLs for a wide range of sink temperatures (80 to 320 K) are investigated and analysed. The model enables us to explain the operating characteristics found in QCLs. This predictive model is expected to be applicable to all QCL material systems operating in pulsed and cw regimes.

Sensitivity Analysis as a Tool to assess Energy-Water Nexus in India

NASA Astrophysics Data System (ADS)

Priyanka, P.; Banerjee, R.

2017-12-01

Rapid urbanization, population growth and related structural changes with-in the economy of a developing country act as a stressor on energy and water demand, which forms a well-established energy-water nexus. Energy-water nexus is thoroughly studied at various spatial scales viz. city level, river basin level and national level- to guide different stakeholders for sustainable management of energy and water. However, temporal dimensions of energy-water nexus at national level have not been thoroughly investigated because of unavailability of relevant time-series data. In this study we investigated energy-water nexus at national level using environmentally-extended input-output tables for Indian economy (2004-2013) as provided by EORA database. Perturbation based sensitivity analysis is proposed to highlight the critical nodes of interactions among economic sectors which is further linked to detect the synergistic effects of energy and water consumption. Technology changes (interpreted as change in value of nodes) results in modification of interactions among economic sectors and synergy is affected through direct as well as indirect effects. Indirect effects are not easily understood through preliminary examination of data, hence sensitivity analysis within an input-output framework is important to understand the indirect effects. Furthermore, time series data helps in developing the understanding on dynamics of synergistic effects. We identified the key sectors and technology changes for Indian economy which will provide the better decision support for policy makers about sustainable use of energy-water resources in India.

A hierarchical dislocation-grain boundary interaction model based on 3D discrete dislocation dynamics and molecular dynamics

NASA Astrophysics Data System (ADS)

Gao, Yuan; Zhuang, Zhuo; You, XiaoChuan

2011-04-01

We develop a new hierarchical dislocation-grain boundary (GB) interaction model to predict the mechanical behavior of polycrystalline metals at micro and submicro scales by coupling 3D Discrete Dislocation Dynamics (DDD) simulation with the Molecular Dynamics (MD) simulation. At the microscales, the DDD simulations are responsible for capturing the evolution of dislocation structures; at the nanoscales, the MD simulations are responsible for obtaining the GB energy and ISF energy which are then transferred hierarchically to the DDD level. In the present model, four kinds of dislocation-GB interactions, i.e. transmission, absorption, re-emission and reflection, are all considered. By this methodology, the compression of a Cu micro-sized bi-crystal pillar is studied. We investigate the characteristic mechanical behavior of the bi-crystal compared with that of the single-crystal. Moreover, the comparison between the present penetrable model of GB and the conventional impenetrable model also shows the accuracy and efficiency of the present model.

Development of many-body polarizable force fields for Li-battery components: 1. Ether, alkane, and carbonate-based solvents.

PubMed

Borodin, Oleg; Smith, Grant D

2006-03-30

Classical many-body polarizable force fields were developed for n-alkanes, perflouroalkanes, polyethers, ketones, and linear and cyclic carbonates on the basis of quantum chemistry dimer energies of model compounds and empirical thermodynamic liquid-state properties. The dependence of the electron correlation contribution to the dimer binding energy on basis-set size and level of theory was investigated as a function of molecular separation for a number of alkane, ether, and ketone dimers. Molecular dynamics (MD) simulations of the force fields accurately predicted structural, dynamic, and transport properties of liquids and unentangled polymer melts. On average, gas-phase dimer binding energies predicted with the force field were between those from MP2/aug-cc-pvDz and MP2/aug-cc-pvTz quantum chemistry calculations.

Influence of the nuclear level density on the odd-even staggering in 56Fe+p spallation at energies from 300 to 1500 MeV/nucleon

NASA Astrophysics Data System (ADS)

Su, Jun; Zhu, Long; Guo, Chenchen

2018-05-01

Background: Special attention has been paid to study the shell effect and odd-even staggering (OES) in the nuclear spallation. Purpose: In this paper, we investigate the influence of the nuclear level density on the OES in the 56Fe+p spallations at energies from 300 to 1500 MeV/nucleon. Method: The isospin-dependent quantum molecular dynamics (IQMD) model is applied to produce the highly excited and equilibrium remnants, which is then de-excited using the statistical model gemini. The excitation energy of the heaviest hot fragments is applied to match the IQMD model with the gemini model. In the gemini model, the statistical description of the evaporation are based on the Hauser-Feshbach formalism, in which level density prescriptions are applied. Results: By investigating the OES of the excited pre-fragments, it is found that the OES originates at the end of the decay process when the excitation energy is close to the nucleon-emission threshold energy, i.e., the smaller value of the neutron separation energy and proton separation energy. The strong influence of level density on the OES is noticed. Two types of the nuclear level densities, the discrepancy of which is only about 7% near the nucleon emission threshold energy, are used in the model. However, the calculated values of the OES differ by the factor of 3 for the relevant nuclei. Conclusions: It is suggested that, although the particle-separation energies play a key role in determining the OES, the level density at excitation energy lower than the particle-separation energies should be taken into consideration

The origin of unequal bond lengths in the C 1B 2 state of SO 2: Signatures of high-lying potential energy surface crossings in the low-lying vibrational structure

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

Park, G. Barratt; Jiang, Jun; Field, Robert W.

Here the C 1B 2 state of SO 2 has a double-minimum potential in the antisymmetric stretch coordinate, such that the minimum energy geometry has nonequivalent SO bond lengths. The asymmetry in the potential energy surface is expressed as a staggering in the energy levels of the v' 3 progression. We have recently made the first observation of low-lying levels with odd quanta of v' 3, which allows us--in the current work--to characterize the origins of the level staggering. Our work demonstrates the usefulness of low-lying vibrational level structure, where the character of the wavefunctions can be relatively easily understood,more » to extract information about dynamically important potential energy surface crossings that occur at much higher energy. The measured staggering pattern is consistent with a vibronic coupling model for the double-minimum, which involves direct coupling to the bound 2 1A 1 state and indirect coupling with the repulsive 3 1A 1 state. The degree of staggering in the v' 3 levels increases with quanta of bending excitation, which is consistent with the approach along the C state potential energy surface to a conical intersection with the 2 1A 1 surface at a bond angle of ~145°.« less

The origin of unequal bond lengths in the C 1B 2 state of SO 2: Signatures of high-lying potential energy surface crossings in the low-lying vibrational structure

DOE PAGES

Park, G. Barratt; Jiang, Jun; Field, Robert W.

2016-04-14

Here the C 1B 2 state of SO 2 has a double-minimum potential in the antisymmetric stretch coordinate, such that the minimum energy geometry has nonequivalent SO bond lengths. The asymmetry in the potential energy surface is expressed as a staggering in the energy levels of the v' 3 progression. We have recently made the first observation of low-lying levels with odd quanta of v' 3, which allows us--in the current work--to characterize the origins of the level staggering. Our work demonstrates the usefulness of low-lying vibrational level structure, where the character of the wavefunctions can be relatively easily understood,more » to extract information about dynamically important potential energy surface crossings that occur at much higher energy. The measured staggering pattern is consistent with a vibronic coupling model for the double-minimum, which involves direct coupling to the bound 2 1A 1 state and indirect coupling with the repulsive 3 1A 1 state. The degree of staggering in the v' 3 levels increases with quanta of bending excitation, which is consistent with the approach along the C state potential energy surface to a conical intersection with the 2 1A 1 surface at a bond angle of ~145°.« less

A monostable piezoelectric energy harvester for broadband low-level excitations

NASA Astrophysics Data System (ADS)

Fan, Kangqi; Tan, Qinxue; Zhang, Yiwei; Liu, Shaohua; Cai, Meiling; Zhu, Yingmin

2018-03-01

This letter presents a monostable piezoelectric energy harvester (PEH) for achieving enhanced energy extraction from low-level excitations. The proposed PEH is realized by introducing symmetric magnetic attraction to a piezoelectric cantilever beam and a pair of stoppers to confine the maximum deflection of the beam. The lumped parameter model of such a system is presented and experimentally validated. Theoretical simulations and experimental measurements demonstrate that the proposed design can bring about a wider operating bandwidth and higher output voltage than the linear PEH. Under a sinusoidal vibration with an amplitude of 3 m/s2, a 54% increase in the operating bandwidth and a 253% increase in the magnitude of output power are achieved compared to its linear counterpart. Moreover, the proposed PEH exhibits rich dynamic features, including the tunable operating bandwidth, adjustable voltage and power levels, and softening hysteresis.

Energy technologies evaluated against climate targets using a cost and carbon trade-off curve.

PubMed

Trancik, Jessika E; Cross-Call, Daniel

2013-06-18

Over the next few decades, severe cuts in emissions from energy will be required to meet global climate-change mitigation goals. These emission reductions imply a major shift toward low-carbon energy technologies, and the economic cost and technical feasibility of mitigation are therefore highly dependent upon the future performance of energy technologies. However, existing models do not readily translate into quantitative targets against which we can judge the dynamic performance of technologies. Here, we present a simple, new model for evaluating energy-supply technologies and their improvement trajectories against climate-change mitigation goals. We define a target for technology performance in terms of the carbon intensity of energy, consistent with emission reduction goals, and show how the target depends upon energy demand levels. Because the cost of energy determines the level of adoption, we then compare supply technologies to one another and to this target based on their position on a cost and carbon trade-off curve and how the position changes over time. Applying the model to U.S. electricity, we show that the target for carbon intensity will approach zero by midcentury for commonly cited emission reduction goals, even under a high demand-side efficiency scenario. For Chinese electricity, the carbon intensity target is relaxed and less certain because of lesser emission reductions and greater variability in energy demand projections. Examining a century-long database on changes in the cost-carbon space, we find that the magnitude of changes in cost and carbon intensity that are required to meet future performance targets is not unprecedented, providing some evidence that these targets are within engineering reach. The cost and carbon trade-off curve can be used to evaluate the dynamic performance of existing and new technologies against climate-change mitigation goals.

Contribution of PsbS Function and Stomatal Conductance to Foliar Temperature in Higher Plants

PubMed Central

Kulasek, Milena; Bernacki, Maciej Jerzy; Ciszak, Kamil; Witoń, Damian; Karpiński, Stanisław

2016-01-01

Natural capacity has evolved in higher plants to absorb and harness excessive light energy. In basic models, the majority of absorbed photon energy is radiated back as fluorescence and heat. For years the proton sensor protein PsbS was considered to play a critical role in non-photochemical quenching (NPQ) of light absorbed by PSII antennae and in its dissipation as heat. However, the significance of PsbS in regulating heat emission from a whole leaf has never been verified before by direct measurement of foliar temperature under changing light intensity. To test its validity, we here investigated the foliar temperature changes on increasing and decreasing light intensity conditions (foliar temperature dynamics) using a high resolution thermal camera and a powerful adjustable light-emitting diode (LED) light source. First, we showed that light-dependent foliar temperature dynamics is correlated with Chl content in leaves of various plant species. Secondly, we compared the foliar temperature dynamics in Arabidopsis thaliana wild type, the PsbS null mutant npq4-1 and a PsbS-overexpressing transgenic line under different transpiration conditions with or without a photosynthesis inhibitor. We found no direct correlations between the NPQ level and the foliar temperature dynamics. Rather, differences in foliar temperature dynamics are primarily affected by stomatal aperture, and rapid foliar temperature increase during irradiation depends on the water status of the leaf. We conclude that PsbS is not directly involved in regulation of foliar temperature dynamics during excessive light energy episodes. PMID:27273581

DC dynamic pull-in instability of a dielectric elastomer balloon: an energy-based approach

NASA Astrophysics Data System (ADS)

Sharma, Atul Kumar; Arora, Nitesh; Joglekar, M. M.

2018-03-01

This paper reports an energy-based method for the dynamic pull-in instability analysis of a spherical dielectric elastomer (DE) balloon subjected to a quasi-statically applied inflation pressure and a Heaviside step voltage across the balloon wall. The proposed technique relies on establishing the energy balance at the point of maximum stretch in an oscillation cycle, followed by the imposition of an instability condition for extracting the threshold parameters. The material models of the Ogden family are employed for describing the hyperelasticity of the balloon. The accuracy of the critical dynamic pull-in parameters is established by examining the saddle-node bifurcation in the transient response of the balloon obtained by integrating numerically the equation of motion, derived using the Euler-Lagrange equation. The parametric study brings out the effect of inflation pressure on the onset of the pull-in instability in the DE balloon. A quantitative comparison between the static and dynamic pull-in parameters at four different levels of the inflation pressure is presented. The results indicate that the dynamic pull-in instability gets triggered at electric fields that are lower than those corresponding to the static instability. The results of the present investigation can find potential use in the design and development of the balloon actuators subjected to transient loading. The method developed is versatile and can be used in the dynamic instability analysis of other conservative systems of interest.

DC dynamic pull-in instability of a dielectric elastomer balloon: an energy-based approach.

PubMed

Sharma, Atul Kumar; Arora, Nitesh; Joglekar, M M

2018-03-01

This paper reports an energy-based method for the dynamic pull-in instability analysis of a spherical dielectric elastomer (DE) balloon subjected to a quasi-statically applied inflation pressure and a Heaviside step voltage across the balloon wall. The proposed technique relies on establishing the energy balance at the point of maximum stretch in an oscillation cycle, followed by the imposition of an instability condition for extracting the threshold parameters. The material models of the Ogden family are employed for describing the hyperelasticity of the balloon. The accuracy of the critical dynamic pull-in parameters is established by examining the saddle-node bifurcation in the transient response of the balloon obtained by integrating numerically the equation of motion, derived using the Euler-Lagrange equation. The parametric study brings out the effect of inflation pressure on the onset of the pull-in instability in the DE balloon. A quantitative comparison between the static and dynamic pull-in parameters at four different levels of the inflation pressure is presented. The results indicate that the dynamic pull-in instability gets triggered at electric fields that are lower than those corresponding to the static instability. The results of the present investigation can find potential use in the design and development of the balloon actuators subjected to transient loading. The method developed is versatile and can be used in the dynamic instability analysis of other conservative systems of interest.

Dynamic analysis of a buckled asymmetric piezoelectric beam for energy harvesting

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

Van Blarigan, Louis, E-mail: louis01@umail.ucsb.edu; Moehlis, Jeff

2016-03-15

A model of a buckled beam energy harvester is analyzed to determine the phenomena behind the transition between high and low power output levels. It is shown that the presence of a chaotic attractor is a sufficient condition to predict high power output, though there are relatively small areas where high output is achieved without a chaotic attractor. The chaotic attractor appears as a product of a period doubling cascade or a boundary crisis. Bifurcation diagrams provide insight into the development of the chaotic region as the input power level is varied, as well as the intermixed periodic windows.

The AquaDEB project (phase I): Analysing the physiological flexibility of aquatic species and connecting physiological diversity to ecological and evolutionary processes by using Dynamic Energy Budgets

NASA Astrophysics Data System (ADS)

Alunno-Bruscia, Marianne; van der Veer, Henk W.; Kooijman, Sebastiaan A. L. M.

2009-08-01

The European Research Project AquaDEB (2007-2011, http://www.ifremer.fr/aquadeb/) is joining skills and expertise of some French and Dutch research institutes and universities to analyse the physiological flexibility of aquatic organisms and to link it to ecological and evolutionary processes within a common theoretical framework for quantitative bioenergetics [Kooijman, S.A.L.M., 2000. Dynamic energy and mass budgets in biological systems. Cambridge University Press, Cambridge]. The main scientific objectives in AquaDEB are i) to study and compare the sensitivity of aquatic species (mainly molluscs and fish) to environmental variability of natural or human origin, and ii) to evaluate the related consequences at different biological levels (individual, population, ecosystem) and temporal scales (life cycle, population dynamics, evolution). At mid-term life, the AquaDEB collaboration has already yielded interesting results by quantifying bio-energetic processes of various aquatic species (e.g. molluscs, fish, crustaceans, algae) with a single mathematical framework. It has also allowed to federate scientists with different backgrounds, e.g. mathematics, microbiology, ecology, chemistry, and working in different fields, e.g. aquaculture, fisheries, ecology, agronomy, ecotoxicology, climate change. For the two coming years, the focus of the AquaDEB collaboration will be in priority: (i) to compare energetic and physiological strategies among species through the DEB parameter values and to identify the factors responsible for any differences in bioenergetics and physiology; and to compare dynamic (DEB) versus static (SEB) energy models to study the physiological performance of aquatic species; (ii) to consider different scenarios of environmental disruption (excess of nutrients, diffuse or massive pollution, exploitation by man, climate change) to forecast effects on growth, reproduction and survival of key species; (iii) to scale up the models for a few species from the individual level up to the level of evolutionary processes.

Continuous-Time Monitoring of Landau-Zener Interference in a Cooper-Pair Box

NASA Astrophysics Data System (ADS)

Sillanpää, Mika; Lehtinen, Teijo; Paila, Antti; Makhlin, Yuriy; Hakonen, Pertti

2006-05-01

Landau-Zener (LZ) tunneling can occur with a certain probability when crossing energy levels of a quantum two-level system are swept across the minimum energy separation. Here we present experimental evidence of quantum interference effects in solid-state LZ tunneling. We used a Cooper-pair box qubit where the LZ tunneling occurs at the charge degeneracy. By employing a weak nondemolition monitoring, we observe interference between consecutive LZ-tunneling events; we find that the average level occupancies depend on the dynamical phase. The system’s unusually strong linear response is explained by interband relaxation. Our interferometer can be used as a high-resolution Mach-Zehnder type detector for phase and charge.

Continuous-time monitoring of Landau-Zener interference in a cooper-pair box.

PubMed

Sillanpää, Mika; Lehtinen, Teijo; Paila, Antti; Makhlin, Yuriy; Hakonen, Pertti

2006-05-12

Landau-Zener (LZ) tunneling can occur with a certain probability when crossing energy levels of a quantum two-level system are swept across the minimum energy separation. Here we present experimental evidence of quantum interference effects in solid-state LZ tunneling. We used a Cooper-pair box qubit where the LZ tunneling occurs at the charge degeneracy. By employing a weak nondemolition monitoring, we observe interference between consecutive LZ-tunneling events; we find that the average level occupancies depend on the dynamical phase. The system's unusually strong linear response is explained by interband relaxation. Our interferometer can be used as a high-resolution Mach-Zehnder-type detector for phase and charge.

Role of wave packet width in quantum molecular dynamics in fusion reactions near barrier

NASA Astrophysics Data System (ADS)

Cao, X. G.; Ma, Y. G.; Zhang, G. Q.; Wang, H. W.; Anastasi, A.; Curciarello, F.; De Leo, V.

2014-05-01

The dynamical fusion process of 48Ca + 144Sm with different impact parameters near barrier is studied by an extended quantum molecular dynamics (EQMD) model, where width of wavepacket is dynamically treated based on variational principle. The time evolution of different energy components such as potential energy, kinetic energy, Coulomb energy and Pauli potential are analyzed when dynamical or fixed width is assumed in calculation. It is found that the dynamical wavepacket width can enhance the dissipation of incident energy and the fluctuations, which are important to form compound nuclei. Moreover, we compare the fusion barrier dependence on the incident energy when it is determined by both dynamical and fixed wavepacket width.

Event-driven Monte Carlo: Exact dynamics at all time scales for discrete-variable models

NASA Astrophysics Data System (ADS)

Mendoza-Coto, Alejandro; Díaz-Méndez, Rogelio; Pupillo, Guido

2016-06-01

We present an algorithm for the simulation of the exact real-time dynamics of classical many-body systems with discrete energy levels. In the same spirit of kinetic Monte Carlo methods, a stochastic solution of the master equation is found, with no need to define any other phase-space construction. However, unlike existing methods, the present algorithm does not assume any particular statistical distribution to perform moves or to advance the time, and thus is a unique tool for the numerical exploration of fast and ultra-fast dynamical regimes. By decomposing the problem in a set of two-level subsystems, we find a natural variable step size, that is well defined from the normalization condition of the transition probabilities between the levels. We successfully test the algorithm with known exact solutions for non-equilibrium dynamics and equilibrium thermodynamical properties of Ising-spin models in one and two dimensions, and compare to standard implementations of kinetic Monte Carlo methods. The present algorithm is directly applicable to the study of the real-time dynamics of a large class of classical Markovian chains, and particularly to short-time situations where the exact evolution is relevant.

Origin of the glass-like dynamics in molecular metals κ-(BEDT-TTF)2X: implications from fluctuation spectroscopy and ab initio calculations

NASA Astrophysics Data System (ADS)

Müller, Jens; Hartmann, Benedikt; Rommel, Robert; Brandenburg, Jens; Winter, Stephen M.; Schlueter, John A.

2015-08-01

We have studied the low-frequency dynamics of the charge carriers in different organic charge-transfer salts κ-(BEDT-TTF)2X with polymeric anions X by using resistance noise spectroscopy. Our aim is to investigate the structural, glass-like transition caused by the conformational degrees of freedom of the BEDT-TTF molecules’ terminal ethylene groups. Although of fundamental importance for studies of the electronic ground-state properties, the phenomenology of the glassy dynamics has been minimally investigated and its origin is not understood. Our systematic studies of fluctuation spectroscopy of various different compounds reveal a universal, pronounced maximum in the resistance noise power spectral density related to the glass transition. The energy scale of this process can be identified with the activation energy of the glass-like ethylene endgroup structural dynamics as determined from thermodynamic and NMR measurements. For the first time for this class of ‘plastic crystals’, we report a typical glassy property of the relaxation time, namely a Vogel-Fulcher-Tammann law, and are able to determine the degree of fragility of the glassy system. Supporting ab initio calculations provide an explanation for the origin and phenomenology of the glassy dynamics in different systems in terms of a simple two-level model, where the relevant energy scales are determined by the coupling of the ethylene endgroups to the anions.

Research on simulation system with the wide range and high-precision laser energy characteristics

NASA Astrophysics Data System (ADS)

Dong, Ke-yan; Lou, Yan; He, Jing-yi; Tong, Shou-feng; Jiang, Hui-lin

2012-10-01

The Hardware-in-the-loop(HWIL) simulation test is one of the important parts for the development and performance testing of semi-active laser-guided weapons. In order to obtain accurate results, the confidence level of the target environment should be provided for a high-seeker during the HWIL simulation test of semi-active laser-guided weapons, and one of the important simulation parameters is the laser energy characteristic. In this paper, based on the semi-active laser-guided weapon guidance principles, an important parameter of simulation of confidence which affects energy characteristics in performance test of HWIL simulation was analyzed. According to the principle of receiving the same energy by using HWIL simulation and in practical application, HWIL energy characteristics simulation systems with the crystal absorption structure was designed. And on this basis, the problems of optimal design of the optical system were also analyzed. The measured results show that the dynamic attenuation range of the system energy is greater than 50dB, the dynamic attenuation stability is less than 5%, and the maximum energy changing rate driven by the servo motor is greater than 20dB/s.

Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching.

PubMed

Glowacki, David R; Rodgers, W J; Shannon, Robin; Robertson, Struan H; Harvey, Jeremy N

2017-04-28

The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH 3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems.This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'. © 2017 The Authors.

Reaction and relaxation at surface hotspots: using molecular dynamics and the energy-grained master equation to describe diamond etching

PubMed Central

Rodgers, W. J.; Shannon, Robin; Robertson, Struan H.; Harvey, Jeremy N.

2017-01-01

The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at ‘hotspots’ that form on the surface of diamond during the chemical vapour deposition process. To explore this, we developed an efficient reactive potential energy surface by fitting an empirical valence bond model to higher-level ab initio electronic structure theory. We then ran 160 000 NVE trajectories on a large slab of diamond, and the results are in reasonable agreement with experiment: they suggest that energy dissipation from surface hotspots is complete within a few hundred femtoseconds, but that a small fraction of CH3 does in fact undergo dissociation prior to the onset of thermal equilibrium. Second, we developed and tested a general procedure to formulate and solve the energy-grained master equation (EGME) for surface chemistry problems. The procedure we outline splits the diamond slab into system and bath components, and then evaluates microcanonical transition-state theory rate coefficients in the configuration space of the system atoms. Energy transfer from the system to the bath is estimated using linear response theory from a single long MD trajectory, and used to parametrize an energy transfer function which can be input into the EGME. Despite the number of approximations involved, the surface EGME results are in reasonable agreement with the NVE MD simulations, but considerably cheaper. The results are encouraging, because they offer a computationally tractable strategy for investigating non-equilibrium reaction dynamics at surfaces for a broader range of systems. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’. PMID:28320908

Temporal switching of homo-FRET pathways in single-chromophore dimer models of π-conjugated polymers.

PubMed

Stangl, Thomas; Bange, Sebastian; Schmitz, Daniela; Würsch, Dominik; Höger, Sigurd; Vogelsang, Jan; Lupton, John M

2013-01-09

A set of π-conjugated oligomer dimers templated in molecular scaffolds is presented as a model system for studying the interactions between chromophores in conjugated polymers (CPs). Single-molecule spectroscopy was used to reveal energy transfer dynamics between two oligomers in either a parallel or oblique-angle geometry. In particular, the conformation of single molecules embedded in a host matrix was investigated via polarized excitation and emission fluorescence microscopy in combination with fluorescence correlation spectroscopy. While the intramolecular interchromophore conformation was found to have no impact on the fluorescence quantum yield, lifetime, or photon statistics (antibunching), the long-term nonequilibrium dynamics of energy transfer within these bichromophoric systems was accessible by studying the linear dichroism in emission at the single-molecule level, which revealed reversible switching of the emission between the two oligomers. In bulk polymer films, interchromophore coupling promotes the migration of excitation energy to quenching sites. Realizing the presence and dynamics of such interactions is crucial for understanding limitations on the quantum efficiency of larger CP materials.

Computational Analysis of AMPK-Mediated Neuroprotection Suggests Acute Excitotoxic Bioenergetics and Glucose Dynamics Are Regulated by a Minimal Set of Critical Reactions.

PubMed

Connolly, Niamh M C; D'Orsi, Beatrice; Monsefi, Naser; Huber, Heinrich J; Prehn, Jochen H M

2016-01-01

Loss of ionic homeostasis during excitotoxic stress depletes ATP levels and activates the AMP-activated protein kinase (AMPK), re-establishing energy production by increased expression of glucose transporters on the plasma membrane. Here, we develop a computational model to test whether this AMPK-mediated glucose import can rapidly restore ATP levels following a transient excitotoxic insult. We demonstrate that a highly compact model, comprising a minimal set of critical reactions, can closely resemble the rapid dynamics and cell-to-cell heterogeneity of ATP levels and AMPK activity, as confirmed by single-cell fluorescence microscopy in rat primary cerebellar neurons exposed to glutamate excitotoxicity. The model further correctly predicted an excitotoxicity-induced elevation of intracellular glucose, and well resembled the delayed recovery and cell-to-cell heterogeneity of experimentally measured glucose dynamics. The model also predicted necrotic bioenergetic collapse and altered calcium dynamics following more severe excitotoxic insults. In conclusion, our data suggest that a minimal set of critical reactions may determine the acute bioenergetic response to transient excitotoxicity and that an AMPK-mediated increase in intracellular glucose may be sufficient to rapidly recover ATP levels following an excitotoxic insult.

Computational Analysis of AMPK-Mediated Neuroprotection Suggests Acute Excitotoxic Bioenergetics and Glucose Dynamics Are Regulated by a Minimal Set of Critical Reactions

PubMed Central

Connolly, Niamh M. C.; D’Orsi, Beatrice; Monsefi, Naser; Huber, Heinrich J.; Prehn, Jochen H. M.

2016-01-01

Loss of ionic homeostasis during excitotoxic stress depletes ATP levels and activates the AMP-activated protein kinase (AMPK), re-establishing energy production by increased expression of glucose transporters on the plasma membrane. Here, we develop a computational model to test whether this AMPK-mediated glucose import can rapidly restore ATP levels following a transient excitotoxic insult. We demonstrate that a highly compact model, comprising a minimal set of critical reactions, can closely resemble the rapid dynamics and cell-to-cell heterogeneity of ATP levels and AMPK activity, as confirmed by single-cell fluorescence microscopy in rat primary cerebellar neurons exposed to glutamate excitotoxicity. The model further correctly predicted an excitotoxicity-induced elevation of intracellular glucose, and well resembled the delayed recovery and cell-to-cell heterogeneity of experimentally measured glucose dynamics. The model also predicted necrotic bioenergetic collapse and altered calcium dynamics following more severe excitotoxic insults. In conclusion, our data suggest that a minimal set of critical reactions may determine the acute bioenergetic response to transient excitotoxicity and that an AMPK-mediated increase in intracellular glucose may be sufficient to rapidly recover ATP levels following an excitotoxic insult. PMID:26840769

Biology-inspired AMO physics

NASA Astrophysics Data System (ADS)

Mathur, Deepak

2015-01-01

This Topical Review presents an overview of increasingly robust interconnects that are being established between atomic, molecular and optical (AMO) physics and the life sciences. AMO physics, outgrowing its historical role as a facilitator—a provider of optical methodologies, for instance—now seeks to partner biology in its quest to link systems-level descriptions of biological entities to insights based on molecular processes. Of course, perspectives differ when AMO physicists and biologists consider various processes. For instance, while AMO physicists link molecular properties and dynamics to potential energy surfaces, these have to give way to energy landscapes in considerations of protein dynamics. But there are similarities also: tunnelling and non-adiabatic transitions occur both in protein dynamics and in molecular dynamics. We bring to the fore some such differences and similarities; we consider imaging techniques based on AMO concepts, like 4D fluorescence microscopy which allows access to the dynamics of cellular processes, multiphoton microscopy which offers a built-in confocality, and microscopy with femtosecond laser beams to saturate the suppression of fluorescence in spatially controlled fashion so as to circumvent the diffraction limit. Beyond imaging, AMO physics contributes with optical traps that probe the mechanical and dynamical properties of single ‘live’ cells, highlighting differences between healthy and diseased cells. Trap methodologies have also begun to probe the dynamics governing of neural stem cells adhering to each other to form neurospheres and, with squeezed light to probe sub-diffusive motion of yeast cells. Strong field science contributes not only by providing a source of energetic electrons and γ-rays via laser-plasma accelerations schemes, but also via filamentation and supercontinuum generation, enabling mainstream collision physics into play in diverse processes like DNA damage induced by low-energy collisions to invoking dissociative attachment in quantification of stress levels in humans. The prognosis is extremely good for more intense interaction of AMO physics and biology; by way of future predictions attention is drawn to only two of very many opportunities for such interactions: application of attosecond techniques and tunnelling experiments to biological problems.

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

PubMed

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of reaction dynamics, which provides a useful tool to study chemical or biochemical systems in solution or enzymes.

Numeric and fluid dynamic representation of tornadic double vortex thunderstorms

NASA Technical Reports Server (NTRS)

Connell, J. R.; Marquart, E. J.; Frost, W.; Boaz, W.

1980-01-01

Current understanding of a double vortex thunderstorm involves a pair of contra-rotating vortices that exists in the dynamic updraft. The pair is believed to be a result of a blocking effect which occurs when a cylindrical thermal updraft of a thunderstorm protrudes into the upper level air and there is a large amount of vertical wind shear between the low level and upper level air layers. A numerical tornado prediction scheme based on the double vortex thunderstorm was developed. The Energy-Shear Index (ESI) is part of the scheme and is calculated from radiosonde measurements. The ESI incorporates parameters representative of thermal instability and blocking effect, and indicates appropriate environments for which the development of double vortex thunderstorms is likely.

Uncertainty evaluation of EnPIs in industrial applications as a key factor in setting improvement actions

NASA Astrophysics Data System (ADS)

D'Emilia, G.; Di Gasbarro, D.; Gaspari, A.; Natale, E.

2015-11-01

A methodology is proposed assuming high-level Energy Performance Indicators (EnPIs) uncertainty as quantitative indicator of the evolution of an Energy Management System (EMS). Motivations leading to the selection of the EnPIs, uncertainty evaluation techniques and criteria supporting decision-making are discussed, in order to plan and pursue reliable measures for energy performance improvement. In this paper, problems, priorities, operative possibilities and reachable improvement limits are examined, starting from the measurement uncertainty assessment. Two different industrial cases are analysed with reference to the following aspects: absence/presence of energy management policy and action plans; responsibility level for the energy issues; employees’ training and motivation in respect of the energy problems; absence/presence of adequate infrastructures for monitoring and sharing of energy information; level of standardization and integration of methods and procedures linked to the energy activities; economic and financial resources for the improvement of energy efficiency. A critic and comparative analysis of the obtained results is realized. The methodology, experimentally validated, allows developing useful considerations for effective, realistic and economically feasible improvement plans, depending on the specific situation. Recursive application of the methodology allows getting reliable and resolved assessment of the EMS status, also in dynamic industrial contexts.

Modeling Energy Efficiency As A Green Logistics Component In Vehicle Assembly Line

NASA Astrophysics Data System (ADS)

Oumer, Abduaziz; Mekbib Atnaw, Samson; Kie Cheng, Jack; Singh, Lakveer

2016-11-01

This paper uses System Dynamics (SD) simulation to investigate the concept green logistics in terms of energy efficiency in automotive industry. The car manufacturing industry is considered to be one of the highest energy consuming industries. An efficient decision making model is proposed that capture the impacts of strategic decisions on energy consumption and environmental sustainability. The sources of energy considered in this research are electricity and fuel; which are the two main types of energy sources used in a typical vehicle assembly plant. The model depicts the performance measurement for process- specific energy measures of painting, welding, and assembling processes. SD is the chosen simulation method and the main green logistics issues considered are Carbon Dioxide (CO2) emission and energy utilization. The model will assist decision makers acquire an in-depth understanding of relationship between high level planning and low level operation activities on production, environmental impacts and costs associated. The results of the SD model signify the existence of positive trade-offs between green practices of energy efficiency and the reduction of CO2 emission.

System level modeling and component level control of fuel cells

NASA Astrophysics Data System (ADS)

Xue, Xingjian

This dissertation investigates the fuel cell systems and the related technologies in three aspects: (1) system-level dynamic modeling of both PEM fuel cell (PEMFC) and solid oxide fuel cell (SOFC); (2) condition monitoring scheme development of PEM fuel cell system using model-based statistical method; and (3) strategy and algorithm development of precision control with potential application in energy systems. The dissertation first presents a system level dynamic modeling strategy for PEM fuel cells. It is well known that water plays a critical role in PEM fuel cell operations. It makes the membrane function appropriately and improves the durability. The low temperature operating conditions, however, impose modeling difficulties in characterizing the liquid-vapor two phase change phenomenon, which becomes even more complex under dynamic operating conditions. This dissertation proposes an innovative method to characterize this phenomenon, and builds a comprehensive model for PEM fuel cell at the system level. The model features the complete characterization of multi-physics dynamic coupling effects with the inclusion of dynamic phase change. The model is validated using Ballard stack experimental result from open literature. The system behavior and the internal coupling effects are also investigated using this model under various operating conditions. Anode-supported tubular SOFC is also investigated in the dissertation. While the Nernst potential plays a central role in characterizing the electrochemical performance, the traditional Nernst equation may lead to incorrect analysis results under dynamic operating conditions due to the current reverse flow phenomenon. This dissertation presents a systematic study in this regard to incorporate a modified Nernst potential expression and the heat/mass transfer into the analysis. The model is used to investigate the limitations and optimal results of various operating conditions; it can also be utilized to perform the optimal design of tubular SOFC. With the system-level dynamic model as a basis, a framework for the robust, online monitoring of PEM fuel cell is developed in the dissertation. The monitoring scheme employs the Hotelling T2 based statistical scheme to handle the measurement noise and system uncertainties and identifies the fault conditions through a series of self-checking and conformal testing. A statistical sampling strategy is also utilized to improve the computation efficiency. Fuel/gas flow control is the fundamental operation for fuel cell energy systems. In the final part of the dissertation, a high-precision and robust tracking control scheme using piezoelectric actuator circuit with direct hysteresis compensation is developed. The key characteristic of the developed control algorithm includes the nonlinear continuous control action with the adaptive boundary layer strategy.

High-Level, First-Principles, Full-Dimensional Quantum Calculation of the Ro-vibrational Spectrum of the Simplest Criegee Intermediate (CH2OO).

PubMed

Li, Jun; Carter, Stuart; Bowman, Joel M; Dawes, Richard; Xie, Daiqian; Guo, Hua

2014-07-03

The ro-vibrational spectrum of the simplest Criegee intermediate (CH2OO) has been determined quantum mechanically based on nine-dimensional potential energy and dipole surfaces for its ground electronic state. The potential energy surface is fitted to more than 50 000 high-level ab initio points with a root-mean-square error of 25 cm(-1), using a recently proposed permutation invariant polynomial neural network method. The calculated rotational constants, vibrational frequencies, and spectral intensities of CH2OO are in excellent agreement with experiment. The potential energy surface provides a valuable platform for studying highly excited vibrational and unimolecular reaction dynamics of this important molecule.

Monolayer phosphorene under time-dependent magnetic field

NASA Astrophysics Data System (ADS)

Nascimento, J. P. G.; Aguiar, V.; Guedes, I.

2018-02-01

We obtain the exact wave function of a monolayer phosphorene under a low-intensity time-dependent magnetic field using the dynamical invariant method. We calculate the quantum-mechanical energy expectation value and the transition probability for a constant and an oscillatory magnetic field. For the former we observe that the Landau level energy varies linearly with the quantum numbers n and m and the magnetic field intensity B0. No transition takes place. For the latter, we observe that the energy oscillates in time, increasing linearly with the Landau level n and m and nonlinearly with the magnetic field. The (k , l) →(n , m) transitions take place only for l = m. We investigate the (0,0) →(n , 0) and (1 , l) and (2 , l) probability transitions.

Intermittency and dynamical Lee-Yang zeros of open quantum systems.

PubMed

Hickey, James M; Flindt, Christian; Garrahan, Juan P

2014-12-01

We use high-order cumulants to investigate the Lee-Yang zeros of generating functions of dynamical observables in open quantum systems. At long times the generating functions take on a large-deviation form with singularities of the associated cumulant generating functions-or dynamical free energies-signifying phase transitions in the ensemble of dynamical trajectories. We consider a driven three-level system as well as the dissipative Ising model. Both systems exhibit dynamical intermittency in the statistics of quantum jumps. From the short-time behavior of the dynamical Lee-Yang zeros, we identify critical values of the counting field which we attribute to the observed intermittency and dynamical phase coexistence. Furthermore, for the dissipative Ising model we construct a trajectory phase diagram and estimate the value of the transverse field where the stationary state changes from being ferromagnetic (inactive) to paramagnetic (active).

Insulin Induces an Increase in Cytosolic Glucose Levels in 3T3-L1 Cells with Inhibited Glycogen Synthase Activation

PubMed Central

Chowdhury, Helena H.; Kreft, Marko; Jensen, Jørgen; Zorec, Robert

2014-01-01

Glucose is an important source of energy for mammalian cells and enters the cytosol via glucose transporters. It has been thought for a long time that glucose entering the cytosol is swiftly phosphorylated in most cell types; hence the levels of free glucose are very low, beyond the detection level. However, the introduction of new fluorescence resonance energy transfer-based glucose nanosensors has made it possible to measure intracellular glucose more accurately. Here, we used the fluorescent indicator protein (FLIPglu-600µ) to monitor cytosolic glucose dynamics in mouse 3T3-L1 cells in which glucose utilization for glycogen synthesis was inhibited. The results show that cells exhibit a low resting cytosolic glucose concentration. However, in cells with inhibited glycogen synthase activation, insulin induced a robust increase in cytosolic free glucose. The insulin-induced increase in cytosolic glucose in these cells is due to an imbalance between the glucose transported into the cytosol and the use of glucose in the cytosol. In untreated cells with sensitive glycogen synthase activation, insulin stimulation did not result in a change in the cytosolic glucose level. This is the first report of dynamic measurements of cytosolic glucose levels in cells devoid of the glycogen synthesis pathway. PMID:25279585

On-the-Fly ab Initio Semiclassical Calculation of Glycine Vibrational Spectrum

PubMed Central

2017-01-01

We present an on-the-fly ab initio semiclassical study of vibrational energy levels of glycine, calculated by Fourier transform of the wavepacket correlation function. It is based on a multiple coherent states approach integrated with monodromy matrix regularization for chaotic dynamics. All four lowest-energy glycine conformers are investigated by means of single-trajectory semiclassical spectra obtained upon classical evolution of on-the-fly trajectories with harmonic zero-point energy. For the most stable conformer I, direct dynamics trajectories are also run for each vibrational mode with energy equal to the first harmonic excitation. An analysis of trajectories evolved up to 50 000 atomic time units demonstrates that, in this time span, conformers II and III can be considered as isolated species, while conformers I and IV show a pretty facile interconversion. Therefore, previous perturbative studies based on the assumption of isolated conformers are often reliable but might be not completely appropriate in the case of conformer IV and conformer I for which interconversion occurs promptly. PMID:28489368

Machine learning of accurate energy-conserving molecular force fields

PubMed Central

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

2017-01-01

Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

Energy and wear optimisation of train longitudinal dynamics and of traction and braking systems

NASA Astrophysics Data System (ADS)

Conti, R.; Galardi, E.; Meli, E.; Nocciolini, D.; Pugi, L.; Rindi, A.

2015-05-01

Traction and braking systems deeply affect longitudinal train dynamics, especially when an extensive blending phase among different pneumatic, electric and magnetic devices is required. The energy and wear optimisation of longitudinal vehicle dynamics has a crucial economic impact and involves several engineering problems such as wear of braking friction components, energy efficiency, thermal load on components, level of safety under degraded or adhesion conditions (often constrained by the current regulation in force on signalling or other safety-related subsystem). In fact, the application of energy storage systems can lead to an efficiency improvement of at least 10% while, as regards the wear reduction, the improvement due to distributed traction systems and to optimised traction devices can be quantified in about 50%. In this work, an innovative integrated procedure is proposed by the authors to optimise longitudinal train dynamics and traction and braking manoeuvres in terms of both energy and wear. The new approach has been applied to existing test cases and validated with experimental data provided by Breda and, for some components and their homologation process, the results of experimental activities derive from cooperation performed with relevant industrial partners such as Trenitalia and Italcertifer. In particular, simulation results are referred to the simulation tests performed on a high-speed train (Ansaldo Breda Emu V250) and on a tram (Ansaldo Breda Sirio Tram). The proposed approach is based on a modular simulation platform in which the sub-models corresponding to different subsystems can be easily customised, depending on the considered application, on the availability of technical data and on the homologation process of different components.

Diagnosing the influence of model structure on the simulation of water, energy and carbon fluxes on bark beetle infested forests

NASA Astrophysics Data System (ADS)

Gochis, D. J.; Gutmann, E. D.; Brooks, P. D.; Reed, D. E.; Ewers, B. E.; Pendall, E.; Biederman, J. A.; Harpold, A. A.; Barnard, H. R.; Hu, J.

2011-12-01

Forest dynamics induced by insect infestation can have a significant, local impact on plant physiological regulation of water, energy and carbon fluxes. Rapid mortality succeeded by more gradually varying land cover changes are presently thought to initiate a cascade of changes to water, energy and carbon budgets at the forest stand scale. Initial model sensitivity results have suggested very strong changes in land-atmosphere exchanges of these variables. Specifically, model results from the Noah land surface model, a relatively simple model, have suggested that loss of transpiration function may result in a nearly 50% increase in seasonal soil moisture values and similar increases in runoff production for locations in the central Rocky Mountains. However, differing model structures, such as the representation of plant canopy architecture, snowpack dynamics, dynamic vegetation and hillslope hydrologic processes, may significantly confound the synthesis of results from different modeling systems. We assess the performance of new suite of model simulations from three different land surface models of differing model structures and complexity levels against a comprehensive set of field observations of land surface flux and state variables. The focus of the analysis is in diagnosing how model structure influences changes in energy, water and carbon budget partitioning prior to and following insect infestation. Specific emphasis in this presentation is placed on verifying variables that characterize top of canopy and within canopy energy and water fluxes. We conclude the presentation with a set of recommendations about the advantages and disadvantages of various model structures in their simulation of insect driven forest dynamics.

Russian Hydrogen-Checking Instrument on Curiosity Fires 2 Millionth Pulse

NASA Image and Video Library

2014-01-29

Dynamic Albedo of Neutrons DAN, measures the flow of neutrons with different energy levels returning from the ground, and their delay times, as an indication of the amount and depth of hydrogen in the ground beneath the NASA rover, Curiosity.

Wind farm and solar park effects on plant-soil carbon cycling: uncertain impacts of changes in ground-level microclimate.

PubMed

Armstrong, Alona; Waldron, Susan; Whitaker, Jeanette; Ostle, Nicholas J

2014-06-01

Global energy demand is increasing as greenhouse gas driven climate change progresses, making renewable energy sources critical to future sustainable power provision. Land-based wind and solar electricity generation technologies are rapidly expanding, yet our understanding of their operational effects on biological carbon cycling in hosting ecosystems is limited. Wind turbines and photovoltaic panels can significantly change local ground-level climate by a magnitude that could affect the fundamental plant-soil processes that govern carbon dynamics. We believe that understanding the possible effects of changes in ground-level microclimates on these phenomena is crucial to reducing uncertainty of the true renewable energy carbon cost and to maximize beneficial effects. In this Opinions article, we examine the potential for the microclimatic effects of these land-based renewable energy sources to alter plant-soil carbon cycling, hypothesize likely effects and identify critical knowledge gaps for future carbon research. © 2013 John Wiley & Sons Ltd.

A new energy transfer channel from carotenoids to chlorophylls in purple bacteria.

PubMed

Feng, Jin; Tseng, Chi-Wei; Chen, Tingwei; Leng, Xia; Yin, Huabing; Cheng, Yuan-Chung; Rohlfing, Michael; Ma, Yuchen

2017-07-10

It is unclear whether there is an intermediate dark state between the S 2 and S 1 states of carotenoids. Previous two-dimensional electronic spectroscopy measurements support its existence and its involvement in the energy transfer from carotenoids to chlorophylls, but there is still considerable debate on the origin of this dark state and how it regulates the energy transfer process. Here we use ab initio calculations on excited-state dynamics and simulated two-dimensional electronic spectrum of carotenoids from purple bacteria to provide evidence supporting that the dark state may be assigned to a new A g + state. Our calculations also indicate that groups on the conjugation backbone of carotenoids may substantially affect the excited-state levels and the energy transfer process. These results contribute to a better understanding of carotenoid excited states.Carotenoids harvest energy from light and transfer it to chlorophylls during photosynthesis. Here, Feng et al. perform ab initio calculations on excited-state dynamics and simulated 2D electronic spectrum of carotenoids, supporting the existence of a new excited state in carotenoids.

Experimental apparatus for overlapping a ground-state cooled ion with ultracold atoms

NASA Astrophysics Data System (ADS)

Meir, Ziv; Sikorsky, Tomas; Ben-shlomi, Ruti; Akerman, Nitzan; Pinkas, Meirav; Dallal, Yehonatan; Ozeri, Roee

2018-03-01

Experimental realizations of charged ions and neutral atoms in overlapping traps are gaining increasing interest due to their wide research application ranging from chemistry at the quantum level to quantum simulations of solid state systems. In this paper, we describe our experimental system in which we overlap a single ground-state cooled ion trapped in a linear Paul trap with a cloud of ultracold atoms such that both constituents are in the ?K regime. Excess micromotion (EMM) currently limits atom-ion interaction energy to the mK energy scale and above. We demonstrate spectroscopy methods and compensation techniques which characterize and reduce the ion's parasitic EMM energy to the ?K regime even for ion crystals of several ions. We further give a substantial review on the non-equilibrium dynamics which governs atom-ion systems. The non-equilibrium dynamics is manifested by a power law distribution of the ion's energy. We also give an overview on the coherent and non-coherent thermometry tools which can be used to characterize the ion's energy distribution after single to many atom-ion collisions.

Cooperative and Integrated Vehicle and Intersection Control for Energy Efficiency (CIVIC-E²)

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

Hou, Yunfei; Seliman, Salaheldeen M. S.; Wang, Enshu

Recent advances in connected vehicle technologies enable vehicles and signal controllers to cooperate and improve the traffic management at intersections. This paper explores the opportunity for cooperative and integrated vehicle and intersection control for energy efficiency (CIVIC-E 2) to contribute to a more sustainable transportation system. We propose a two-level approach that jointly optimizes the traffic signal timing and vehicles' approach speed, with the objective being to minimize total energy consumption for all vehicles passing through an isolated intersection. More specifically, at the intersection level, a dynamic programming algorithm is designed to find the optimal signal timing by explicitly consideringmore » the arrival time and energy profile of each vehicle. At the vehicle level, a model predictive control strategy is adopted to ensure that vehicles pass through the intersection in a timely fashion. Our simulation study has shown that the proposed CIVIC-E 2 system can significantly improve intersection performance under various traffic conditions. Compared with conventional fixed-time and actuated signal control strategies, the proposed algorithm can reduce energy consumption and queue length by up to 31% and 95%, respectively.« less

Cooperative and Integrated Vehicle and Intersection Control for Energy Efficiency (CIVIC-E²)

DOE PAGES

Hou, Yunfei; Seliman, Salaheldeen M. S.; Wang, Enshu; ...

2018-02-15

Recent advances in connected vehicle technologies enable vehicles and signal controllers to cooperate and improve the traffic management at intersections. This paper explores the opportunity for cooperative and integrated vehicle and intersection control for energy efficiency (CIVIC-E 2) to contribute to a more sustainable transportation system. We propose a two-level approach that jointly optimizes the traffic signal timing and vehicles' approach speed, with the objective being to minimize total energy consumption for all vehicles passing through an isolated intersection. More specifically, at the intersection level, a dynamic programming algorithm is designed to find the optimal signal timing by explicitly consideringmore » the arrival time and energy profile of each vehicle. At the vehicle level, a model predictive control strategy is adopted to ensure that vehicles pass through the intersection in a timely fashion. Our simulation study has shown that the proposed CIVIC-E 2 system can significantly improve intersection performance under various traffic conditions. Compared with conventional fixed-time and actuated signal control strategies, the proposed algorithm can reduce energy consumption and queue length by up to 31% and 95%, respectively.« less

Numerical simulation of hydrogen fluorine overtone chemical lasers

NASA Astrophysics Data System (ADS)

Chen, Jinbao; Jiang, Zhongfu; Hua, Weihong; Liu, Zejin; Shu, Baihong

1998-08-01

A two-dimensional program was applied to simulate the chemical dynamic process, gas dynamic process and lasing process of a combustion-driven CW HF overtone chemical lasers. Some important parameters in the cavity were obtained. The calculated results included HF molecule concentration on each vibration energy level while lasing, averaged pressure and temperature, zero power gain coefficient of each spectral line, laser spectrum, the averaged laser intensity, output power, chemical efficiency and the length of lasing zone.

Mixotrophy and intraguild predation - dynamic consequences of shifts between food web motifs

NASA Astrophysics Data System (ADS)

Karnatak, Rajat; Wollrab, Sabine

2017-06-01

Mixotrophy is ubiquitous in microbial communities of aquatic systems with many flagellates being able to use autotroph as well as heterotroph pathways for energy acquisition. The usage of one over the other pathway is associated with resource availability and the coupling of alternative pathways has strong implications for system stability. We investigated the impact of dominance of different energy pathways related to relative resource availability on system dynamics in the setting of a tritrophic food web motif. This motif consists of a mixotroph feeding on a purely autotroph species while competing for a shared resource. In addition, the autotroph can use an additional exclusive food source. By changing the relative abundance of shared vs. exclusive food source, we shift the food web motif from an intraguild predation motif to a food chain motif. We analyzed the dependence of system dynamics on absolute and relative resource availability. In general, the system exhibits a transition from stable to oscillatory dynamics with increasing nutrient availability. However, this transition occurs at a much lower nutrient level for the food chain in comparison to the intraguild predation motif. A similar transition is also observed with variations in the relative abundance of food sources for a range of nutrient levels. We expect this shift in food web motifs to occur frequently in microbial communities and therefore the results from our study are highly relevant for natural systems.

Ab Initio Molecular Dynamics Study on the Interactions between Carboxylate Ions and Metal Ions in Water.

PubMed

Mehandzhiyski, Aleksandar Y; Riccardi, Enrico; van Erp, Titus S; Trinh, Thuat T; Grimes, Brian A

2015-08-20

The interaction between a carboxylate anion (deprotonated propanoic acid) and the divalent Mg(2+), Ca(2+), Sr(2+), Ba(2+) metal ions is studied via ab initio molecular dynamics. The main focus of the study is the selectivity of the carboxylate-metal ion interaction in aqueous solution. The interaction is modeled by explicitly accounting for the solvent molecules on a DFT level. The hydration energies of the metal ions along with their diffusion and mobility coefficients are determined and a trend correlated with their ionic radius is found. Subsequently, a series of 16 constrained molecular dynamics simulations for every ion is performed, and the interaction free energy is obtained from thermodynamic integration of the forces between the metal ion and the carboxylate ion. The results indicate that the magnesium ion interacts most strongly with the carboxylate, followed by calcium, strontium, and barium. Because the interaction free energy is not enough to explain the selectivity of the reaction observed experimentally, more detailed analysis is performed on the simulation trajectories to understand the steric changes in the reaction complex during dissociation. The solvent dynamics appear to play an important role during the dissociation of the complex and also in the observed selectivity behavior of the divalent ions.

The positron excess as a smoking gun for dynamical dark matter?

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

Dienes, Keith R.; Kumar, Jason; Thomas, Brooks

One of the most puzzling aspects of recent data from the AMS-02 experiment is an apparent rise in the cosmic-ray positron fraction as a function of energy. This feature is observed out to energies of approximately 350 GeV. One explanation of these results interprets the extra positrons as arising from the decays of dark-matter particles. This in turn typically requires that such particles have rather heavy TeV-scale masses and not undergo simple two-body decays to leptons. In this talk, by contrast, we show that Dynamical Dark Matter (DDM) can not only match existing AMS-02 data on the positron excess, butmore » also accomplish this feat with significantly lighter dark-matter constituents undergoing simple two-body decays to leptons. We also demonstrate that the Dynamical Dark Matter framework makes a fairly robust prediction that the positron fraction should level off and then remain roughly constant out to approximately 1 TeV, without experiencing any sharp downturns. Thus, if we interpret the positron excess in terms of decaying dark matter, the existence of a plateau in the positron fraction at energies less than 1 TeV may be taken as a “smoking gun” of Dynamical Dark Matter.« less

Real-time visualization of the vibrational wavepacket dynamics in electronically excited pyrimidine via femtosecond time-resolved photoelectron imaging

NASA Astrophysics Data System (ADS)

Li, Shuai; Long, Jinyou; Ling, Fengzi; Wang, Yanmei; Song, Xinli; Zhang, Song; Zhang, Bing

2017-07-01

The vibrational wavepacket dynamics at the very early stages of the S1-T1 intersystem crossing in photoexcited pyrimidine is visualized in real time by femtosecond time-resolved photoelectron imaging and time-resolved mass spectroscopy. A coherent superposition of the vibrational states is prepared by the femtosecond pump pulse at 315.3 nm, resulting in a vibrational wavepacket. The composition of the prepared wavepacket is directly identified by a sustained quantum beat superimposed on the parent-ion transient, possessing a frequency in accord with the energy separation between the 6a1 and 6b2 states. The dephasing time of the vibrational wavepacket is determined to be 82 ps. More importantly, the variable Franck-Condon factors between the wavepacket components and the dispersed cation vibrational levels are experimentally illustrated to identify the dark state and follow the energy-flow dynamics on the femtosecond time scale. The time-dependent intensities of the photoelectron peaks originated from the 6a1 vibrational state exhibit a clear quantum beating pattern with similar periodicity but a phase shift of π rad with respect to those from the 6b2 state, offering an unambiguous picture of the restricted intramolecular vibrational energy redistribution dynamics in the 6a1/6b2 Fermi resonance.

Hint of nonstandard Mikheyev-Smirnov-Wolfenstein dynamics in solar neutrino conversion

NASA Astrophysics Data System (ADS)

Palazzo, Antonio

2011-05-01

Motivated by the recent low-threshold measurements of the solar B8 neutrino spectrum performed by Borexino, Super-Kamiokande and the Sudbury Neutrino Observatory—all now monitoring the transition regime between low-energy (vacuumlike) and high-energy (matter-dominated) flavor conversions—we consider the role of subdominant dynamical terms induced by new flavor-changing interactions. We find that the presence of such perturbations with strength ˜10-1GF is now favored, offering a better description of the anomalous behavior suggested by the new results, whose spectrum shows no sign of the typical low-energy upturn predicted by the standard Mikheyev-Smirnov-Wolfenstein (MSW) mechanism. Our findings, if interpreted in a 2-flavor scheme, provide a hint of such new interactions at the ˜2σ level, which is rather robust with respect to 3-flavor effects possibly induced by nonzero θ13.

The Development of Two Composite Energy Absorbers for Use in a Transport Rotorcraft Airframe Crash Testbed (TRACT 2) Full-Scale Crash Test

NASA Technical Reports Server (NTRS)

Littell, Justin D.; Jackson, Karen E.; Annett, Martin S.; Seal, Michael D.; Fasanella, Edwin L.

2015-01-01

Two composite energy absorbers were developed and evaluated at NASA Langley Research Center through multi-level testing and simulation performed under the Transport Rotorcraft Airframe Crash Testbed (TRACT) research program. A conical-shaped energy absorber, designated the conusoid, was evaluated that consisted of four layers of hybrid carbon-Kevlar plain weave fabric oriented at [+45deg/-45deg/-45deg/+45deg] with respect to the vertical direction. A sinusoidal-shaped energy absorber, designated the sinusoid, was developed that consisted of hybrid carbon-Kevlar plain weave fabric face sheets, two layers for each face sheet oriented at +/-45deg with respect to the vertical direction, and a closed-cell ELFOAM P200 polyisocyanurate (2.0-lb/cu ft) foam core. The design goal for the energy absorbers was to achieve average floor-level accelerations of between 25- and 40-g during the full-scale crash test of a retrofitted CH-46E helicopter airframe, designated TRACT 2. Variations in both designs were assessed through dynamic crush testing of component specimens. Once the designs were finalized, subfloor beams of each configuration were fabricated and retrofitted into a barrel section of a CH-46E helicopter. A vertical drop test of the barrel section was conducted onto concrete to evaluate the performance of the energy absorbers prior to retrofit into TRACT 2. The retrofitted airframe was crash tested under combined forward and vertical velocity conditions onto soft soil. Finite element models were developed of all test articles and simulations were performed using LS-DYNA, a commercial nonlinear explicit transient dynamic finite element code. Test-analysis results are presented for each energy absorber as comparisons of time-history responses, as well as predicted and experimental structural deformations and progressive damage under impact loading for each evaluation level.

Generalization of the Bogoliubov-Zubarev Theorem for Dynamic Pressure to the Case of Compressibility

NASA Astrophysics Data System (ADS)

Rudoi, Yu. G.

2018-01-01

We present the motivation, formulation, and modified proof of the Bogoliubov-Zubarev theorem connecting the pressure of a dynamical object with its energy within the framework of a classical description and obtain a generalization of this theorem to the case of dynamical compressibility. In both cases, we introduce the volume of the object into consideration using a singular addition to the Hamiltonian function of the physical object, which allows using the concept of the Bogoliubov quasiaverage explicitly already on a dynamical level of description. We also discuss the relation to the same result known as the Hellmann-Feynman theorem in the framework of the quantum description of a physical object.

Indirect dynamics in SN2@N: insight into the influence of central atoms.

PubMed

Liu, Xu; Zhao, Chenyang; Yang, Li; Zhang, Jiaxu; Sun, Rui

2017-08-30

Central atoms have a significant influence on the reaction kinetics and dynamics of nucleophilic substitution (S N 2). Herein, atomistic dynamics of a prototype S N 2@N reaction F - + NH 2 Cl is uncovered employing direct dynamics simulations that show strikingly distinct features from those determined for a S N 2@C congener F - + CH 3 Cl. Indirect scattering is found to prevail, which proceeds predominantly through a hydrogen-bonded F - -HNHCl complex in the reactant entrance channel. This unexpected finding of a pronounced contribution of indirect reaction dynamics, even at a high collision energy, is in strong contrast to a general evolution from indirect to direct dynamics with enhanced energy that characterizes S N 2@C. This result suggests that the relative importance of different atomic-level mechanisms may depend essentially on the interaction potential of reactive encounters and the coupling between inter- and intramolecular modes of the pre-reaction complex. For F - + NH 2 Cl the proton transfer pathway is less competitive than S N 2. A remarkable finding is that the more favorable energetics for NH 2 Cl proton transfer, as compared to that for CH 3 Cl, does not manifest itself in the reaction dynamics. The present work sheds light on the underlying reaction dynamics of S N 2@N, which remain largely unclear compared to well-studied S N 2@C.

Probing the kinetic energy-release dynamics of H-atom products from the gas-phase reaction of O(3P) with vinyl radical C2H3.

PubMed

Jang, Su-Chan; Choi, Jong-Ho

2014-11-21

The gas-phase radical-radical reaction dynamics of ground-state atomic oxygen O((3)P) with vinyl radicals C2H3 has been studied by combining the results of vacuum-ultraviolet laser-induced fluorescence spectroscopy in a crossed beam configuration with ab initio calculations. The two radical reactants O((3)P) and C2H3 were produced by photolysis of NO2 and supersonic flash pyrolysis of C2H3I, respectively. Doppler profile analysis of the kinetic energy release of the nascent H-atom products from the title reaction O((3)P) + C2H3→ H((2)S) + CH2CO (ketene) revealed that the average translational energy of the products and the average fraction of the total available energy were 7.03 ± 0.30 kcal mol(-1) and 7.2%. The empirical data combined with CBS-QB3 level ab initio theory and statistical calculations demonstrated that the title oxygen-hydrogen exchange reaction is a major reaction channel, through an addition-elimination mechanism involving the formation of a short-lived, dynamical complex on the doublet potential energy surface. On the basis of systematic comparison with several exchange reactions of hydrocarbon radicals, the observed kinetic energy release can be explained in terms of the weak impulse at the moment of decomposition in the loose transition state with a product-like geometry and a small reverse barrier along the exit channel.

Foundations of metabolic organization: coherence as a basis of computational properties in metabolic networks.

PubMed

Igamberdiev, A U

1999-04-01

Biological organization is based on the coherent energy transfer allowing for macromolecules to operate with high efficiency and realize computation. Computation is executed with virtually 100% efficiency via the coherent operation of molecular machines in which low-energy recognitions trigger energy-driven non-equilibrium dynamic processes. The recognition process is of quantum mechanical nature being a non-demolition measurement. It underlies the enzymatic conversion of a substrate into the product (an elementary metabolic phenomenon); the switching via separation of the direct and reverse routes in futile cycles provides the generation and complication of metabolic networks (coherence within cycles is maintained by the supramolecular organization of enzymes); the genetic level corresponding to the appearance of digital information is based on reflective arrows (catalysts realize their own self-reproduction) and operation of hypercycles. Every metabolic cycle via reciprocal regulation of both its halves can generate rhythms and spatial structures (resulting from the temporally organized depositions from the cycles). Via coherent events which percolate from the elementary submolecular level to organismic entities, self-assembly based on the molecular complementarity is realized and the dynamic informational field operating within the metabolic network is generated.

Sensor Measurement Strategies for Monitoring Offshore Wind and Wave Energy Devices

NASA Astrophysics Data System (ADS)

O'Donnell, Deirdre; Srbinovsky, Bruno; Murphy, Jimmy; Popovici, Emanuel; Pakrashi, Vikram

2015-07-01

While the potential of offshore wind and wave energy devices is well established and accepted, operations and maintenance issues are still not very well researched or understood. In this regard, scaled model testing has gained popularity over time for such devices at various technological readiness levels. The dynamic response of these devices are typically measured by different instruments during such scaled tests but agreed sensor choice, measurement and placement guidelines are still not in place. This paper compared the dynamic responses of some of these sensors from a scaled ocean wave testing to highlight the importance of sensor measurement strategies. The possibility of using multiple, cheaper sensors of seemingly inferior performance as opposed to the deployment of a small number of expensive and accurate sensors are also explored. An energy aware adaptive sampling theory is applied to highlight the possibility of more efficient computing when large volumes of data are available from the tested structures. Efficient sensor measurement strategies are expected to have a positive impact on the development of an device at different technological readiness levels while it is expected to be helpful in reducing operation and maintenance costs if such an approach is considered for the devices when they are in operation.

Three electron beams from a laser-plasma wakefield accelerator and the energy apportioning question

PubMed Central

Yang, X.; Brunetti, E.; Gil, D. Reboredo; Welsh, G. H.; Li, F. Y.; Cipiccia, S.; Ersfeld, B.; Grant, D. W.; Grant, P. A.; Islam, M. R.; Tooley, M. P.; Vieux, G.; Wiggins, S. M.; Sheng, Z. M.; Jaroszynski, D. A.

2017-01-01

Laser-wakefield accelerators are compact devices capable of delivering ultra-short electron bunches with pC-level charge and MeV-GeV energy by exploiting the ultra-high electric fields arising from the interaction of intense laser pulses with plasma. We show experimentally and through numerical simulations that a high-energy electron beam is produced simultaneously with two stable lower-energy beams that are ejected in oblique and counter-propagating directions, typically carrying off 5–10% of the initial laser energy. A MeV, 10s nC oblique beam is ejected in a 30°–60° hollow cone, which is filled with more energetic electrons determined by the injection dynamics. A nC-level, 100s keV backward-directed beam is mainly produced at the leading edge of the plasma column. We discuss the apportioning of absorbed laser energy amongst the three beams. Knowledge of the distribution of laser energy and electron beam charge, which determine the overall efficiency, is important for various applications of laser-wakefield accelerators, including the development of staged high-energy accelerators. PMID:28281679

Dynamic modeling, experimental evaluation, optimal design and control of integrated fuel cell system and hybrid energy systems for building demands

NASA Astrophysics Data System (ADS)

Nguyen, Gia Luong Huu

Fuel cells can produce electricity with high efficiency, low pollutants, and low noise. With the advent of fuel cell technologies, fuel cell systems have since been demonstrated as reliable power generators with power outputs from a few watts to a few megawatts. With proper equipment, fuel cell systems can produce heating and cooling, thus increased its overall efficiency. To increase the acceptance from electrical utilities and building owners, fuel cell systems must operate more dynamically and integrate well with renewable energy resources. This research studies the dynamic performance of fuel cells and the integration of fuel cells with other equipment in three levels: (i) the fuel cell stack operating on hydrogen and reformate gases, (ii) the fuel cell system consisting of a fuel reformer, a fuel cell stack, and a heat recovery unit, and (iii) the hybrid energy system consisting of photovoltaic panels, fuel cell system, and energy storage. In the first part, this research studied the steady-state and dynamic performance of a high temperature PEM fuel cell stack. Collaborators at Aalborg University (Aalborg, Denmark) conducted experiments on a high temperature PEM fuel cell short stack at steady-state and transients. Along with the experimental activities, this research developed a first-principles dynamic model of a fuel cell stack. The dynamic model developed in this research was compared to the experimental results when operating on different reformate concentrations. Finally, the dynamic performance of the fuel cell stack for a rapid increase and rapid decrease in power was evaluated. The dynamic model well predicted the performance of the well-performing cells in the experimental fuel cell stack. The second part of the research studied the dynamic response of a high temperature PEM fuel cell system consisting of a fuel reformer, a fuel cell stack, and a heat recovery unit with high thermal integration. After verifying the model performance with the obtained experimental data, the research studied the control of airflow to regulate the temperature of reactors within the fuel processor. The dynamic model provided a platform to test the dynamic response for different control gains. With sufficient sensing and appropriate control, a rapid response to maintain the temperature of the reactor despite an increase in power was possible. The third part of the research studied the use of a fuel cell in conjunction with photovoltaic panels, and energy storage to provide electricity for buildings. This research developed an optimization framework to determine the size of each device in the hybrid energy system to satisfy the electrical demands of buildings and yield the lowest cost. The advantage of having the fuel cell with photovoltaic and energy storage was the ability to operate the fuel cell at baseload at night, thus reducing the need for large battery systems to shift the solar power produced in the day to the night. In addition, the dispatchability of the fuel cell provided an extra degree of freedom necessary for unforeseen disturbances. An operation framework based on model predictive control showed that the method is suitable for optimizing the dispatch of the hybrid energy system.

Accurate potential energy surface for the 1(2)A' state of NH(2): scaling of external correlation versus extrapolation to the complete basis set limit.

PubMed

Li, Y Q; Varandas, A J C

2010-09-16

An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system which is suitable for dynamics and kinetics studies of the reactions of N(2D) + H2(X1Sigmag+) NH(a1Delta) + H(2S) and their isotopomeric variants. It is obtained by fitting ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set, after slightly correcting semiempirically the dynamical correlation using the double many-body expansion-scaled external correlation method. The function so obtained is compared in detail with a potential energy surface of the same family obtained by extrapolating the calculated raw energies to the complete basis set limit. The topographical features of the novel global potential energy surface are examined in detail and found to be in general good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. The novel function has been built so as to become degenerate at linear geometries with the ground-state potential energy surface of A'' symmetry reported by our group, where both form a Renner-Teller pair.

Acoustic energy harvesting using an electromechanical Helmholtz resonator.

PubMed

Liu, Fei; Phipps, Alex; Horowitz, Stephen; Ngo, Khai; Cattafesta, Louis; Nishida, Toshikazu; Sheplak, Mark

2008-04-01

This paper presents the development of an acoustic energy harvester using an electromechanical Helmholtz resonator (EMHR). The EMHR consists of an orifice, cavity, and a piezoelectric diaphragm. Acoustic energy is converted to mechanical energy when sound incident on the orifice generates an oscillatory pressure in the cavity, which in turns causes the vibration of the diaphragm. The conversion of acoustic energy to electrical energy is achieved via piezoelectric transduction in the diaphragm of the EMHR. Moreover, the diaphragm is coupled with energy reclamation circuitry to increase the efficiency of the energy conversion. Lumped element modeling of the EMHR is used to provide physical insight into the coupled energy domain dynamics governing the energy reclamation process. The feasibility of acoustic energy reclamation using an EMHR is demonstrated in a plane wave tube for two power converter topologies. The first is comprised of only a rectifier, and the second uses a rectifier connected to a flyback converter to improve load matching. Experimental results indicate that approximately 30 mW of output power is harvested for an incident sound pressure level of 160 dB with a flyback converter. Such power level is sufficient to power a variety of low power electronic devices.

Effect of dynamic surface polarization on the oxidative stability of solvents in nonaqueous Li-O 2 batteries

NASA Astrophysics Data System (ADS)

Khetan, Abhishek; Pitsch, Heinz; Viswanathan, Venkatasubramanian

2017-09-01

Polarization-induced renormalization of the frontier energy levels of interacting molecules and surfaces can cause significant shifts in the excitation and transport behavior of electrons. This phenomenon is crucial in determining the oxidative stability of nonaqueous electrolytes in high-energy density electrochemical systems such as the Li-O2 battery. On the basis of partially self-consistent first-principles Sc G W0 calculations, we systematically study how the electronic energy levels of four commonly used solvent molecules, namely, dimethylsulfoxide (DMSO), dimethoxyethane (DME), tetrahydrofuran (THF), and acetonitrile (ACN), renormalize when physisorbed on the different stable surfaces of Li2O2 , the main discharge product. Using band level alignment arguments, we propose that the difference between the solvent's highest occupied molecular orbital (HOMO) level and the surface's valence-band maximum (VBM) is a refined metric of oxidative stability. This metric and a previously used descriptor, solvent's gas phase HOMO level, agree quite well for physisorbed cases on pristine surfaces where ACN is oxidatively most stable followed by DME, THF, and DMSO. However, this effect is intrinsically linked to the surface chemistry of the solvent's interaction with the surface states and defects, and depends strongly on their nature. We conclusively show that the propensity of solvent molecules to oxidize will be significantly higher on Li2O2 surfaces with defects as compared to pristine surfaces. This suggests that the oxidative stability of a solvent is dynamic and is a strong function of surface electronic properties. Thus, while gas phase HOMO levels could be used for preliminary solvent candidate screening, a more refined picture of solvent stability requires mapping out the solvent stability as a function of the state of the surface under operating conditions.

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations

PubMed Central

2016-01-01

The epidermal growth factor receptor (EGFR) is a dimeric membrane protein that regulates key aspects of cellular function. Activation of the EGFR is linked to changes in the conformation of the transmembrane (TM) domain, brought about by changes in interactions of the TM helices of the membrane lipid bilayer. Using an advanced computational approach that combines Coarse-Grained molecular dynamics and well-tempered MetaDynamics (CG-MetaD), we characterize the large-scale motions of the TM helices, simulating multiple association and dissociation events between the helices in membrane, thus leading to a free energy landscape of the dimerization process. The lowest energy state of the TM domain is a right-handed dimer structure in which the TM helices interact through the N-terminal small-X3-small sequence motif. In addition to this state, which is thought to correspond to the active form of the receptor, we have identified further low-energy states that allow us to integrate with a high level of detail a range of previous experimental observations. These conformations may lead to the active state via two possible activation pathways, which involve pivoting and rotational motions of the helices, respectively. Molecular dynamics also reveals correlation between the conformational changes of the TM domains and of the intracellular juxtamembrane domains, paving the way for a comprehensive understanding of EGFR signaling at the cell membrane. PMID:27459426

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations.

PubMed

Lelimousin, Mickaël; Limongelli, Vittorio; Sansom, Mark S P

2016-08-24

The epidermal growth factor receptor (EGFR) is a dimeric membrane protein that regulates key aspects of cellular function. Activation of the EGFR is linked to changes in the conformation of the transmembrane (TM) domain, brought about by changes in interactions of the TM helices of the membrane lipid bilayer. Using an advanced computational approach that combines Coarse-Grained molecular dynamics and well-tempered MetaDynamics (CG-MetaD), we characterize the large-scale motions of the TM helices, simulating multiple association and dissociation events between the helices in membrane, thus leading to a free energy landscape of the dimerization process. The lowest energy state of the TM domain is a right-handed dimer structure in which the TM helices interact through the N-terminal small-X3-small sequence motif. In addition to this state, which is thought to correspond to the active form of the receptor, we have identified further low-energy states that allow us to integrate with a high level of detail a range of previous experimental observations. These conformations may lead to the active state via two possible activation pathways, which involve pivoting and rotational motions of the helices, respectively. Molecular dynamics also reveals correlation between the conformational changes of the TM domains and of the intracellular juxtamembrane domains, paving the way for a comprehensive understanding of EGFR signaling at the cell membrane.

Application of a sodium sulfur cell with dynamic sulfur electrode to a battery system

NASA Astrophysics Data System (ADS)

Tokoi, H.; Takahashi, K.; Shimoyashiki, S.

1992-01-01

The construction and performance of a sodium sulfur battery system with dynamic sulfur electrodes are described. Three cells were first connected in parallel, then two such groups were connected in series. Each cell included a liquid sodium-filled beta-double-prime-alumina tube and a system to feed liquid sulfur into the annular cathode. Low-resistance graphite felt was tightly packed around the beta-double-prime-alumina tube. Sodium pentasulfide was removed from the sulfur electrode. The battery was operated automatically and stably charged and discharged in the two-phase region. The discharged energy was 4372 Wh (capacity 1170 Ah) during a continuous operation of 19.5 h. The discharge/charge energy efficiency of the battery was 82 percent at an averaged current density of 100 mA/sq cm and operating temperature of 350 C. The deviation of the cell current in a parallel chain was less than 7 percent, and this was induced by the difference in internal resistance. In the daily charge/discharge cycle, cell capacity with the dynamic sulfur electrode was 1.5 times higher than that with the static sulfur electrode using the same active surface of beta-double-prime-alumina, because the internal resistance of the former cell was constant regardless of cell capacity. This battery system with a dynamic sulfur electrode can be applied to energy storage systems,such as large scale load leveling systems, electric vehicle batteries, and solar energy systems.

Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Chaubey, Amit Kumar; Dubey, Kshatresh Dutta; Ojha, Rajendra Prasad

2012-03-01

Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, which are the fundamental in protecting the cell from recombination and degradation. Telomeric DNA sequences can form four stranded quadruplex structures, which are involved in the structure of telomere ends. The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadrulex as an attractive target for cancer therapeutic intervention. Molecular dynamic simulation offers the prospects of detailed description of the dynamical structure with ion and water at molecular level. In this work we have taken a oligomeric part of human telomeric DNA, d(TAGGGT) to form different monomeric quadruplex structures d(TAGGGT)4. Here we report the relative stabilities of these structures under K+ ion conditions and binding interaction between the strands, as determined by molecular dynamic simulations followed by energy calculation. We have taken locked nucleic acid (LNA) in this study. The free energy molecular mechanics Poission Boltzman surface area calculations are performed for the determination of most stable complex structure between all modified structures. We calculated binding free energy for the combination of different strands as the ligand and receptor for all structures. The energetic study shows that, a mixed hybrid type quadruplex conformation in which two parallel strands are bind with other two antiparallel strands, are more stable than other conformations. The possible mechanism for the inhibition of the cancerous growth has been discussed. Such studies may be helpful for the rational drug designing.

Probing spin dynamics and quantum relaxation in Li Y0.998 Ho0.002 F4 via 19F NMR

NASA Astrophysics Data System (ADS)

Graf, M. J.; Lascialfari, A.; Borsa, F.; Tkachuk, A. M.; Barbara, B.

2006-01-01

We report measurements of F19 nuclear spin-lattice relaxation 1/T1 as a function of temperature and external magnetic field in a LiY0.998Ho0.002F4 single crystal, a single-ion magnet exhibiting interesting quantum effects. The F19 1/T1 is found to depend on the coupling with the diluted rare-earth (RE) moments, making it an effective probe of the rare-earth spin dynamics. The results for 1/T1 show a behavior similar to that observed in molecular nanomagnets, a result which we attribute to the discreteness of the energy levels in both cases. At intermediate temperatures the lifetime broadening of the crystal field split RE magnetic levels follows a T3 power law. At low temperature the field dependence of 1/T1 shows peaks in correspondence to the critical magnetic fields for energy level crossings (LC). A key result of this study is that the broadening of the levels at LC is found to become extremely small at low temperatures, about 1.7mT , a value which is comparable to the weak dipolar fields at the RE lattice positions. Thus, unlike the molecular magnets, decoherence effects are strongly suppressed, and it may be possible to measure directly the level repulsions at avoided level crossings.

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

Vijayakumar, M.; Nie, Zimin; Walter, Eric D.

Redox flow battery (RFB) is a promising candidate for energy storage component in designing resilient grid scale power supply due to the advantage of the separation of power and energy. However, poorly understood chemical and thermal stability issues of electrolytes currently limit the performance of RFB. Designing of high performance stable electrolytes requires comprehensive knowledge about the molecular level solvation structure and dynamics of their redox active species. The molecular level understanding of detrimental V2O5 precipitation process led to successful designing of mixed acid based electrolytes for vanadium redox flow batteries (VRFB). The higher stability of mixed acid based electrolytesmore » is attributed to the choice of hydrochloric acid as optimal co-solvent, which provides chloride anions for ligand exchange process in vanadium solvation structure. The role of chloride counter anion on solvation structure and dynamics of vanadium species were studied using combined magnetic resonance spectroscopy and DFT based theoretical methods. Finally, the solvation phenomenon of multiple vanadium species and their impact on VRFB electrolyte chemical stability were discussed.« less

Theoretical study on mechanisms of structural rearrangement and ionic dissociation in the HCl(H 2O) 4 cluster with path-integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sugawara, Shuichi; Yoshikawa, Takehiro; Takayanagi, Toshiyuki; Tachikawa, Masanori

2011-01-01

The structural rearrangement process for the HCl(H2O)4 cluster has been studied by path-integral molecular dynamics simulations, where 'on-the-fly' calculation of the potential energy surface is done with the PM3-MAIS semiempirical level. The mechanisms of the rearrangement were analyzed using appropriate collective coordinates as well as detailed potential energy diagrams derived from low-lying stationary points. It was found that the vibrational entropy mainly determines the stability of the cluster structure especially at high temperatures. We have also found that the acidity of HCl in the cluster correlates with the coordination number of chlorine with respect water molecules.

Tuning ultrafast electron injection dynamics at organic-graphene/metal interfaces.

PubMed

Ravikumar, Abhilash; Kladnik, Gregor; Müller, Moritz; Cossaro, Albano; Bavdek, Gregor; Patera, Laerte L; Sánchez-Portal, Daniel; Venkataraman, Latha; Morgante, Alberto; Brivio, Gian Paolo; Cvetko, Dean; Fratesi, Guido

2018-05-03

We compare the ultrafast charge transfer dynamics of molecules on epitaxial graphene and bilayer graphene grown on Ni(111) interfaces through first principles calculations and X-ray resonant photoemission spectroscopy. We use 4,4'-bipyridine as a prototypical molecule for these explorations as the energy level alignment of core-excited molecular orbitals allows ultrafast injection of electrons from a substrate to a molecule on a femtosecond timescale. We show that the ultrafast injection of electrons from the substrate to the molecule is ∼4 times slower on weakly coupled bilayer graphene than on epitaxial graphene. Through our experiments and calculations, we can attribute this to a difference in the density of states close to the Fermi level between graphene and bilayer graphene. We therefore show how graphene coupling with the substrate influences charge transfer dynamics between organic molecules and graphene interfaces.

Energy Levels and Co-evolution of Product Innovation in Supply Chain Clusters

NASA Astrophysics Data System (ADS)

Ji, Guojun

In the last decade supply chain clusters phenomenon has emerged as a new approach in product innovation studies. This article makes three contributions to the approach by addressing some open issues. The first contribution is to explicitly incorporate the energy levels in the analysis. Hence, the unit of analysis is widened from sectoral systems of innovation to socio-technical systems. Hence, the unit of analysis is widened from sectoral systems of innovation to socio-technical systems. The second contribution is to suggest an analytical distinction between different evolution method, actors involved in them, and the institutions which guide actor's perceptions and activities. Thirdly, the article opens up the black box of institutions, making them an integral part of supply chain. The article provides a coherent conceptual multi-level perspective, using insights from sociology, institutional theory and innovation studies. The perspective is particularly useful to analyze long-term dynamics supply chain clusters phenomenon, shifts from one energy level to another and the co-evolution of product innovation.

Influence of the steady background turbulence level on second sound dynamics in He II II

NASA Astrophysics Data System (ADS)

Dalban-Canassy, M.; Hilton, D. K.; Sciver, S. W. Van

2007-01-01

We report complementary results to our previous publication [Dalban-Canassy M, Hilton DK, Van Sciver SW. Influence of the steady background turbulence level on second sound dynamics in He II. Adv Cryo Eng 2006;51:371-8], both of which are aimed at determining the influence of background turbulence on the breakpoint energy of second sound pulses in He II. The apparatus consists of a channel 175 mm long and 242 mm 2 in cross section immersed in a saturated bath of He II at 1.7 K. A heater at the bottom end generates both background turbulence, through a low level steady heat flux (up to qs = 2.6 kW/m 2), and high intensity square second sound pulses ( qp = 100 or 200 kW/m 2) of variable duration Δ t0 (up to 1 ms). Two superconducting filament sensors, located 25.4 mm and 127 mm above the heater, measure the temperature profiles of the traveling pulses. We present here an analysis of the measurements gathered on the top sensor, and compare them to similar results for the bottom sensor [1]. The strong dependence of the breakpoint energy on the background heat flux previously illustrated is also observed on the top sensor. The present work shows that the ratio of energy received at the top sensor to that at the bottom sensor diminishes with increasing background heat flux.

Potential energy surface and quantum dynamics study of rovibrational states for HO(3) (X (2)A'').

PubMed

Braams, Bastiaan J; Yu, Hua-Gen

2008-06-07

An analytic potential energy surface has been constructed by fitting to about 28 thousand energy points for the electronic ground-state (X (2)A'') of HO(3). The energy points are calculated using a hybrid density functional HCTH and a large basis set aug-cc-pVTZ, i.e., a HCTH/aug-cc-pVTZ density functional theory (DFT) method. The DFT calculations show that the trans-HO(3) isomer is the global minimum with a potential well depth of 9.94 kcal mol(-1) with respect to the OH + O(2) asymptote. The equilibrium geometry of the cis-HO(3) conformer is located 1.08 kcal mol(-1) above that of the trans-HO(3) one with an isomerization barrier of 2.41 kcal mol(-1) from trans- to cis-HO(3). By using this surface, a rigorous quantum dynamics (QD) study has been carried out for computing the rovibrational energy levels of HO(3). The calculated results determine a dissociation energy of 6.15 kcal mol(-1), which is in excellent agreement with the experimental value of Lester et al. [J. Phys. Chem. A, 2007, 111, 4727.].

Simulating Energy Relaxation in Pump-Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids.

PubMed

Dettori, Riccardo; Ceriotti, Michele; Hunger, Johannes; Melis, Claudio; Colombo, Luciano; Donadio, Davide

2017-03-14

We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale. The method is applied to hydrogen-bonded molecular liquids, specifically deuterated methanol and water, providing a robust picture of energy relaxation at the molecular scale.

Dynamic analysis of the urban-based low-carbon policy using system dynamics: Focused on housing and green space

NASA Astrophysics Data System (ADS)

Hong, Taehoon; Kim, Jimin; Koo, Choongwan; Jeong, Kwangbok

2015-02-01

To systematically manage the energy consumption of existing buildings, the government has to enforce greenhouse gas reduction policies. However, most of the policies are not properly executed because they do not consider various factors from the urban level perspective. Therefore, this study aimed to conduct a dynamic analysis of an urban-based low-carbon policy using system dynamics, with a specific focus on housing and green space. This study was conducted in the following steps: (i) establishing the variables of urban-based greenhouse gases (GHGs) emissions; (ii) creating a stock/flow diagram of urban-based GHGs emissions; (iii) conducting an information analysis using the system dynamics; and (iv) proposing the urban-based low-carbon policy. If a combined energy policy that uses the housing sector (30%) and the green space sector (30%) at the same time is implemented, 2020 CO2 emissions will be 7.23 million tons (i.e., 30.48% below 2020 business-as-usual), achieving the national carbon emissions reduction target (26.9%). The results of this study could contribute to managing and improving the fundamentals of the urban-based low-carbon policies to reduce greenhouse gas emissions.

Nuclear Dynamics at Molecule–Metal Interfaces: A Pseudoparticle Perspective

DOE PAGES

Galperin, Michael; Nitzan, Abraham

2015-11-20

We discuss nuclear dynamics at molecule-metal interfaces including nonequilibrium molecular junctions. Starting from the many-body states (pseudoparticle) formulation of the molecule-metal system in the molecular vibronic basis, we introduce gradient expansion to reduce the adiabatic nuclear dynamics (that is, nuclear dynamics on a single molecular potential surface) into its semiclassical form while maintaining the effect of the nonadiabatic electronic transitions between different molecular charge states. Finally, this yields a set of equations for the nuclear dynamics in the presence of these nonadiabatic transitions, which reproduce the surface-hopping formulation in the limit of small metal-molecule coupling (where broadening of the molecularmore » energy levels can be disregarded) and Ehrenfest dynamics (motion on the potential of mean force) when information on the different charging states is traced out.« less

Symmetry-Based Techniques for Qualitative Understanding of Rovibrational Effects in Spherical-Top Molecular Spectra and Dynamics

NASA Astrophysics Data System (ADS)

Mitchell, Justin Chadwick

2011-12-01

Using light to probe the structure of matter is as natural as opening our eyes. Modern physics and chemistry have turned this art into a rich science, measuring the delicate interactions possible at the molecular level. Perhaps the most commonly used tool in computational spectroscopy is that of matrix diagonalization. While this is invaluable for calculating everything from molecular structure and energy levels to dipole moments and dynamics, the process of numerical diagonalization is an opaque one. This work applies symmetry and semi-classical techniques to elucidate numerical spectral analysis for high-symmetry molecules. Semi-classical techniques, such as the Potential Energy Surfaces, have long been used to help understand molecular vibronic and rovibronic spectra and dynamics. This investigation focuses on newer semi-classical techniques that apply Rotational Energy Surfaces (RES) to rotational energy level clustering effects in high-symmetry molecules. Such clusters exist in rigid rotor molecules as well as deformable spherical tops. This study begins by using the simplicity of rigid symmetric top molecules to clarify the classical-quantum correspondence of RES semi-classical analysis and then extends it to a more precise and complete theory of modern high-resolution spectra. RES analysis is extended to molecules having more complex and higher rank tensorial rotational and rovibrational Hamiltonians than were possible to understand before. Such molecules are shown to produce an extraordinary range of rotational level clusters, corresponding to a panoply of symmetries ranging from C4v to C2 and C1 (no symmetry) with a corresponding range of new angular momentum localization and J-tunneling effects. Using RES topography analysis and the commutation duality relations between symmetry group operators in the lab-frame to those in the body-frame, it is shown how to better describe and catalog complex splittings found in rotational level clusters. Symmetry character analysis is generalized to give analytic eigensolutions. An appendix provides vibrational analogies. For the first time, interactions between molecular vibrations (polyads) are described semi-classically by multiple RES. This is done for the nu 3/2nu4 dyad of CF4. The nine-surface RES topology of the U(9)-dyad agrees with both computational and experimental work. A connection between this and a simpler U(2) example is detailed in an Appendix.

Macroturbulence in Very High Resolution Atmospheric Models: Evidence for Two Scaling Regimes

NASA Astrophysics Data System (ADS)

Straus, D. M.

2010-12-01

The macro-turbulent properties of the atmosphere's circulation are examined in a number of very high resolution seasonal simulations using the global Nonhydrostatic ICosahedral Atmospheric Model (NICAM) at 7-km horizontal resolution (40 levels), and the forecast model of the European Centre for Medium-Range Weather Forecasts (ECMWF) at T1279 and T2047 spectral resolutions (90-levels). These simulations were carried out as part of an extraordinary collaborative project between the Center for Ocean-Land-Atmosphere Studies (COLA), the University of Tokyo, the Japan Agency for Marine-Earth Science and Technology (JAMSTEC), ECMWF, and the National Institute of Computational Sciences (NICS) The goals of the analysis are to document the rotational and divergence kinetic energy spectral characteristics, to shed light on the different scaling regimes obtained and the role of non-hydrostatic dynamics, and to asses the effects of the smallest scales on the cascades of energy. Simulations with all the models show some evidence of two scaling regimes (power law with steep slope, and a distinctly more shallow slope at smaller scales) for both rotational and divergent kinetic energy. The strength of the evidence for the two-regimes, as well as the wavenumber ranges in which they occur, do differ between models. Analysis of different time scale contributions to the spectra lend insight into the energy transfer mechanism. The implications for dynamical theories of turbulent energy exchange are discussed, as well as difference in approach to compared with multiplicative cascade theories.

Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation

NASA Technical Reports Server (NTRS)

Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.

2007-01-01

The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.

Application of the Hilbert space average method on heat conduction models.

PubMed

Michel, Mathias; Gemmer, Jochen; Mahler, Günter

2006-01-01

We analyze closed one-dimensional chains of weakly coupled many level systems, by means of the so-called Hilbert space average method (HAM). Subject to some concrete conditions on the Hamiltonian of the system, our theory predicts energy diffusion with respect to a coarse-grained description for almost all initial states. Close to the respective equilibrium, we investigate this behavior in terms of heat transport and derive the heat conduction coefficient. Thus, we are able to show that both heat (energy) diffusive behavior as well as Fourier's law follows from and is compatible with a reversible Schrödinger dynamics on the complete level of description.

Relative complexation energies for Li(+) ion in solution: molecular level solvation versus polarizable continuum model study.

PubMed

Eilmes, Andrzej; Kubisiak, Piotr

2010-01-21

Relative complexation energies for the lithium cation in acetonitrile and diethyl ether have been studied. Quantum-chemical calculations explicitly describing the solvation of Li(+) have been performed based on structures obtained from molecular dynamics simulations. The effect of an increasing number of solvent molecules beyond the first solvation shell has been found to consist in reduction of the differences in complexation energies for different coordination numbers. Explicit-solvation data have served as a benchmark to the results of polarizable continuum model (PCM) calculations. It has been demonstrated that the PCM approach can yield relative complexation energies comparable to the predictions based on molecular-level solvation, but at significantly lower computational cost. The best agreement between the explicit-solvation and the PCM results has been obtained when the van der Waals surface was adopted to build the molecular cavity.

Effects of Imidacloprid and Varroa destructor on survival and health of European honey bees, Apis mellifera.

PubMed

Abbo, Pendo M; Kawasaki, Joshua K; Hamilton, Michele; Cook, Steven C; DeGrandi-Hoffman, Gloria; Li, Wen Feng; Liu, Jie; Chen, Yan Ping

2017-06-01

There has been growing concern over declines in populations of honey bees and other pollinators which are a vital part to our food security. It is imperative to identify factors responsible for accelerated declines in bee populations and develop solutions for reversing bee losses. While exact causes of colony losses remain elusive, risk factors thought to play key roles are ectoparasitic mites Varroa destructor and neonicotinoid pesticides. The present study aims to investigate effects of a neonicotinoid pesticide Imidacloprid and Varroa mites individually on survivorship, growth, physiology, virus dynamics and immunity of honey bee workers. Our study provides clear evidence that the exposure to sublethal doses of Imidacloprid could exert a significantly negative effect on health and survival of honey bees. We observed a significant reduction in the titer of vitellogenin (Vg), an egg yolk precursor that regulates the honey bees development and behavior and often are linked to energy homeostasis, in bees exposed to Imidacloprid. This result indicates that sublethal exposure to neonicotinoid could lead to increased energy usage in honey bees as detoxification is a energy-consuming metabolic process and suggests that Vg could be a useful biomarker for measuring levels of energy stress and sublethal effects of pesticides on honey bees. Measurement of the quantitative effects of different levels of Varroa mite infestation on the replication dynamic of Deformed wing virus (DWV), an RNA virus associated with Varroa infestation, and expression level of immune genes yields unique insights into how honey bees respond to stressors under laboratory conditions. © 2016 Institute of Zoology, Chinese Academy of Sciences.

Dynamical Jahn-Teller effect of fullerene anions

NASA Astrophysics Data System (ADS)

Liu, Dan; Iwahara, Naoya; Chibotaru, Liviu F.

2018-03-01

The dynamical Jahn-Teller effect of C60n - anions (n =1 -5) is studied using the numerical diagonalization of the linear pn⊗8 d Jahn-Teller Hamiltonian with the currently established coupling parameters. It is found that in all anions the Jahn-Teller effect stabilizes the low-spin states, resulting in the violation of Hund's rule. The energy gain due to the Jahn-Teller dynamics is found to be comparable to the static Jahn-Teller stabilization. The Jahn-Teller dynamics influences the thermodynamic properties via strong variation of the density of vibronic states with energy. Thus the large vibronic entropy in the low-spin states enhances the effective spin gap of C603 - quenching the spin crossover. From the calculations of the effective spin gap as a function of the Hund's rule coupling, we found that the latter should amount 40 ±5 meV in order to cope with the violation of Hund's rule and to reproduce the large spin gap. With the obtained numerical solutions, the matrix elements of electronic operators for the low-lying vibronic levels and the vibronic reduction factors are calculated for all anions.

An Energy-Aware Trajectory Optimization Layer for sUAS

NASA Astrophysics Data System (ADS)

Silva, William A.

The focus of this work is the implementation of an energy-aware trajectory optimization algorithm that enables small unmanned aircraft systems (sUAS) to operate in unknown, dynamic severe weather environments. The software is designed as a component of an Energy-Aware Dynamic Data Driven Application System (EA-DDDAS) for sUAS. This work addresses the challenges of integrating and executing an online trajectory optimization algorithm during mission operations in the field. Using simplified aircraft kinematics, the energy-aware algorithm enables extraction of kinetic energy from measured winds to optimize thrust use and endurance during flight. The optimization layer, based upon a nonlinear program formulation, extracts energy by exploiting strong wind velocity gradients in the wind field, a process known as dynamic soaring. The trajectory optimization layer extends the energy-aware path planner developed by Wenceslao Shaw-Cortez te{Shaw-cortez2013} to include additional mission configurations, simulations with a 6-DOF model, and validation of the system with flight testing in June 2015 in Lubbock, Texas. The trajectory optimization layer interfaces with several components within the EA-DDDAS to provide an sUAS with optimal flight trajectories in real-time during severe weather. As a result, execution timing, data transfer, and scalability are considered in the design of the software. Severe weather also poses a measure of unpredictability to the system with respect to communication between systems and available data resources during mission operations. A heuristic mission tree with different cost functions and constraints is implemented to provide a level of adaptability to the optimization layer. Simulations and flight experiments are performed to assess the efficacy of the trajectory optimization layer. The results are used to assess the feasibility of flying dynamic soaring trajectories with existing controllers as well as to verify the interconnections between EA-DDDAS components. Results also demonstrate the usage of the trajectory optimization layer in conjunction with a lattice-based path planner as a method of guiding the optimization layer and stitching together subsequent trajectories.

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

Santos, A.F., E-mail: alesandroferreira@fisica.ufmt.br; Department of Physics and Astronomy, University of Victoria, 3800 Finnerty Road Victoria, BC; Khanna, Faqir C., E-mail: khannaf@uvic.ca

Dynamics between particles is governed by Lorentz and CPT symmetry. There is a violation of Parity (P) and CP symmetry at low levels. The unified theory, that includes particle physics and quantum gravity, may be expected to be covariant with Lorentz and CPT symmetry. At high enough energies, will the unified theory display violation of any symmetry? The Standard Model Extension (SME), with Lorentz and CPT violating terms, has been suggested to include particle dynamics. The minimal SME in the pure photon sector is considered in order to calculate the Casimir effect at finite temperature.

Vibration-rotation alchemy in acetylene (12C2H2), ? at low vibrational excitation: from high resolution spectroscopy to fast intramolecular dynamics

NASA Astrophysics Data System (ADS)

Perry, David S.; Miller, Anthony; Amyay, Badr; Fayt, André; Herman, Michel

2010-04-01

The link between energy-resolved spectra and time-resolved dynamics is explored quantitatively for acetylene (12C2H2), ? with up to 8600 cm-1 of vibrational energy. This comparison is based on the extensive and reliable knowledge of the vibration-rotation energy levels and on the model Hamiltonian used to fit them to high precision [B. Amyay, S. Robert, M. Herman, A. Fayt, B. Raghavendra, A. Moudens, J. Thiévin, B. Rowe, and R. Georges, J. Chem. Phys. 131, 114301 (2009)]. Simulated intensity borrowing features in high resolution absorption spectra and predicted survival probabilities in intramolecular vibrational redistribution (IVR) are first investigated for the v 4 + v 5 and v 3 bright states, for J = 2, 30 and 100. The dependence of the results on the rotational quantum number and on the choice of vibrational bright state reflects the interplay of three kinds of off-diagonal resonances: anharmonic, rotational l-type, and Coriolis. The dynamical quantities used to characterize the calculated time-dependent dynamics are the dilution factor φ d, the IVR lifetime τ IVR , and the recurrence time τ rec. For the two bright states v 3 + 2v 4 and 7v 4, the collisionless dynamics for thermally averaged rotational distributions at T = 27, 270 and 500 K were calculated from the available spectroscopic data. For the 7v 4 bright state, an apparent irreversible decay of is found. In all cases, the model Hamiltonian allows a detailed calculation of the energy flow among all of the coupled zeroth-order vibration-rotation states.

Automated Dynamic Demand Response Implementation on a Micro-grid

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

Kuppannagari, Sanmukh R.; Kannan, Rajgopal; Chelmis, Charalampos

In this paper, we describe a system for real-time automated Dynamic and Sustainable Demand Response with sparse data consumption prediction implemented on the University of Southern California campus microgrid. Supply side approaches to resolving energy supply-load imbalance do not work at high levels of renewable energy penetration. Dynamic Demand Response (D 2R) is a widely used demand-side technique to dynamically adjust electricity consumption during peak load periods. Our D 2R system consists of accurate machine learning based energy consumption forecasting models that work with sparse data coupled with fast and sustainable load curtailment optimization algorithms that provide the ability tomore » dynamically adapt to changing supply-load imbalances in near real-time. Our Sustainable DR (SDR) algorithms attempt to distribute customer curtailment evenly across sub-intervals during a DR event and avoid expensive demand peaks during a few sub-intervals. It also ensures that each customer is penalized fairly in order to achieve the targeted curtailment. We develop near linear-time constant-factor approximation algorithms along with Polynomial Time Approximation Schemes (PTAS) for SDR curtailment that minimizes the curtailment error defined as the difference between the target and achieved curtailment values. Our SDR curtailment problem is formulated as an Integer Linear Program that optimally matches customers to curtailment strategies during a DR event while also explicitly accounting for customer strategy switching overhead as a constraint. We demonstrate the results of our D 2R system using real data from experiments performed on the USC smartgrid and show that 1) our prediction algorithms can very accurately predict energy consumption even with noisy or missing data and 2) our curtailment algorithms deliver DR with extremely low curtailment errors in the 0.01-0.05 kWh range.« less

Multi-Site λ-dynamics for simulated Structure-Activity Relationship studies

PubMed Central

Knight, Jennifer L.; Brooks, Charles L.

2011-01-01

Multi-Site λ-dynamics (MSλD) is a new free energy simulation method that is based on λ-dynamics. It has been developed to enable multiple substituents at multiple sites on a common ligand core to be modeled simultaneously and their free energies assessed. The efficacy of MSλD for estimating relative hydration free energies and relative binding affinties is demonstrated using three test systems. Model compounds representing multiple identical benzene, dihydroxybenzene and dimethoxybenzene molecules show total combined MSλD trajectory lengths of ~1.5 ns are sufficient to reliably achieve relative hydration free energy estimates within 0.2 kcal/mol and are less sensitive to the number of trajectories that are used to generate these estimates for hybrid ligands that contain up to ten substituents modeled at a single site or five substituents modeled at each of two sites. Relative hydration free energies among six benzene derivatives calculated from MSλD simulations are in very good agreement with those from alchemical free energy simulations (with average unsigned differences of 0.23 kcal/mol and R2=0.991) and experiment (with average unsigned errors of 1.8 kcal/mol and R2=0.959). Estimates of the relative binding affinities among 14 inhibitors of HIV-1 reverse transcriptase obtained from MSλD simulations are in reasonable agreement with those from traditional free energy simulations and experiment (average unsigned errors of 0.9 kcal/mol and R2=0.402). For the same level of accuracy and precision MSλD simulations are achieved ~20–50 times faster than traditional free energy simulations and thus with reliable force field parameters can be used effectively to screen tens to hundreds of compounds in structure-based drug design applications. PMID:22125476

Mixed quantum-classical studies of energy partitioning in unimolecular chemical reactions

NASA Astrophysics Data System (ADS)

Bladow, Landon Lowell

A mixed quantum-classical reaction path Hamiltonian method is utilized to study the dynamics of unimolecular reactions. The method treats motion along the reaction path classically and treats the transverse vibrations quantum mechanically. The theory leads to equations that predict the disposai of the exit-channel potential energy to product translation and vibration. In addition, vibrational state distributions are obtained for the product normal modes. Vibrational excitation results from the curvature of the minimum energy reaction path. The method is applied to six unimolecular reactions: HF elimination from fluoroethane, 1,1-difluoroethane, 1,1-difluoroethene, and trifluoromethane; and HCl elimination from chloroethane and acetyl chloride. The minimum energy paths were calculated at either the MP2 or B3LYP level of theory. In all cases, the majority of the vibrational excitation of the products occurs in the HX fragment. The results are compared to experimental data and other theoretical results, where available. The best agreement between the experimental and calculated HX vibrational distributions is found for the halogenated ethanes, and the experimental deduction that the majority of the HX vibrational excitation arises from the potential energy release is supported. It is believed that the excess energy provided in experiments contributes to the poorer agreement between experiment and theory observed for HF elimination from 1,1-difluoroethene and trifluoromethane. An attempt is described to incorporate a treatment of the excess energy into the present method. However, the sign of the curvature coupling elements is then found to affect the dynamics. Overall, the method appears to be an efficient dynamical tool for modeling the disposal of the exit-channel potential energy in unimolecular reactions.

Frontiers of controlling energy levels at interfaces

NASA Astrophysics Data System (ADS)

Koch, Norbert

The alignment of electron energy levels at interfaces between semiconductors, dielectrics, and electrodes determines the function and efficiency of all electronic and optoelectronic devices. Reliable guidelines for predicting the level alignment for a given material combination and methods to adjust the intrinsic energy landscape are needed to enable efficient engineering approaches. These are sufficiently understood for established electronic materials, e.g., Si, but for the increasing number of emerging materials, e.g., organic and 2D semiconductors, perovskites, this is work in progress. The intrinsic level alignment and the underlying mechanisms at interfaces between organic and inorganic semiconductors are discussed first. Next, methods to alter the level alignment are introduced, which all base on proper charge density rearrangement at a heterojunction. As interface modification agents we use molecular electron acceptors and donors, as well as molecular photochromic switches that add a dynamic aspect and allow device multifunctionality. For 2D semiconductors surface transfer doping with molecular acceptors/donors transpires as viable method to locally tune the Fermi-level position in the energy gap. The fundamental electronic properties of a prototypical 1D interface between intrinsic and p-doped 2D semiconductor regions are derived from local (scanning probe) and area-averaged (photoemission) spectroscopy experiments. Future research opportunities for attaining unsurpassed interface control through charge density management are discussed.

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

Benson, Stephen V.; Marhauser, Frank; Douglas, David R.

A method for the suppression of upstream-directed field emission in RF accelerators. The method is not restricted to a certain number of cavity cells, but requires similar operating field levels in all cavities to efficiently annihilate the once accumulated energy. Such a field balance is desirable to minimize dynamic RF losses, but not necessarily achievable in reality depending on individual cavity performance, such as early Q.sub.0-drop or quench field. The method enables a significant energy reduction for upstream-directed electrons within a relatively short distance. As a result of the suppression of upstream-directed field emission, electrons will impact surfaces at rathermore » low energies leading to reduction of dark current and less issues with heating and damage of accelerator components as well as radiation levels including neutron generation and thus radio-activation.« less

Deformed supersymmetric quantum mechanics with spin variables

NASA Astrophysics Data System (ADS)

Fedoruk, Sergey; Ivanov, Evgeny; Sidorov, Stepan

2018-01-01

We quantize the one-particle model of the SU(2|1) supersymmetric multiparticle mechanics with the additional semi-dynamical spin degrees of freedom. We find the relevant energy spectrum and the full set of physical states as functions of the mass-dimension deformation parameter m and SU(2) spin q\\in (Z_{>0,}1/2+Z_{≥0}) . It is found that the states at the fixed energy level form irreducible multiplets of the supergroup SU(2|1). Also, the hidden superconformal symmetry OSp(4|2) of the model is revealed in the classical and quantum cases. We calculate the OSp(4|2) Casimir operators and demonstrate that the full set of the physical states belonging to different energy levels at fixed q are unified into an irreducible OSp(4|2) multiplet.

Analytical Tools for Investigating and Modeling Agent-Based Systems

DTIC Science & Technology

2005-06-01

of Black Holes Cluster 10 : Juan M. Maldacena (1924), Journal of High Energy Physics Field theory models for tachyon and gauge field string dy...namics; Super-Poincare Invariant Superstring Field The- ory; Level Four Approximation to the Tachyon Potential in Superstring Field Theory; SO(32) Spinors

Background history and cosmic perturbations for a general system of self-conserved dynamical dark energy and matter

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

Gómez-Valent, Adrià; Karimkhani, Elahe; Solà, Joan, E-mail: adriagova@ecm.ub.edu, E-mail: e.karimkhani91@basu.ac.ir, E-mail: sola@ecm.ub.edu

We determine the Hubble expansion and the general cosmic perturbation equations for a general system consisting of self-conserved matter, ρ{sub m}, and self-conserved dark energy (DE), ρ{sub D}. While at the background level the two components are non-interacting, they do interact at the perturbations level. We show that the coupled system of matter and DE perturbations can be transformed into a single, third order, matter perturbation equation, which reduces to the (derivative of the) standard one in the case that the DE is just a cosmological constant. As a nontrivial application we analyze a class of dynamical models whose DEmore » density ρ{sub D}(H) consists of a constant term, C{sub 0}, and a series of powers of the Hubble rate. These models were previously analyzed from the point of view of dynamical vacuum models, but here we treat them as self-conserved DE models with a dynamical equation of state. We fit them to the wealth of expansion history and linear structure formation data and compare their fit quality with that of the concordance ΛCDM model. Those with C{sub 0}=0 include the so-called ''entropic-force'' and ''QCD-ghost'' DE models, as well as the pure linear model ρ{sub D}∼H, all of which appear strongly disfavored. The models with C{sub 0}≠0 , in contrast, emerge as promising dynamical DE candidates whose phenomenological performance is highly competitive with the rigid Λ-term inherent to the ΛCDM.« less

Heat dissipation guides activation in signaling proteins.

PubMed

Weber, Jeffrey K; Shukla, Diwakar; Pande, Vijay S

2015-08-18

Life is fundamentally a nonequilibrium phenomenon. At the expense of dissipated energy, living things perform irreversible processes that allow them to propagate and reproduce. Within cells, evolution has designed nanoscale machines to do meaningful work with energy harnessed from a continuous flux of heat and particles. As dictated by the Second Law of Thermodynamics and its fluctuation theorem corollaries, irreversibility in nonequilibrium processes can be quantified in terms of how much entropy such dynamics produce. In this work, we seek to address a fundamental question linking biology and nonequilibrium physics: can the evolved dissipative pathways that facilitate biomolecular function be identified by their extent of entropy production in general relaxation processes? We here synthesize massive molecular dynamics simulations, Markov state models (MSMs), and nonequilibrium statistical mechanical theory to probe dissipation in two key classes of signaling proteins: kinases and G-protein-coupled receptors (GPCRs). Applying machinery from large deviation theory, we use MSMs constructed from protein simulations to generate dynamics conforming to positive levels of entropy production. We note the emergence of an array of peaks in the dynamical response (transient analogs of phase transitions) that draw the proteins between distinct levels of dissipation, and we see that the binding of ATP and agonist molecules modifies the observed dissipative landscapes. Overall, we find that dissipation is tightly coupled to activation in these signaling systems: dominant entropy-producing trajectories become localized near important barriers along known biological activation pathways. We go on to classify an array of equilibrium and nonequilibrium molecular switches that harmonize to promote functional dynamics.

Six degree-of-freedom analysis of hip, knee, ankle and foot provides updated understanding of biomechanical work during human walking.

PubMed

Zelik, Karl E; Takahashi, Kota Z; Sawicki, Gregory S

2015-03-01

Measuring biomechanical work performed by humans and other animals is critical for understanding muscle-tendon function, joint-specific contributions and energy-saving mechanisms during locomotion. Inverse dynamics is often employed to estimate joint-level contributions, and deformable body estimates can be used to study work performed by the foot. We recently discovered that these commonly used experimental estimates fail to explain whole-body energy changes observed during human walking. By re-analyzing previously published data, we found that about 25% (8 J) of total positive energy changes of/about the body's center-of-mass and >30% of the energy changes during the Push-off phase of walking were not explained by conventional joint- and segment-level work estimates, exposing a gap in our fundamental understanding of work production during gait. Here, we present a novel Energy-Accounting analysis that integrates various empirical measures of work and energy to elucidate the source of unexplained biomechanical work. We discovered that by extending conventional 3 degree-of-freedom (DOF) inverse dynamics (estimating rotational work about joints) to 6DOF (rotational and translational) analysis of the hip, knee, ankle and foot, we could fully explain the missing positive work. This revealed that Push-off work performed about the hip may be >50% greater than conventionally estimated (9.3 versus 6.0 J, P=0.0002, at 1.4 m s(-1)). Our findings demonstrate that 6DOF analysis (of hip-knee-ankle-foot) better captures energy changes of the body than more conventional 3DOF estimates. These findings refine our fundamental understanding of how work is distributed within the body, which has implications for assistive technology, biomechanical simulations and potentially clinical treatment. © 2015. Published by The Company of Biologists Ltd.

Simultaneous integrated boost to intraprostatic lesions using different energy levels of intensity-modulated radiotherapy and volumetric-arc therapy

PubMed Central

Sonmez, S; Erbay, G; Guler, O C; Arslan, G

2014-01-01

Objective: This study compared the dosimetry of volumetric-arc therapy (VMAT) and intensity-modulated radiotherapy (IMRT) with a dynamic multileaf collimator using the Monte Carlo algorithm in the treatment of prostate cancer with and without simultaneous integrated boost (SIB) at different energy levels. Methods: The data of 15 biopsy-proven prostate cancer patients were evaluated. The prescribed dose was 78 Gy to the planning target volume (PTV78) including the prostate and seminal vesicles and 86 Gy (PTV86) in 39 fractions to the intraprostatic lesion, which was delineated by MRI or MR-spectroscopy. Results: PTV dose homogeneity was better for IMRT than VMAT at all energy levels for both PTV78 and PTV86. Lower rectum doses (V30–V50) were significantly higher with SIB compared with PTV78 plans in both IMRT and VMAT plans at all energy levels. The bladder doses at high dose level (V60–V80) were significantly higher in IMRT plans with SIB at all energy levels compared with PTV78 plans, but no significant difference was observed in VMAT plans. VMAT plans resulted in a significant decrease in the mean monitor units (MUs) for 6, 10, and 15 MV energy levels both in plans with and those without SIB. Conclusion: Dose escalation to intraprostatic lesions with 86 Gy is safe without causing serious increase in organs at risk (OARs) doses. VMAT is advantageous in sparing OARs and requiring less MU than IMRT. Advances in knowledge: VMAT with SIB to intraprostatic lesion is a feasible method in treating prostate cancer. Additionally, no dosimetric advantage of higher energy is observed. PMID:24319009

Scattering study of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction on an ab initio based analytical potential energy surface

NASA Astrophysics Data System (ADS)

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N.

2016-01-01

Initial state selected dynamics of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]+ structure lying 0.72 eV below the Ne + NeH+ asymptote is found to be the most stable geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.

Optical turbulence and transverse rogue waves in a cavity with triple-quantum-dot molecules

NASA Astrophysics Data System (ADS)

Eslami, M.; Khanmohammadi, M.; Kheradmand, R.; Oppo, G.-L.

2017-09-01

We show that optical turbulence extreme events can exist in the transverse dynamics of a cavity containing molecules of triple quantum dots under conditions close to tunneling-induced transparency. These nanostructures, when coupled via tunneling, form a four-level configuration with tunable energy-level separations. We show that such a system exhibits multistability and bistability of Turing structures in instability domains with different critical wave vectors. By numerical simulation of the mean-field equation that describes the transverse dynamics of the system, we show that the simultaneous presence of two transverse solutions with opposite nonlinearities gives rise to a series of turbulent structures with the capability of generating two-dimensional rogue waves.

When the ball is in the female's court: How the scramble-competition mating system of the North American red squirrel has shaped male physiology and testosterone dynamics.

PubMed

Boonstra, Rudy; Dušek, Adam; Lane, Jeffrey E; Boutin, Stan

2017-10-01

Male reproductive success in most mammals is determined by their success in direct inter-male competition through aggression and conflict, resulting in female-defense mating systems being predominant. This is linked to male testosterone levels and its dynamics. However, in certain environments, a scramble-competition mating system has evolved, where female reproductive behavior takes precedence and male testosterone dynamics are unlikely to be related to inter-male competition. We studied the North American red squirrel (Tamiasciurus hudsonicus), a species with a well-established scramble-competition system. Using an ACTH hormonal challenge protocol as a proxy for competitive interactions, we compared the testosterone dynamics in breeding males in late winter with that in nonbreeding males in late spring in the Yukon. To gain an integrated picture of their physiological state, we also assessed changes in their stress response, body mass, energy mobilization, and indices of immune function. Testosterone levels at the base bleed were high in breeding males (2.72ng/mL) and virtually absent in non-breeding males (0.04ng/mL). Breeding males were in better condition (heavier body mass, higher hematocrit, and higher erythrocytes), had higher indices of immune function (neutrophil:lymphocyte ratio), but a similar ability to mobilize energy (glucose) compared with non-breeding males. Though total cortisol was higher in non-breeding males, free cortisol was twice as high in breeding males as their corticosteroid binding globulin levels were half as high. In response to the ACTH challenge, testosterone levels in breeding males declined 49% over the first hour and increased 36% over the next hour; in non-breeding males levels showed no change. Free cortisol increased only modestly (26% in breeding males; 23% in non-breeding males). Glucose levels changed similarly in breeding and nonbreeding males, declining for the first 30min and then increasing for the next 60min. Thus, testosterone and components of the stress axis function in a profoundly different manner in male red squirrels than in males of mammals with female-defense mating systems. There are four probable interrelated reasons for these adaptations in male red squirrels: the marginal benefits of each mating, the constraints of mate searching away from their own resource-based territories, energy mobilization in a harsh environment, and a long life span. Copyright © 2017 Elsevier Inc. All rights reserved.

Efficient Construction of Free Energy Profiles of Breathing Metal–Organic Frameworks Using Advanced Molecular Dynamics Simulations

PubMed Central

2017-01-01

In order to reliably predict and understand the breathing behavior of highly flexible metal–organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials. PMID:29131647

Efficient Construction of Free Energy Profiles of Breathing Metal-Organic Frameworks Using Advanced Molecular Dynamics Simulations.

PubMed

Demuynck, Ruben; Rogge, Sven M J; Vanduyfhuys, Louis; Wieme, Jelle; Waroquier, Michel; Van Speybroeck, Veronique

2017-12-12

In order to reliably predict and understand the breathing behavior of highly flexible metal-organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials.

Study of soil aggregate breakdown dynamics under low dispersive ultrasonic energies with sedimentation and X-ray attenuation**

PubMed Central

Schomakers, Jasmin; Zehetner, Franz; Mentler, Axel; Ottner, Franz; Mayer, Herwig

2016-01-01

It has been increasingly recognized that soil organic matter stabilization is strongly controlled by physical binding within soil aggregates. It is therefore essential to measure soil aggregate stability reliably over a wide range of disruptive energies and different aggregate sizes. To this end, we tested high-accuracy ultrasonic dispersion in combination with subsequent sedimentation and X-ray attenuation. Three arable topsoils (notillage) from Central Europe were subjected to ultrasound at four different specific energy levels: 0.5, 6.7, 100 and 500 J cm−3, and the resulting suspensions were analyzed for aggregate size distribution by wet sieving (2 000-63 μm) and sedimentation/X-ray attenuation (63-2 μm). The combination of wet sieving and sedimentation technique allowed for a continuous analysis, at high resolution, of soil aggregate breakdown dynamics after defined energy inputs. Our results show that aggregate size distribution strongly varied with sonication energy input and soil type. The strongest effects were observed in the range of low specific energies (< 10 J cm−3), which previous studies have largely neglected. This shows that low ultrasonic energies are required to capture the full range of aggregate stability and release of soil organic matter upon aggregate breakdown. PMID:27099408

PCB Food Web Dynamics Quantify Nutrient and Energy Flow in Aquatic Ecosystems.

PubMed

McLeod, Anne M; Paterson, Gordon; Drouillard, Ken G; Haffner, G Douglas

2015-11-03

Measuring in situ nutrient and energy flows in spatially and temporally complex aquatic ecosystems represents a major ecological challenge. Food web structure, energy and nutrient budgets are difficult to measure, and it is becoming more important to quantify both energy and nutrient flow to determine how food web processes and structure are being modified by multiple stressors. We propose that polychlorinated biphenyl (PCB) congeners represent an ideal tracer to quantify in situ energy and nutrient flow between trophic levels. Here, we demonstrate how an understanding of PCB congener bioaccumulation dynamics provides multiple direct measurements of energy and nutrient flow in aquatic food webs. To demonstrate this novel approach, we quantified nitrogen (N), phosphorus (P) and caloric turnover rates for Lake Huron lake trout, and reveal how these processes are regulated by both growth rate and fish life history. Although minimal nutrient recycling was observed in young growing fish, slow growing, older lake trout (>5 yr) recycled an average of 482 Tonnes·yr(-1) of N, 45 Tonnes·yr(-1) of P and assimilated 22 TJ yr(-1) of energy. Compared to total P loading rates of 590 Tonnes·yr(-1), the recycling of primarily bioavailable nutrients by fish plays an important role regulating the nutrient states of oligotrophic lakes.

Study of soil aggregate breakdown dynamics under low dispersive ultrasonic energies with sedimentation and X-ray attenuation

NASA Astrophysics Data System (ADS)

Schomakers, Jasmin; Zehetner, Franz; Mentler, Axel; Ottner, Franz; Mayer, Herwig

2015-10-01

It has been increasingly recognized that soil organic matter stabilization is strongly controlled by physical binding within soil aggregates. It is therefore essential to measure soil aggregate stability reliably over a wide range of disruptive energies and different aggregate sizes. To this end, we tested highaccuracy ultrasonic dispersion in combination with subsequent sedimentation and X-ray attenuation. Three arable topsoils (notillage) from Central Europe were subjected to ultrasound at four different specific energy levels: 0.5, 6.7, 100 and 500 J cm-3, and the resulting suspensions were analyzed for aggregate size distribution by wet sieving (2 000-63 μm) and sedimentation/X-ray attenuation (63-2 μm). The combination of wet sieving and sedimentation technique allowed for a continuous analysis, at high resolution, of soil aggregate breakdown dynamics after defined energy inputs. Our results show that aggregate size distribution strongly varied with sonication energy input and soil type. The strongest effects were observed in the range of low specific energies (< 10 J cm-3), which previous studies have largely neglected. This shows that low ultrasonic energies are required to capture the full range of aggregate stability and release of soil organic matter upon aggregate breakdown.

Protocols Utilizing Constant pH Molecular Dynamics to Compute pH-Dependent Binding Free Energies

PubMed Central

2015-01-01

In protein–ligand binding, the electrostatic environments of the two binding partners may vary significantly in bound and unbound states, which may lead to protonation changes upon binding. In cases where ligand binding results in a net uptake or release of protons, the free energy of binding is pH-dependent. Nevertheless, conventional free energy calculations and molecular docking protocols typically do not rigorously account for changes in protonation that may occur upon ligand binding. To address these shortcomings, we present a simple methodology based on Wyman’s binding polynomial formalism to account for the pH dependence of binding free energies and demonstrate its use on cucurbit[7]uril (CB[7]) host–guest systems. Using constant pH molecular dynamics and a reference binding free energy that is taken either from experiment or from thermodynamic integration computations, the pH-dependent binding free energy is determined. This computational protocol accurately captures the large pKa shifts observed experimentally upon CB[7]:guest association and reproduces experimental binding free energies at different levels of pH. We show that incorrect assignment of fixed protonation states in free energy computations can give errors of >2 kcal/mol in these host–guest systems. Use of the methods presented here avoids such errors, thus suggesting their utility in computing proton-linked binding free energies for protein–ligand complexes. PMID:25134690

Intramolecular Vibrational Energy Redistribution (ivr) in Selected S_{1} Levels above 1000 cm^{-1} in Para-Fluorotoluene

NASA Astrophysics Data System (ADS)

Whalley, Laura E.; Gardner, Adrian M.; Tuttle, William Duncan; Davies, Julia A.; Reid, Katharine L.; Wright, Timothy G.

2017-06-01

With increasing vibrational wavenumber, the density of states of a molecule is expected to rise dramatically, especially so when low wavenumber torsions (internal rotations) are present, as in the case of para-fluorotoluene (pFT). This in turn is expected to lead to more opportunities for coupling between vibrational modes, which is the driving force for intramolecular vibrational energy redistribution (IVR). Previous studies at higher energies have focussed on the two close lying vibrational levels at 1200 cm^{-1} in the S_{1} electronic state of pFT which were assigned to two zero-order bright states (ZOBSs), whose characters predominantly involve C-CH_{3} and C-F stretching modes. A surprising result of these studies was that the photoelectron spectra showed evidence that IVR is more extensive following excitation of the C-F mode than it is following excitation of the C-CH_{3} mode, despite these levels being separated by only 35 cm^{-1}. This observation provides evidence that the IVR dynamics are mode-specific, which in turn may be a consequence of the IVR route being dependent on couplings to nearby states that are only available to the C-F mode. In this work, in order to further investigate this behaviour, we have employed resonance-enhanced multiphoton ionisation (REMPI) spectroscopy and zero-kinetic-energy (ZEKE) spectroscopy to probe S_{1} levels above 1000 cm^{-1} in pFT. Such ZEKE spectra have been recorded via a number of S_{1} intermediate levels allowing the character and coupling between vibrations to be unravelled; the consequence of this coupling will be discussed with a view to understanding any IVR dynamics seen. C. J. Hammond, V. L. Ayles, D. E. Bergeron, K. L. Reid and T. G. Wright, J. Chem. Phys., 125, 124308 (2006) J. A. Davies, A. M. Green, A. M. Gardner, C. D. Withers, T. G. Wright and K. L. Reid, Phys. Chem. Chem. Phys., 16, 430 (2014)

Low-Dimensional Models of "Neuro-Glio-Vascular Unit" for Describing Neural Dynamics under Normal and Energy-Starved Conditions.

PubMed

Chhabria, Karishma; Chakravarthy, V Srinivasa

2016-01-01

The motivation of developing simple minimal models for neuro-glio-vascular (NGV) system arises from a recent modeling study elucidating the bidirectional information flow within the NGV system having 89 dynamic equations (1). While this was one of the first attempts at formulating a comprehensive model for neuro-glio-vascular system, it poses severe restrictions in scaling up to network levels. On the contrary, low--dimensional models are convenient devices in simulating large networks that also provide an intuitive understanding of the complex interactions occurring within the NGV system. The key idea underlying the proposed models is to describe the glio-vascular system as a lumped system, which takes neural firing rate as input and returns an "energy" variable (analogous to ATP) as output. To this end, we present two models: biophysical neuro-energy (Model 1 with five variables), comprising KATP channel activity governed by neuronal ATP dynamics, and the dynamic threshold (Model 2 with three variables), depicting the dependence of neural firing threshold on the ATP dynamics. Both the models show different firing regimes, such as continuous spiking, phasic, and tonic bursting depending on the ATP production coefficient, ɛp, and external current. We then demonstrate that in a network comprising such energy-dependent neuron units, ɛp could modulate the local field potential (LFP) frequency and amplitude. Interestingly, low-frequency LFP dominates under low ɛp conditions, which is thought to be reminiscent of seizure-like activity observed in epilepsy. The proposed "neuron-energy" unit may be implemented in building models of NGV networks to simulate data obtained from multimodal neuroimaging systems, such as functional near infrared spectroscopy coupled to electroencephalogram and functional magnetic resonance imaging coupled to electroencephalogram. Such models could also provide a theoretical basis for devising optimal neurorehabilitation strategies, such as non-invasive brain stimulation for stroke patients.

Dissipation of 'dark energy' by cortex in knowledge retrieval.

PubMed

Capolupo, Antonio; Freeman, Walter J; Vitiello, Giuseppe

2013-03-01

We have devised a thermodynamic model of cortical neurodynamics expressed at the classical level by neural networks and at the quantum level by dissipative quantum field theory. Our model is based on features in the spatial images of cortical activity newly revealed by high-density electrode arrays. We have incorporated the mechanism and necessity for so-called dark energy in knowledge retrieval. We have extended the model first using the Carnot cycle to define our measures for energy, entropy and temperature, and then using the Rankine cycle to incorporate criticality and phase transitions. We describe the dynamics of two interactive fields of neural activity that express knowledge, one at high and the other at low energy density, and the two operators that create and annihilate the fields. We postulate that the extremely high density of energy sequestered briefly in cortical activity patterns can account for the vividness, richness of associations, and emotional intensity of memories recalled by stimuli. Copyright © 2013 Elsevier B.V. All rights reserved.

Characterization of biosurfactant produced by petrofilic bacteria isolated from hydrocarbon impacted soil and its potential application in bioremediation

NASA Astrophysics Data System (ADS)

Arsyah, D. M.; Kardena, E.; Helmy, Q.

2018-01-01

The study adopts a multi-level perspective in technology transition to analyse how the transition process in the development of geothermal energy in Indonesia is able to compete against the incumbent fossil-fuelled energy sources. Three levels of multi-level perspective are socio-technical landscape (ST-landscape), socio-technical regime (ST-regime) and niche innovations in Indonesia geothermal development. The identification, mapping and analysis of the dynamic relationship between each level are the important pillars of the multi-level perspective framework. The analysis considers the set of rules, actors and controversies that may arise in the technological transition process. The identified geothermal resource risks are the basis of the emerging geothermal technological innovations in Indonesian geothermal. The analysis of this study reveals the transition pathway, which yields a forecast for the Indonesian geothermal technology transition in the form of scenarios and probable impacts.

Chemical reactivity and spectroscopy explored from QM/MM molecular dynamics simulations using the LIO code

NASA Astrophysics Data System (ADS)

Marcolongo, Juan P.; Zeida, Ari; Semelak, Jonathan A.; Foglia, Nicolás O.; Morzan, Uriel N.; Estrin, Dario A.; González Lebrero, Mariano C.; Scherlis, Damián A.

2018-03-01

In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.

Intramolecular energy transfer and the driving mechanisms for large-amplitude collective motions of clusters

NASA Astrophysics Data System (ADS)

Yanao, Tomohiro; Koon, Wang Sang; Marsden, Jerrold E.

2009-04-01

This paper uncovers novel and specific dynamical mechanisms that initiate large-amplitude collective motions in polyatomic molecules. These mechanisms are understood in terms of intramolecular energy transfer between modes and driving forces. Structural transition dynamics of a six-atom cluster between a symmetric and an elongated isomer is highlighted as an illustrative example of what is a general message. First, we introduce a general method of hyperspherical mode analysis to analyze the energy transfer among internal modes of polyatomic molecules. In this method, the (3n-6) internal modes of an n-atom molecule are classified generally into three coarse level gyration-radius modes, three fine level twisting modes, and (3n-12) fine level shearing modes. We show that a large amount of kinetic energy flows into the gyration-radius modes when the cluster undergoes structural transitions by changing its mass distribution. Based on this fact, we construct a reactive mode as a linear combination of the three gyration-radius modes. It is shown that before the reactive mode acquires a large amount of kinetic energy, activation or inactivation of the twisting modes, depending on the geometry of the isomer, plays crucial roles for the onset of a structural transition. Specifically, in a symmetric isomer with a spherical mass distribution, activation of specific twisting modes drives the structural transition into an elongated isomer by inducing a strong internal centrifugal force, which has the effect of elongating the mass distribution of the system. On the other hand, in an elongated isomer, inactivation of specific twisting modes initiates the structural transition into a symmetric isomer with lower potential energy by suppressing the elongation effect of the internal centrifugal force and making the effects of the potential force dominant. This driving mechanism for reactions as well as the present method of hyperspherical mode analysis should be widely applicable to molecular reactions in which a system changes its overall mass distribution in a significant way.

Statistical errors in molecular dynamics averages

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

Schiferl, S.K.; Wallace, D.C.

1985-11-15

A molecular dynamics calculation produces a time-dependent fluctuating signal whose average is a thermodynamic quantity of interest. The average of the kinetic energy, for example, is proportional to the temperature. A procedure is described for determining when the molecular dynamics system is in equilibrium with respect to a given variable, according to the condition that the mean and the bandwidth of the signal should be sensibly constant in time. Confidence limits for the mean are obtained from an analysis of a finite length of the equilibrium signal. The role of serial correlation in this analysis is discussed. The occurence ofmore » unstable behavior in molecular dynamics data is noted, and a statistical test for a level shift is described.« less

Understanding the interactions of human follicle stimulating hormone with single-walled carbon nanotubes by molecular dynamics simulation and free energy analysis.

PubMed

Mahmoodi, Yasaman; Mehrnejad, Faramarz; Khalifeh, Khosrow

2018-01-01

Interactions of carbon nanotubes (CNTs) and blood proteins are of interest for nanotoxicology and nanomedicine. It is believed that the interactions of blood proteins and glycoproteins with CNTs may have important biological effects. In spite of many experimental studies of single-walled carbon nanotubes (SWCNT) and glycoproteins with different methods, little is known about the atomistic details of their association process or of structural alterations occurring in adsorbed glycoproteins. In this study, we have applied molecular dynamics simulation to investigate the interaction of follicle stimulating hormone (hFSH) with SWCNT. The aim of this work is to investigate possible mechanisms of nanotoxicity at a molecular level. We present details of the molecular dynamics, structure, and free energy of binding of hFSH on the surface of SWCNT. We find that hFSH in aqueous solution strongly adsorbs onto SWCNT via their concave surface as evidenced by high binding free energies for residues in both protein subunits. It was found that hydrophobic, π-cation, and π-π stacking interactions are the main driving forces for the adsorption of the protein at the nanotube surface.

Rotational and translational effects in collisions of electronically excited diatomic hydrides

NASA Technical Reports Server (NTRS)

Crosley, David R.

1988-01-01

Collisional quenching and vibrational energy proceed competitively with rotational energy transfer for several excited states of the diatomic radicals OH, NH, and CH. This occurs for a wide variety of molecular collision partners. This phenomenon permits the examination of the influence of rotational motion on the collision dynamics of these theoretically tractable species. Measurements can also be made as a function of temperature, i.e., collision velocity. In OH (sup 2 sigma +), both vibrational transfer and quenching are found to decrease with an increase in rotational level, while quenching decreases with increasing temperature. This behavior indicates that for OH, anisotropic attractive forces govern the entrance channel dynamics for these collisions. The quenching of NH (sup 3 pi sub i) by many (although not all) collision partners also decreases with increasing rotational and translational energy, and NH (sup 1 pi) behaves much like OH (sup 2 sigma +). However, the quenching of CH (sup 2 delta) appears to decrease with increasing rotation but increases with increasing temperature, suggesting in this case anisotropic forces involving a barrier or repulsive wall. Such similarities and differences should furnish useful comparisons with both simple and detailed theoretical pictures of the appropriate collision dynamics.

General Trends of Dihedral Conformational Transitions in a Globular Protein

PubMed Central

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; McCammon, J. Andrew

2017-01-01

Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and Adaptive Biasing Force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions ~2 times faster on average using dihedral boost, and ~3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the Bend, Coil and Turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein sidechains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Sidechains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins. PMID:26799251

Reshaping the energy industry

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

Payne, F.W.

1988-01-01

Our energy industry has gone through the dynamic restructuring. The changes taking place in the energy industry will affect the pocketbooks, thus the lives, of every American, at every level. The geopolitical/militaristic intrigues which surround the international oil segment of this industry must be left to the dubious talents of others. But as motivators, planners, and executors of the powerful changes which are restructuring the other aspects of our industry, the author believes the American people share grave responsibilities. The author defines the scope, the meaning, the results of these changes, and applies the new techniques and technologies they provide.

The Differential Gibbs Free Energy of Activation and its Implications in the Transition-State of Enzymatic Reactions

NASA Astrophysics Data System (ADS)

Maggi, F.; Riley, W. J.

2016-12-01

We propose a mathematical framework to introduce the concept of differential free energy of activation in enzymatically catalyzed reactions, and apply it to N uptake by microalgae and bacteria. This framework extends the thermodynamic capabilities of the classical transition-state theory in and harmonizes the consolidated definitions of kinetic parameters with their thermodynamic and physical meaning. Here, the activation energy is assumed to be a necessary energetic level for equilibrium complexation between reactants and activated complex; however, an additional energy contribution is required for the equilibrium activated complex to release reaction products. We call this "differential free energy of activation"; it can be described by a Boltzmann distribution, and corresponds to a free energy level different from that of complexation. Whether this level is above or below the free energy of activation depends on the reaction, and defines energy domains that correspond to "superactivated", "activated", and "subactivated" complexes. The activated complex reaching one of those states will eventually release the products from an energy level different than that of activation. The concept of differential free energy of activation was tested on 57 independent experiments of NH­4+ and NO3- uptake by various microalgae and bacteria at temperatures ranging between 1 and 45oC. Results showed that the complexation equilibrium always favored the activated complex, but the differential energy of activation led to an apparent energy barrier consistent with observations. Temperature affected all energy levels within this framework but did not alter substantially these thermodynamic features. Overall the approach: (1) provides a thermodynamic and mathematical link between Michaelis-Menten and rate constants; (2) shows that both kinetic parameters can be described or approximated by Arrhenius' like equations; (3) describes the likelihood of formation of sub-, super-, and activated complexes; and (4) shows direction and thermodynamic likelihood of each reaction branch within the transition state. The approach suites particularly well for calibration of kinetic parameters against experimentally acquired reaction dynamics measurements of nutrient biogeochemical cycles.

A Piezoelectric PZT Ceramic Mulitlayer Stack for Energy Harvesting Under Dynamic Forces

NASA Technical Reports Server (NTRS)

Xu, Tian-Bing; Siochi, Emilie J.; Kang, Jin Ho; Zuo, Lei; Zhou, Wanlu; Tang, Xiudong; Jiang, Xiaoning

2011-01-01

Piezoelectric energy harvesting transducers (PEHTs) are commonly used in motion/vibration energy scavenging devices. To date, most researchers have focused on energy harvesting at narrow bandwidths around the mechanical resonance frequency, and most piezoelectric harvesting devices reported in the literature have very low effective piezoelectric coefficient (d(sub eff)) (< 10(exp 4) pC/N). For instance, more than 80% of PEHT related papers are on transverse "31" mode cantilever beam type PEHTs (CBPEHTs) having piezoelectric coefficients of about 100 pC/N. The level of harvested electrical power for CBPEHTs is on the order of microW even at resonance mode. In order to harvest more electrical energy across broader bandwidth, high effective piezoelectric coefficient structures are needed. In this study, we investigate a "33" longitudinal mode, piezoelectric PZT ceramic multilayer stack (PZT-Stack) with high effective piezoelectric coefficient for high-performance PEHTs. The PZT-Stack is composed of 300 layers of 0.1 mm thick PZT plates, with overall dimensions of 32.4 mm X 7.0 mm X 7.0 mm. Experiments were carried out with dynamic forces in a broad bandwidth ranging from 0.5 Hz to 25 kHz. The measured results show that the effective piezoelectric coefficient of the PZT-stack is about 1 X 10(exp 5) pC/N at off-resonance frequencies and 1.39 X 10(exp 6) pC/N at resonance, which is order of magnitude larger than that of traditional PEHTs. The effective piezoelectric coefficients (d(sub eff)) do not change significantly with applied dynamic forces having root mean square (RMS) values ranging from 1 N to 40 N. In resonance mode, 231 mW of electrical power was harvested at 2479 Hz with a dynamic force of 11.6 N(sub rms), and 7.6 mW of electrical power was generated at a frequency of 2114 Hz with 1 N(sub rms) dynamic force. In off-resonance mode, an electrical power of 18.7 mW was obtained at 680 Hz with a 40 N(sub rms) dynamic force. A theoretical model of energy harvesting for the PZT-Stack is established. The modeled results matched well with experimental measurements. This study demonstrated that high effective piezoelectric coefficient structures enable PEHTs to harvest more electrical energy from mechanical vibrations or motions, suggesting an effective design for high-performance low-footprint PEHTs with potential applications in military, aerospace, and portable electronics. In addition, this study provides a route for using piezoelectric multilayer stacks for active or semi-active adaptive control to damp, harvest or transform unwanted dynamic vibrations into useful electrical energy.

LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)

DTIC Science & Technology

2014-03-01

LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E) by James P. Larentzos, John K. Brennan, Joshua D. Moore, and...MD 21005-5069 ARL-TR-6863 March 2014 LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E) James P...13 September 2013 4. TITLE AND SUBTITLE LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E) 5a. CONTRACT NUMBER 5b

System-level view of geospace dynamics: Challenges for high-latitude ground-based observations

NASA Astrophysics Data System (ADS)

Donovan, E.

2014-12-01

Increasingly, research programs including GEM, CEDAR, GEMSIS, GO Canada, and others are focusing on how geospace works as a system. Coupling sits at the heart of system level dynamics. In all cases, coupling is accomplished via fundamental processes such as reconnection and plasma waves, and can be between regions, energy ranges, species, scales, and energy reservoirs. Three views of geospace are required to attack system level questions. First, we must observe the fundamental processes that accomplish the coupling. This "observatory view" requires in situ measurements by satellite-borne instruments or remote sensing from powerful well-instrumented ground-based observatories organized around, for example, Incoherent Scatter Radars. Second, we need to see how this coupling is controlled and what it accomplishes. This demands quantitative observations of the system elements that are being coupled. This "multi-scale view" is accomplished by networks of ground-based instruments, and by global imaging from space. Third, if we take geospace as a whole, the system is too complicated, so at the top level we need time series of simple quantities such as indices that capture important aspects of the system level dynamics. This requires a "key parameter view" that is typically provided through indices such as AE and DsT. With the launch of MMS, and ongoing missions such as THEMIS, Cluster, Swarm, RBSP, and ePOP, we are entering a-once-in-a-lifetime epoch with a remarkable fleet of satellites probing processes at key regions throughout geospace, so the observatory view is secure. With a few exceptions, our key parameter view provides what we need. The multi-scale view, however, is compromised by space/time scales that are important but under-sampled, combined extent of coverage and resolution that falls short of what we need, and inadequate conjugate observations. In this talk, I present an overview of what we need for taking system level research to its next level, and how high latitude ground based observations can address these challenges.

Linking point scale process non-linearity, catchment organization and linear system dynamics in a thermodynamic state space

NASA Astrophysics Data System (ADS)

Zehe, Erwin; Loritz, Ralf; Ehret, Uwe; Westhoff, Martijn; Kleidon, Axel; Savenije, Hubert

2017-04-01

It is flabbergasting to note that catchment systems often behave almost linearly, despite of the strong non-linearity of point scale soil water characteristics. In the present study we provide evidence that a thermodynamic treatment of environmental system dynamics is the key to understand how particularly a stronger spatial organization of catchments leads to a more linear rainfall runoff behavior. Our starting point is that water fluxes in a catchment are associated with fluxes of kinetic and potential energy while changes in subsurface water stocks go along with changes in potential energy and chemical energy of subsurface water. Steady state/local equilibrium of the entire system can be defined as a state of minimum free energy, reflecting an equilibrium subsurface water storage, which is determined catchment topography, soil water characteristics and water levels in the stream. Dynamics of the entire system, i.e. deviations from equilibrium storage, are 'pseudo' oscillations in a thermodynamic state space. Either to an excess potential energy in case of wetting while subsequent relaxation back to equilibrium requires drainage/water export. Or to an excess in capillary binding energy in case of driving, while relaxation back to equilibrium requires recharge of the subsurface water stock. While system dynamics is highly non-linear on the 'too dry branch' it is essentially linear on the 'too wet branch' in case of potential energy excess. A steepened topography, which reflects a stronger spatial organization, reduces the equilibrium storage of the catchment system to smaller values, thereby it increases the range of states where the systems behaves linearly due to an excess in potential energy. Contrarily to this a shift to finer textured soils increases the equilibrium storage, which implies that the range of states where the systems behaves linearly is reduced. In this context it is important to note that an increased internal organization of the system due to an elevated density of the preferential flow paths, imply a less non-linear system behavior. This is because they avoid persistence of very dry states system states by facilitating recharge of the soil moisture stock. Based on the proposed approach we compare dynamics of four distinctly different catchments in their respective state space and demonstrate the feasibility of the approach to explain differences and similarities in their rainfall runoff regimes.

First principles molecular dynamics study of nitrogen vacancy complexes in boronitrene

NASA Astrophysics Data System (ADS)

Ukpong, A. M.; Chetty, N.

2012-07-01

We present the results of first principles molecular dynamics simulations of nitrogen vacancy complexes in monolayer hexagonal boron nitride. The threshold for local structure reconstruction is found to be sensitive to the presence of a substitutional carbon impurity. We show that activated nitrogen dynamics triggers the annihilation of defects in the layer through formation of Stone-Wales-type structures. The lowest energy state of nitrogen vacancy complexes is negatively charged and spin polarized. Using the divacancy complex, we show that their formation induces spontaneous magnetic moments, which is tunable by electron or hole injection. The Fermi level s-resonant defect state is identified as a unique signature of the ground state of the divacancy complex. Due to their ability to enhance structural cohesion, only the divacancy and the nitrogen vacancy carbon-antisite complexes are able to suppress the Fermi level resonant defect state to open a gap between the conduction and valence bands.

Self-balancing dynamic scheduling of electrical energy for energy-intensive enterprises

NASA Astrophysics Data System (ADS)

Gao, Yunlong; Gao, Feng; Zhai, Qiaozhu; Guan, Xiaohong

2013-06-01

Balancing production and consumption with self-generation capacity in energy-intensive enterprises has huge economic and environmental benefits. However, balancing production and consumption with self-generation capacity is a challenging task since the energy production and consumption must be balanced in real time with the criteria specified by power grid. In this article, a mathematical model for minimising the production cost with exactly realisable energy delivery schedule is formulated. And a dynamic programming (DP)-based self-balancing dynamic scheduling algorithm is developed to obtain the complete solution set for such a multiple optimal solutions problem. For each stage, a set of conditions are established to determine whether a feasible control trajectory exists. The state space under these conditions is partitioned into subsets and each subset is viewed as an aggregate state, the cost-to-go function is then expressed as a function of initial and terminal generation levels of each stage and is proved to be a staircase function with finite steps. This avoids the calculation of the cost-to-go of every state to resolve the issue of dimensionality in DP algorithm. In the backward sweep process of the algorithm, an optimal policy is determined to maximise the realisability of energy delivery schedule across the entire time horizon. And then in the forward sweep process, the feasible region of the optimal policy with the initial and terminal state at each stage is identified. Different feasible control trajectories can be identified based on the region; therefore, optimising for the feasible control trajectory is performed based on the region with economic and reliability objectives taken into account.

Exploring the Origin of Differential Binding Affinities of Human Tubulin Isotypes αβII, αβIII and αβIV for DAMA-Colchicine Using Homology Modelling, Molecular Docking and Molecular Dynamics Simulations

PubMed Central

Panda, Dulal; Kunwar, Ambarish

2016-01-01

Tubulin isotypes are found to play an important role in regulating microtubule dynamics. The isotype composition is also thought to contribute in the development of drug resistance as tubulin isotypes show differential binding affinities for various anti-cancer agents. Tubulin isotypes αβII, αβIII and αβIV show differential binding affinity for colchicine. However, the origin of differential binding affinity is not well understood at the molecular level. Here, we investigate the origin of differential binding affinity of a colchicine analogue N-deacetyl-N-(2-mercaptoacetyl)-colchicine (DAMA-colchicine) for human αβII, αβIII and αβIV isotypes, employing sequence analysis, homology modeling, molecular docking, molecular dynamics simulation and MM-GBSA binding free energy calculations. The sequence analysis study shows that the residue compositions are different in the colchicine binding pocket of αβII and αβIII, whereas no such difference is present in αβIV tubulin isotypes. Further, the molecular docking and molecular dynamics simulations results show that residue differences present at the colchicine binding pocket weaken the bonding interactions and the correct binding of DAMA-colchicine at the interface of αβII and αβIII tubulin isotypes. Post molecular dynamics simulation analysis suggests that these residue variations affect the structure and dynamics of αβII and αβIII tubulin isotypes, which in turn affect the binding of DAMA-colchicine. Further, the binding free-energy calculation shows that αβIV tubulin isotype has the highest binding free-energy and αβIII has the lowest binding free-energy for DAMA-colchicine. The order of binding free-energy for DAMA-colchicine is αβIV ≃ αβII >> αβIII. Thus, our computational approaches provide an insight into the effect of residue variations on differential binding of αβII, αβIII and αβIV tubulin isotypes with DAMA-colchicine and may help to design new analogues with higher binding affinities for tubulin isotypes. PMID:27227832

Effects of wind energy generation and white-nose syndrome on the viability of the Indiana bat

USGS Publications Warehouse

Erickson, Richard A.; Thogmartin, Wayne E.; Diffendorfer, James E.; Russell, Robin E.; Szymanski, Jennifer A.

2016-01-01

Wind energy generation holds the potential to adversely affect wildlife populations. Species-wide effects are difficult to study and few, if any, studies examine effects of wind energy generation on any species across its entire range. One species that may be affected by wind energy generation is the endangered Indiana bat (Myotis sodalis), which is found in the eastern and midwestern United States. In addition to mortality from wind energy generation, the species also faces range-wide threats from the emerging infectious fungal disease, white-nose syndrome (WNS). White-nose syndrome, caused by Pseudogymnoascus destructans, disturbs hibernating bats leading to high levels of mortality. We used a spatially explicit full-annual-cycle model to investigate how wind turbine mortality and WNS may singly and then together affect population dynamics of this species. In the simulation, wind turbine mortality impacted the metapopulation dynamics of the species by causing extirpation of some of the smaller winter colonies. In general, effects of wind turbines were localized and focused on specific spatial subpopulations. Conversely, WNS had a depressive effect on the species across its range. Wind turbine mortality interacted with WNS and together these stressors had a larger impact than would be expected from either alone, principally because these stressors together act to reduce species abundance across the spectrum of population sizes. Our findings illustrate the importance of not only prioritizing the protection of large winter colonies as is currently done, but also of protecting metapopulation dynamics and migratory connectivity.

Effects of wind energy generation and white-nose syndrome on the viability of the Indiana bat.

PubMed

Erickson, Richard A; Thogmartin, Wayne E; Diffendorfer, Jay E; Russell, Robin E; Szymanski, Jennifer A

2016-01-01

Wind energy generation holds the potential to adversely affect wildlife populations. Species-wide effects are difficult to study and few, if any, studies examine effects of wind energy generation on any species across its entire range. One species that may be affected by wind energy generation is the endangered Indiana bat ( Myotis sodalis ), which is found in the eastern and midwestern United States. In addition to mortality from wind energy generation, the species also faces range-wide threats from the emerging infectious fungal disease, white-nose syndrome (WNS). White-nose syndrome, caused by Pseudogymnoascus destructans , disturbs hibernating bats leading to high levels of mortality. We used a spatially explicit full-annual-cycle model to investigate how wind turbine mortality and WNS may singly and then together affect population dynamics of this species. In the simulation, wind turbine mortality impacted the metapopulation dynamics of the species by causing extirpation of some of the smaller winter colonies. In general, effects of wind turbines were localized and focused on specific spatial subpopulations. Conversely, WNS had a depressive effect on the species across its range. Wind turbine mortality interacted with WNS and together these stressors had a larger impact than would be expected from either alone, principally because these stressors together act to reduce species abundance across the spectrum of population sizes. Our findings illustrate the importance of not only prioritizing the protection of large winter colonies as is currently done, but also of protecting metapopulation dynamics and migratory connectivity.

The Cl + O3 reaction: a detailed QCT simulation of molecular beam experiments.

PubMed

Menéndez, M; Castillo, J F; Martínez-Haya, B; Aoiz, F J

2015-10-14

We have studied in detail the dynamics of the Cl + O3 reaction in the 1-56 kcal mol(-1) collision energy range using quasi-classical trajectory (QCT) calculations on a recent potential energy surface (PES) [J. F. Castillo et al., Phys. Chem. Chem. Phys., 2011, 13, 8537]. The main goal of this work has been to assess the accuracy of the PES and the reliability of the QCT method by comparison with the existing crossed molecular beam results [J. Zhang and Y. T. Lee J. Phys. Chem. A, 1997, 101, 6485]. For this purpose, we have developed a methodology that allows us to determine the experimental observables in crossed molecular beam experiments (integral and differential cross sections, recoil velocity distributions, scattering angle-recoil velocity polar maps, etc.) as continuous functions of the collision energy. Using these distributions, raw experimental data in the laboratory frame (angular distributions and time-of-flight spectra) have been simulated from first principles with the sole information on the instrumental parameters and taking into account the energy spread. A general good agreement with the experimental data has been found, thereby demonstrating the adequacy of the QCT method and the quality of the PES to describe the dynamics of this reaction at the level of resolution of the existing crossed beam experiments. Some features which are apparent in the differential cross sections have also been analysed in terms of the dynamics of the reaction and its evolution with the collision energy.

Use of Direct Dynamics Simulations to Determine Unimolecular Reaction Paths and Arrhenius Parameters for Large Molecules.

PubMed

Yang, Li; Sun, Rui; Hase, William L

2011-11-08

In a previous study (J. Chem. Phys.2008, 129, 094701) it was shown that for a large molecule, with a total energy much greater than its barrier for decomposition and whose vibrational modes are harmonic oscillators, the expressions for the classical Rice-Ramsperger-Kassel-Marcus (RRKM) (i.e., RRK) and classical transition-state theory (TST) rate constants become equivalent. Using this relationship, a molecule's unimolecular rate constants versus temperature may be determined from chemical dynamics simulations of microcanonical ensembles for the molecule at different total energies. The simulation identifies the molecule's unimolecular pathways and their Arrhenius parameters. In the work presented here, this approach is used to study the thermal decomposition of CH3-NH-CH═CH-CH3, an important constituent in the polymer of cross-linked epoxy resins. Direct dynamics simulations, at the MP2/6-31+G* level of theory, were used to investigate the decomposition of microcanonical ensembles for this molecule. The Arrhenius A and Ea parameters determined from the direct dynamics simulation are in very good agreement with the TST Arrhenius parameters for the MP2/6-31+G* potential energy surface. The simulation method applied here may be particularly useful for large molecules with a multitude of decomposition pathways and whose transition states may be difficult to determine and have structures that are not readily obvious.

Zero-Point Energy Constraint for Unimolecular Dissociation Reactions. Giving Trajectories Multiple Chances To Dissociate Correctly.

PubMed

Paul, Amit K; Hase, William L

2016-01-28

A zero-point energy (ZPE) constraint model is proposed for classical trajectory simulations of unimolecular decomposition and applied to CH4* → H + CH3 decomposition. With this model trajectories are not allowed to dissociate unless they have ZPE in the CH3 product. If not, they are returned to the CH4* region of phase space and, if necessary, given additional opportunities to dissociate with ZPE. The lifetime for dissociation of an individual trajectory is the time it takes to dissociate with ZPE in CH3, including multiple possible returns to CH4*. With this ZPE constraint the dissociation of CH4* is exponential in time as expected for intrinsic RRKM dynamics and the resulting rate constant is in good agreement with the harmonic quantum value of RRKM theory. In contrast, a model that discards trajectories without ZPE in the reaction products gives a CH4* → H + CH3 rate constant that agrees with the classical and not quantum RRKM value. The rate constant for the purely classical simulation indicates that anharmonicity may be important and the rate constant from the ZPE constrained classical trajectory simulation may not represent the complete anharmonicity of the RRKM quantum dynamics. The ZPE constraint model proposed here is compared with previous models for restricting ZPE flow in intramolecular dynamics, and connecting product and reactant/product quantum energy levels in chemical dynamics simulations.

Probing Dirac fermion dynamics in topological insulator Bi2Se3 films with a scanning tunneling microscope.

PubMed

Song, Can-Li; Wang, Lili; He, Ke; Ji, Shuai-Hua; Chen, Xi; Ma, Xu-Cun; Xue, Qi-Kun

2015-05-01

Scanning tunneling microscopy and spectroscopy have been used to investigate the femtosecond dynamics of Dirac fermions in the topological insulator Bi2Se3 ultrathin films. At the two-dimensional limit, bulk electrons become quantized and the quantization can be controlled by the film thickness at a single quintuple layer level. By studying the spatial decay of standing waves (quasiparticle interference patterns) off steps, we measure directly the energy and film thickness dependence of the phase relaxation length lϕ and inelastic scattering lifetime τ of topological surface-state electrons. We find that τ exhibits a remarkable (E - EF)(-2) energy dependence and increases with film thickness. We show that the features revealed are typical for electron-electron scattering between surface and bulk states.

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

PubMed

Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

2016-08-05

The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Late time cosmological dynamics with a nonminimal extension of the mimetic matter scenario

NASA Astrophysics Data System (ADS)

Hosseinkhan, N.; Nozari, K.

2018-02-01

We investigate an extension of mimetic gravity in which mimetic matter is nonminimally coupled to the Ricci scalar. We derive the background field equations and show that, as the minimal case, the nonminimal mimetic matter can behave as dark matter or dark energy. By adopting some well-known potentials, we study the dynamics of the scale factor and the equation of state parameter in detail. As the effective mimetic dark energy, this model explains the late time cosmic acceleration and its equation of state parameter crosses the phantom divide. We extend our analysis to the dynamical system approach and the phase space trajectories of the model. We obtain an attractor line which corresponds to the late time cosmic acceleration. By comparing this nonminimal mimetic matter scenario with observational data for the LCDM, we show that the confidence levels of this model overlap with those of Planck 2015 TT, TE, EE + Low P + Lensing + BAO data in the LCDM model.

Bidirectionality and compartmentation of metabolic fluxes are revealed in the dynamics of isotopomer networks.

PubMed

Schryer, David W; Peterson, Pearu; Paalme, Toomas; Vendelin, Marko

2009-04-17

Isotope labeling is one of the few methods of revealing the in vivo bidirectionality and compartmentalization of metabolic fluxes within metabolic networks. We argue that a shift from steady state to dynamic isotopomer analysis is required to deal with these cellular complexities and provide a review of dynamic studies of compartmentalized energy fluxes in eukaryotic cells including cardiac muscle, plants, and astrocytes. Knowledge of complex metabolic behaviour on a molecular level is prerequisite for the intelligent design of genetically modified organisms able to realize their potential of revolutionizing food, energy, and pharmaceutical production. We describe techniques to explore the bidirectionality and compartmentalization of metabolic fluxes using information contained in the isotopic transient, and discuss the integration of kinetic models with MFA. The flux parameters of an example metabolic network were optimized to examine the compartmentalization of metabolites and and the bidirectionality of fluxes in the TCA cycle of Saccharomyces uvarum for steady-state respiratory growth.

Measuring the dynamic structure factor of a quantum gas undergoing a structural phase transition

PubMed Central

Landig, Renate; Brennecke, Ferdinand; Mottl, Rafael; Donner, Tobias; Esslinger, Tilman

2015-01-01

The dynamic structure factor is a central quantity describing the physics of quantum many-body systems, capturing structure and collective excitations of a material. In condensed matter, it can be measured via inelastic neutron scattering, which is an energy-resolving probe for the density fluctuations. In ultracold atoms, a similar approach could so far not be applied because of the diluteness of the system. Here we report on a direct, real-time and nondestructive measurement of the dynamic structure factor of a quantum gas exhibiting cavity-mediated long-range interactions. The technique relies on inelastic scattering of photons, stimulated by the enhanced vacuum field inside a high finesse optical cavity. We extract the density fluctuations, their energy and lifetime while the system undergoes a structural phase transition. We observe an occupation of the relevant quasi-particle mode on the level of a few excitations, and provide a theoretical description of this dissipative quantum many-body system. PMID:25944151

Communication: An accurate global potential energy surface for the ground electronic state of ozone

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

Dawes, Richard, E-mail: dawesr@mst.edu, E-mail: hguo@unm.edu; Lolur, Phalgun; Li, Anyang

We report a new full-dimensional and global potential energy surface (PES) for the O + O{sub 2} → O{sub 3} ozone forming reaction based on explicitly correlated multireference configuration interaction (MRCI-F12) data. It extends our previous [R. Dawes, P. Lolur, J. Ma, and H. Guo, J. Chem. Phys. 135, 081102 (2011)] dynamically weighted multistate MRCI calculations of the asymptotic region which showed the widely found submerged reef along the minimum energy path to be the spurious result of an avoided crossing with an excited state. A spin-orbit correction was added and the PES tends asymptotically to the recently developed long-rangemore » electrostatic model of Lepers et al. [J. Chem. Phys. 137, 234305 (2012)]. This PES features: (1) excellent equilibrium structural parameters, (2) good agreement with experimental vibrational levels, (3) accurate dissociation energy, and (4) most-notably, a transition region without a spurious reef. The new PES is expected to allow insight into the still unresolved issues surrounding the kinetics, dynamics, and isotope signature of ozone.« less

Ultrasound acoustic wave energy transfer and harvesting

NASA Astrophysics Data System (ADS)

Shahab, Shima; Leadenham, Stephen; Guillot, François; Sabra, Karim; Erturk, Alper

2014-04-01

This paper investigates low-power electricity generation from ultrasound acoustic wave energy transfer combined with piezoelectric energy harvesting for wireless applications ranging from medical implants to naval sensor systems. The focus is placed on an underwater system that consists of a pulsating source for spherical wave generation and a harvester connected to an external resistive load for quantifying the electrical power output. An analytical electro-acoustic model is developed to relate the source strength to the electrical power output of the harvester located at a specific distance from the source. The model couples the energy harvester dynamics (piezoelectric device and electrical load) with the source strength through the acoustic-structure interaction at the harvester-fluid interface. Case studies are given for a detailed understanding of the coupled system dynamics under various conditions. Specifically the relationship between the electrical power output and system parameters, such as the distance of the harvester from the source, dimensions of the harvester, level of source strength, and electrical load resistance are explored. Sensitivity of the electrical power output to the excitation frequency in the neighborhood of the harvester's underwater resonance frequency is also reported.

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences.

PubMed

Best, Robert B; Mittal, Jeetain

2011-04-01

Although it is now possible to fold peptides and miniproteins in molecular dynamics simulations, it is well appreciated that force fields are not all transferable to different proteins. Here, we investigate the influence of the protein force field and the solvent model on the folding energy landscape of a prototypical two-state folder, the GB1 hairpin. We use extensive replica-exchange molecular dynamics simulations to characterize the free-energy surface as a function of temperature. Most of these force fields appear similar at a global level, giving a fraction folded at 300 K between 0.2 and 0.8 in all cases, which is a difference in stability of 2.8 kT, and are generally consistent with experimental data at this temperature. The most significant differences appear in the unfolded state, where there are different residual secondary structures which are populated, and the overall dimensions of the unfolded states, which in most of the force fields are too collapsed relative to experimental Förster Resonance Energy Transfer (FRET) data.

Molecular dynamics study of radiation damage and microstructure evolution of zigzag single-walled carbon nanotubes under carbon ion incidence

NASA Astrophysics Data System (ADS)

Li, Huan; Tang, Xiaobin; Chen, Feida; Huang, Hai; Liu, Jian; Chen, Da

2016-07-01

The radiation damage and microstructure evolution of different zigzag single-walled carbon nanotubes (SWCNTs) were investigated under incident carbon ion by molecular dynamics (MD) simulations. The radiation damage of SWCNTs under incident carbon ion with energy ranging from 25 eV to 1 keV at 300 K showed many differences at different incident sites, and the defect production increased to the maximum value with the increase in incident ion energy, and slightly decreased but stayed fairly stable within the majority of the energy range. The maximum damage of SWCNTs appeared when the incident ion energy reached 200 eV and the level of damage was directly proportional to incident ion fluence. The radiation damage was also studied at 100 K and 700 K and the defect production decreased distinctly with rising temperature because radiation-induced defects would anneal and recombine by saturating dangling bonds and reconstructing carbon network at the higher temperature. Furthermore, the stability of a large-diameter tube surpassed that of a thin one under the same radiation environments.

Distributed Coordination of Energy Storage with Distributed Generators

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

Yang, Tao; Wu, Di; Stoorvogel, Antonie A.

2016-07-18

With a growing emphasis on energy efficiency and system flexibility, a great effort has been made recently in developing distributed energy resources (DER), including distributed generators and energy storage systems. This paper first formulates an optimal coordination problem considering constraints at both system and device levels, including power balance constraint, generator output limits, storage energy and power capacity and charging/discharging efficiencies. An algorithm is then proposed to dynamically and automatically coordinate DERs in a distributed manner. With the proposed algorithm, the agent at each DER only maintains a local incremental cost and updates it through information exchange with a fewmore » neighbors, without relying on any central decision maker. Simulation results are used to illustrate and validate the proposed algorithm.« less

Excited-state quantum phase transitions in systems with two degrees of freedom: Level density, level dynamics, thermal properties

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

Stránský, Pavel; Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, 04510, México, D.F.; Macek, Michal

2014-06-15

Quantum systems with a finite number of freedom degrees f develop robust singularities in the energy spectrum of excited states as the system’s size increases to infinity. We analyze the general form of these singularities for low f, particularly f=2, clarifying the relation to classical stationary points of the corresponding potential. Signatures in the smoothed energy dependence of the quantum state density and in the flow of energy levels with an arbitrary control parameter are described along with the relevant thermodynamical consequences. The general analysis is illustrated with specific examples of excited-state singularities accompanying the first-order quantum phase transition. --more » Highlights: •ESQPTs found in infinite-size limit of systems with low numbers of freedom degrees f. •ESQPTs related to non-analytical evolutions of classical phase–space properties. •ESQPT signatures analyzed for general f, particularly f=2, extending known case f=1. •ESQPT signatures identified in smoothened density and flow of energy spectrum. •ESQPTs shown to induce a new type of thermodynamic anomalies.« less

Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations.

PubMed

Li, Chun-Xiang; Guo, Wei-Wei; Xie, Bin-Bin; Cui, Ganglong

2016-08-21

Herein we have used combined static electronic structure calculations and "on-the-fly" global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the (1)ππ(∗), (1)nπ(∗), and S0 states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated (1)ππ(∗) system. The first is the diabatic ESIPT process along the (1)ππ(∗) potential energy profile. The generated (1)ππ(∗) keto species then decays to the S0 state via the keto (1)ππ(∗)/gs conical intersection. The second is internal conversion to the dark (1)nπ(∗) state near the (1)ππ(∗) /(1)nπ(∗) crossing point in the course of the diabatic (1)ππ(∗) ESIPT process. Our following dynamics simulations have shown that the ESIPT and (1)ππ(∗) → S0 internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the (1)ππ(∗) → S0 internal conversion in the keto region, the (1)ππ(∗) → (1)nπ(∗) internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone.

Photodynamics of oxybenzone sunscreen: Nonadiabatic dynamics simulations

NASA Astrophysics Data System (ADS)

Li, Chun-Xiang; Guo, Wei-Wei; Xie, Bin-Bin; Cui, Ganglong

2016-08-01

Herein we have used combined static electronic structure calculations and "on-the-fly" global-switching trajectory surface-hopping dynamics simulations to explore the photochemical mechanism of oxybenzone sunscreen. We have first employed the multi-configurational CASSCF method to optimize minima, conical intersections, and minimum-energy reaction paths related to excited-state intramolecular proton transfer (ESIPT) and excited-state decays in the 1ππ∗, 1nπ∗, and S0 states (energies are refined at the higher MS-CASPT2 level). According to the mapped potential energy profiles, we have identified two ultrafast excited-state deactivation pathways for the initially populated 1ππ∗ system. The first is the diabatic ESIPT process along the 1ππ∗ potential energy profile. The generated 1ππ∗ keto species then decays to the S0 state via the keto 1ππ∗/gs conical intersection. The second is internal conversion to the dark 1nπ∗ state near the 1ππ∗ /1nπ∗ crossing point in the course of the diabatic 1ππ∗ ESIPT process. Our following dynamics simulations have shown that the ESIPT and 1ππ∗ → S0 internal conversion times are 104 and 286 fs, respectively. Finally, our present work demonstrates that in addition to the ESIPT process and the 1ππ∗ → S0 internal conversion in the keto region, the 1ππ∗ → 1nπ∗ internal conversion in the enol region plays as well an important role for the excited-state relaxation dynamics of oxybenzone.

A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories

PubMed Central

2015-01-01

Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics. PMID:25988351

A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories.

PubMed

Ramanathan, Ravishankar; Muñoz, Victor

2015-06-25

Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics.

Energy Absorbing Seat System for an Agricultural Aircraft

NASA Technical Reports Server (NTRS)

Kellas, Sotiris; Jones, Lisa E. (Technical Monitor)

2002-01-01

A task was initiated to improve the energy absorption capability of an existing aircraft seat through cost-effective retrofitting, while keeping seat-weight increase to a minimum. This task was undertaken as an extension of NASA ongoing safety research and commitment to general aviation customer needs. Only vertical crash scenarios have been considered in this task which required the energy absorbing system to protect the seat occupant in a range of crash speeds up to 31 ft/sec. It was anticipated that, the forward and/or side crash accelerations could be attenuated with the aid of airbags, the technology of which is currently available in automobiles and military helicopters. Steps which were followed include, preliminary crush load determination, conceptual design of cost effective energy absorbers, fabrication and testing (static and dynamic) of energy absorbers, system analysis, design and fabrication of dummy seat/rail assembly, dynamic testing of dummy seat/rail assembly, and finally, testing of actual modified seat system with a dummy occupant. A total of ten full scale tests have been performed including three of the actual aircraft seat. Results from full-scale tests indicated that occupant loads were attenuated successfully to survivable levels.

Mass and energy budgets of animals: Behavioral and ecological implications

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

Porter, W.P.

1991-11-01

The two major aims of our lab are as follows: First, to develop and field-test general mechanistic models that predict animal life history characteristics as influenced by climate and the physical, physiological behavioral characteristics of species. This involves: understanding how animal time and energy budgets are affected by climate and animal properties; predicting growth and reproductive potential from time and energy budgets; predicting mortality based on climate and time and energy budgets; and linking these individual based models to population dynamics. Second to conduct empirical studies of animal physiological ecology, particularly the effects of temperature on time and energy budgets.more » The physiological ecology of individual animals is the key link between the physical environment and population-level phenomena. We address the macroclimate to microclimate linkage on a broad spatial scale; address the links between individuals and population dynamics for lizard species; test the endotherm energetics and behavior model using beaver; address the spatial variation in climate and its effects on individual energetics, growth and reproduction; and address patchiness in the environment and constraints they may impose on individual energetics, growth and reproduction. These projects are described individually in the following section. 24 refs., 9 figs.« less

Operations and thermodynamics of an artificial rotary molecular motor in solution.

PubMed

Moro, Lorenzo; di Giosia, Matteo; Calvaresi, Matteo; Bakalis, Evangelos; Zerbetto, Francesco

2014-06-23

A general framework is provided that makes possible the estimation of time-dependent properties of a stochastic system moving far from equilibrium. The process is investigated and discussed in general terms of nonequilibrium thermodynamics. The approach is simple and can be exploited to gain insight into the dynamics of any molecular-level machine. As a case study, the dynamics of an artificial molecular rotary motor, similar to the inversion of a helix, which drives the motor from a metastable state to equilibrium, are examined. The energy path that the motor walks was obtained from the results of atomistic calculations. The motor undergoes unidirectional rotation and its entropy, internal energy, free energy, and net exerted force are given as a function of time, starting from the solution of Smoluchowski's equation. The rather low value of the organization index, that is, the ratio of the work done by the particle against friction during the unidirectional motion per available free energy, reveals that the motion is mainly subject to randomness, and the amount of energy converted to heat due to the directional motion is very small. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SIMWEST - A simulation model for wind energy storage systems

NASA Technical Reports Server (NTRS)

Edsinger, R. W.; Warren, A. W.; Gordon, L. H.; Chang, G. C.

1978-01-01

This paper describes a comprehensive and efficient computer program for the modeling of wind energy systems with storage. The level of detail of SIMWEST (SImulation Model for Wind Energy STorage) is consistent with evaluating the economic feasibility as well as the general performance of wind energy systems with energy storage options. The software package consists of two basic programs and a library of system, environmental, and control components. The first program is a precompiler which allows the library components to be put together in building block form. The second program performs the technoeconomic system analysis with the required input/output, and the integration of system dynamics. An example of the application of the SIMWEST program to a current 100 kW wind energy storage system is given.

Developing a framework for energy technology portfolio selection

NASA Astrophysics Data System (ADS)

Davoudpour, Hamid; Ashrafi, Maryam

2012-11-01

Today, the increased consumption of energy in world, in addition to the risk of quick exhaustion of fossil resources, has forced industrial firms and organizations to utilize energy technology portfolio management tools viewed both as a process of diversification of energy sources and optimal use of available energy sources. Furthermore, the rapid development of technologies, their increasing complexity and variety, and market dynamics have made the task of technology portfolio selection difficult. Considering high level of competitiveness, organizations need to strategically allocate their limited resources to the best subset of possible candidates. This paper presents the results of developing a mathematical model for energy technology portfolio selection at a R&D center maximizing support of the organization's strategy and values. The model balances the cost and benefit of the entire portfolio.

Dynamic analysis of combined photovoltaic source and synchronous generator connected to power grid

NASA Astrophysics Data System (ADS)

Mahabal, Divya

In the world of expanding economy and technology, the energy demand is likely to increase even with the global efforts of saving and increasing energy efficiency. Higher oil prices, effects of greenhouse gases, and concerns over other environmental impacts gave way to Distributed Generation (DG). With adequate awareness and support, DG's can meet these rising energy demands at lower prices compared to conventional methods. Extensive research is taking place in different areas like fuel cells, photovoltaic cells, wind turbines, and gas turbines. DG's when connected to a grid increase the overall efficiency of the power grid. It is believed that three-fifth of the world's electricity would account for renewable energy by middle of 21st century. This thesis presents the dynamic analysis of a grid connected photovoltaic (PV) system and synchronous generator. A grid is considered as an infinite bus. The photovol-taic system and synchronous generator act as small scale distributed energy resources. The output of the photovoltaic system depends on the light intensity, temperature, and irradiance levels of sun. The maximum power point tracking and DC/AC converter are also modeled for the photovoltaic system. The PV system is connected to the grid through DC/AC system. Different combinations of PV and synchronous generator are modeled with the grid to study the dynamics of the proposed system. The dynamics of the test system is analyzed by subjecting the system to several disturbances under various conditions. All modules are individually modeled and con-nected using MATLAB/Simulink software package. Results from the study show that, as the penetration of renewable energy sources like PV increases into the power system, the dynamics of the system becomes faster. When considering cases such as load switching, PV cannot deliver more power as the performance of PV depends on environmental conditions. Synchronous generator in power system can produce the required amount of power. As the main aim of this research is to use renewable sources like PV in the system, it is advantageous to use a combination of both PV and synchronous generator in the system.

Ion-neutral chemistry at ultralow energies: dynamics of reactive collisions between laser-cooled Ca+ ions and Rb atoms in an ion-atom hybrid trap†

NASA Astrophysics Data System (ADS)

Hall, Felix H. J.; Eberle, Pascal; Hegi, Gregor; Raoult, Maurice; Aymar, Mireille; Dulieu, Olivier; Willitsch, Stefan

2013-08-01

Cold chemical reactions between laser-cooled Ca+ ions and Rb atoms were studied in an ion-atom hybrid trap. Reaction rate constants were determined in the range of collision energies ⟨E coll⟩/k B=20 mK-20 K. The lowest energies were achieved in experiments using single localised Ca+ ions. Product branching ratios were studied using resonant-excitation mass spectrometry. The dynamics of the reactive processes in this system (non-radiative and radiative charge transfer as well as radiative association leading to the formation of CaRb+ molecular ions) have been analysed using high-level quantum-chemical calculations of the potential energy curves of CaRb+ and quantum-scattering calculations for the radiative channels. For the present low-energy scattering experiments, it is shown that the energy dependence of the reaction rate constants is governed by long-range interactions in line with the classical Langevin model, but their magnitude is determined by short-range non-adiabatic and radiative couplings which only weakly depend on the asymptotic energy. The quantum character of the collisions is predicted to manifest itself in the occurrence of narrow shape resonances at well-defined collision energies. The present results highlight both universal and system-specific phenomena in cold ion-neutral reactive collisions.

Energy and Quality-Aware Multimedia Signal Processing

NASA Astrophysics Data System (ADS)

Emre, Yunus

Today's mobile devices have to support computation-intensive multimedia applications with a limited energy budget. In this dissertation, we present architecture level and algorithm-level techniques that reduce energy consumption of these devices with minimal impact on system quality. First, we present novel techniques to mitigate the effects of SRAM memory failures in JPEG2000 implementations operating in scaled voltages. We investigate error control coding schemes and propose an unequal error protection scheme tailored for JPEG2000 that reduces overhead without affecting the performance. Furthermore, we propose algorithm-specific techniques for error compensation that exploit the fact that in JPEG2000 the discrete wavelet transform outputs have larger values for low frequency subband coefficients and smaller values for high frequency subband coefficients. Next, we present use of voltage overscaling to reduce the data-path power consumption of JPEG codecs. We propose an algorithm-specific technique which exploits the characteristics of the quantized coefficients after zig-zag scan to mitigate errors introduced by aggressive voltage scaling. Third, we investigate the effect of reducing dynamic range for datapath energy reduction. We analyze the effect of truncation error and propose a scheme that estimates the mean value of the truncation error during the pre-computation stage and compensates for this error. Such a scheme is very effective for reducing the noise power in applications that are dominated by additions and multiplications such as FIR filter and transform computation. We also present a novel sum of absolute difference (SAD) scheme that is based on most significant bit truncation. The proposed scheme exploits the fact that most of the absolute difference (AD) calculations result in small values, and most of the large AD values do not contribute to the SAD values of the blocks that are selected. Such a scheme is highly effective in reducing the energy consumption of motion estimation and intra-prediction kernels in video codecs. Finally, we present several hybrid energy-saving techniques based on combination of voltage scaling, computation reduction and dynamic range reduction that further reduce the energy consumption while keeping the performance degradation very low. For instance, a combination of computation reduction and dynamic range reduction for Discrete Cosine Transform shows on average, 33% to 46% reduction in energy consumption while incurring only 0.5dB to 1.5dB loss in PSNR.

Perspective: chemical dynamics simulations of non-statistical reaction dynamics

PubMed Central

Ma, Xinyou; Hase, William L.

2017-01-01

Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’. PMID:28320906

Relationship between dynamical entropy and energy dissipation far from thermodynamic equilibrium.

PubMed

Green, Jason R; Costa, Anthony B; Grzybowski, Bartosz A; Szleifer, Igal

2013-10-08

Connections between microscopic dynamical observables and macroscopic nonequilibrium (NE) properties have been pursued in statistical physics since Boltzmann, Gibbs, and Maxwell. The simulations we describe here establish a relationship between the Kolmogorov-Sinai entropy and the energy dissipated as heat from a NE system to its environment. First, we show that the Kolmogorov-Sinai or dynamical entropy can be separated into system and bath components and that the entropy of the system characterizes the dynamics of energy dissipation. Second, we find that the average change in the system dynamical entropy is linearly related to the average change in the energy dissipated to the bath. The constant energy and time scales of the bath fix the dynamical relationship between these two quantities. These results provide a link between microscopic dynamical variables and the macroscopic energetics of NE processes.

Relationship between dynamical entropy and energy dissipation far from thermodynamic equilibrium

PubMed Central

Green, Jason R.; Costa, Anthony B.; Grzybowski, Bartosz A.; Szleifer, Igal

2013-01-01

Connections between microscopic dynamical observables and macroscopic nonequilibrium (NE) properties have been pursued in statistical physics since Boltzmann, Gibbs, and Maxwell. The simulations we describe here establish a relationship between the Kolmogorov–Sinai entropy and the energy dissipated as heat from a NE system to its environment. First, we show that the Kolmogorov–Sinai or dynamical entropy can be separated into system and bath components and that the entropy of the system characterizes the dynamics of energy dissipation. Second, we find that the average change in the system dynamical entropy is linearly related to the average change in the energy dissipated to the bath. The constant energy and time scales of the bath fix the dynamical relationship between these two quantities. These results provide a link between microscopic dynamical variables and the macroscopic energetics of NE processes. PMID:24065832

Eutectic-based wafer-level-packaging technique for piezoresistive MEMS accelerometers and bond characterization using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Aono, T.; Kazama, A.; Okada, R.; Iwasaki, T.; Isono, Y.

2018-03-01

We developed a eutectic-based wafer-level-packaging (WLP) technique for piezoresistive micro-electromechanical systems (MEMS) accelerometers on the basis of molecular dynamics analyses and shear tests of WLP accelerometers. The bonding conditions were experimentally and analytically determined to realize a high shear strength without solder material atoms diffusing to adhesion layers. Molecular dynamics (MD) simulations and energy dispersive x-ray (EDX) spectrometry done after the shear tests clarified the eutectic reaction of the solder materials used in this research. Energy relaxation calculations in MD showed that the diffusion of solder material atoms into the adhesive layer was promoted at a higher temperature. Tensile creep MD simulations also suggested that the local potential energy in a solder material model determined the fracture points of the model. These numerical results were supported by the shear tests and EDX analyses for WLP accelerometers. Consequently, a bonding load of 9.8 kN and temperature of 300 °C were found to be rational conditions because the shear strength was sufficient to endure the polishing process after the WLP process and there was little diffusion of solder material atoms to the adhesion layer. Also, eutectic-bonding-based WLP was effective for controlling the attenuation of the accelerometers by determining the thickness of electroplated solder materials that played the role of a cavity between the accelerometers and lids. If the gap distance between the two was less than 6.2 µm, the signal gains for x- and z-axis acceleration were less than 20 dB even at the resonance frequency due to air-damping.

Mechanical energy absorber

NASA Technical Reports Server (NTRS)

Wesselski, Clarence J. (Inventor)

1993-01-01

An energy absorbing system for controlling the force where a moving object engages a stationary stop and where the system utilized telescopic tubular members, energy absorbing diaphragm elements, force regulating disc springs, and a return spring to return the telescoping member to its start position after stroking is presented. The energy absorbing system has frusto-conical diaphragm elements frictionally engaging the shaft and are opposed by a force regulating set of disc springs. In principle, this force feedback mechanism serves to keep the stroking load at a reasonable level even if the friction coefficient increases greatly. This force feedback device also serves to desensitize the singular and combined effects of manufacturing tolerances, sliding surface wear, temperature changes, dynamic effects, and lubricity.

Production of Entanglement Entropy by Decoherence

NASA Astrophysics Data System (ADS)

Merkli, M.; Berman, G. P.; Sayre, R. T.; Wang, X.; Nesterov, A. I.

We examine the dynamics of entanglement entropy of all parts in an open system consisting of a two-level dimer interacting with an environment of oscillators. The dimer-environment interaction is almost energy conserving. We find the precise link between decoherence and production of entanglement entropy. We show that not all environment oscillators carry significant entanglement entropy and we identify the oscillator frequency regions which contribute to the production of entanglement entropy. For energy conserving dimer-environment interactions the models are explicitly solvable and our results hold for all dimer-environment coupling strengths. We carry out a mathematically rigorous perturbation theory around the energy conserving situation in the presence of small non-energy conserving interactions.

Deep Throttle Turbopump Technology Design Concepts

NASA Technical Reports Server (NTRS)

Guinzburg, Adiel; Williams, Morgan; Ferguson, Tom; Garcia, Roberto (Technical Monitor)

2002-01-01

The objective of this project is to increase the throttling range of turbopumps from 30 to 120% of the design value, while maintaining high performance levels. Details are given on wide flow range issues, H-Q characteristics, stall characteristics, energy levels, pressure fluctuations at impeller exit, WFR impeller characteristics, commercial diffuser pumps, slotted or tandem vanes, leading edge characteristics, leading edge models, throat models, diffusion passage models, computational fluid dynamics (CFD) methodologies, and CFD flow cases.

The potential energy landscape contribution to the dynamic heat capacity

NASA Astrophysics Data System (ADS)

Brown, Jonathan R.; McCoy, John D.

2011-05-01

The dynamic heat capacity of a simple polymeric, model glassformer was computed using molecular dynamics simulations by sinusoidally driving the temperature and recording the resultant energy. The underlying potential energy landscape of the system was probed by taking a time series of particle positions and quenching them. The resulting dynamic heat capacity demonstrates that the long time relaxation is the direct result of dynamics resulting from the potential energy landscape. Moreover, the equilibrium (low frequency) portion of the potential energy landscape contribution to the heat capacity is found to increase rapidly at low temperatures and at high packing fractions. This increase in the heat capacity is explained by a statistical mechanical model based on the distribution of minima in the potential energy landscape.

Exact master equation and non-Markovian decoherence dynamics of Majorana zero modes under gate-induced charge fluctuations

NASA Astrophysics Data System (ADS)

Lai, Hon-Lam; Yang, Pei-Yun; Huang, Yu-Wei; Zhang, Wei-Min

2018-02-01

In this paper, we use the exact master equation approach to investigate the decoherence dynamics of Majorana zero modes in the Kitaev model, a 1D p -wave spinless topological superconducting chain (TSC) that is disturbed by gate-induced charge fluctuations. The exact master equation is derived by extending Feynman-Vernon influence functional technique to fermionic open systems involving pairing excitations. We obtain the exact master equation for the zero-energy Bogoliubov quasiparticle (bogoliubon) in the TSC, and then transfer it into the master equation for the Majorana zero modes. Within this exact master equation formalism, we can describe in detail the non-Markovian decoherence dynamics of the zero-energy bogoliubon as well as Majorana zero modes under local perturbations. We find that at zero temperature, local charge fluctuations induce level broadening to one of the Majorana zero modes but there is an isolated peak (localized bound state) located at zero energy that partially protects the Majorana zero mode from decoherence. At finite temperatures, the zero-energy localized bound state does not precisely exist, but the coherence of the Majorana zero mode can still be partially but weakly protected, due to the sharp dip of the spectral density near the zero frequency. The decoherence will be enhanced as one increases the charge fluctuations and/or the temperature of the gate.

Dynamic EROI Assessment of the IPCC 21st Century Electricity Production Scenario

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

Neumeyer, Charles; Goldston, Robert

Abstract: The Energy Return on Investment (EROI) is an important measure of the energy gain of an electrical power generating facility that is typically evaluated based on the life cycle energy balance of a single facility. The EROI concept can be extended to cover a collection of facilities that comprise a complete power system and used to assess the expansion and evolution of a power system as it transitions from one portfolio mix of technologies to another over time. In this study we develop a dynamic EROI model that simulates the evolution of a power system and we perform anmore » EROI simulation of one of the electricity production scenarios developed under the auspices of the Intergovernmental Panel on Climate Change (IPCC) covering the global supply of electricity in the 21st century. Our analytic tool provides the means for evaluation of dynamic EROI based on arbitrary time-dependent demand scenarios by modeling the required expansion of power generation, including the plowback needed for new construction and to replace facilities as they are retired. The results provide insight into the level of installed and delivered power, above and beyond basic consumer demand, that is required to support construction during expansion, as well as the supplementary power that may be required if plowback constraints are imposed. In addition, sensitivity to EROI parameters, and the impact of energy storage efficiency are addressed.« less

Dynamic EROI Assessment of the IPCC 21st Century Electricity Production Scenario

DOE PAGES

Neumeyer, Charles; Goldston, Robert

2016-04-28

Abstract: The Energy Return on Investment (EROI) is an important measure of the energy gain of an electrical power generating facility that is typically evaluated based on the life cycle energy balance of a single facility. The EROI concept can be extended to cover a collection of facilities that comprise a complete power system and used to assess the expansion and evolution of a power system as it transitions from one portfolio mix of technologies to another over time. In this study we develop a dynamic EROI model that simulates the evolution of a power system and we perform anmore » EROI simulation of one of the electricity production scenarios developed under the auspices of the Intergovernmental Panel on Climate Change (IPCC) covering the global supply of electricity in the 21st century. Our analytic tool provides the means for evaluation of dynamic EROI based on arbitrary time-dependent demand scenarios by modeling the required expansion of power generation, including the plowback needed for new construction and to replace facilities as they are retired. The results provide insight into the level of installed and delivered power, above and beyond basic consumer demand, that is required to support construction during expansion, as well as the supplementary power that may be required if plowback constraints are imposed. In addition, sensitivity to EROI parameters, and the impact of energy storage efficiency are addressed.« less

Modelling southern elephant seals Mirounga leonina using an individual-based model coupled with a dynamic energy budget

PubMed Central

Melbourne-Thomas, Jessica; Corney, Stuart P.; McMahon, Clive R.; Hindell, Mark A.

2018-01-01

Higher trophic-level species are an integral component of any marine ecosystem. Despite their importance, methods for representing these species in end-to-end ecosystem models often have limited representation of life histories, energetics and behaviour. We built an individual-based model coupled with a dynamic energy budget for female southern elephant seals Mirounga leonina to demonstrate a method for detailed representation of marine mammals. We aimed to develop a model which could i) simulate energy use and life histories, as well as breeding traits of southern elephant seals in an emergent manner, ii) project a stable population over time, and iii) have realistic population dynamics and structure based on emergent life history features (such as age at first breeding, lifespan, fecundity and (yearling) survival). We evaluated the model’s ability to represent a stable population over long time periods (>10 generations), including the sensitivity of the emergent properties to variations in key parameters. Analyses indicated that the model is sensitive to changes in resource availability and energy requirements for the transition from pup to juvenile, and juvenile to adult stage. This was particularly the case for breeding success and yearling survival. This model is suitable for use as a standalone tool for investigating the impacts of changes to behaviour and population responses of southern elephant seals. PMID:29596456

Interpolating moving least-squares methods for fitting potential energy surfaces: using classical trajectories to explore configuration space.

PubMed

Dawes, Richard; Passalacqua, Alessio; Wagner, Albert F; Sewell, Thomas D; Minkoff, Michael; Thompson, Donald L

2009-04-14

We develop two approaches for growing a fitted potential energy surface (PES) by the interpolating moving least-squares (IMLS) technique using classical trajectories. We illustrate both approaches by calculating nitrous acid (HONO) cis-->trans isomerization trajectories under the control of ab initio forces from low-level HF/cc-pVDZ electronic structure calculations. In this illustrative example, as few as 300 ab initio energy/gradient calculations are required to converge the isomerization rate constant at a fixed energy to approximately 10%. Neither approach requires any preliminary electronic structure calculations or initial approximate representation of the PES (beyond information required for trajectory initial conditions). Hessians are not required. Both approaches rely on the fitting error estimation properties of IMLS fits. The first approach, called IMLS-accelerated direct dynamics, propagates individual trajectories directly with no preliminary exploratory trajectories. The PES is grown "on the fly" with the computation of new ab initio data only when a fitting error estimate exceeds a prescribed tight tolerance. The second approach, called dynamics-driven IMLS fitting, uses relatively inexpensive exploratory trajectories to both determine and fit the dynamically accessible configuration space. Once exploratory trajectories no longer find configurations with fitting error estimates higher than the designated accuracy, the IMLS fit is considered to be complete and usable in classical trajectory calculations or other applications.

Dissociation of polycyclic aromatic hydrocarbons: molecular dynamics studies

NASA Astrophysics Data System (ADS)

Simon, A.; Rapacioli, M.; Rouaut, G.; Trinquier, G.; Gadéa, F. X.

2017-03-01

We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC-DFTB) level of theory. The SCC-DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene , pyrene and coronene at several energies. Such studies enable one to derive significant trends on branching ratios, kinetics, structures and hints on the formation mechanism of the ejected neutral fragments. In particular, dependence of branching ratios on PAH size and energy were retrieved. The losses of H and C2H2 (recognized as the ethyne molecule) were identified as major dissociation channels. The H/C2H2 ratio was found to increase with PAH size and to decrease with energy. For , which is the most interesting PAH from the astrophysical point of view, the loss of H was found as the quasi-only channel for an internal energy of 30 eV. Overall, in line with experimental trends, decreasing the internal energy or increasing the PAH size will favour the hydrogen loss channels with respect to carbonaceous fragments. This article is part of the themed issue 'Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces'.

Proton transfer reactions and dynamics in CH(3)OH-H(3)O(+)-H(2)O complexes.

PubMed

Sagarik, Kritsana; Chaiwongwattana, Sermsiri; Vchirawongkwin, Viwat; Prueksaaroon, Supakit

2010-01-28

Proton transfer reactions and dynamics in hydrated complexes formed from CH(3)OH, H(3)O(+) and H(2)O were studied using theoretical methods. The investigations began with searching for equilibrium structures at low hydration levels using the DFT method, from which active H-bonds in the gas phase and continuum aqueous solution were characterized and analyzed. Based on the asymmetric stretching coordinates (Deltad(DA)), four H-bond complexes were identified as potential transition states, in which the most active unit is represented by an excess proton nearly equally shared between CH(3)OH and H(2)O. These cannot be definitive due to the lack of asymmetric O-H stretching frequencies (nu(OH)) which are spectral signatures of transferring protons. Born-Oppenheimer molecular dynamics (BOMD) simulations revealed that, when the thermal energy fluctuations and dynamics were included in the model calculations, the spectral signatures at nu(OH) approximately 1000 cm(-1) appeared. In continuum aqueous solution, the H-bond complex with incomplete water coordination at charged species turned out to be the only active transition state. Based on the assumption that the thermal energy fluctuations and dynamics could temporarily break the H-bonds linking the transition state complex and water molecules in the second hydration shell, elementary reactions of proton transfer were proposed. The present study showed that, due to the coupling among various vibrational modes, the discussions on proton transfer reactions cannot be made based solely on static proton transfer potentials. Inclusion of thermal energy fluctuations and dynamics in the model calculations, as in the case of BOMD simulations, together with systematic IR spectral analyses, have been proved to be the most appropriate theoretical approaches.

Study of Z scaling of runaway electron plateau final loss energy deposition into wall of DIII-D

DOE PAGES

Hollmann, Eric M.; Commaux, Nicolas; Eidietis, Nicholas; ...

2017-06-12

Here, controlled runaway electron (RE) plateau-wall strikes with different initial impurity levels are used to study the effect of background plasma ion charge Z (resistivity) on RE-­wall loss dynamics. It is found that Joule heating (magnetic to kinetic energy conversion) during the final loss does not go up monotonically with increasing Z, but peaks at intermediate Z ~ 6. Joule heating and overall time scales of the RE final loss are found to be reasonably well-described by a basic 0D coupled-circuit model, with only the loss time as a free parameter. This loss time is found to be fairly wellmore » correlated with the avalanche time, possibly suggesting that the RE final loss rate is limited by the avalanche rate. First attempts at measuring total energy deposition to the vessel walls by REs during the final loss are made. At higher plasma impurity levels Z > 5, energy deposition to the wall appears be consistent with modeling, at least within the large uncertainties of the measurement. At low impurity levels Z < 5, however, local energy deposition appears around 5-­20× less than expected, suggesting that the RE energy dissipation at low Z is not fully understood.« less

Study of Z scaling of runaway electron plateau final loss energy deposition into wall of DIII-D

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

Hollmann, Eric M.; Commaux, Nicolas; Eidietis, Nicholas

Here, controlled runaway electron (RE) plateau-wall strikes with different initial impurity levels are used to study the effect of background plasma ion charge Z (resistivity) on RE-­wall loss dynamics. It is found that Joule heating (magnetic to kinetic energy conversion) during the final loss does not go up monotonically with increasing Z, but peaks at intermediate Z ~ 6. Joule heating and overall time scales of the RE final loss are found to be reasonably well-described by a basic 0D coupled-circuit model, with only the loss time as a free parameter. This loss time is found to be fairly wellmore » correlated with the avalanche time, possibly suggesting that the RE final loss rate is limited by the avalanche rate. First attempts at measuring total energy deposition to the vessel walls by REs during the final loss are made. At higher plasma impurity levels Z > 5, energy deposition to the wall appears be consistent with modeling, at least within the large uncertainties of the measurement. At low impurity levels Z < 5, however, local energy deposition appears around 5-­20× less than expected, suggesting that the RE energy dissipation at low Z is not fully understood.« less

Lifetimes and wave functions of ozone metastable vibrational states near the dissociation limit in a full-symmetry approach

NASA Astrophysics Data System (ADS)

Lapierre, David; Alijah, Alexander; Kochanov, Roman; Kokoouline, Viatcheslav; Tyuterev, Vladimir

2016-10-01

Energies and lifetimes (widths) of vibrational states above the lowest dissociation limit of O163 were determined using a previously developed efficient approach, which combines hyperspherical coordinates and a complex absorbing potential. The calculations are based on a recently computed potential energy surface of ozone determined with a spectroscopic accuracy [Tyuterev et al., J. Chem. Phys. 139, 134307 (2013), 10.1063/1.4821638]. The effect of permutational symmetry on rovibrational dynamics and the density of resonance states in O3 is discussed in detail. Correspondence between quantum numbers appropriate for short- and long-range parts of wave functions of the rovibrational continuum is established. It is shown, by symmetry arguments, that the allowed purely vibrational (J =0 ) levels of O163 and O183, both made of bosons with zero nuclear spin, cannot dissociate on the ground-state potential energy surface. Energies and wave functions of bound states of the ozone isotopologue O163 with rotational angular momentum J =0 and 1 up to the dissociation threshold were also computed. For bound levels, good agreement with experimental energies is found: The rms deviation between observed and calculated vibrational energies is 1 cm-1. Rotational constants were determined and used for a simple identification of vibrational modes of calculated levels.

Overtone-induced dissociation and isomerization dynamics of the hydroxymethyl radical (CH2OH and CD2OH). I. A theoretical study

NASA Astrophysics Data System (ADS)

Kamarchik, E.; Rodrigo, C.; Bowman, J. M.; Reisler, H.; Krylov, A. I.

2012-02-01

The dissociation of the hydroxymethyl radical, CH2OH, and its isotopolog, CD2OH, following the excitation of high OH stretch overtones is studied by quasi-classical molecular dynamics calculations using a global potential energy surface (PES) fitted to ab initio calculations. The PES includes CH2OH and CH3O minima, dissociation products, and all relevant barriers. Its analysis shows that the transition states for OH bond fission and isomerization are both very close in energy to the excited vibrational levels reached in recent experiments and involve significant geometry changes relative to the CH2OH equilibrium structure. The energies of key stationary points are refined using high-level electronic structure calculations. Vibrational energies and wavefunctions are computed by coupled anharmonic vibrational calculations. They show that high OH-stretch overtones are mixed with other modes. Consequently, trajectory calculations carried out at energies about ˜3000 cm-1 above the barriers reveal that despite initial excitation of the OH stretch, the direct OH bond fission is relatively slow (10 ps) and a considerable fraction of the radicals undergoes isomerization to the methoxy radical. The computed dissociation energies are: D0(CH2OH → CH2O + H) = 10 188 cm-1, D0(CD2OH → CD2O + H) = 10 167 cm-1, D0(CD2OH → CHDO + D) = 10 787 cm-1. All are in excellent agreement with the experimental results. For CH2OH, the barriers for the direct OH bond fission and isomerization are: 14 205 and 13 839 cm-1, respectively.

Emergent Irreversibility and Entanglement Spectrum Statistics

NASA Astrophysics Data System (ADS)

Chamon, Claudio; Hamma, Alioscia; Mucciolo, Eduardo R.

2014-06-01

We study the problem of irreversibility when the dynamical evolution of a many-body system is described by a stochastic quantum circuit. Such evolution is more general than a Hamiltonian one, and since energy levels are not well defined, the well-established connection between the statistical fluctuations of the energy spectrum and irreversibility cannot be made. We show that the entanglement spectrum provides a more general connection. Irreversibility is marked by a failure of a disentangling algorithm and is preceded by the appearance of Wigner-Dyson statistical fluctuations in the entanglement spectrum. This analysis can be done at the wave-function level and offers an alternative route to study quantum chaos and quantum integrability.

The impact of economic complexity on carbon emissions: evidence from France.

PubMed

Can, Muhlis; Gozgor, Giray

2017-07-01

This paper reanalyzes the determinants of the CO 2 emissions in France. For this purpose, it considers the unit root test with two structural breaks and a dynamic ordinary least squares estimation. The paper also considers the effects of the energy consumption and the economic complexity on CO 2 emissions. First, it is observed that the EKC hypothesis is valid in France. Second, the positive effect of the energy consumption on CO 2 emissions is obtained. Third, it is observed that a higher economic complexity suppresses the level of CO 2 emissions in the long run. The findings imply noteworthy environmental policy implications to decrease the level of CO 2 emissions in France.

Investigation of high-energy ion-irradiated MA957 using synchrotron radiation under in-situ tension

DOE PAGES

Mo, Kun; Yun, Di; Miao, Yinbin; ...

2016-01-02

In this paper, an MA957 oxide dispersion-strengthened (ODS) alloy was irradiated with high-energy ions in the Argonne Tandem Linac Accelerator System. Fe ions at an energy of 84 MeV bombarded MA957 tensile specimens, creating a damage region similar to 7.5 μm in depth; the peak damage (similar to 40 dpa) was estimated to be at similar to 7 μm from the surface. Following the irradiation, in-situ high-energy X-ray diffraction measurements were performed at the Advanced Photon Source in order to study the dynamic deformation behavior of the specimens after ion irradiation damage. In-situ X-ray measurements taken during tensile testing ofmore » the ion-irradiated MA957 revealed a difference in loading behavior between the irradiated and un-irradiated regions of the specimen. At equivalent applied stresses, lower lattice strains were found in the radiation-damaged region than those in the un-irradiated region. This might be associated with a higher level of Type II stresses as a result of radiation hardening. The study has demonstrated the feasibility of combining high-energy ion radiation and high-energy synchrotron X-ray diffraction to study materials' radiation damage in a dynamic manner.« less

Bio-inspired energy-harvesting mechanisms and patterns of dynamic soaring.

PubMed

Liu, Duo-Neng; Hou, Zhong-Xi; Guo, Zheng; Yang, Xi-Xiang; Gao, Xian-Zhong

2017-01-30

Albatrosses can make use of the dynamic soaring technique extracting energy from the wind field to achieve large-scale movement without a flap, which stimulates interest in effortless flight with small unmanned aerial vehicles (UAVs). However, mechanisms of energy harvesting in terms of the energy transfer from the wind to the flyer (albatross or UAV) are still indeterminate and controversial when using different reference frames in previous studies. In this paper, the classical four-phase Rayleigh cycle, includes sequentially upwind climb, downwind turn, downwind dive and upwind turn, is introduced in analyses of energy gain with the albatross's equation of motions and the simulated trajectory in dynamic soaring. Analytical and numerical results indicate that the energy gain in the air-relative frame mostly originates from large wind gradients at lower part of the climb and dive, while the energy gain in the inertial frame comes from the lift vector inclined to the wind speed direction during the climb, dive and downwind turn at higher altitude. These two energy-gain mechanisms are not equivalent in terms of energy sources and reference frames but have to be simultaneously satisfied in terms of the energy-neutral dynamic soaring cycle. For each reference frame, energy-loss phases are necessary to connect energy-gain ones. Based on these four essential phases in dynamic soaring and the albatrosses' flight trajectory, different dynamic soaring patterns are schematically depicted and corresponding optimal trajectories are computed. The optimal dynamic soaring trajectories are classified into two closed patterns including 'O' shape and '8' shape, and four travelling patterns including 'Ω' shape, 'α' shape, 'C' shape and 'S' shape. The correlation among these patterns are analysed and discussed. The completeness of the classification for different patterns is confirmed by listing and summarising dynamic soaring trajectories shown in studies over the past decades.

Influence of chemical disorder on energy dissipation and defect evolution in concentrated solid solution alloys

DOE PAGES

Zhang, Yanwen; Stocks, George Malcolm; Jin, Ke; ...

2015-10-28

A long-standing objective in materials research is to understand how energy is dissipated in both the electronic and atomic subsystems in irradiated materials, and how related non-equilibrium processes may affect defect dynamics and microstructure evolution. Here we show that alloy complexity in concentrated solid solution alloys having both an increasing number of principal elements and altered concentrations of specific elements can lead to substantial reduction in the electron mean free path and thermal conductivity, which has a significant impact on energy dissipation and consequentially on defect evolution during ion irradiation. Enhanced radiation resistance with increasing complexity from pure nickel tomore » binary and to more complex quaternary solid solutions is observed under ion irradiation up to an average damage level of 1 displacement per atom. Understanding how materials properties can be tailored by alloy complexity and their influence on defect dynamics may pave the way for new principles for the design of radiation tolerant structural alloys.« less

Variationally Optimized Free-Energy Flooding for Rate Calculation.

PubMed

McCarty, James; Valsson, Omar; Tiwary, Pratyush; Parrinello, Michele

2015-08-14

We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of several collective variables that is designed to flood the associated free energy surface up to a predefined level. The resulting bias potential effectively accelerates transitions between metastable free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates to be obtained. We test the method on a few illustrative systems for which we obtain an order of magnitude improvement in efficiency relative to previous approaches and several orders of magnitude relative to unbiased molecular dynamics. We expect an even larger improvement in more complex systems. This and the ability of the variational approach to deal efficiently with a large number of collective variables will greatly enhance the scope of these calculations. This work is a vindication of the potential that the variational principle has if applied in innovative ways.

Resource Management in Constrained Dynamic Situations

NASA Astrophysics Data System (ADS)

Seok, Jinwoo

Resource management is considered in this dissertation for systems with limited resources, possibly combined with other system constraints, in unpredictably dynamic environments. Resources may represent fuel, power, capabilities, energy, and so on. Resource management is important for many practical systems; usually, resources are limited, and their use must be optimized. Furthermore, systems are often constrained, and constraints must be satisfied for safe operation. Simplistic resource management can result in poor use of resources and failure of the system. Furthermore, many real-world situations involve dynamic environments. Many traditional problems are formulated based on the assumptions of given probabilities or perfect knowledge of future events. However, in many cases, the future is completely unknown, and information on or probabilities about future events are not available. In other words, we operate in unpredictably dynamic situations. Thus, a method is needed to handle dynamic situations without knowledge of the future, but few formal methods have been developed to address them. Thus, the goal is to design resource management methods for constrained systems, with limited resources, in unpredictably dynamic environments. To this end, resource management is organized hierarchically into two levels: 1) planning, and 2) control. In the planning level, the set of tasks to be performed is scheduled based on limited resources to maximize resource usage in unpredictably dynamic environments. In the control level, the system controller is designed to follow the schedule by considering all the system constraints for safe and efficient operation. Consequently, this dissertation is mainly divided into two parts: 1) planning level design, based on finite state machines, and 2) control level methods, based on model predictive control. We define a recomposable restricted finite state machine to handle limited resource situations and unpredictably dynamic environments for the planning level. To obtain a policy, dynamic programing is applied, and to obtain a solution, limited breadth-first search is applied to the recomposable restricted finite state machine. A multi-function phased array radar resource management problem and an unmanned aerial vehicle patrolling problem are treated using recomposable restricted finite state machines. Then, we use model predictive control for the control level, because it allows constraint handling and setpoint tracking for the schedule. An aircraft power system management problem is treated that aims to develop an integrated control system for an aircraft gas turbine engine and electrical power system using rate-based model predictive control. Our results indicate that at the planning level, limited breadth-first search for recomposable restricted finite state machines generates good scheduling solutions in limited resource situations and unpredictably dynamic environments. The importance of cooperation in the planning level is also verified. At the control level, a rate-based model predictive controller allows good schedule tracking and safe operations. The importance of considering the system constraints and interactions between the subsystems is indicated. For the best resource management in constrained dynamic situations, the planning level and the control level need to be considered together.

Dynamic modeling and control of a solid-sorbent CO{sub 2} capture process with two-stage bubbling fluidized bed adsorber reactor

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

Modekurti, S.; Bhattacharyya, D.; Zitney, S.

2012-01-01

Solid-sorbent-based CO{sub 2} capture processes have strong potential for reducing the overall energy penalty for post-combustion capture from the flue gas of a conventional pulverized coal power plant. However, the commercial success of this technology is contingent upon it operating over a wide range of capture rates, transient events, malfunctions, and disturbances, as well as under uncertainties. To study these operational aspects, a dynamic model of a solid-sorbent-based CO{sub 2} capture process has been developed. In this work, a one-dimensional (1D), non-isothermal, dynamic model of a two-stage bubbling fluidized bed (BFB) adsorber-reactor system with overflow-type weir configuration has been developedmore » in Aspen Custom Modeler (ACM). The physical and chemical properties of the sorbent used in this study are based on a sorbent (32D) developed at National Energy Technology Laboratory (NETL). Each BFB is divided into bubble, emulsion, and cloud-wake regions with the assumptions that the bubble region is free of solids while both gas and solid phases coexist in the emulsion and cloud-wake regions. The BFB dynamic model includes 1D partial differential equations (PDEs) for mass and energy balances, along with comprehensive reaction kinetics. In addition to the two BFB models, the adsorber-reactor system includes 1D PDE-based dynamic models of the downcomer and outlet hopper, as well as models of distributors, control valves, and other pressure-drop devices. Consistent boundary and initial conditions are considered for simulating the dynamic model. Equipment items are sized and appropriate heat transfer options, wherever needed, are provided. Finally, a valid pressure-flow network is developed and a lower-level control system is designed. Using ACM, the transient responses of various process variables such as flue gas and sorbent temperatures, overall CO{sub 2} capture, level of solids in the downcomer and hopper have been studied by simulating typical disturbances such as change in the temperature, flowrate, and composition of the flue gas. To maintain the overall CO{sub 2} capture at a desired level in face of the typical disturbances, two control strategies were considered–a proportional-integral-derivative (PID)-based feedback control strategy and a feedforward-augmented feedback control strategy. Dynamic simulation results show that both the strategies result in unacceptable overshoot/undershoot and a long settling time. To improve the control system performance, a linear model predictive controller (LMPC) is designed. In summary, the overall results illustrate how optimizing the operation and control of carbon capture systems can have a significant impact on the extent and the rate at which commercial-scale capture processes will be scaled-up, deployed, and used in the years to come.« less

Energy Cascade Analysis: from Subscale Eddies to Mean Flow

NASA Astrophysics Data System (ADS)

Cheikh, Mohamad Ibrahim; Wonnell, Louis; Chen, James

2017-11-01

Understanding the energy transfer between eddies and mean flow can provide insights into the energy cascade process. Much work has been done to investigate the energy cascade at the level of the smallest eddies using different numerical techniques derived from the Navier-Stokes equations. These methodologies, however, prove to be computationally inefficient when producing energy spectra for a wide range of length scales. In this regard, Morphing Continuum Theory (MCT) resolves the length-scales issues by assuming the fluid continuum to be composed of inner structures that play the role of subscale eddies. The current study show- cases the capabilities of MCT in capturing the dynamics of energy cascade at the level of subscale eddies, through a supersonic turbulent flow of Mach 2.93 over an 8× compression ramp. Analysis of the results using statistical averaging procedure shows the existence of a statistical coupling of the internal and translational kinetic energy fluctuations with the corresponding rotational kinetic energy of the subscale eddies, indicating a multiscale transfer of energy. The results show that MCT gives a new characterization of the energy cascade within compressible turbulence without the use of excessive computational resources. This material is based upon work supported by the Air Force Office of Scientific Research under Award Number FA9550-17-1-0154.

A systemic approach to explore the flexibility of energy stores at the cellular scale: Examples from muscle cells.

PubMed

Taghipoor, Masoomeh; van Milgen, Jaap; Gondret, Florence

2016-09-07

Variations in energy storage and expenditure are key elements for animals adaptation to rapidly changing environments. Because of the multiplicity of metabolic pathways, metabolic crossroads and interactions between anabolic and catabolic processes within and between different cells, the flexibility of energy stores in animal cells is difficult to describe by simple verbal, textual or graphic terms. We propose a mathematical model to study the influence of internal and external challenges on the dynamic behavior of energy stores and its consequence on cell energy status. The role of the flexibility of energy stores on the energy equilibrium at the cellular level is illustrated through three case studies: variation in eating frequency (i.e., glucose input), level of physical activity (i.e., ATP requirement), and changes in cell characteristics (i.e., maximum capacity of glycogen storage). Sensitivity analysis has been performed to highlight the most relevant parameters of the model; model simulations have then been performed to illustrate how variation in these key parameters affects cellular energy balance. According to this analysis, glycogen maximum accumulation capacity and homeostatic energy demand are among the most important parameters regulating muscle cell metabolism to ensure its energy equilibrium. Copyright © 2016 Elsevier Ltd. All rights reserved.

Numerical research of dynamic characteristics in tower solar cavity receiver based on step-change radiation flux

NASA Astrophysics Data System (ADS)

Chen, Zhengwei; Wang, Yueshe; Hao, Yun; Wang, Qizhi

2013-07-01

The solar cavity receiver is an important light-energy to thermal-energy convector in the tower solar thermal power plant system. The heat flux in the inner surface of the cavity will show the characteristics of non-continuous step change especially in non-normal and transient weather conditions, which may result in a continuous dynamic variation of the characteristic parameters. Therefore, the research of dynamic characteristics of the receiver plays a very important role in the operation and the control safely in solar cavity receiver system. In this paper, based on the non-continuous step change of radiation flux, a non-linear dynamic model is put forward to obtain the effects of the non-continuous step change radiation flux and step change feed water flow on the receiver performance by sequential modular approach. The subject investigated in our study is a 1MW solar power station constructed in Yanqing County, Beijing. This study has obtained the dynamic responses of the characteristic parameters in the cavity receiver, such as drum pressure, drum water level, main steam flow and main steam enthalpy under step change radiation flux. And the influence law of step-change feed water flow to the dynamic characteristics in the receiver also has been analyzed. The results have a reference value for the safe operation and the control in solar cavity receiver system.

The effects of graded levels of calorie restriction: I. impact of short term calorie and protein restriction on body composition in the C57BL/6 mouse.

PubMed

Mitchell, Sharon E; Tang, Zhanhui; Kerbois, Celine; Delville, Camille; Konstantopedos, Penelope; Bruel, Aurélie; Derous, Davina; Green, Cara; Aspden, Richard M; Goodyear, Simon R; Chen, Luonan; Han, Jackie J D; Wang, Yingchun; Promislow, Daniel E L; Lusseau, David; Douglas, Alex; Speakman, John R

2015-06-30

Faced with reduced levels of food, animals must adjust to the consequences of the shortfall in energy. We explored how C57BL/6 mice withdrew energy from different body tissues during three months of food restriction at graded levels up to 40% (calorie restriction: CR). We compared this to the response to equivalent levels of protein restriction (PR) without a shortfall in calories. Under CR there was a dynamic change in body mass over 30 days and thereafter it stabilized. The time to reach stability was independent of the level of restriction. At the end of three months whole body dissections revealed differential utilization of the different tissues. Adipose tissue depots were the most significantly utilized tissue, and provided 55.8 to 60.9% of the total released energy. In comparison, reductions in the sizes of structural tissues contributed between 29.8 and 38.7% of the energy. The balance was made up by relatively small changes in the vital organs. The components of the alimentary tract grew slightly under restriction, particularly the stomach, and this was associated with a parallel increase in assimilation efficiency of the food (averaging 1.73%). None of the changes under CR were recapitulated by equivalent levels of PR.

The effects of graded levels of calorie restriction: I. impact of short term calorie and protein restriction on body composition in the C57BL/6 mouse

PubMed Central

Mitchell, Sharon E.; Tang, Zhanhui; Kerbois, Celine; Delville, Camille; Konstantopedos, Penelope; Bruel, Aurélie; Derous, Davina; Green, Cara; Aspden, Richard M.; Goodyear, Simon R.; Chen, Luonan; Han, Jackie J.D.; Wang, Yingchun; Promislow, Daniel E.L.; Lusseau, David; Douglas, Alex; Speakman, John R.

2015-01-01

Faced with reduced levels of food, animals must adjust to the consequences of the shortfall in energy. We explored how C57BL/6 mice withdrew energy from different body tissues during three months of food restriction at graded levels up to 40% (calorie restriction: CR). We compared this to the response to equivalent levels of protein restriction (PR) without a shortfall in calories. Under CR there was a dynamic change in body mass over 30 days and thereafter it stabilized. The time to reach stability was independent of the level of restriction. At the end of three months whole body dissections revealed differential utilization of the different tissues. Adipose tissue depots were the most significantly utilized tissue, and provided 55.8 to 60.9% of the total released energy. In comparison, reductions in the sizes of structural tissues contributed between 29.8 and 38.7% of the energy. The balance was made up by relatively small changes in the vital organs. The components of the alimentary tract grew slightly under restriction, particularly the stomach, and this was associated with a parallel increase in assimilation efficiency of the food (averaging 1.73%). None of the changes under CR were recapitulated by equivalent levels of PR. PMID:26079539

Electronic Characterization of Defects in Narrow Gap Semiconductors-Comparison of Electronic Energy Levels and Formation Energies in Mercury Cadmium Telluride, Mercury Zinc Telluride, and Mercury Zinc Selenide

NASA Technical Reports Server (NTRS)

Patterson, James D.

1996-01-01

We have used a Green's function technique to calculate the energy levels and formation energy of deep defects in the narrow gap semiconductors mercury cadmium telluride (MCT), mercury zinc telluride (MZT) and mercury zinc selenide (MZS). The formation energy is calculated from the difference between the total energy with an impurity cluster and the total energy for the perfect crystal. Substitutional (including antisite), interstitial (self and foreign), and vacancy deep defects are considered. Relaxation effects are calculated (with molecular dynamics). By use of a pseudopotential, we generalize the ideal vacancy model so as to be able to consider relaxation for vacancies. Different charge states are considered and the charged state energy shift (as computed by a modified Haldane-Anderson model) can be twice that due to relaxation. Different charged states for vacancies were not calculated to have much effect on the formation energy. For all cases we find deep defects in the energy gap only for cation site s-like orbitals or anion site p-like orbitals, and for the substitutional case only the latter are appreciably effected by relaxation. For most cases for MCT, MZT, MZS, we consider x (the concentration of Cd or Zn) in the range appropriate for a band gap of 0.1 eV. For defect energy levels, the absolute accuracy of our results is limited, but the precision is good, and hence chemical trends are accurately predicted. For the same reason, defect formation energies are more accurately predicted than energy level position. We attempt, in Appendix B, to calculate vacancy formation energies using relatively simple chemical bonding ideas due to Harrison. However, these results are only marginally accurate for estimating vacancy binding energies. Appendix C lists all written reports and publications produced for the grant. We include abstracts and a complete paper that summarizes our work which is not yet available.

Effective surface Debye temperature for NiMnSb(100) epitaxial films

NASA Astrophysics Data System (ADS)

Borca, C. N.; Komesu, Takashi; Jeong, Hae-kyung; Dowben, P. A.; Ristoiu, D.; Hordequin, Ch.; Pierre, J.; Nozières, J. P.

2000-07-01

The surface Debye temperature of the NiMnSb (100) epitaxial films has been obtained using low energy electron diffraction, inverse photoemission, and core-level photoemission. The normal dynamic motion of the (100) surface results in a value for the effective surface Debye temperature of 145±13 K. This is far smaller than the bulk Debye temperature of 312±5 K obtained from wave vector dependent inelastic neutron scattering. The large difference between these measures of surface and bulk dynamic motion indicates a soft and compositionally different (100) surface.

Dynamics of harpooning studied by transition state spectroscopy. II. LiṡṡFH

NASA Astrophysics Data System (ADS)

Hudson, A. J.; Oh, H. B.; Polanyi, J. C.; Piecuch, P.

2000-12-01

The van der Waals complex LiṡṡFH was formed in crossed beams and the transition state of the excited-state reaction, Li*(2p 2P)+HF→LiF+H, was accessed by photoexcitation of this complex. The dynamics of the excited-state reaction were probed by varying the excitation wavelength over the range 570-970 nm while recording the photodepletion of the complex. The findings were interpreted using high-level ab initio calculations of the ground and lowest excited-state potential-energy surfaces.

Sensitivity Analysis of Flux Determination in Heart by H2 18O -provided Labeling Using a Dynamic Isotopologue Model of Energy Transfer Pathways

PubMed Central

Schryer, David W.; Peterson, Pearu; Illaste, Ardo; Vendelin, Marko

2012-01-01

To characterize intracellular energy transfer in the heart, two organ-level methods have frequently been employed: inversion and saturation transfer, and dynamic labeling. Creatine kinase (CK) fluxes obtained by following oxygen labeling have been considerably smaller than the fluxes determined by saturation transfer. It has been proposed that dynamic labeling determines net flux through CK shuttle, whereas saturation transfer measures total unidirectional flux. However, to our knowledge, no sensitivity analysis of flux determination by oxygen labeling has been performed, limiting our ability to compare flux distributions predicted by different methods. Here we analyze oxygen labeling in a physiological heart phosphotransfer network with active CK and adenylate kinase (AdK) shuttles and establish which fluxes determine the labeling state. A mathematical model consisting of a system of ordinary differential equations was composed describing enrichment in each phosphoryl group and inorganic phosphate. By varying flux distributions in the model and calculating the labeling, we analyzed labeling sensitivity to different fluxes in the heart. We observed that the labeling state is predominantly sensitive to total unidirectional CK and AdK fluxes and not to net fluxes. We conclude that measuring dynamic incorporation of into the high-energy phosphotransfer network in heart does not permit unambiguous determination of energetic fluxes with a higher magnitude than the ATP synthase rate when the bidirectionality of fluxes is taken into account. Our analysis suggests that the flux distributions obtained using dynamic labeling, after removing the net flux assumption, are comparable with those from inversion and saturation transfer. PMID:23236266

Ab Initio Vibrational Levels For HO2 and Vibrational Splittings for Hydrogen Atom Transfer

NASA Technical Reports Server (NTRS)

Barclay, V. J.; Dateo, Christopher E.; Hamilton, I. P.; Arnold, James O. (Technical Monitor)

1994-01-01

We calculate vibrational levels and wave functions for HO2 using the recently reported ab initio potential energy surface of Walch and Duchovic. There is intramolecular hydrogen atom transfer when the hydrogen atom tunnels through a T-shaped saddle point separating two equivalent equilibrium geometries, and correspondingly, the energy levels are split. We focus on vibrational levels and wave functions with significant splitting. The first three vibrational levels with splitting greater than 2/cm are (15 0), (0 7 1) and (0 8 0) where V(sub 2) is the O-O-H bend quantum number. We discuss the dynamics of hydrogen atom transfer; in particular, the O-O distances at which hydrogen atom transfer is most probable for these vibrational levels. The material of the proposed presentation was reviewed and the technical content will not reveal any information not already in the public domain and will not give any foreign industry or government a competitive advantage.

27ps DFTMD Simulations of Maltose using a Reduced Basis Set

USDA-ARS?s Scientific Manuscript database

The disaccharide, a-maltose, has been studied using constant energy density functional molecular dynamics (DFTMD) at the B3LYP/6-31+G*/4-31G+COSMO (solvent) level of theory. Maltose is of particular interest as the variation in glycosidic dihedral angles has been found to be dependent upon the star...

PHYSICAL EFFECTS OCCURRING DURING GENERATION AND AMPLIFICATION OF LASER RADIATION: Dynamics of population of the A3∑u+ nitrogen metastable state in a self-sustained volume discharge of a pulsed CO2 laser

NASA Astrophysics Data System (ADS)

Apollonov, V. V.; Baĭtsur, G. G.; Ermachenko, A. V.; Raspopov, N. A.; Sviridenkov, É. A.; Semenov, S. K.; Firsov, K. N.

1989-02-01

Intracavity laser spectroscopy was used to study the dynamics of population of the ν = 2-8 vibrational levels of the A3∑u+ state in order to establish the possible influence of multistage ionization on the evolution of instability in a self-sustained volume discharge in CO2 laser active mixtures. The populations of the nitrogen vibrational levels Nν were calculated taking into account the real output pulse profile of a dye laser. It was found that multistage ionization can only influence the duration of stable operation of a self-sustained volume discharge by increasing the rate of growth of the spark channel in the discharge gap. This is why the addition of readily ionized substances to the gas that reduce the electron energy and therefore lower Nν can substantially improve the stability of the volume discharge and increase the active volume and output energy of a CO2 laser.

Enhanced sampling techniques in molecular dynamics simulations of biological systems.

PubMed

Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

2015-05-01

Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

Scattering study of the Ne + NeH{sup +}(v{sub 0} = 0, j{sub 0} = 0) → NeH{sup +} + Ne reaction on an ab initio based analytical potential energy surface

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

Koner, Debasish; Panda, Aditya N., E-mail: adi07@iitg.ernet.in; Barrios, Lizandra

2016-01-21

Initial state selected dynamics of the Ne + NeH{sup +}(v{sub 0} = 0, j{sub 0} = 0) → NeH{sup +} + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]{sup +} structure lying 0.72 eV below the Ne + NeH{sup +} asymptote is found to be the most stablemore » geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.« less

Molecular dynamic simulation study of plasma etching L10 FePt media in embedded mask patterning (EMP) process

NASA Astrophysics Data System (ADS)

Zhu, Jianxin; Quarterman, P.; Wang, Jian-Ping

2017-05-01

Plasma etching process of single-crystal L10-FePt media [H. Wang et al., Appl. Phys. Lett. 102(5) (2013)] is studied using molecular dynamic simulation. Embedded-Atom Method [M. S. Daw and M. I. Baskes, Phy. Rev. B 29, 6443 (1984); X. W. Zhou, R. A. Johnson and H. N. G. Wadley, Phy. Rev. B 69, 144113 (2004)] is used to calculate the interatomic potential within atoms in FePt alloy, and ZBL potential [J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon,1985] in comparison with conventional Lennard-Jones "12-6" potential is applied to interactions between etching gas ions and metal atoms. It is shown the post-etch structure defects can include amorphized surface layer and lattice interstitial point defects that caused by etchant ions passed through the surface layer. We show that the amorphized or damaged FePt lattice surface layer (or "magnetic dead-layer") thickness after etching increases with ion energy for Ar ion impacts, but significantly small for He ions at up to 250eV ion energy. However, we showed that He sputtering creates more interstitial defects at lower energy levels and defects are deeper below the surface compared to Ar sputtering. We also calculate the interstitial defect level and depth as dependence on ion energy for both Ar and He ions. Media magnetic property loss due to these defects is also discussed.

Energy harvesting based on piezoelectric Ericsson cycles in a piezoceramic material

NASA Astrophysics Data System (ADS)

Zhang, B.; Ducharne, B.; Guyomar, D.; Sebald, G.

2013-09-01

The possibility of recycling ambient energies with electric generators instead of using batteries with limited life spans has stimulated important research efforts over the past years. The integration of such generators into mainly autonomous low-power systems, for various industrial or domestic applications is envisioned. In particular, the present work deals with energy harvesting from mechanical vibrations. It is shown here that direct piezoelectric energy harvesting (short circuiting on an adapted resistance, for example) leads to relatively weak energy levels that are insufficient for an industrial development. By coupling an electric field and mechanical excitation on Ericsson-based cycles, the amplitude of the harvested energy can be highly increased, and can reach a maximum close to 100 times its initial value. To obtain such a gain, one needs to employ high electrical field levels (high amplitude, high frequency), which induce a non-linearity through the piezoceramic. A special dynamic hysteresis model has been developed to correctly take into account the material properties, and to provide a real estimation of the harvested energy. A large number of theoretical predictions and experimental results have been compared and are discussed herein, in order to validate the proposed solution.

Holidays in lights: Tracking cultural patterns in demand for energy services

NASA Astrophysics Data System (ADS)

Román, Miguel O.; Stokes, Eleanor C.

2015-06-01

Successful climate change mitigation will involve not only technological innovation, but also innovation in how we understand the societal and individual behaviors that shape the demand for energy services. Traditionally, individual energy behaviors have been described as a function of utility optimization and behavioral economics, with price restructuring as the dominant policy lever. Previous research at the macro-level has identified economic activity, power generation and technology, and economic role as significant factors that shape energy use. However, most demand models lack basic contextual information on how dominant social phenomenon, the changing demographics of cities, and the sociocultural setting within which people operate, affect energy decisions and use patterns. Here we use high-quality Suomi-NPP VIIRS nighttime environmental products to: (1) observe aggregate human behavior through variations in energy service demand patterns during the Christmas and New Year's season and the Holy Month of Ramadan and (2) demonstrate that patterns in energy behaviors closely track sociocultural boundaries at the country, city, and district level. These findings indicate that energy decision making and demand is a sociocultural process as well as an economic process, often involving a combination of individual price-based incentives and societal-level factors. While nighttime satellite imagery has been used to map regional energy infrastructure distribution, tracking daily dynamic lighting demand at three major scales of urbanization is novel. This methodology can enrich research on the relative importance of drivers of energy demand and conservation behaviors at fine scales. Our initial results demonstrate the importance of seating energy demand frameworks in a social context.

Holiday in Lights: Tracking Cultural Patterns in Demand for Energy Services

NASA Technical Reports Server (NTRS)

Roman, Miguel O.; Stokes, Eleanor C.

2015-01-01

Successful climate change mitigation will involve not only technological innovation, but also innovation in how we understand the societal and individual behaviors that shape the demand for energy services. Traditionally, individual energy behaviors have been described as a function of utility optimization and behavioral economics, with price restructuring as the dominant policy lever. Previous research at the macro-level has identified economic activity, power generation and technology, and economic role as significant factors that shape energy use. However, most demand models lack basic contextual information on how dominant social phenomenon, the changing demographics of cities, and the sociocultural setting within which people operate, affect energy decisions and use patterns. Here we use high-quality Suomi-NPP VIIRS nighttime environmental products to: (1) observe aggregate human behavior through variations in energy service demand patterns during the Christmas and New Year's season and the Holy Month of Ramadan and (2) demonstrate that patterns in energy behaviors closely track sociocultural boundaries at the country, city, and district level. These findings indicate that energy decision making and demand is a sociocultural process as well as an economic process, often involving a combination of individual price-based incentives and societal-level factors. While nighttime satellite imagery has been used to map regional energy infrastructure distribution, tracking daily dynamic lighting demand at three major scales of urbanization is novel. This methodology can enrich research on the relative importance of drivers of energy demand and conservation behaviors at fine scales. Our initial results demonstrate the importance of seating energy demand frameworks in a social context.

Holidays in lights: Tracking cultural patterns in demand for energy services.

PubMed

Román, Miguel O; Stokes, Eleanor C

2015-06-01

Successful climate change mitigation will involve not only technological innovation, but also innovation in how we understand the societal and individual behaviors that shape the demand for energy services. Traditionally, individual energy behaviors have been described as a function of utility optimization and behavioral economics, with price restructuring as the dominant policy lever. Previous research at the macro-level has identified economic activity, power generation and technology, and economic role as significant factors that shape energy use. However, most demand models lack basic contextual information on how dominant social phenomenon, the changing demographics of cities, and the sociocultural setting within which people operate, affect energy decisions and use patterns. Here we use high-quality Suomi-NPP VIIRS nighttime environmental products to: (1) observe aggregate human behavior through variations in energy service demand patterns during the Christmas and New Year's season and the Holy Month of Ramadan and (2) demonstrate that patterns in energy behaviors closely track sociocultural boundaries at the country, city, and district level. These findings indicate that energy decision making and demand is a sociocultural process as well as an economic process, often involving a combination of individual price-based incentives and societal-level factors. While nighttime satellite imagery has been used to map regional energy infrastructure distribution, tracking daily dynamic lighting demand at three major scales of urbanization is novel. This methodology can enrich research on the relative importance of drivers of energy demand and conservation behaviors at fine scales. Our initial results demonstrate the importance of seating energy demand frameworks in a social context.

Atomistic potentials based energy flux integral criterion for dynamic adiabatic shear banding

NASA Astrophysics Data System (ADS)

Xu, Yun; Chen, Jun

2015-02-01

The energy flux integral criterion based on atomistic potentials within the framework of hyperelasticity-plasticity is proposed for dynamic adiabatic shear banding (ASB). System Helmholtz energy decomposition reveals that the dynamic influence on the integral path dependence is originated from the volumetric strain energy and partial deviatoric strain energy, and the plastic influence only from the rest part of deviatoric strain energy. The concept of critical shear banding energy is suggested for describing the initiation of ASB, which consists of the dynamic recrystallization (DRX) threshold energy and the thermal softening energy. The criterion directly relates energy flux to the basic physical processes that induce shear instability such as dislocation nucleations and multiplications, without introducing ad-hoc parameters in empirical constitutive models. It reduces to the classical path independent J-integral for quasi-static loading and elastic solids. The atomistic-to-continuum multiscale coupling method is used to simulate the initiation of ASB. Atomic configurations indicate that DRX induced microstructural softening may be essential to the dynamic shear localization and hence the initiation of ASB.

Nonlinear Modeling and Characterization of the Villari Effect and Model-guided Development of Magnetostrictive Energy Harvesters and Dampers

NASA Astrophysics Data System (ADS)

Deng, Zhangxian

The Villari effect, through which mechanical energy is transferred to magnetic energy in magnetostrictive materials can be utilized in energy harvester and damper designs. Significant research has been conducted on two magnetostrictive materials, Terfenol-D (TbxDy1-xFe2.0, x ≈ 0.3) and Galfenol (Fe1-xGax, 0.15 ≤ x ≤ 0.3), due to their high magnetomechanical coupling. Both materials have strengths and weaknesses. Terfenol-D exhibits low eddy current loss, but it is brittle and difficult to machine. Terfenol-D also provides higher magnetostriction while requiring a large magnetic field. On the other hand, Galfenol is mechanically robust, and thus can be machined, welded, and formed into complex geometries. However, due to its severe eddy current effect, lamination is necessary in high frequency applications. This work first characterized the Villari effect of Galfenol in terms of the piezo-magnetic constant d33* and hysteresis loss. The stress-flux density loops of oriented, polycrystalline Fe18.4Ga81.6 Galfenol were measured at quasi-static and dynamic regimes (up to 800 Hz). Advanced modeling tools are necessary for magnetostrictive device development. On the material level, this work proposed a dynamic, discrete energy-averaged (DEA) model incorporating time-dependent volume fractions into the static DEA framework. This dynamic DEA model took eddy current loss, mechanical loss, and pinning site loss into account and accurately simulated the measured Villari effect up to 600 Hz. On the system level, this work integrated a hysteresis static DEA model with a 3D finite element (FE) framework, and accurately modeled stress-flux density minor loops in a quasi-static state. Based on the assumption that the magnetostriction and magnetization are uniaxial, this work also proposed an efficient 2D FE framework describing nonlinear magnetostrictive responses via interpolation functions. This enhanced knowledge of the Villari effect facilitates magnetostrictive vibration energy harvester designs. A Galfenol unimorph, bonding passive stainless steel on a Galfenol beam, was investigated. The performance of the proposed unimorph harvesters, subjected to impulsive and periodic excitations, was evaluated for different types of electrical loads. The maximum average output power density P¯ and the maximum energy conversion efficiency were 24.4 mW/cm3 and 5.9%, respectively. The fully coupled 2D FE model, incorporating magnetic, mechanical, and electrical dynamics, was validated using impulsive responses. A simplified and more efficient FE approach, which decoupled the electrical dynamics from the magnetostrictive coupling and utilized a two-step procedure to eliminate transient responses, was also presented, as was a comprehensive parametric study targeting coil size, magnet location, magnet strength, thickness ratio, and tip mass. The maximum P&barbelow;P¯ was improved by 15.2% via optimization. Energy harvester's bandwidth is another essential parameter that often needs to be optimized. This work conducted preliminary experiments on a nonlinear buckled unimorph beam, and achieved a 300% bandwidth improvement. Besides its applications in energy harvesting, the Villari effect dissipates mechanical energy and thus can be implemented in dampers. This work conceptually proposed possible magnetostrictive dampers to attenuate noise in gearboxes. The loss factors eta of Terfenol-D and Galfenol damping units were first compared numerically in COMSOL Multiphysics. Based on the finite element results, the damping effect of Terfenol-D was then quantified experimentally. The maximum eta at 750 Hz was 0.2136 and 0.3679 for purely resistive and capacitive loads, respectively.

Urban sustainable energy development: A case study of the city of Philadelphia

NASA Astrophysics Data System (ADS)

Argyriou, Iraklis

This study explores the role of cities in sustainable energy development through a governance-informed analysis. Despite the leading position of municipalities in energy sustainability, cities have been mostly conceptualized as sites where energy development is shaped by external policy scales, i.e. the national level. A growing body of research, however, critiques this analytical perspective, and seeks to better understand the type of factors and dynamics that influence energy sustainability within a multi-level policy context for urban energy. Given that particular circumstances are applicable across cities, a context-specific analysis can provide insight regarding how sustainable energy development takes place in urban areas. In applying such an analytical perspective on urban energy sustainability, this study undertakes a qualitative case study analysis for the city of Philadelphia, Pennsylvania, by looking at four key local policy initiatives relevant to building energy efficiency and solar electricity development at the municipal government and city-wide level. The evaluation of the initiatives suggests that renewable electricity use has increased substantially in the city over the last years but the installed capacity of local renewable electricity systems, including solar photovoltaics, is low. On the other hand, although the city has made little progress in meeting its building energy efficiency targets, more comprehensive action is taken in this area. The study finds that the above outcomes have been shaped mainly by four factors. The first is the city government's incremental policy approach aiming to develop a facilitative context for local action. The second is the role that a diverse set of stakeholders have in local sustainable energy development. The third is the constraints that systemic policy barriers create for solar power development. The fourth is the ways through which the relevant multi-level policy environment structures the city's possibilities on sustainable energy. In this context, the study identifies four areas of policy recommendation that could enhance Philadelphia's prospects for energy sustainability: integrated municipal energy planning; stable financing for market development; enhanced actor interactions; and multi-level policymaking that facilitates local action. These policy directions could be of interest to a broader body of metropolitan cities regarding their efforts in sustainable energy development.

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules

NASA Astrophysics Data System (ADS)

Hamelberg, Donald; Mongan, John; McCammon, J. Andrew

2004-06-01

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.

An adaptive interpolation scheme for molecular potential energy surfaces

NASA Astrophysics Data System (ADS)

Kowalewski, Markus; Larsson, Elisabeth; Heryudono, Alfa

2016-08-01

The calculation of potential energy surfaces for quantum dynamics can be a time consuming task—especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm based on polyharmonic splines combined with a partition of unity approach. The adaptive node refinement allows to greatly reduce the number of sample points by employing a local error estimate. The algorithm and its scaling behavior are evaluated for a model function in 2, 3, and 4 dimensions. The developed algorithm allows for a more rapid and reliable interpolation of a potential energy surface within a given accuracy compared to the non-adaptive version.

Free energy landscapes of a highly structured β-hairpin peptide and its single mutant

NASA Astrophysics Data System (ADS)

Kim, Eunae; Yang, Changwon; Jang, Soonmin; Pak, Youngshang

2008-10-01

We investigated the free energy landscapes of a highly structured β-hairpin peptide (MBH12) and a less structured peptide with a single mutation of Tyr6 to Asp6 (MBH10). For the free energy mapping, starting from an extended conformation, the replica exchange molecular dynamic simulations for two β-hairpins were performed using a modified version of an all-atom force field employing an implicit solvation (param99MOD5/GBSA). With the present simulation approach, we demonstrated that detailed stability changes associated with the sequence modification from MBH12 to MBH10 are quantitatively well predicted at the all-atom level.

Hole localization, water dissociation mechanisms, and band alignment at aqueous-titania interfaces

NASA Astrophysics Data System (ADS)

Lyons, John L.

Photocatalytic water splitting is a promising method for generating clean energy, but materials that can efficiently act as photocatalysts are scarce. This is in part due to the fact that exposure to water can strongly alter semiconductor surfaces and therefore photocatalyst performance. Many materials are not stable in aqueous environments; in other cases, local changes in structure may occur, affecting energy-level alignment. Even in the simplest case, dynamic fluctuations modify the organization of interface water. Accounting for such effects requires knowledge of the dominant local structural motifs and also accurate semiconductor band-edge positions, making quantitative prediction of energy-level alignments computationally challenging. Here we employ a combined theoretical approach to study the structure, energy alignment, and hole localization at aqueous-titania interfaces. We calculate the explicit aqueous-semiconductor interface using ab initio molecular dynamics, which provides the fluctuating atomic structure, the extent of water dissociation, and the resulting electrostatic potential. For both anatase and rutile TiO2 we observe spontaneous water dissociation and re-association events that occur via distinct mechanisms. We also find a higher-density water layer occurring on anatase. In both cases, we find that the second monolayer of water plays a crucial role in controlling the extent of water dissociation. Using hybrid functional calculations, we then investigate the propensity for dissociated waters to stabilize photo-excited carriers, and compare the results of rutile and anatase aqueous interfaces. Finally, we use the GW approach from many-body perturbation theory to obtain the position of semiconductor band edges relative to the occupied 1b1 level and thus the redox levels of water, and examine how local structural modifications affect these offsets. This work was performed in collaboration with N. Kharche, M. Z. Ertem, J. T. Muckerman, and M. S. Hybertsen. It made use of resources at the Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility, at Brookhaven National Lab.

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

PubMed

Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf

2016-06-30

In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level

PubMed Central

Olsson, Martin A.; Söderhjelm, Pär

2016-01-01

In this article, the convergence of quantum mechanical (QM) free‐energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa‐acid deep‐cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158–224 atoms). We use single‐step exponential averaging (ssEA) and the non‐Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi‐empirical PM6‐DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free‐energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27117350

Long-term shifts in life-cycle energy efficiency and carbon intensity.

PubMed

Yeh, Sonia; Mishra, Gouri Shankar; Morrison, Geoff; Teter, Jacob; Quiceno, Raul; Gillingham, Kenneth; Riera-Palou, Xavier

2013-03-19

The quantity of primary energy needed to support global human activity is in large part determined by how efficiently that energy is converted to a useful form. We estimate the system-level life-cycle energy efficiency (EF) and carbon intensity (CI) across primary resources for 2005-2100. Our results underscore that although technological improvements at each energy conversion process will improve technology efficiency and lead to important reductions in primary energy use, market mediated effects and structural shifts toward less efficient pathways and pathways with multiple stages of conversion will dampen these efficiency gains. System-level life-cycle efficiency may decrease as mitigation efforts intensify, since low-efficiency renewable systems with high output have much lower GHG emissions than some high-efficiency fossil fuel systems. Climate policies accelerate both improvements in EF and the adoption of renewable technologies, resulting in considerably lower primary energy demand and GHG emissions. Life-cycle EF and CI of useful energy provide a useful metric for understanding dynamics of implementing climate policies. The approaches developed here reiterate the necessity of a combination of policies that target efficiency and decarbonized energy technologies. We also examine life-cycle exergy efficiency (ExF) and find that nearly all of the qualitative results hold regardless of whether we use ExF or EF.

Internal swells in the tropics: Near-inertial wave energy fluxes and dissipation during CINDY

NASA Astrophysics Data System (ADS)

Soares, S. M.; Natarov, A.; Richards, K. J.

2016-05-01

A developing MJO event in the tropical Indian Ocean triggered wind disturbances that generated inertial oscillations in the surface mixed layer. Subsequent radiation of near-inertial waves below the mixed layer produced strong turbulence in the pycnocline. Linear plane wave dynamics and spectral analysis are used to explain these observations, with the ultimate goal of estimating the wave energy flux in relation to both the energy input by the wind and the dissipation by turbulence. The results indicate that the wave packets carry approximately 30-40% of the wind input of inertial kinetic energy, and propagate in an environment conducive to the occurrence of a critical level set up by a combination of vertical gradients in background relative vorticity and Doppler shifting of wave frequency. Turbulent kinetic energy dissipation measurements demonstrate that the waves lose energy as they propagate in the transition layer as well as in the pycnocline, where approaching this critical level may have dissipated approximately 20% of the wave packet energy in a single event. Our analysis, therefore, supports the notion that appreciable amounts of wind-induced inertial kinetic energy escape the surface boundary layer into the interior. However, a large fraction of wave energy is dissipated within the pycnocline, limiting its penetration into the abyssal ocean.

Dissipation of ‘dark energy’ by cortex in knowledge retrieval

NASA Astrophysics Data System (ADS)

Capolupo, Antonio; Freeman, Walter J.; Vitiello, Giuseppe

2013-03-01

We have devised a thermodynamic model of cortical neurodynamics expressed at the classical level by neural networks and at the quantum level by dissipative quantum field theory. Our model is based on features in the spatial images of cortical activity newly revealed by high-density electrode arrays. We have incorporated the mechanism and necessity for so-called dark energy in knowledge retrieval. We have extended the model first using the Carnot cycle to define our measures for energy, entropy and temperature, and then using the Rankine cycle to incorporate criticality and phase transitions. We describe the dynamics of two interactive fields of neural activity that express knowledge, one at high and the other at low energy density, and the two operators that create and annihilate the fields. We postulate that the extremely high density of energy sequestered briefly in cortical activity patterns can account for the vividness, richness of associations, and emotional intensity of memories recalled by stimuli.

Fluorescence properties and energy transfer study of Er3+/Nd3+ doped fluorophosphate glass pumped at 800 and 980 nm for mid-infrared laser applications

NASA Astrophysics Data System (ADS)

Tian, Ying; Xu, Rongrong; Hu, Lili; Zhang, Junjie

2012-04-01

The fluorescence properties of 2.7 μm emission as well as near infrared emissions in Er3+/Nd3+ doped fluorophosphate glasses are investigated under 800 and 980 nm excitation. The fluorescence dynamics and energy transfer processes between Er and Nd ions in different pumping schemes are reported. Three Judd-Ofelt intensity parameters, energy transfer microparameters, and efficiency have been determined using the Judd-Ofelt and Förster-Dexter theories. The calculated energy transfer efficiency of the Er3+:4I13/2 level to the Nd3+:4I15/2 level is as high as 83.91%. The results indicate that Nd3+ may be an efficient sensitizer for Er3+ to obtain mid-infrared emission and the more suitable pumping scheme of 2.7 μm laser applications for Er3+/Nd3+ doped fluorophosphate glass is 980 nm excitation.

Spectra- and temperature-dependent dynamics of directly end-pumped holmium lasers

NASA Astrophysics Data System (ADS)

Ji, Encai; Shen, Yijie; Nie, Mingming; Fu, Xing; Liu, Qiang

2017-04-01

We develop a theoretical model with high accuracy for directly end-pumped Ho3+ laser system considering the influences of ground-state depletion, energy transfer up-conversion, temperature-dependent cross sections, and pump spectra shift. The heat generation in our model is precisely evaluated by calculating the transition rates of non-radiation relaxation processes among manifolds and in-band relaxation processes based on a detailed analysis of energy levels structure of holmium ions. A spatial dynamic thermal iteration method, just developed by our group, is applied to describe the coupled influences between spatial thermal effects and pump spectra. This model is verified to both adapt to the narrow-band good beam-quality pumped case and the broad-band bad beam-quality pumped case, which is in accordance with our previous reported experimental results.

Feasibility of Traveling Wave Direct Energy Conversion of Fission Reaction Fragments

NASA Technical Reports Server (NTRS)

Tarditi, A. G.; George, J. A.; Miley, G. H.; Scott, J. H.

2013-01-01

Fission fragment direct energy conversion has been considered in the past for the purpose of increasing nuclear power plant efficiency and for advanced space propulsion. Since the fragments carry electric charge (typically in the order of 20 e) and have 100 MeV-range kinetic energy, techniques utilizing very high-voltage DC electrodes have been considered. This study is focused on a different approach: the kinetic energy of the charged fission fragments is converted into alternating current by means of a traveling wave coupling scheme (Traveling Wave Direct Energy Converter, TWDEC), thereby not requiring the utilization of high voltage technology. A preliminary feasibility analysis of the concept is introduced based on a conceptual level study and on a particle simulation model of the beam dynamics.

Mixed quantum-classical electrodynamics: Understanding spontaneous decay and zero-point energy

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

Li, Tao E.; Nitzan, Abraham; Sukharev, Maxim

The dynamics of an electronic two-level system coupled to an electromagnetic field are simulated explicitly for one- and three-dimensional systems through semiclassical propagation of the Maxwell-Liouville equations. Here, we consider three flavors of mixed quantum-classical dynamics: (i) the classical path approximation (CPA), (ii) Ehrenfest dynamics, and (iii) symmetrical quasiclassical (SQC) dynamics. Our findings are as follows: (i) The CPA fails to recover a consistent description of spontaneous emission, (ii) a consistent “spontaneous” emission can be obtained from Ehrenfest dynamics, provided that one starts in an electronic superposition state, and (iii) spontaneous emission is always obtained using SQC dynamics. Using themore » SQC and Ehrenfest frameworks, we further calculate the dynamics following an incoming pulse, but here we find very different responses: SQC and Ehrenfest dynamics deviate sometimes strongly in the calculated rate of decay of the transient excited state. Nevertheless, our work confirms the earlier observations by Miller [J. Chem. Phys. 69, 2188 (1978)] that Ehrenfest dynamics can effectively describe some aspects of spontaneous emission and highlights interesting possibilities for studying light-matter interactions with semiclassical mechanics.« less

Mixed quantum-classical electrodynamics: Understanding spontaneous decay and zero-point energy

NASA Astrophysics Data System (ADS)

Li, Tao E.; Nitzan, Abraham; Sukharev, Maxim; Martinez, Todd; Chen, Hsing-Ta; Subotnik, Joseph E.

2018-03-01

The dynamics of an electronic two-level system coupled to an electromagnetic field are simulated explicitly for one- and three-dimensional systems through semiclassical propagation of the Maxwell-Liouville equations. We consider three flavors of mixed quantum-classical dynamics: (i) the classical path approximation (CPA), (ii) Ehrenfest dynamics, and (iii) symmetrical quasiclassical (SQC) dynamics. Our findings are as follows: (i) The CPA fails to recover a consistent description of spontaneous emission, (ii) a consistent "spontaneous" emission can be obtained from Ehrenfest dynamics, provided that one starts in an electronic superposition state, and (iii) spontaneous emission is always obtained using SQC dynamics. Using the SQC and Ehrenfest frameworks, we further calculate the dynamics following an incoming pulse, but here we find very different responses: SQC and Ehrenfest dynamics deviate sometimes strongly in the calculated rate of decay of the transient excited state. Nevertheless, our work confirms the earlier observations by Miller [J. Chem. Phys. 69, 2188 (1978), 10.1063/1.436793] that Ehrenfest dynamics can effectively describe some aspects of spontaneous emission and highlights interesting possibilities for studying light-matter interactions with semiclassical mechanics.

Mixed quantum-classical electrodynamics: Understanding spontaneous decay and zero-point energy

DOE PAGES

Li, Tao E.; Nitzan, Abraham; Sukharev, Maxim; ...

2018-03-12

The dynamics of an electronic two-level system coupled to an electromagnetic field are simulated explicitly for one- and three-dimensional systems through semiclassical propagation of the Maxwell-Liouville equations. Here, we consider three flavors of mixed quantum-classical dynamics: (i) the classical path approximation (CPA), (ii) Ehrenfest dynamics, and (iii) symmetrical quasiclassical (SQC) dynamics. Our findings are as follows: (i) The CPA fails to recover a consistent description of spontaneous emission, (ii) a consistent “spontaneous” emission can be obtained from Ehrenfest dynamics, provided that one starts in an electronic superposition state, and (iii) spontaneous emission is always obtained using SQC dynamics. Using themore » SQC and Ehrenfest frameworks, we further calculate the dynamics following an incoming pulse, but here we find very different responses: SQC and Ehrenfest dynamics deviate sometimes strongly in the calculated rate of decay of the transient excited state. Nevertheless, our work confirms the earlier observations by Miller [J. Chem. Phys. 69, 2188 (1978)] that Ehrenfest dynamics can effectively describe some aspects of spontaneous emission and highlights interesting possibilities for studying light-matter interactions with semiclassical mechanics.« less

Energy exchange dynamics across L–H transitions in NSTX

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

Diallo, A.; Banerjee, S.; Zweben, S. J.

Here, we studied the energy exchange dynamics across the low-to-high-confinement (L–H) transition in NSTX discharges using the gas-puff imaging (GPI) diagnostic. The investigation focused on the energy exchange between flows and turbulence to help clarify the mechanism of the L–H transition. We applied this study to three types of heating schemes, including a total of 17 shots from the NSTX 2010 campaign run. Results show that the edge fluctuation characteristics (fluctuation levels, radial and poloidal correlation lengths) measured using GPI do not vary just prior to the H-mode transition, but change after the transition. Using a velocimetry approach (orthogonal-dynamics programming), velocity fields of amore » $$24\\times 30$$ cm GPI view during the L–H transition were obtained with good spatial (~1 cm) and temporal (~2.5 μs) resolutions. Analysis using these velocity fields shows that the production term is systematically negative just prior to the L–H transition, indicating a transfer from mean flows to turbulence, which is inconsistent with the predator–prey paradigm. Moreover, the inferred absolute value of the production term is two orders of magnitude too small to explain the observed rapid L–H transition. These discrepancies are further reinforced by consideration of the ratio between the kinetic energy in the mean flow to the thermal free energy, which is estimated to be much less than 1, suggesting again that the turbulence depletion mechanism may not play an important role in the transition to the H-mode. Although the Reynolds work therefore appears to be too small to directly deplete the turbulent free energy reservoir, order-of-magnitude analysis shows that the Reynolds stress may still make a non-negligible contribution to the observed poloidal flows.« less

Energy exchange dynamics across L-H transitions in NSTX

NASA Astrophysics Data System (ADS)

Diallo, A.; Banerjee, S.; Zweben, S. J.; Stoltzfus-Dueck, T.

2017-06-01

We studied the energy exchange dynamics across the low-to-high-confinement (L-H) transition in NSTX discharges using the gas-puff imaging (GPI) diagnostic. The investigation focused on the energy exchange between flows and turbulence to help clarify the mechanism of the L-H transition. We applied this study to three types of heating schemes, including a total of 17 shots from the NSTX 2010 campaign run. Results show that the edge fluctuation characteristics (fluctuation levels, radial and poloidal correlation lengths) measured using GPI do not vary just prior to the H-mode transition, but change after the transition. Using a velocimetry approach (orthogonal-dynamics programming), velocity fields of a 24× 30 cm GPI view during the L-H transition were obtained with good spatial (˜1 cm) and temporal (˜2.5 μs) resolutions. Analysis using these velocity fields shows that the production term is systematically negative just prior to the L-H transition, indicating a transfer from mean flows to turbulence, which is inconsistent with the predator-prey paradigm. Moreover, the inferred absolute value of the production term is two orders of magnitude too small to explain the observed rapid L-H transition. These discrepancies are further reinforced by consideration of the ratio between the kinetic energy in the mean flow to the thermal free energy, which is estimated to be much less than 1, suggesting again that the turbulence depletion mechanism may not play an important role in the transition to the H-mode. Although the Reynolds work therefore appears to be too small to directly deplete the turbulent free energy reservoir, order-of-magnitude analysis shows that the Reynolds stress may still make a non-negligible contribution to the observed poloidal flows.

Energy exchange dynamics across L–H transitions in NSTX

DOE PAGES

Diallo, A.; Banerjee, S.; Zweben, S. J.; ...

2017-05-10

Here, we studied the energy exchange dynamics across the low-to-high-confinement (L–H) transition in NSTX discharges using the gas-puff imaging (GPI) diagnostic. The investigation focused on the energy exchange between flows and turbulence to help clarify the mechanism of the L–H transition. We applied this study to three types of heating schemes, including a total of 17 shots from the NSTX 2010 campaign run. Results show that the edge fluctuation characteristics (fluctuation levels, radial and poloidal correlation lengths) measured using GPI do not vary just prior to the H-mode transition, but change after the transition. Using a velocimetry approach (orthogonal-dynamics programming), velocity fields of amore » $$24\\times 30$$ cm GPI view during the L–H transition were obtained with good spatial (~1 cm) and temporal (~2.5 μs) resolutions. Analysis using these velocity fields shows that the production term is systematically negative just prior to the L–H transition, indicating a transfer from mean flows to turbulence, which is inconsistent with the predator–prey paradigm. Moreover, the inferred absolute value of the production term is two orders of magnitude too small to explain the observed rapid L–H transition. These discrepancies are further reinforced by consideration of the ratio between the kinetic energy in the mean flow to the thermal free energy, which is estimated to be much less than 1, suggesting again that the turbulence depletion mechanism may not play an important role in the transition to the H-mode. Although the Reynolds work therefore appears to be too small to directly deplete the turbulent free energy reservoir, order-of-magnitude analysis shows that the Reynolds stress may still make a non-negligible contribution to the observed poloidal flows.« less

Effect of structural mount dynamics on a pair of operating Stirling Convertors

NASA Astrophysics Data System (ADS)

Goodnight, Thomas W.; Suárez, Vicente J.; Hughes, William O.; Samorezov, Sergey

2002-01-01

The U.S. Department of Energy (DOE), in conjunction with NASA John H. Glenn Research Center and Stirling Technology Company, are currently developing a Stirling convertor for a Stirling Radioisotope Generator (SRG). NASA Headquarters and DOE have identified the SRG for potential use as an advanced spacecraft power system for future NASA deep-space and Mars surface missions. Low-level dynamic base-shake tests were conducted on a dynamic simulation of the structural mount for a pair of Operating Stirling Convertors. These tests were conducted at NASA Glenn Research Center's Structural Dynamics Laboratory as part of the development of this technology. The purpose of these tests was to identify the changes in transmissibility and the effect on structural dynamic response on a pair of operating Stirling Technology Demonstration Convertors (TDCs). This paper addresses the base-shake test, setup, procedure and results conducted on the Stirling TDC mount simulator in April 2001. .

Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials.

PubMed

Bistafa, Carlos; Kitamura, Yukichi; Martins-Costa, Marilia T C; Nagaoka, Masataka; Ruiz-López, Manuel F

2018-06-12

We describe a method to locate stationary points in the free-energy hypersurface of complex molecular systems using high-level correlated ab initio potentials. In this work, we assume a combined QM/MM description of the system although generalization to full ab initio potentials or other theoretical schemes is straightforward. The free-energy gradient (FEG) is obtained as the mean force acting on relevant nuclei using a dual level strategy. First, a statistical simulation is carried out using an appropriate, low-level quantum mechanical force-field. Free-energy perturbation (FEP) theory is then used to obtain the free-energy derivatives for the target, high-level quantum mechanical force-field. We show that this composite FEG-FEP approach is able to reproduce the results of a standard free-energy minimization procedure with high accuracy, while simultaneously allowing for a drastic reduction of both computational and wall-clock time. The method has been applied to study the structure of the water molecule in liquid water at the QCISD/aug-cc-pVTZ level of theory, using the sampling from QM/MM molecular dynamics simulations at the B3LYP/6-311+G(d,p) level. The obtained values for the geometrical parameters and for the dipole moment of the water molecule are within the experimental error, and they also display an excellent agreement when compared to other theoretical estimations. The developed methodology represents therefore an important step toward the accurate determination of the mechanism, kinetics, and thermodynamic properties of processes in solution, in enzymes, and in other disordered chemical systems using state-of-the-art ab initio potentials.

Effects of wind energy generation and white-nose syndrome on the viability of the Indiana bat

PubMed Central

Thogmartin, Wayne E.; Diffendorfer, Jay E.; Russell, Robin E.; Szymanski, Jennifer A.

2016-01-01

Wind energy generation holds the potential to adversely affect wildlife populations. Species-wide effects are difficult to study and few, if any, studies examine effects of wind energy generation on any species across its entire range. One species that may be affected by wind energy generation is the endangered Indiana bat (Myotis sodalis), which is found in the eastern and midwestern United States. In addition to mortality from wind energy generation, the species also faces range-wide threats from the emerging infectious fungal disease, white-nose syndrome (WNS). White-nose syndrome, caused by Pseudogymnoascus destructans, disturbs hibernating bats leading to high levels of mortality. We used a spatially explicit full-annual-cycle model to investigate how wind turbine mortality and WNS may singly and then together affect population dynamics of this species. In the simulation, wind turbine mortality impacted the metapopulation dynamics of the species by causing extirpation of some of the smaller winter colonies. In general, effects of wind turbines were localized and focused on specific spatial subpopulations. Conversely, WNS had a depressive effect on the species across its range. Wind turbine mortality interacted with WNS and together these stressors had a larger impact than would be expected from either alone, principally because these stressors together act to reduce species abundance across the spectrum of population sizes. Our findings illustrate the importance of not only prioritizing the protection of large winter colonies as is currently done, but also of protecting metapopulation dynamics and migratory connectivity. PMID:28028486

Estimation of dynamic energy budget parameters for the Mediterranean toothcarp (Aphanius fasciatus)

NASA Astrophysics Data System (ADS)

Rinaldi, A.; Montalto, V.; Lika, K.; Sanfilippo, M.; Manganaro, A.; Sarà, G.

2014-11-01

Organisms adopt different sets of physiological, behavioural and morphological trade-offs in order to cope with natural environmental fluctuations. This has consequential rebounds on ecological processes and population dynamics. Such aspects become crucial for sex-dimorphic species, where sex-specific growth variation could mirror different tactics both in energy acquisition and investment between maximum female and male body size with cascading effects on population demography. To date, different approaches have been used in order to understand the causes of individual growth rate changes in ectotherm indeterminate growers, most of which failed. Here, we propose the use of a mechanistic model based on the Dynamic Energy Budget theory (DEB; Koojiman, 2010) to investigate potential differences in energy allocation strategies adopted by individuals of different genders with the Mediterranean toothcarp Aphanius fasciatus (Valenciennes, 1821) as the model species. We collected literature and field data in order to study differences in energy allocation strategies between females and males of the same species by generating projections of possible growth performances: (1) throughout their entire life span and (2) under a context of varying functional responses. Generally, the present exercise of simulations returned different patterns of growth performance among females and males of A. fasciatus, with the former being able to better optimize energetic trade-offs under optimal environmental conditions. The present DEB parameterization exercise represents an essential step towards developing a mechanistic approach to depict metabolic strategies, which are at the base of observed sexual differences, and how such differences may impair ultimate fitness at individual and, therefore, population levels.

Modeling energy consumption in membrane bioreactors for wastewater treatment in north Africa.

PubMed

Skouterisl, George; Arnot, Tom C; Jraou, Mouna; Feki, Firas; Sayadi, Sami

2014-03-01

Two pilot-scale membrane bioreactors were operated alongside a full-sized activated sludge plant in Tunisia in order to compare specific energy demand and treated water quality. Energy consumption rates were measured for the complete membrane bioreactor systems and for their different components. Specific energy demand was measured for the systems and compared with the activated sludge plant, which operated at around 3 kWh m(-3). A model was developed for each membrane bioreactor based on both dynamic and steady-state mass balances, microbial kinetics and stoichiometry, and energy balance. Energy consumption was evaluated as a function of mixed-liquor suspended solids concentration, net permeate fluxes, and the resultant treated water quality. This work demonstrates the potential for using membrane bioreactors in decentralised domestic water treatment in North Africa, at energy consumption levels similar or lower than conventional activated sludge systems, with the added benefit of producing treated water suitable for unrestricted crop irrigation.

Coordinating Resource Usage through Adaptive Service Provisioning in Wireless Sensor Networks

NASA Astrophysics Data System (ADS)

Fok, Chien-Liang; Roman, Gruia-Catalin; Lu, Chenyang

Wireless sensor networks (WSNs) exhibit high levels of network dynamics and consist of devices with limited energy. This results in the need to coordinate applications not only at the functional level, as is traditionally done, but also in terms of resource utilization. In this paper, we present a middleware that does this using adaptive service provisioning. Novel service binding strategies automatically adapt application behavior when opportunities for energy savings surface, and switch providers when the network topology changes. The former is accomplished by providing limited information about the energy consumption associated with using various services, systematically exploiting opportunities for sharing service invocations, and exploiting the broadcast nature of wireless communication in WSNs. The middleware has been implemented and evaluated on two disparate WSN platforms, the TelosB and Imote2. Empirical results show that adaptive service provisioning can enable energy-aware service binding decisions that result in increased energy efficiency and significantly increase service availability, while imposing minimal additional burden on the application, service, and device developers. Two applications, medical patient monitoring and structural health monitoring, demonstrate the middleware's efficacy.

Energy management of an experimental microgrid coupled to a V2G system

NASA Astrophysics Data System (ADS)

Mendes, Paulo R. C.; Isorna, Luis Valverde; Bordons, Carlos; Normey-Rico, Julio E.

2016-09-01

This paper presents an algorithm for economic optimization of a laboratory microgrid. The microgrid incorporates a hybrid storage system composed of a battery bank and a hydrogen storage and it has a connection with the external electrical network and a charging station for electric vehicles. To study the impact of use of renewable energy power systems, the microgrid has a programmable power supply that can emulate the dynamic behavior of a wind turbine and/or a photovoltaic field. The system modeling was carried out using the Energy Hubs methodology. A hierarchical control structure is proposed based on Model Predictive Control and acting in different time scales, where the first level is responsible for maintaining the microgrid stability and the second level has the task of performing the management of electricity purchase and sale to the power grid, maximize the use of renewable energy sources, manage the use of energy storages and perform the charge of the parked vehicles. Practical experiments were performed with different weather conditions of solar irradiation and wind. The results show a reliable operation of the proposed control system.

General trends of dihedral conformational transitions in a globular protein.

PubMed

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C; McCammon, J Andrew

2016-04-01

Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ∼ 3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins. © 2016 Wiley Periodicals, Inc.

General trends of dihedral conformational transitions in a globular protein

DOE PAGES

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; ...

2016-02-15

In this paper, dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ~3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed bymore » the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. In conclusion, these general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.« less

Identification of structural motifs as tunneling two-level systems in amorphous alumina at low temperatures

NASA Astrophysics Data System (ADS)

Paz, Alejandro Pérez; Lebedeva, Irina V.; Tokatly, Ilya V.; Rubio, Angel

2014-12-01

One of the most accepted models that describe the anomalous thermal behavior of amorphous materials at temperatures below 1 K relies on the quantum mechanical tunneling of atoms between two nearly equivalent potential energy wells forming a two-level system (TLS). Indirect evidence for TLSs is widely available. However, the atomistic structure of these TLSs remains an unsolved topic in the physics of amorphous materials. Here, using classical molecular dynamics, we found several hitherto unknown bistable structural motifs that may be key to understanding the anomalous thermal properties of amorphous alumina at low temperatures. We show through free energy profiles that the complex potential energy surface can be reduced to canonical TLSs. The tunnel splitting predicted from instanton theory, the number density, dipole moment, and coupling to external strain of the discovered motifs are consistent with experiments.

MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU system

PubMed Central

Ruymgaart, A. Peter; Cardenas, Alfredo E.; Elber, Ron

2011-01-01

We report an optimized version of the molecular dynamics program MOIL that runs on a shared memory system with OpenMP and exploits the power of a Graphics Processing Unit (GPU). The model is of heterogeneous computing system on a single node with several cores sharing the same memory and a GPU. This is a typical laboratory tool, which provides excellent performance at minimal cost. Besides performance, emphasis is made on accuracy and stability of the algorithm probed by energy conservation for explicit-solvent atomically-detailed-models. Especially for long simulations energy conservation is critical due to the phenomenon known as “energy drift” in which energy errors accumulate linearly as a function of simulation time. To achieve long time dynamics with acceptable accuracy the drift must be particularly small. We identify several means of controlling long-time numerical accuracy while maintaining excellent speedup. To maintain a high level of energy conservation SHAKE and the Ewald reciprocal summation are run in double precision. Double precision summation of real-space non-bonded interactions improves energy conservation. In our best option, the energy drift using 1fs for a time step while constraining the distances of all bonds, is undetectable in 10ns simulation of solvated DHFR (Dihydrofolate reductase). Faster options, shaking only bonds with hydrogen atoms, are also very well behaved and have drifts of less than 1kcal/mol per nanosecond of the same system. CPU/GPU implementations require changes in programming models. We consider the use of a list of neighbors and quadratic versus linear interpolation in lookup tables of different sizes. Quadratic interpolation with a smaller number of grid points is faster than linear lookup tables (with finer representation) without loss of accuracy. Atomic neighbor lists were found most efficient. Typical speedups are about a factor of 10 compared to a single-core single-precision code. PMID:22328867

Enhancement of the dynamic Casimir effect within a metal photonic crystal

NASA Astrophysics Data System (ADS)

Ueta, Tsuyoshi

2013-05-01

If the counterposed metal plates are vibrated, when the gap between the plates becomes narrow, the energy of stationary states between the plates increases, and when it spreads, the energy decreases. Light with the energy for this energy difference arises. This is called dynamical Casimir effect. The author has so far investigated the interaction between lattice vibration and light in a one-dimensional metal photonic crystal whose stacked components are artificially vibrated by using actuators. A simple model was numerically analyzed, and the following novel phenomena were found out. The lattice vibration generates the light of frequency which added the integral multiple of the vibration frequency to that of the incident wave and also amplifies the incident wave resonantly. On a resonance, the amplification factor increases very rapidly with the number of layers. Resonance frequencies change with the phases of lattice vibration. The amplification phenomenon was analytically discussed for low frequency of the lattice vibration and is confirmed by numerical works. The lattice-vibrating metal photonic crystal is a system of dynamical Casimir effect connected in series, and so we can expect that a dynamical Casimir effect is enhanced by the photonic band effect. In the present study, when an electromagnetic field between metal plates is in the ground state in a one-dimensional metal photonic crystal, the radiation of electromagnetic wave in excited states has been investigated by artificially introducing lattice vibration to the photonic crystal. In this case as well as a dynamical Casimir effect, it has been shown that the harmonics of a ground state are generated just by vibrating a photonic crystal even without an incident wave. The dependencies of the radiating power on the number of layers and on the wavenumber of the lattice vibration are remarkable. It has found that the radiation amplitude on lower excited states is not necessarily large and radiation on specific excited levels is large.

Calculations of kaonic nuclei based on chiral meson-baryon amplitudes

NASA Astrophysics Data System (ADS)

Gazda, Daniel; Mareš, Jiří

2013-09-01

In-medium KbarN scattering amplitudes developed within a chirally motivated coupled-channel model are used to construct K- nuclear potentials for calculations of K- nuclear quasi-bound states. Self-consistent evaluations yield K- potential depths -Re VK(ρ0) of order 100 MeV. Dynamical polarization effects and two-nucleon KbarNN→YN absorption modes are discussed. The widths ΓK of allK- nuclear quasi-bound states are comparable or even larger than the corresponding binding energies BK, exceeding considerably the energy level spacing.

Surveys of research in the Chemistry Division, Argonne National Laboratory

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

Grazis, B.M.

1992-01-01

Research reports are presented on reactive intermediates in condensed phase (radiation chemistry, photochemistry), electron transfer and energy conversion, photosynthesis and solar energy conversion, metal cluster chemistry, chemical dynamics in gas phase, photoionization-photoelectrons, characterization and reactivity of coal and coal macerals, premium coal sample program, chemical separations, heavy elements coordination chemistry, heavy elements photophysics/photochemistry, f-electron interactions, radiation chemistry of high-level wastes (gas generation in waste tanks), ultrafast molecular electronic devices, and nuclear medicine. Separate abstracts have been prepared. Accelerator activites and computer system/network services are also reported.

Surveys of research in the Chemistry Division, Argonne National Laboratory

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

Grazis, B.M.

1992-11-01

Research reports are presented on reactive intermediates in condensed phase (radiation chemistry, photochemistry), electron transfer and energy conversion, photosynthesis and solar energy conversion, metal cluster chemistry, chemical dynamics in gas phase, photoionization-photoelectrons, characterization and reactivity of coal and coal macerals, premium coal sample program, chemical separations, heavy elements coordination chemistry, heavy elements photophysics/photochemistry, f-electron interactions, radiation chemistry of high-level wastes (gas generation in waste tanks), ultrafast molecular electronic devices, and nuclear medicine. Separate abstracts have been prepared. Accelerator activites and computer system/network services are also reported.

From individuals to populations to communities: a dynamic energy budget model of marine ecosystem size-spectrum including life history diversity.

PubMed

Maury, Olivier; Poggiale, Jean-Christophe

2013-05-07

Individual metabolism, predator-prey relationships, and the role of biodiversity are major factors underlying the dynamics of food webs and their response to environmental variability. Despite their crucial, complementary and interacting influences, they are usually not considered simultaneously in current marine ecosystem models. In an attempt to fill this gap and determine if these factors and their interaction are sufficient to allow realistic community structure and dynamics to emerge, we formulate a mathematical model of the size-structured dynamics of marine communities which integrates mechanistically individual, population and community levels. The model represents the transfer of energy generated in both time and size by an infinite number of interacting fish species spanning from very small to very large species. It is based on standard individual level assumptions of the Dynamic Energy Budget theory (DEB) as well as important ecological processes such as opportunistic size-based predation and competition for food. Resting on the inter-specific body-size scaling relationships of the DEB theory, the diversity of life-history traits (i.e. biodiversity) is explicitly integrated. The stationary solutions of the model as well as the transient solutions arising when environmental signals (e.g. variability of primary production and temperature) propagate through the ecosystem are studied using numerical simulations. It is shown that in the absence of density-dependent feedback processes, the model exhibits unstable oscillations. Density-dependent schooling probability and schooling-dependent predatory and disease mortalities are proposed to be important stabilizing factors allowing stationary solutions to be reached. At the community level, the shape and slope of the obtained quasi-linear stationary spectrum matches well with empirical studies. When oscillations of primary production are simulated, the model predicts that the variability propagates along the spectrum in a given frequency-dependent size range before decreasing for larger sizes. At the species level, the simulations show that small and large species dominate the community successively (small species being more abundant at small sizes and large species being more abundant at large sizes) and that the total biomass of a species decreases with its maximal size which again corroborates empirical studies. Our results indicate that the simultaneous consideration of individual growth and reproduction, size-structured trophic interactions, the diversity of life-history traits and a density-dependent stabilizing process allow realistic community structure and dynamics to emerge without any arbitrary prescription. As a logical consequence of our model construction and a basis for future studies, we define the function Φ as the relative contribution of each species to the total biomass of the ecosystem, for any given size. We argue that this function is a measure of the functional role of biodiversity characterizing the impact of the structure of the community (its species composition) on its function (the relative proportions of losses, dissipation and biological work). Copyright © 2013 Elsevier Ltd. All rights reserved.

Regulation of mitochondrial bioenergetics by the non-canonical roles of mitochondrial dynamics proteins in the heart.

PubMed

Wang, Wang; Fernandez-Sanz, Celia; Sheu, Shey-Shing

2018-05-01

Recent advancement in mitochondrial research has significantly extended our knowledge on the role and regulation of mitochondria in health and disease. One important breakthrough is the delineation of how mitochondrial morphological changes, termed mitochondrial dynamics, are coupled to the bioenergetics and signaling functions of mitochondria. In general, it is believed that fusion leads to an increased mitochondrial respiration efficiency and resistance to stress-induced dysfunction while fission does the contrary. This concept seems not applicable to adult cardiomyocytes. The mitochondria in adult cardiomyocytes exhibit fragmented morphology (tilted towards fission) and show less networking and movement as compared to other cell types. However, being the most energy-demanding cells, cardiomyocytes in the adult heart possess vast number of mitochondria, high level of energy flow, and abundant mitochondrial dynamics proteins. This apparent discrepancy could be explained by recently identified new functions of the mitochondrial dynamics proteins. These "non-canonical" roles of mitochondrial dynamics proteins range from controlling inter-organelle communication to regulating cell viability and survival under metabolic stresses. Here, we summarize the newly identified non-canonical roles of mitochondrial dynamics proteins. We focus on how these fission and fusion independent roles of dynamics proteins regulate mitochondrial bioenergetics. We also discuss potential molecular mechanisms, unique intracellular location, and the cardiovascular disease relevance of these non-canonical roles of the dynamics proteins. We propose that future studies are warranted to differentiate the canonical and non-canonical roles of dynamics proteins and to identify new approaches for the treatment of heart diseases. This article is part of a Special issue entitled Cardiac adaptations to obesity, diabetes and insulin resistance, edited by Professors Jan F.C. Glatz, Jason R.B. Dyck and Christine Des Rosiers. Copyright © 2017 Elsevier B.V. All rights reserved.

Tunneling Splittings in Vibronic Structure of CH_3F^+ ( X^2E): Studied by High Resolution Photoelectron Spectra and AB Initio Theoretical Method

NASA Astrophysics Data System (ADS)

Mo, Yuxiang; Gao, Shuming; Dai, Zuyang; Li, Hua

2013-06-01

We report a combined experimental and theoretical study on the vibronic structure of CH_3F^+. The results show that the tunneling splittings of vibrational energy levels occur in CH_3F^+ due to the Jahn-Teller effect. Experimentally, we have measured a high resolution ZEKE spectrum of CH_3F up to 3500 cm^-^1 above the ground state. Theoretically, we performed an ab initio calculation based on the diabatic model. The adiabatic potential energy surfaces (APES) of CH_3F^+ have been calculated at the MRCI/CAS/avq(t)z level and expressed by Taylor expansions with normal coordinates as variables. The energy gradients for the lower and upper APES, the derivative couplings between them and also the energies of the APES have been used to determine the coefficients in the Taylor expansion. The spin-vibronic energy levels have been calculated by accounting all six vibrational modes and their couplings. The experimental ZEKE spectra were assigned based on the theoretical calculations. W. Domcke, D. R. Yarkony, and H. Köpple (Eds.), Conical Intersections: Eletronic Structure, Dynamics and Spectroscopy (World Scientific, Singapore, 2004). M. S. Schuurman, D. E. Weinberg, and D. R. Yarkony, J. Chem. Phys. 127, 104309 (2007).

Characteristics of level-spacing statistics in chaotic graphene billiards.

PubMed

Huang, Liang; Lai, Ying-Cheng; Grebogi, Celso

2011-03-01

A fundamental result in nonrelativistic quantum nonlinear dynamics is that the spectral statistics of quantum systems that possess no geometric symmetry, but whose classical dynamics are chaotic, are described by those of the Gaussian orthogonal ensemble (GOE) or the Gaussian unitary ensemble (GUE), in the presence or absence of time-reversal symmetry, respectively. For massless spin-half particles such as neutrinos in relativistic quantum mechanics in a chaotic billiard, the seminal work of Berry and Mondragon established the GUE nature of the level-spacing statistics, due to the combination of the chirality of Dirac particles and the confinement, which breaks the time-reversal symmetry. A question is whether the GOE or the GUE statistics can be observed in experimentally accessible, relativistic quantum systems. We demonstrate, using graphene confinements in which the quasiparticle motions are governed by the Dirac equation in the low-energy regime, that the level-spacing statistics are persistently those of GOE random matrices. We present extensive numerical evidence obtained from the tight-binding approach and a physical explanation for the GOE statistics. We also find that the presence of a weak magnetic field switches the statistics to those of GUE. For a strong magnetic field, Landau levels become influential, causing the level-spacing distribution to deviate markedly from the random-matrix predictions. Issues addressed also include the effects of a number of realistic factors on level-spacing statistics such as next nearest-neighbor interactions, different lattice orientations, enhanced hopping energy for atoms on the boundary, and staggered potential due to graphene-substrate interactions.

Dynamic Modeling of Learning in Emerging Energy Industries: The Example of Advanced Biofuels in the United States; NREL (National Renewable Energy Laboratory)

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

Peterson, Steve; Bush, Brian; Vimmerstedt, Laura

This paper (and its supplemental model) presents novel approaches to modeling interactions and related policies among investment, production, and learning in an emerging competitive industry. New biomass-to-biofuels pathways are being developed and commercialized to support goals for U.S. advanced biofuel use, such as those in the Energy Independence and Security Act of 2007. We explore the impact of learning rates and techno-economics in a learning model excerpted from the Biomass Scenario Model (BSM), developed by the U.S. Department of Energy and the National Renewable Energy Laboratory to explore the impact of biofuel policy on the evolution of the biofuels industry.more » The BSM integrates investment, production, and learning among competing biofuel conversion options that are at different stages of industrial development. We explain the novel methods used to simulate the impact of differing assumptions about mature industry techno-economics and about learning rates while accounting for the different maturity levels of various conversion pathways. A sensitivity study shows that the parameters studied (fixed capital investment, process yield, progress ratios, and pre-commercial investment) exhibit highly interactive effects, and the system, as modeled, tends toward market dominance of a single pathway due to competition and learning dynamics.« less

Visualizing Energy on Target: Molecular Dynamics Simulations

DTIC Science & Technology

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

Probing dark energy dynamics from current and future cosmological observations

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

Zhao Gongbo; Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6; Zhang Xinmin

2010-02-15

We report the constraints on the dark energy equation-of-state w(z) using the latest 'Constitution' SNe sample combined with the WMAP5 and Sloan Digital Sky Survey data. Assuming a flat Universe, and utilizing the localized principal component analysis and the model selection criteria, we find that the {Lambda}CDM model is generally consistent with the current data, yet there exists a weak hint of the possible dynamics of dark energy. In particular, a model predicting w(z)<-1 at z is an element of [0.25,0.5) and w(z)>-1 at z is an element of [0.5,0.75), which means that w(z) crosses -1 in the range ofmore » z is an element of [0.25,0.75), is mildly favored at 95% confidence level. Given the best fit model for current data as a fiducial model, we make future forecast from the joint data sets of Joint Dark Energy Mission, Planck, and Large Synoptic Survey Telescope, and we find that the future surveys can reduce the error bars on the w bins by roughly a factor of 10 for a 5-w-bin model.« less

Properties of inhibitors of methane hydrate formation via molecular dynamics simulations.

PubMed

Anderson, Brian J; Tester, Jefferson W; Borghi, Gian Paolo; Trout, Bernhardt L

2005-12-21

Within the framework of a proposed two-step mechanism for hydrate inhibition, the energy of binding of four inhibitor molecules (PEO, PVP, PVCap, and VIMA) to a hydrate surface is estimated with molecular dynamic simulations. One key feature of this proposed mechanism is that the binding of an inhibitor molecule to the surface of an ensuing hydrate crystal disrupts growth and therein crystallization. It is found through the molecular dynamic simulations that inhibitor molecules that experimentally exhibit better inhibition strength also have higher free energies of binding, an indirect confirmation of our proposed mechanism. Inhibitors increasing in effectiveness, PEO < PVP < PVCap < VIMA, have increasingly negative (exothermic) binding energies of -0.2 < -20.6 < -37.5 < -45.8 kcal/mol and binding free energies of increasing favorability (+0.4 approximately = +0.5 < -9.4 < -15.1 kcal/mol). Furthermore, the effect of an inhibitor molecule on the local liquid water structure under hydrate-forming conditions was examined and correlated to the experimental effectiveness of the inhibitors. Two molecular characteristics that lead to strongly binding inhibitors were found: (1) a charge distribution on the edge of the inhibitor that mimics the charge separation in the water molecules on the surface of the hydrate and (2) the congruence of the size of the inhibitor with respect to the available space at the hydrate-surface binding site. Equipped with this molecular-level understanding of the process of hydrate inhibition via low-dosage kinetic hydrate inhibitors we can design new, more effective inhibitor molecules.

Predicting the Dynamics of Protein Abundance

PubMed Central

Mehdi, Ahmed M.; Patrick, Ralph; Bailey, Timothy L.; Bodén, Mikael

2014-01-01

Protein synthesis is finely regulated across all organisms, from bacteria to humans, and its integrity underpins many important processes. Emerging evidence suggests that the dynamic range of protein abundance is greater than that observed at the transcript level. Technological breakthroughs now mean that sequencing-based measurement of mRNA levels is routine, but protocols for measuring protein abundance remain both complex and expensive. This paper introduces a Bayesian network that integrates transcriptomic and proteomic data to predict protein abundance and to model the effects of its determinants. We aim to use this model to follow a molecular response over time, from condition-specific data, in order to understand adaptation during processes such as the cell cycle. With microarray data now available for many conditions, the general utility of a protein abundance predictor is broad. Whereas most quantitative proteomics studies have focused on higher organisms, we developed a predictive model of protein abundance for both Saccharomyces cerevisiae and Schizosaccharomyces pombe to explore the latitude at the protein level. Our predictor primarily relies on mRNA level, mRNA–protein interaction, mRNA folding energy and half-life, and tRNA adaptation. The combination of key features, allowing for the low certainty and uneven coverage of experimental observations, gives comparatively minor but robust prediction accuracy. The model substantially improved the analysis of protein regulation during the cell cycle: predicted protein abundance identified twice as many cell-cycle-associated proteins as experimental mRNA levels. Predicted protein abundance was more dynamic than observed mRNA expression, agreeing with experimental protein abundance from a human cell line. We illustrate how the same model can be used to predict the folding energy of mRNA when protein abundance is available, lending credence to the emerging view that mRNA folding affects translation efficiency. The software and data used in this research are available at http://bioinf.scmb.uq.edu.au/proteinabundance/. PMID:24532840

Predicting the dynamics of protein abundance.

PubMed

Mehdi, Ahmed M; Patrick, Ralph; Bailey, Timothy L; Bodén, Mikael

2014-05-01

Protein synthesis is finely regulated across all organisms, from bacteria to humans, and its integrity underpins many important processes. Emerging evidence suggests that the dynamic range of protein abundance is greater than that observed at the transcript level. Technological breakthroughs now mean that sequencing-based measurement of mRNA levels is routine, but protocols for measuring protein abundance remain both complex and expensive. This paper introduces a Bayesian network that integrates transcriptomic and proteomic data to predict protein abundance and to model the effects of its determinants. We aim to use this model to follow a molecular response over time, from condition-specific data, in order to understand adaptation during processes such as the cell cycle. With microarray data now available for many conditions, the general utility of a protein abundance predictor is broad. Whereas most quantitative proteomics studies have focused on higher organisms, we developed a predictive model of protein abundance for both Saccharomyces cerevisiae and Schizosaccharomyces pombe to explore the latitude at the protein level. Our predictor primarily relies on mRNA level, mRNA-protein interaction, mRNA folding energy and half-life, and tRNA adaptation. The combination of key features, allowing for the low certainty and uneven coverage of experimental observations, gives comparatively minor but robust prediction accuracy. The model substantially improved the analysis of protein regulation during the cell cycle: predicted protein abundance identified twice as many cell-cycle-associated proteins as experimental mRNA levels. Predicted protein abundance was more dynamic than observed mRNA expression, agreeing with experimental protein abundance from a human cell line. We illustrate how the same model can be used to predict the folding energy of mRNA when protein abundance is available, lending credence to the emerging view that mRNA folding affects translation efficiency. The software and data used in this research are available at http://bioinf.scmb.uq.edu.au/proteinabundance/.

Dynamics of charged particle motion in the vicinity of three dimensional magnetic null points: Energization and chaos

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

Gascoyne, Andrew, E-mail: a.d.gascoyne@sheffield.ac.uk

2015-03-15

Using a full orbit test particle approach, we analyse the motion of a single proton in the vicinity of magnetic null point configurations which are solutions to the kinematic, steady state, resistive magnetohydrodynamics equations. We consider two magnetic configurations, namely, the sheared and torsional spine reconnection regimes [E. R. Priest and D. I. Pontin, Phys. Plasmas 16, 122101 (2009); P. Wyper and R. Jain, Phys. Plasmas 17, 092902 (2010)]; each produce an associated electric field and thus the possibility of accelerating charged particles to high energy levels, i.e., > MeV, as observed in solar flares [R. P. Lin, Space Sci. Rev. 124,more » 233 (2006)]. The particle's energy gain is strongly dependent on the location of injection and is characterised by the angle of approach β, with optimum angle of approach β{sub opt} as the value of β which produces the maximum energy gain. We examine the topological features of each regime and analyse the effect on the energy gain of the proton. We also calculate the complete Lyapunov spectrum for the considered dynamical systems in order to correctly quantify the chaotic nature of the particle orbits. We find that the sheared model is a good candidate for the acceleration of particles, and for increased shear, we expect a larger population to be accelerated to higher energy levels. In the strong electric field regime (E{sub 0}=1500 V/m), the torsional model produces chaotic particle orbits quantified by the calculation of multiple positive Lyapunov exponents in the spectrum, whereas the sheared model produces chaotic orbits only in the neighbourhood of the null point.« less

One and two hydrogen molecules in the large cage of the structure II clathrate hydrate: quantum translation-rotation dynamics close to the cage wall.

PubMed

Sebastianelli, Francesco; Xu, Minzhong; Kanan, Dalal K; Bacić, Zlatko

2007-07-19

We have performed a rigorous theoretical study of the quantum translation-rotation (T-R) dynamics of one and two H2 and D2 molecules confined inside the large hexakaidecahedral (5(12)6(4)) cage of the sII clathrate hydrate. For a single encapsulated H2 and D2 molecule, accurate quantum five-dimensional calculations of the T-R energy levels and wave functions are performed that include explicitly, as fully coupled, all three translational and the two rotational degrees of freedom of the hydrogen molecule, while the cage is taken to be rigid. In addition, the ground-state properties, energetics, and spatial distribution of one and two p-H2 and o-D2 molecules in the large cage are calculated rigorously using the diffusion Monte Carlo method. These calculations reveal that the low-energy T-R dynamics of hydrogen molecules in the large cage are qualitatively different from that inside the small cage, studied by us recently. This is caused by the following: (i) The large cage has a cavity whose diameter is about twice that of the small cage for the hydrogen molecule. (ii) In the small cage, the potential energy surface (PES) for H2 is essentially flat in the central region, while in the large cage the PES has a prominent maximum at the cage center, whose height exceeds the T-R zero-point energy of H2/D2. As a result, the guest molecule is excluded from the central part of the large cage, its wave function localized around the off-center global minimum. Peculiar quantum dynamics of the hydrogen molecule squeezed between the central maximum and the cage wall manifests in the excited T-R states whose energies and wave functions differ greatly from those for the small cage. Moreover, they are sensitive to the variations in the hydrogen-bonding topology, which modulate the corrugation of the cage wall.

Application configuration selection for energy-efficient execution on multicore systems

DOE PAGES

Wang, Shinan; Luo, Bing; Shi, Weisong; ...

2015-09-21

Balanced performance and energy consumption are incorporated in the design of modern computer systems. Several runtime factors, such as concurrency levels, thread mapping strategies, and dynamic voltage and frequency scaling (DVFS) should be considered in order to achieve optimal energy efficiency fora workload. Selecting appropriate run-time factors, however, is one of the most challenging tasks because the run-time factors are architecture-specific and workload-specific. And while most existing works concentrate on either static analysis of the workload or run-time prediction results, we present a hybrid two-step method that utilizes concurrency levels and DVFS settings to achieve the energy efficiency configuration formore » a worldoad. The experimental results based on a Xeon E5620 server with NPB and PARSEC benchmark suites show that the model is able to predict the energy efficient configuration accurately. On average, an additional 10% EDP (Energy Delay Product) saving is obtained by using run-time DVFS for the entire system. An off-line optimal solution is used to compare with the proposed scheme. Finally, the experimental results show that the average extra EDP saved by the optimal solution is within 5% on selective parallel benchmarks.« less

Using a biased qubit to probe complex systems

NASA Astrophysics Data System (ADS)

Pollock, Felix A.; Checińska, Agata; Pascazio, Saverio; Modi, Kavan

2016-09-01

Complex mesoscopic systems play increasingly important roles in modern science, from understanding biological functions at the molecular level to designing solid-state information processing devices. The operation of these systems typically depends on their energetic structure, yet probing their energy landscape can be extremely challenging; they have many degrees of freedom, which may be hard to isolate and measure independently. Here, we show that a qubit (a two-level quantum system) with a biased energy splitting can directly probe the spectral properties of a complex system, without knowledge of how they couple. Our work is based on the completely positive and trace-preserving map formalism, which treats any unknown dynamics as a "black-box" process. This black box contains information about the system with which the probe interacts, which we access by measuring the survival probability of the initial state of the probe as function of the energy splitting and the process time. Fourier transforming the results yields the energy spectrum of the complex system. Without making assumptions about the strength or form of its coupling, our probe could determine aspects of a complex molecule's energy landscape as well as, in many cases, test for coherent superposition of its energy eigenstates.

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

Demidov, V. E.; Dzyapko, O.; Demokritov, S. O.

The room-temperature dynamics of a magnon gas driven by short microwave pumping pulses is studied. An overpopulation of the lowest energy level of the system following the pumping is observed. Using the sensitivity of the Brillouin light scattering technique to the coherence degree of the scattering magnons we demonstrate the spontaneous emergence of coherence of the magnons at the lowest level, if their density exceeds a critical value. This finding is clear proof of the quantum nature of the observed phenomenon and direct evidence of Bose-Einstein condensation of magnons at room temperature.

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

Yoshii, Kazutomo; Llopis, Pablo; Zhang, Kaicheng

As CMOS scaling nears its end, parameter variations (process, temperature and voltage) are becoming a major concern. To overcome parameter variations and provide stability, modern processors are becoming dynamic, opportunistically adjusting voltage and frequency based on thermal and energy constraints, which negatively impacts traditional bulk-synchronous parallelism-minded hardware and software designs. As node-level architecture is growing in complexity, implementing variation control mechanisms only with hardware can be a challenging task. In this paper we investigate a software strategy to manage hardwareinduced variations, leveraging low-level monitoring/controlling mechanisms.

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

PubMed

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.

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

NASA Astrophysics Data System (ADS)

Humeniuk, Alexander; Mitrić, Roland

2017-12-01

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

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

Hong, Taehoon, E-mail: hong7@yonsei.ac.kr; Kim, Jimin, E-mail: cookie6249@yonsei.ac.kr; Jeong, Kwangbok, E-mail: kbjeong7@yonsei.ac.kr

To systematically manage the energy consumption of existing buildings, the government has to enforce greenhouse gas reduction policies. However, most of the policies are not properly executed because they do not consider various factors from the urban level perspective. Therefore, this study aimed to conduct a dynamic analysis of an urban-based low-carbon policy using system dynamics, with a specific focus on housing and green space. This study was conducted in the following steps: (i) establishing the variables of urban-based greenhouse gases (GHGs) emissions; (ii) creating a stock/flow diagram of urban-based GHGs emissions; (iii) conducting an information analysis using the systemmore » dynamics; and (iv) proposing the urban-based low-carbon policy. If a combined energy policy that uses the housing sector (30%) and the green space sector (30%) at the same time is implemented, 2020 CO{sub 2} emissions will be 7.23 million tons (i.e., 30.48% below 2020 business-as-usual), achieving the national carbon emissions reduction target (26.9%). The results of this study could contribute to managing and improving the fundamentals of the urban-based low-carbon policies to reduce greenhouse gas emissions.« less

Modeling of metal thin film growth: Linking angstrom-scale molecular dynamics results to micron-scale film topographies

NASA Astrophysics Data System (ADS)

Hansen, U.; Rodgers, S.; Jensen, K. F.

2000-07-01

A general method for modeling ionized physical vapor deposition is presented. As an example, the method is applied to growth of an aluminum film in the presence of an ionized argon flux. Molecular dynamics techniques are used to examine the surface adsorption, reflection, and sputter reactions taking place during ionized physical vapor deposition. We predict their relative probabilities and discuss their dependence on energy and incident angle. Subsequently, we combine the information obtained from molecular dynamics with a line of sight transport model in a two-dimensional feature, incorporating all effects of reemission and resputtering. This provides a complete growth rate model that allows inclusion of energy- and angular-dependent reaction rates. Finally, a level-set approach is used to describe the morphology of the growing film. We thus arrive at a computationally highly efficient and accurate scheme to model the growth of thin films. We demonstrate the capabilities of the model predicting the major differences on Al film topographies between conventional and ionized sputter deposition techniques studying thin film growth under ionized physical vapor deposition conditions with different Ar fluxes.

Possible signals of vacuum dynamics in the Universe

NASA Astrophysics Data System (ADS)

Peracaula, Joan Solà; de Cruz Pérez, Javier; Gómez-Valent, Adrià

2018-05-01

We study a generic class of time-evolving vacuum models which can provide a better phenomenological account of the overall cosmological observations as compared to the ΛCDM. Among these models, the running vacuum model (RVM) appears to be the most motivated and favored one, at a confidence level of ˜3σ. We further support these results by computing the Akaike and Bayesian information criteria. Our analysis also shows that we can extract fair signals of dynamical dark energy (DDE) by confronting the same set of data to the generic XCDM and CPL parametrizations. In all cases we confirm that the combined triad of modern observations on Baryonic Acoustic Oscillations, Large Scale Structure formation, and the Cosmic Microwave Background, provide the bulk of the signal sustaining a possible vacuum dynamics. In the absence of any of these three crucial data sources, the DDE signal can not be perceived at a significant confidence level. Its possible existence could be a cure for some of the tensions existing in the ΛCDM when confronted to observations.

2n-emission from 205Pb* nucleus using clusterization approach at Ebeam˜14-20 MeV

NASA Astrophysics Data System (ADS)

Kaur, Amandeep; Sandhu, Kiran; Sharma, Manoj Kumar

2016-05-01

The dynamics involved in n-induced reaction with 204Pb target is analyzed and the decay of the composite system 205Pb* is governed within the collective clusterization approach of the Dynamical Cluster-decay Model (DCM). The experimental data for 2n-evaporation channel is available for neutron energy range of 14-20 MeV and is addressed by optimizing the only parameter of the model, the neck-length parameter (ΔR). The calculations are done by taking the quadrupole (β2) deformations of the decaying fragments and the calculated 2n-emission cross-sections find nice agreement with available data. An effort is made to study the role of level density parameter in the decay of hot-rotating nucleus, and the mass dependence in level density parameter is exercised for the first time in DCM based calculations. It is to be noted that the effect of deformation, temperature and angular momentum etc. is studied to extract better description of the dynamics involved.

Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

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

Geng, Hua Y., E-mail: huay.geng@gmail.com; Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853

A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate ismore » about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.« less

Quantum dynamics of tunneling dominated reactions at low temperatures

NASA Astrophysics Data System (ADS)

Hazra, Jisha; Balakrishnan, N.

2015-05-01

We report a quantum dynamics study of the Li + HF → LiF + H reaction at low temperatures of interest to cooling and trapping experiments. Contributions from non-zero partial waves are analyzed and results show narrow resonances in the energy dependence of the cross section that survive partial wave summation. The computations are performed using the ABC code and a simple modification of the ABC code that enables separate energy cutoffs for the reactant and product rovibrational energy levels is found to dramatically reduce the basis set size and computational expense. Results obtained using two ab initio electronic potential energy surfaces for the LiHF system show strong sensitivity to the choice of the potential. In particular, small differences in the barrier heights of the two potential surfaces are found to dramatically influence the reaction cross sections at low energies. Comparison with recent measurements of the reaction cross section (Bobbenkamp et al 2011 J. Chem. Phys. 135 204306) shows similar energy dependence in the threshold regime and an overall good agreement with experimental data compared to previous theoretical results. Also, usefulness of a recently introduced method for ultracold reactions that employ the quantum close-coupling method at short-range and the multichannel quantum defect theory at long-range, is demonstrated in accurately evaluating product state-resolved cross sections for D + H2 and H + D2 reactions.

A heat receiver design for solar dynamic space power systems

NASA Technical Reports Server (NTRS)

Baker, Karl W.; Dustin, Miles O.; Crane, Roger

1990-01-01

An advanced heat pipe receiver designed for a solar dynamic space power system is described. The power system consists of a solar concentrator, solar heat receiver, Stirling heat engine, linear alternator and waste heat radiator. The solar concentrator focuses the sun's energy into a heat receiver. The engine and alternator convert a portion of this energy to electric power and the remaining heat is rejected by a waste heat radiator. Primary liquid metal heat pipes transport heat energy to the Stirling engine. Thermal energy storage allows this power system to operate during the shade portion of an orbit. Lithium fluoride/calcium fluoride eutectic is the thermal energy storage material. Thermal energy storage canisters are attached to the midsection of each heat pipe. The primary heat pipes pass through a secondary vapor cavity heat pipe near the engine and receiver interface. The secondary vapor cavity heat pipe serves three important functions. First, it smooths out hot spots in the solar cavity and provides even distribution of heat to the engine. Second, the event of a heat pipe failure, the secondary heat pipe cavity can efficiently transfer heat from other operating primary heat pipes to the engine heat exchanger of the defunct heat pipe. Third, the secondary heat pipe vapor cavity reduces temperature drops caused by heat flow into the engine. This unique design provides a high level of reliability and performance.

Supersonic Localized Excitations Mediate Microscopic Dynamic Failure

NASA Astrophysics Data System (ADS)

Ghaffari, H. O.; Griffith, W. A.; Pec, M.

2017-12-01

A moving rupture front activates a fault patch by increasing stress above a threshold strength level. Subsequent failure yields fast slip which releases stored energy in the rock. A fraction of the released energy is radiated as seismic waves carrying information about the earthquake source. While this simplified model is widely accepted, the detailed evolution from the onset of dynamic failure to eventual re-equilibration is still poorly understood. To study dynamic failure of brittle solids we indented thin sheets of single mineral crystals and recorded the emitted ultrasound signals (high frequency analogues to seismic waves) using an array of 8 to 16 ultrasound probes. The simple geometry of the experiments allows us to unravel details of dynamic stress history of the laboratory earthquake sources. A universal pattern of failure is observed. First, stress increases over a short time period (1 - 2 µs), followed by rapid weakening (≈ 15 µs). Rapid weakening is followed by two distinct relaxation phases: a temporary quasi-steady state phase (10 µs) followed by a long-term relaxation phase (> 50 µs). We demonstrate that the dynamic stress history during failure is governed by formation and interaction of local non-dispersive excitations, or solitons. The formation and annihilation of solitons mediates the microscopic fast weakening phase, during which extreme acceleration and collision of solitons lead to non-Newtonian behavior and Lorentz contraction, i.e. shortening of solitons' characteristic length. Interestingly, a soliton can propagate as fast as 37 km/s, much faster than the p-wave velocity, implying that a fraction of the energy transmits through soliton excitations. The quasi-steady state phase delays the long-term ageing of the damaged crystal, implying a potentially weaker material. Our results open new horizons for understanding the complexity of earthquake sources, and, more generally, non-equilibrium relaxation of many body systems.

Nonadiabatic dynamics in intense continuous wave laser fields and real-time observation of the associated wavepacket bifurcation in terms of spectrogram of induced photon emission.

PubMed

Mizuno, Yuta; Arasaki, Yasuki; Takatsuka, Kazuo

2016-11-14

We propose a theoretical principle to directly monitor the bifurcation of quantum wavepackets passing through nonadiabatic regions of a molecule that is placed in intense continuous wave (CW) laser fields. This idea makes use of the phenomenon of laser-driven photon emission from molecules that can undergo nonadiabatic transitions between ionic and covalent potential energy surfaces like Li + F - and LiF. The resultant photon emission spectra are of anomalous yet characteristic frequency and intensity, if pumped to an energy level in which the nonadiabatic region is accessible and placed in a CW laser field. The proposed method is designed to take the time-frequency spectrogram with an appropriate time-window from this photon emission to detect the time evolution of the frequency and intensity, which depends on the dynamics and location of the relevant nuclear wavepackets. This method is specifically designed for the study of dynamics in intense CW laser fields and is rather limited in scope than other techniques for femtosecond chemical dynamics in vacuum. The following characteristic features of dynamics can be mapped onto the spectrogram: (1) the period of driven vibrational motion (temporally confined vibrational states in otherwise dissociative channels, the period and other states of which dramatically vary depending on the CW driving lasers applied), (2) the existence of multiple nuclear wavepackets running individually on the field-dressed potential energy surfaces, (3) the time scale of coherent interaction between the nuclear wavepackets running on ionic and covalent electronic states after their branching (the so-called coherence time in the terminology of the theory of nonadiabatic interaction), and so on.

Nonadiabatic dynamics in intense continuous wave laser fields and real-time observation of the associated wavepacket bifurcation in terms of spectrogram of induced photon emission

NASA Astrophysics Data System (ADS)

Mizuno, Yuta; Arasaki, Yasuki; Takatsuka, Kazuo

2016-11-01

We propose a theoretical principle to directly monitor the bifurcation of quantum wavepackets passing through nonadiabatic regions of a molecule that is placed in intense continuous wave (CW) laser fields. This idea makes use of the phenomenon of laser-driven photon emission from molecules that can undergo nonadiabatic transitions between ionic and covalent potential energy surfaces like Li+ F- and LiF. The resultant photon emission spectra are of anomalous yet characteristic frequency and intensity, if pumped to an energy level in which the nonadiabatic region is accessible and placed in a CW laser field. The proposed method is designed to take the time-frequency spectrogram with an appropriate time-window from this photon emission to detect the time evolution of the frequency and intensity, which depends on the dynamics and location of the relevant nuclear wavepackets. This method is specifically designed for the study of dynamics in intense CW laser fields and is rather limited in scope than other techniques for femtosecond chemical dynamics in vacuum. The following characteristic features of dynamics can be mapped onto the spectrogram: (1) the period of driven vibrational motion (temporally confined vibrational states in otherwise dissociative channels, the period and other states of which dramatically vary depending on the CW driving lasers applied), (2) the existence of multiple nuclear wavepackets running individually on the field-dressed potential energy surfaces, (3) the time scale of coherent interaction between the nuclear wavepackets running on ionic and covalent electronic states after their branching (the so-called coherence time in the terminology of the theory of nonadiabatic interaction), and so on.

Molecular dynamics simulations of thermally activated edge dislocation unpinning from voids in α -Fe

NASA Astrophysics Data System (ADS)

Byggmästar, J.; Granberg, F.; Nordlund, K.

2017-10-01

In this study, thermal unpinning of edge dislocations from voids in α -Fe is investigated by means of molecular dynamics simulations. The activation energy as a function of shear stress and temperature is systematically determined. Simulations with a constant applied stress are compared with dynamic simulations with a constant strain rate. We found that a constant applied stress results in a temperature-dependent activation energy. The temperature dependence is attributed to the elastic softening of iron. If the stress is normalized with the softening of the specific shear modulus, the activation energy is shown to be temperature-independent. From the dynamic simulations, the activation energy as a function of critical shear stress was determined using previously developed methods. The results from the dynamic simulations are in good agreement with the constant stress simulations, after the normalization. This indicates that the computationally more efficient dynamic method can be used to obtain the activation energy as a function of stress and temperature. The obtained relation between stress, temperature, and activation energy can be used to introduce a stochastic unpinning event in larger-scale simulation methods, such as discrete dislocation dynamics.

Convective storms and non-classical low-level jets during high ozone level episodes in the Amazon region: An ARM/GOAMAZON case study

NASA Astrophysics Data System (ADS)

Dias-Junior, Cléo Q.; Dias, Nelson Luís; Fuentes, José D.; Chamecki, Marcelo

2017-04-01

In this work, we investigate the ozone dynamics during the occurrence of both downdrafts associated with mesoscale convective storms and non-classical low-level jets. Extensive data sets, comprised of air chemistry and meteorological observations made in the Amazon region of Brazil over the course of 2014-15, are analyzed to address several questions. A first objective is to investigate the atmospheric thermodynamic and dynamic conditions associated with storm-generated ozone enhancements in the Amazon region. A second objective is to determine the magnitude and the frequency of ground-level ozone enhancements related to low-level jets. Ozone enhancements are analyzed as a function of wind shear, low-level jet maximum wind speed, and altitude of jet core. Strong and sudden increases in ozone levels are associated with simultaneous changes in variables such as horizontal wind speed, convective available potential energy, turbulence intensity and vertical velocity skewness. Rapid increases in vertical velocity skewness give support to the hypothesis that the ozone enhancements are directly related to downdrafts. Low-level jets associated with advancing density currents are often present during and after storm downdrafts that transport ozone-enriched air from aloft to the surface.

Experimental and theoretical studies of the npσ1Σu+ and npπ1 Πu+ (n ⩾ 4,N‧ = 1 -6) states of D2: Energies, natural widths, absorption line intensities, and dynamics

NASA Astrophysics Data System (ADS)

Glass-Maujean, M.; Jungen, Ch.; Vasserot, A. M.; Schmoranzer, H.; Knie, A.; Kübler, S.; Ehresmann, A.; Ubachs, W.

2017-08-01

Over a thousand spectral lines in the photoexcitation spectrum of molecular deuterium (D2) to np1 Σu+ and 1Πu+ Rydberg levels (n ⩾ 4) were measured for rotational levels N‧ = 1 -6 in the 117 000-137 000 cm-1 spectral range by two different types of experiments at two synchrotron radiation sources: a vacuum ultraviolet (VUV) Fourier-transform (FT) spectrometer at SOLEIL, Paris and a 10 m-normal-incidence monochromator (NIM) at BESSY II, Berlin. The experimental energies, the absorption cross sections, Einstein A-coefficients, and line widths are compared with ab initio multi-channel quantum defect (MQDT) calculations for these levels. More than 350 R(0) or P(2) lines were assigned, some 280 R(1) or P(3) lines, some 270 R(2) or P(4) lines, over 100 R(3) or P(5) lines, over 90 R(4) lines, and 24 R(5) lines to extract information on the N‧ = 1 -6 excited levels. Transition energies were determined up to excitation energies of 137 000 cm-1 above the ground state, thereby extending earlier work by various authors and considerably improving the spectral accuracy (< 0.1 cm-1), leading to several reassignments. The absorption and the dissociation, ionization and fluorescence excitation cross sections from the NIM experiment are measured on absolute scale and are used to calibrate intensities in the VUV-FT spectra. The overall agreement between experiment and first principles calculations, without adjustable parameters, is excellent in view of the multi-state interferences treated within the MQDT-framework: For the low N‧ values the averaged deviations between those observed in the FT-SOLEIL spectra and those calculated with MQDT are ∼ 0.1 cm-1 with a spread of ∼ 0.5 cm-1. The line intensities in terms of Einstein coefficients are well represented in the MQDT-framework, as are the level widths representing the lifetimes associated with the sum of the three decay channels. These line intensities follow, in general, the 1 /n3 scaling behavior as characteristic in Rydberg series, but deviations occur and those are explained by MQDT. The decay dynamics of the excited N Rydberg levels is analyzed on the basis of the measured quantum yields for ionization, dissociation and fluorescence observed in the NIM experiment in terms of absolute cross sections for the distinctive channels. In particular in the n = 4 manifolds dissociation is found to play a major role, where in the n = 5 manifolds the behavior is most erratic due to strong competition between decay channels. At n = 6 , ionization takes over as the dominant channel. Despite the excellent agreement between observations and the outcome of the MQDT calculations for both level energies and dynamics, some pronounced deviations are found as in the splitting of the 5 pπ, v = 4 -6, N‧ = 1 levels. The shortcomings of the MQDT calculations are ascribed to the treatment of the excited states in terms of a 1 snp single electron configuration, therewith neglecting possible interferences with 1 snf or 2 s core excited states. Some 27 lines remained unassigned; in view of their observation in fluorescence it is stipulated that these lines probe levels in the nf manifold.

Improving energy efficiency via smart building energy management systems. A comparison with policy measures

DOE PAGES

Rocha, Paula; Siddiqui, Afzal; Stadler, Michael

2014-12-09

In this study, to foster the transition to more sustainable energy systems, policymakers have been approving measures to improve energy efficiency as well as promoting smart grids. In this setting, building managers are encouraged to adapt their energy operations to real-time market and weather conditions. Yet, most fail to do so as they rely on conventional building energy management systems (BEMS) that have static temperature set points for heating and cooling equipment. In this paper, we investigate how effective policy measures are at improving building-level energy efficiency compared to a smart BEMS with dynamic temperature set points. To this end,more » we present an integrated optimisation model mimicking the smart BEMS that combines decisions on heating and cooling systems operations with decisions on energy sourcing. Using data from an Austrian and a Spanish building, we find that the smart BEMS results in greater reduction in energy consumption than a conventional BEMS with policy measures.« less

Determination of the formation of dark state via depleted spontaneous emission in a complex solvated molecule.

PubMed

Guo, Xunmin; Wang, Sufan; Xia, Andong; Su, Hongmei

2007-07-05

We present a general two-color two-pulse femtosecond pump-dump approach to study the specific population transfer along the reaction coordinate through the higher vibrational energy levels of excited states of a complex solvated molecule via the depleted spontaneous emission. The time-dependent fluorescence depletion provides the correlated dynamical information between the monitored fluorescence state and the SEP "dumped" dark states, and therefore allow us to obtain the dynamics of the formation of the dark states corresponding to the ultrafast photoisomerization processes. The excited-state dynamics of LDS 751 have been investigated as a function of solvent viscosity and solvent polarity, where a cooperative two-step isomerization process is clearly identified within LDS 751 upon excitation.

Impact Testing of a Stirling Converter's Linear Alternator

NASA Technical Reports Server (NTRS)

Suarez, Vicente J.; Goodnight, Thomas W.; Hughes, William O.; Samorezov, Sergey

2002-01-01

The U.S. Department of Energy (DOE), in conjunction with the NASA John H. Glenn Research Center and Stirling Technology Company, are currently developing a Stirling convertor for a Stirling Radioisotope Generator (SRG). NASA Headquarters and DOE have identified the SRG for potential use as an advanced spacecraft power system for future NASA deep-space and Mars surface missions. Low-level dynamic impact tests were conducted at NASA Glenn Research Center's Structural Dynamics Laboratory as part of the development of this technology. The purpose of this test was to identify dynamic structural characteristics of the Stirling Technology Demonstration Convertor (TDC). This paper addresses the test setup, procedure, and results of the impact testing conducted on the Stirling TDC in May 2001.

Impact testing of a Stirling convertor's linear alternator

NASA Astrophysics Data System (ADS)

Suárez, Vicente J.; Goodnight, Thomas W.; Hughes, William O.; Samorezov, Sergey

2002-01-01

The U.S. Department of Energy (DOE), in conjunction with NASA John H. Glenn Research Center and Stirling Technology Company, are currently developing a Stirling convertor for a Stirling Radioisotope Generator (SRG). NASA Headquarters and DOE have identified the SRG for potential use as an advanced spacecraft power system for future NASA deep-space and Mars surface missions. Low-level dynamic impact tests were conducted at NASA Glenn Research Center's Structural Dynamics Laboratory as part of the development of this technology. The purpose of this test was to identify dynamic structural characteristics of the Stirling Technology Demonstration Convertor (TDC). This paper addresses the test setup, procedure and results of the impact testing conducted on the Stirling TDC in May 2001. .

Control of chemical dynamics by lasers: theoretical considerations.

PubMed

Kondorskiy, Alexey; Nanbu, Shinkoh; Teranishi, Yoshiaki; Nakamura, Hiroki

2010-06-03

Theoretical ideas are proposed for laser control of chemical dynamics. There are the following three elementary processes in chemical dynamics: (i) motion of the wave packet on a single adiabatic potential energy surface, (ii) excitation/de-excitation or pump/dump of wave packet, and (iii) nonadiabatic transitions at conical intersections of potential energy surfaces. A variety of chemical dynamics can be controlled, if we can control these three elementary processes as we desire. For (i) we have formulated the semiclassical guided optimal control theory, which can be applied to multidimensional real systems. The quadratic or periodic frequency chirping method can achieve process (ii) with high efficiency close to 100%. Concerning process (iii) mentioned above, the directed momentum method, in which a predetermined momentum vector is given to the initial wave packet, makes it possible to enhance the desired transitions at conical intersections. In addition to these three processes, the intriguing phenomenon of complete reflection in the nonadiabatic-tunneling-type of potential curve crossing can also be used to control a certain class of chemical dynamics. The basic ideas and theoretical formulations are provided for the above-mentioned processes. To demonstrate the effectiveness of these controlling methods, numerical examples are shown by taking the following processes: (a) vibrational photoisomerization of HCN, (b) selective and complete excitation of the fine structure levels of K and Cs atoms, (c) photoconversion of cyclohexadiene to hexatriene, and (d) photodissociation of OHCl to O + HCl.

Alternation of regular and chaotic dynamics in a simple two-degree-of-freedom system with nonlinear inertial coupling.

PubMed

Sigalov, G; Gendelman, O V; AL-Shudeifat, M A; Manevitch, L I; Vakakis, A F; Bergman, L A

2012-03-01

We show that nonlinear inertial coupling between a linear oscillator and an eccentric rotator can lead to very interesting interchanges between regular and chaotic dynamical behavior. Indeed, we show that this model demonstrates rather unusual behavior from the viewpoint of nonlinear dynamics. Specifically, at a discrete set of values of the total energy, the Hamiltonian system exhibits non-conventional nonlinear normal modes, whose shape is determined by phase locking of rotatory and oscillatory motions of the rotator at integer ratios of characteristic frequencies. Considering the weakly damped system, resonance capture of the dynamics into the vicinity of these modes brings about regular motion of the system. For energy levels far from these discrete values, the motion of the system is chaotic. Thus, the succession of resonance captures and escapes by a discrete set of the normal modes causes a sequence of transitions between regular and chaotic behavior, provided that the damping is sufficiently small. We begin from the Hamiltonian system and present a series of Poincaré sections manifesting the complex structure of the phase space of the considered system with inertial nonlinear coupling. Then an approximate analytical description is presented for the non-conventional nonlinear normal modes. We confirm the analytical results by numerical simulation and demonstrate the alternate transitions between regular and chaotic dynamics mentioned above. The origin of the chaotic behavior is also discussed.

The physics of symbols: bridging the epistemic cut.

PubMed

Pattee, H H

2001-01-01

Evolution requires the genotype-phenotype distinction, a primeval epistemic cut that separates energy-degenerate, rate-independent genetic symbols from the rate-dependent dynamics of construction that they control. This symbol-matter or subject-object distinction occurs at all higher levels where symbols are related to a referent by an arbitrary code. The converse of control is measurement in which a rate-dependent dynamical state is coded into quiescent symbols. Non-integrable constraints are one necessary condition for bridging the epistemic cut by measurement, control, and coding. Additional properties of heteropolymer constraints are necessary for biological evolution.

Universal shape characteristics for the mesoscopic star-shaped polymer via dissipative particle dynamics simulations

NASA Astrophysics Data System (ADS)

Kalyuzhnyi, O.; Ilnytskyi, J. M.; Holovatch, Yu; von Ferber, C.

2018-05-01

In this paper we study the shape characteristics of star-like polymers in various solvent quality using a mesoscopic level of modeling. The dissipative particle dynamics simulations are performed for the homogeneous and four different heterogeneous star polymers with the same molecular weight. We analyse the gyration radius and asphericity at the poor, good and θ-solvent regimes. Detailed explanation based on interplay between enthalpic and entropic contributions to the free energy and analyses on of the asphericity of individual branches are provided to explain the increase of the apsphericity in θ-solvent regime.

Picking the Best from the All-Resources Menu: Advanced Tools for Resource Planning

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

Palmintier, Bryan S

Introduces the wide range of electric power systems modeling types and associated questions they can help answer. The presentation focusses on modeling needs for high levels of Distributed Energy Resources (DERs), renewables, and inverter-based technologies as alternatives to traditional centralized power systems. Covers Dynamics, Production Cost/QSTS, Metric Assessment, Resource Planning, and Integrated Simulations with examples drawn from NREL's past and on-going projects. Presented at the McKnight Foundation workshop on 'An All-Resources Approach to Planning for a More Dynamic, Low-Carbon Grid' exploring grid modernization options to replace retiring coal plants in Minnesota.

Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

PubMed

Ding, Xinqiang; Vilseck, Jonah Z; Hayes, Ryan L; Brooks, Charles L

2017-06-13

λ-dynamics is a generalized ensemble method for alchemical free energy calculations. In traditional λ-dynamics, the alchemical switch variable λ is treated as a continuous variable ranging from 0 to 1 and an empirical estimator is utilized to approximate the free energy. In the present article, we describe an alternative formulation of λ-dynamics that utilizes the Gibbs sampler framework, which we call Gibbs sampler-based λ-dynamics (GSLD). GSLD, like traditional λ-dynamics, can be readily extended to calculate free energy differences between multiple ligands in one simulation. We also introduce a new free energy estimator, the Rao-Blackwell estimator (RBE), for use in conjunction with GSLD. Compared with the current empirical estimator, the advantage of RBE is that RBE is an unbiased estimator and its variance is usually smaller than the current empirical estimator. We also show that the multistate Bennett acceptance ratio equation or the unbinned weighted histogram analysis method equation can be derived using the RBE. We illustrate the use and performance of this new free energy computational framework by application to a simple harmonic system as well as relevant calculations of small molecule relative free energies of solvation and binding to a protein receptor. Our findings demonstrate consistent and improved performance compared with conventional alchemical free energy methods.

The North American Energy System: Chapter 3 of SOCCR-2

NASA Astrophysics Data System (ADS)

Gurney, K. R.; Marcotullio, P. J.; McGlynn, E.; Bruhwiler, L.; Davis, K. J.; Davis, S. J.; Engel-Cox, J.; Field, J.; Gately, C.; Kammen, D. M.; McMahon, J.; Morrow, W.; Torrie, R.

2017-12-01

North America (Canada, Mexico and the United States), has a large and complex energy system, which in this case includes the extraction and conversion of primary energy sources and their storage, transmission, distribution and ultimate end use in the building, transportation and industrial sectors. The presentation assesses the contribution of this energy system to the carbon cycle. The assessment includes the identification of CO2 emissions from fossil fuel use in the different end use, changes over the past 10 years (since the last SOCCR) and the drivers of change. The assessment focuses on our understanding of the energy trends and system feedback dynamics, key drivers of change as a basis for carbon management. The energy systems' carbon emissions from the North American system are placed in global context and a review of scenarios into the future emissions levels, which demonstrate the requirements for de-carbonization in the medium and longer term.

Interactions between metabolic and reproductive functions in the resumption of postpartum fecundity

PubMed Central

Valeggia, Claudia; Ellison, Peter T.

2012-01-01

Lactation has long been recognized as a major determinant of interbirth intervals. The temporal pattern of nursing has been proposed as the mechanism behind lactational amenorrhea. We present a new model of the dynamic regulation of lactational amenorrhea that identifies maternal energy availability as the main determinant of ovarian resumption. Variation in the intensity of lactation remains a component of the model as a determinant of the absolute energetic cost of milk production. But maternal energy supply determines net energy availability; a larger energy supply leaves a greater net energy surplus than a smaller energy supply (lactation costs being equal). We characterize the hormonal postpartum profile of 70 lactating Toba women of Argentina. We use C-peptide, which reflects maternal insulin production, as a measure of energy availability. Initially low, insulin production rises as the postpartum period progresses, reflecting the declining metabolic load of lactation. A short period of supernormal insulin production precedes menstrual resumption. The high levels of insulin may play a role in stimulating the resumption of ovarian activity, which in turn may help to resolve the transient period of insulin resistance. The dynamics of insulin sensitivity during lactation would aid in synchronizing the resumption of ovarian function with a reduction in the energy demands of milk production. This hypothesis is supported by the sustained weight gain experienced by lactating women during the months preceding the first postpartum menses. The link between fecundity and energy balance could serve as a mechanism for adjusting the duration of lactational amenorrhea to the relative metabolic load of lactation. PMID:19298003

Sampling the energy landscape of Pt13 with metadynamics

NASA Astrophysics Data System (ADS)

Pavan, Luca; Di Paola, Cono; Baletto, Francesca

2013-02-01

The potential energy surface of a metallic nanoparticle formed by 13 atoms of platinum is efficiently explored using metadynamics in combination with empirical potential molecular dynamics. The scenario obtained is wider and more complex of what was previously reported: more than thirty independent energy basins are found, corresponding to different local minima of Pt. It is demonstrated that in almost all the cases these motifs are local minima even at ab-initio level, hence proving the effectiveness of the method to sample the energy landscape. A classification of the minima in structural families is proposed, and a discussion regarding the shape and the connections between energy basins is reported. ISSPIC 16 - 16th International Symposium on Small Particles and Inorganic Clusters, edited by Kristiaan Temst, Margriet J. Van Bael, Ewald Janssens, H.-G. Boyen and Françoise Remacle.

Quantum Tunneling in Testosterone 6β-Hydroxylation by Cytochrome P450: Reaction Dynamics Calculations Employing Multiconfiguration Molecular-Mechanical Potential Energy Surfaces

NASA Astrophysics Data System (ADS)

Zhang, Yan; Lin, Hai

2009-05-01

Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6β-hydrogen abstraction and the 6β-d1-testosterone 6β-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.

Understanding glass formation and ion transport in polymeric ionic liquids using computer simulations

NASA Astrophysics Data System (ADS)

Patra, Tarak; Yang, Junhong; Cheng, Yiz; Simmons, David

Polymeric ionic liquids (PILs) are very promising materials to enable more environmentally stable high density energy storage devices. Realization of PILs providing high environmental and mechanical stability while maximizing ion conductivity would be accelerated by an improved molecular level understanding of their structure and dynamics. Extensive evidence suggests that both mechanical properties and ion conductivity in anhydrous PILs are intimately related to the PIL's glass formation behavior. This represents a major challenge to the rational design of these materials, given that the basic nature of glass formation and its connection to molecular properties remains a substantial open question in polymer and condensed matter physics. Here we describe coarse-grained and atomistic molecular dynamics simulations probing the relationship between PIL architecture and interactions, glass formation behavior, and ion transport characteristics. These studies provide guidance towards the design of PILs with improved stability and ion conductivity for future energy applications.

Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

1997-01-01

Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

Structure, Energetics, and Dynamics of Screw Dislocations in Even n-Alkane Crystals.

PubMed

Olson, Isabel A; Shtukenberg, Alexander G; Hakobyan, Gagik; Rohl, Andrew L; Raiteri, Paolo; Ward, Michael D; Kahr, Bart

2016-08-18

Spiral hillocks on n-alkane crystal surfaces were observed immediately after Frank recognized the importance of screw dislocations for crystal growth, yet their structures and energies in molecular crystals remain ill-defined. To illustrate the structural chemistry of screw dislocations that are responsible for plasticity in organic crystals and upon which the organic electronics and pharmaceutical industries depend, molecular dynamics was used to examine heterochiral dislocation pairs with Burgers vectors along [001] in n-hexane, n-octane, and n-decane crystals. The cores were anisotropic and elongated in the (110) slip plane, with significant local changes in molecular position, orientation, conformation, and energy. This detailed atomic level picture produced a distribution of strain consistent with linear elastic theory, giving confidence in the simulations. Dislocations with doubled Burgers vectors split into pairs with elementary displacements. These results suggest a pathway to understanding the mechanical properties and failure associated with elastic and plastic deformation in soft crystals.

Effect of mutation at the interface of Trp-repressor dimeric protein: a steered molecular dynamics simulation.

PubMed

Miño, German; Baez, Mauricio; Gutierrez, Gonzalo

2013-09-01

The strength of key interfacial contacts that stabilize protein-protein interactions have been studied by computer simulation. Experimentally, changes in the interface are evaluated by generating specific mutations at one or more points of the protein structure. Here, such an evaluation is performed by means of steered molecular dynamics and use of a dimeric model of tryptophan repressor and in-silico mutants as a test case. Analysis of four particular cases shows that, in principle, it is possible to distinguish between wild-type and mutant forms by examination of the total energy and force-extension profiles. In particular, detailed atomic level structural analysis indicates that specific mutations at the interface of the dimeric model (positions 19 and 39) alter interactions that appear in the wild-type form of tryptophan repressor, reducing the energy and force required to separate both subunits.

Band-Edge Exciton Fine Structure and Recombination Dynamics in InP/ZnS Colloidal Nanocrystals.

PubMed

Biadala, Louis; Siebers, Benjamin; Beyazit, Yasin; Tessier, Mickaël D; Dupont, Dorian; Hens, Zeger; Yakovlev, Dmitri R; Bayer, Manfred

2016-03-22

We report on a temperature-, time-, and spectrally resolved study of the photoluminescence of type-I InP/ZnS colloidal nanocrystals with varying core size. By studying the exciton recombination dynamics we assess the exciton fine structure in these systems. In addition to the typical bright-dark doublet, the photoluminescence stems from an upper bright state in spite of its large energy splitting (∼100 meV). This striking observation results from dramatically lengthened thermalization processes among the fine structure levels and points to optical-phonon bottleneck effects in InP/ZnS nanocrystals. Furthermore, our data show that the radiative recombination of the dark exciton scales linearly with the bright-dark energy splitting for CdSe and InP nanocrystals. This finding strongly suggests a universal dangling bonds-assisted recombination of the dark exciton in colloidal nanostructures.

Instability in interacting dark sector: an appropriate holographic Ricci dark energy model

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

Herrera, Ramón; Hipólito-Ricaldi, W.S.; Videla, Nelson, E-mail: ramon.herrera@pucv.cl, E-mail: wiliam.ricaldi@ufes.br, E-mail: nelson.videla@ing.uchile.cl

In this paper we investigate the consequences of phantom crossing considering the perturbative dynamics in models with interaction in their dark sector. By mean of a general study of gauge-invariant variables in comoving gauge, we relate the sources of instabilities in the structure formation process with the phantom crossing. In order to illustrate these relations and its consequences in more detail, we consider a specific case of an holographic dark energy interacting with dark matter. We find that in spite of the model is in excellent agreement with observational data at background level, however it is plagued of instabilities inmore » its perturbative dynamics. We reconstruct the model in order to avoid these undesirable instabilities, and we show that this implies a modification of the concordance model at background. Also we find drastic changes on the parameters space in our model when instabilities are avoided.« less

Quantum gravitational collapse as a Dirac particle on the half line

NASA Astrophysics Data System (ADS)

Hassan, Syed Moeez; Husain, Viqar; Ziprick, Jonathan

2018-05-01

We show that the quantum dynamics of a thin spherical shell in general relativity is equivalent to the Coulomb-Dirac equation on the half line. The Hamiltonian has a one-parameter family of self-adjoint extensions with a discrete energy spectrum |E |m , where m is the rest mass of the shell and E is the Arnowitt-Deser-Misner mass. For sufficiently large m , the ground state energy level is negative. This suggests that classical positivity of energy does not survive quantization. The scattering states provide a realization of singularity avoidance. We speculate on the consequences of these results for black hole radiation.

An adaptive interpolation scheme for molecular potential energy surfaces

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

Kowalewski, Markus, E-mail: mkowalew@uci.edu; Larsson, Elisabeth; Heryudono, Alfa

The calculation of potential energy surfaces for quantum dynamics can be a time consuming task—especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm based on polyharmonic splines combined with a partition of unity approach. The adaptive node refinement allows to greatly reduce the number of sample points by employing a local error estimate. The algorithm and its scaling behavior are evaluated for a model function in 2, 3, and 4 dimensions. The developed algorithm allows for a more rapid and reliable interpolation of a potential energy surface within amore » given accuracy compared to the non-adaptive version.« less

Peculiarities of the third natural frequency vibrations of a cantilever for the improvement of energy harvesting.

PubMed

Ostasevicius, Vytautas; Janusas, Giedrius; Milasauskaite, Ieva; Zilys, Mindaugas; Kizauskiene, Laura

2015-05-28

This paper focuses on several aspects extending the dynamical efficiency of a cantilever beam vibrating in the third mode. A few ways of producing this mode stimulation, namely vibro-impact or forced excitation, as well as its application for energy harvesting devices are proposed. The paper presents numerical and experimental analyses of novel structural dynamics effects along with an optimal configuration of the cantilever beam. The peculiarities of a cantilever beam vibrating in the third mode are related to the significant increase of the level of deformations capable of extracting significant additional amounts of energy compared to the conventional harvester vibrating in the first mode. Two types of a piezoelectric vibrating energy harvester (PVEH) prototype are analysed in this paper: the first one without electrode segmentation, while the second is segmented using electrode segmentation at the strain nodes of the third vibration mode to achieve effective operation at the third resonant frequency. The results of this research revealed that the voltage generated by any segment of the segmented PVEH prototype excited at the third resonant frequency demonstrated a 3.4-4.8-fold increase in comparison with the non-segmented prototype. Simultaneously, the efficiency of the energy harvester prototype also increased at lower resonant frequencies from 16% to 90%. The insights presented in the paper may serve for the development and fabrication of advanced piezoelectric energy harvesters which would be able to generate a considerably increased amount of electrical energy independently of the frequency of kinematical excitation.

Control of retinal isomerization in bacteriorhodopsin in the high-intensity regime

PubMed Central

Florean, Andrei C.; Cardoza, David; White, James L.; Lanyi, J. K.; Sension, Roseanne J.; Bucksbaum, Philip H.

2009-01-01

A learning algorithm was used to manipulate optical pulse shapes and optimize retinal isomerization in bacteriorhodopsin, for excitation levels up to 1.8 × 1016 photons per square centimeter. Below 1/3 the maximum excitation level, the yield was not sensitive to pulse shape. Above this level the learning algorithm found that a Fourier-transform-limited (TL) pulse maximized the 13-cis population. For this optimal pulse the yield increases linearly with intensity well beyond the saturation of the first excited state. To understand these results we performed systematic searches varying the chirp and energy of the pump pulses while monitoring the isomerization yield. The results are interpreted including the influence of 1-photon and multiphoton transitions. The population dynamics in each intermediate conformation and the final branching ratio between the all-trans and 13-cis isomers are modified by changes in the pulse energy and duration. PMID:19564608

The influence of wave energy and sediment transport on seagrass distribution

USGS Publications Warehouse

Stevens, Andrew W.; Lacy, Jessica R.

2012-01-01

A coupled hydrodynamic and sediment transport model (Delft3D) was used to simulate the water levels, waves, and currents associated with a seagrass (Zostera marina) landscape along a 4-km stretch of coast in Puget Sound, WA, USA. A hydroacoustic survey of seagrass percent cover and nearshore bathymetry was conducted, and sediment grain size was sampled at 53 locations. Wave energy is a primary factor controlling seagrass distribution at the site, accounting for 73% of the variability in seagrass minimum depth and 86% of the variability in percent cover along the shallow, sandy portions of the coast. A combination of numerical simulations and a conceptual model of the effect of sea-level rise on the cross-shore distribution of seagrass indicates that the area of seagrass habitat may initially increase and that wave dynamics are an important factor to consider in predicting the effect of sea-level rise on seagrass distributions in wave-exposed areas.

Processing-Induced Electrically Active Defects in Black Silicon Nanowire Devices.

PubMed

Carapezzi, Stefania; Castaldini, Antonio; Mancarella, Fulvio; Poggi, Antonella; Cavallini, Anna

2016-04-27

Silicon nanowires (Si NWs) are widely investigated nowadays for implementation in advanced energy conversion and storage devices, as well as many other possible applications. Black silicon (BSi)-NWs are dry etched NWs that merge the advantages related to low-dimensionality with the special industrial appeal connected to deep reactive ion etching (RIE). In fact, RIE is a well established technique in microelectronics manufacturing. However, RIE processing could affect the electrical properties of BSi-NWs by introducing deep states into their forbidden gap. This work applies deep level transient spectroscopy (DLTS) to identify electrically active deep levels and the associated defects in dry etched Si NW arrays. Besides, the successful fitting of DLTS spectra of BSi-NWs-based Schottky barrier diodes is an experimental confirmation that the same theoretical framework of dynamic electronic behavior of deep levels applies in bulk as well as in low dimensional structures like NWs, when quantum confinement conditions do not occur. This has been validated for deep levels associated with simple pointlike defects as well as for deep levels associated with defects with richer structures, whose dynamic electronic behavior implies a more complex picture.

Empirical valence bond models for reactive potential energy surfaces: a parallel multilevel genetic program approach.

PubMed

Bellucci, Michael A; Coker, David F

2011-07-28

We describe a new method for constructing empirical valence bond potential energy surfaces using a parallel multilevel genetic program (PMLGP). Genetic programs can be used to perform an efficient search through function space and parameter space to find the best functions and sets of parameters that fit energies obtained by ab initio electronic structure calculations. Building on the traditional genetic program approach, the PMLGP utilizes a hierarchy of genetic programming on two different levels. The lower level genetic programs are used to optimize coevolving populations in parallel while the higher level genetic program (HLGP) is used to optimize the genetic operator probabilities of the lower level genetic programs. The HLGP allows the algorithm to dynamically learn the mutation or combination of mutations that most effectively increase the fitness of the populations, causing a significant increase in the algorithm's accuracy and efficiency. The algorithm's accuracy and efficiency is tested against a standard parallel genetic program with a variety of one-dimensional test cases. Subsequently, the PMLGP is utilized to obtain an accurate empirical valence bond model for proton transfer in 3-hydroxy-gamma-pyrone in gas phase and protic solvent. © 2011 American Institute of Physics

Computational evaluation of sub-nanometer cluster activity of singly exposed copper atom with various coordinative environment in catalytic CO2 transformation

NASA Astrophysics Data System (ADS)

Shanmugam, Ramasamy; Thamaraichelvan, Arunachalam; Ganesan, Tharumeya Kuppusamy; Viswanathan, Balasubramanian

2017-02-01

Metal cluster, at sub-nanometer level has a unique property in the activation of small molecules, in contrast to that of bulk surface. In the present work, singly exposed active site of copper metal cluster at sub-nanometer level was designed to arrive at the energy minimised configurations, binding energy, electrostatic potential map, frontier molecular orbitals and partial density of states. The ab initio molecular dynamics was carried out to probe the catalytic nature of the cluster. Further, the stability of the metal cluster and its catalytic activity in the electrochemical reduction of CO2 to CO were evaluated by means of computational hydrogen electrode via calculation of the free energy profile using DFT/B3LYP level of theory in vacuum. The activity of the cluster is ascertained from the fact that the copper atom, present in a two coordinative environment, performs a more selective conversion of CO2 to CO at an applied potential of -0.35 V which is comparatively lower than that of higher coordinative sites. The present study helps to design any sub-nano level metal catalyst for electrochemical reduction of CO2 to various value added chemicals.

Structure, dynamics and stability of water/scCO 2/mineral interfaces from ab initio molecular dynamics simulations

DOE PAGES

Lee, Mal -Soon; Peter McGrail, B.; Rousseau, Roger; ...

2015-10-12

Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivitymore » and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO 2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca 2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO 2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences, Geosciences and Biosciences (R.R.), and performed at the Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated for DOE by Battelle. Computational resources were provided by PNNL’s Platform for Institutional Computing (PIC), the W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at PNNL and the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory.« less

Coupled dynamic systems and Le Chatelier's principle in noise control

NASA Astrophysics Data System (ADS)

Maidanik, G.; Becker, K. J.

2004-05-01

Investigation of coupling an externally driven dynamic system-a master dynamic system-to a passive one-an adjunct dynamic system-reveals that the response of the adjunct dynamic system affects the precoupled response of the master dynamic system. The responses, in the two dynamic systems when coupled, are estimated by the stored energies (Es) and (E0), respectively. Since the adjunct dynamic system, prior to coupling, was with zero (0) stored energy, E0s=0, the precoupled stored energy (E00) in the master dynamic system is expected to be reduced to (E0) when coupling is instituted; i.e., one expects E0

Unsteady locomotion: integrating muscle function with whole body dynamics and neuromuscular control

PubMed Central

Biewener, Andrew A.; Daley, Monica A.

2009-01-01

Summary By integrating studies of muscle function with analysis of whole body and limb dynamics, broader appreciation of neuromuscular function can be achieved. Ultimately, such studies need to address non-steady locomotor behaviors relevant to animals in their natural environments. When animals move slowly they likely rely on voluntary coordination of movement involving higher brain centers. However, when moving fast, their movements depend more strongly on responses controlled at more local levels. Our focus here is on control of fast-running locomotion. A key observation emerging from studies of steady level locomotion is that simple spring-mass dynamics, which help to economize energy expenditure, also apply to stabilization of unsteady running. Spring-mass dynamics apply to conditions that involve lateral impulsive perturbations, sudden changes in terrain height, and sudden changes in substrate stiffness or damping. Experimental investigation of unsteady locomotion is challenging, however, due to the variability inherent in such behaviors. Another emerging principle is that initial conditions associated with postural changes following a perturbation define different context-dependent stabilization responses. Distinct stabilization modes following a perturbation likely result from proximo-distal differences in limb muscle architecture, function and control strategy. Proximal muscles may be less sensitive to sudden perturbations and appear to operate, in such circumstances, under feed-forward control. In contrast, multiarticular distal muscles operate, via their tendons, to distribute energy among limb joints in a manner that also depends on the initial conditions of limb contact with the ground. Intrinsic properties of these distal muscle–tendon elements, in combination with limb and body dynamics, appear to provide rapid initial stabilizing mechanisms that are often consistent with spring-mass dynamics. These intrinsic mechanisms likely help to simplify the neural control task, in addition to compensating for delays inherent to subsequent force- and length-dependent neural feedback. Future work will benefit from integrative biomechanical approaches that employ a combination of modeling and experimental techniques to understand how the elegant interplay of intrinsic muscle properties, body dynamics and neural control allows animals to achieve stability and agility over a variety of conditions. PMID:17704070

Suppression of chaos via control of energy flow

NASA Astrophysics Data System (ADS)

Guo, Shengli; Ma, Jun; Alsaedi, Ahmed

2018-03-01

Continuous energy supply is critical and important to support oscillating behaviour; otherwise, the oscillator will die. For nonlinear and chaotic circuits, enough energy supply is also important to keep electric devices working. In this paper, Hamilton energy is calculated for dimensionless dynamical system (e.g., the chaotic Lorenz system) using Helmholtz's theorem. The Hamilton energy is considered as a new variable and then the dynamical system is controlled by using the scheme of energy feedback. It is found that chaos can be suppressed even when intermittent feedback scheme is applied. This scheme is effective to control chaos and to stabilise other dynamical systems.

Peptide probes derived from pertuzumab by molecular dynamics modeling for HER2 positive tumor imaging.

PubMed

Yang, Xiaoliang; Wang, Zihua; Xiang, Zhichu; Li, Dan; Hu, Zhiyuan; Cui, Wei; Geng, Lingling; Fang, Qiaojun

2017-04-01

A high level of HER2 expression in breast cancer correlates with a higher tumor growth rate, high metastatic potential, and a poor long-term patient survival rate. Pertuzumab, a human monoclonal antibody, can reduce the effect of HER2 overexpression by preventing HER2 dimerization. In this study, a combination protocol of molecular dynamics modeling and MM/GBSA binding free energy calculations was applied to design peptides that interact with HER2 based on the HER2/pertuzumab crystal structure. Based on a β hairpin in pertuzumab from Glu46 to Lys65-which plays a key role in interacting with HER2-mutations were carried out in silico to improve the binding free energy of the hairpin that interacts with the Phe256-Lys314 of the HER2 protein. Combined the use of one-bead-one-compound library screening, among all the mutations, a peptide (58F63Y) with the lowest binding free energy was confirmed experimentally to have the highest affinity, and it may be used as a new probe in diagnosing and treating HER2-positive breast cancer.

Deformation-mechanism map for nanocrystalline metals by molecular-dynamics simulation.

PubMed

Yamakov, V; Wolf, D; Phillpot, S R; Mukherjee, A K; Gleiter, H

2004-01-01

Molecular-dynamics simulations have recently been used to elucidate the transition with decreasing grain size from a dislocation-based to a grain-boundary-based deformation mechanism in nanocrystalline f.c.c. metals. This transition in the deformation mechanism results in a maximum yield strength at a grain size (the 'strongest size') that depends strongly on the stacking-fault energy, the elastic properties of the metal, and the magnitude of the applied stress. Here, by exploring the role of the stacking-fault energy in this crossover, we elucidate how the size of the extended dislocations nucleated from the grain boundaries affects the mechanical behaviour. Building on the fundamental physics of deformation as exposed by these simulations, we propose a two-dimensional stress-grain size deformation-mechanism map for the mechanical behaviour of nanocrystalline f.c.c. metals at low temperature. The map captures this transition in both the deformation mechanism and the related mechanical behaviour with decreasing grain size, as well as its dependence on the stacking-fault energy, the elastic properties of the material, and the applied stress level.

A spatial-temporal method for assessing the energy balance dynamics of partially sealed surfaces.

NASA Astrophysics Data System (ADS)

Pipkins, Kyle; Kleinschmit, Birgit; Wessolek, Gerd

2017-04-01

The effects of different types of sealed surfaces on the surface energy balance have been well-studied in the past. However, these field studies typically aggregate these surfaces into continuous units. The proposed method seeks to disaggregate such surfaces into paving and seam areas using spatial methods, and to consider the temperature dynamics under wet and dry conditions between these two components. This experimental work is undertaken using a thermal camera to record a time series of images over two lysimeters with differing levels of surface sealing. The images are subsequently decomposed into component materials using object-based image analysis and compared on the basis of both the surface materials as well as the spatial configuration of materials. Finally, a surface energy balance method is used to estimate evaporation rates from the surfaces, both separately for the different surface components as well as using the total surface mean. Results are validated using the output of the weighing lysimeter. Our findings will determine whether the explicitly spatial method is an improvement over the mean aggregate method.

A dynamic agent-based analysis for the environmental impacts of conventional and novel book retailing.

PubMed

Xu, Ming; Allenby, Braden; Kim, Junbeum; Kahhat, Ramzy

2009-04-15

The dynamics of an e-commerce market and the associated environmental impacts from a bottom-up perspective using an agent-based model is explored. A conceptual meta-theory from psychology is adopted to form the behavioral rules of artificial consumers choosing different methods of buying a book, including conventional bookstores, e-commerce, and a proposed self-pick-up option. Given the energy and emissions savings that result from a shift to e-commerce from bookstore purchase, it appears that reductions in environmental impacts are relatively probable. Additionally, our results suggest that the shift to e-commerce is mainly due to the growth of Internet users, which ties energy and emissions savings to Internet penetration. Moreover, under any scenario, the energy and emissions savings will be provided by the introduction of the proposed self-pick-up option. Our model thus provides insights into market behaviors and related environmental impacts of the growing use of e-commerce systems at the retail level, and provides a basis for the development and implementation of more sustainable policies and practices.

Correlation, Breit and Quantum Electrodynamics effects on energy level and transition properties of W54+ ion

NASA Astrophysics Data System (ADS)

Ding, Xiaobin; Sun, Rui; Koike, Fumihiro; Kato, Daiji; Murakami, Izumi; Sakaue, Hiroyuki A.; Dong, Chenzhong

2017-03-01

The electron correlation effects and Breit interaction as well as Quantum Electro-Dynamics (QED) effects were expected to have important contribution to the energy level and transition properties of heavy highly charged ions. The ground states [Ne]3s23p63d2 and first excited states [Ne]3s23p53d3 of W54+ ion have been studied by using Multi-Configuration Dirac-Fock method with the implementation of Grasp2K package. A restricted active space method was employed to investigate the correlation contribution from different models. The Breit interaction and QED effects were taken into account in the relativistic configuration interaction calculation with the converged wavefunction. It is found that the correlation contribution from 3s and 3p orbital have important contribution to the energy level, transition wavelength and probability of the ground and the first excited state of W54+ ion. Contribution to the Topical Issue "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, Grzegorz Karwasz.

Vibration Analysis of a Split Path Gearbox

NASA Technical Reports Server (NTRS)

Krantz, Timothy L.; Rashidi, Majid

1995-01-01

Split path gearboxes can be attractive alternatives to the common planetary designs for rotorcraft, but because they have seen little use, they are relatively high risk designs. To help reduce the risk of fielding a rotorcraft with a split path gearbox, the vibration and dynamic characteristics of such a gearbox were studied. A mathematical model was developed by using the Lagrangian method, and it was applied to study the effect of three design variables on the natural frequencies and vibration energy of the gearbox. The first design variable, shaft angle, had little influence on the natural frequencies. The second variable, mesh phasing, had a strong effect on the levels of vibration energy, with phase angles of 0 deg and 180 deg producing low vibration levels. The third design variable, the stiffness of the shafts connecting the spur gears to the helical pinions, strongly influenced the natural frequencies of some of the vibration modes, including two of the dominant modes. We found that, to achieve the lowest level of vibration energy, the natural frequencies of these two dominant modes should be less than those of the main excitation sources.

Structure and Dynamics of Confined C-O-H Fluids Relevant to the Subsurface: Application of Magnetic Resonance, Neutron Scattering and Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Gautam, Siddharth S.; Ok, Salim; Cole, David R.

2017-06-01

Geo-fluids consisting of C-O-H volatiles are the main mode of transport of mass and energy throughout the lithosphere and are commonly found confined in pores, grain boundaries and fractures. The confinement of these fluids by porous media at the length scales of a few nanometers gives rise to numerous physical and chemical properties that deviate from the bulk behavior. Studying the structural and dynamical properties of these confined fluids at the length and time scales of nanometers and picoseconds respectively forms an important component of understanding their behavior. To study confined fluids, non-destructive penetrative probes are needed. Nuclear magnetic resonance (NMR) by virtue of its ability to monitor longitudinal and transverse magnetization relaxations of spins, and chemical shifts brought about by the chemical environment of a nucleus, and measuring diffusion coefficient provides a good opportunity to study dynamics and chemical structure at the molecular length and time scales. Another technique that gives insights into the dynamics and structure at these length and time scales is neutron scattering (NS). This is because the wavelength and energies of cold and thermal neutrons used in scattering experiments are in the same range as the spatial features and energies involved in the dynamical processes occurring at the molecular level. Molecular Dynamics (MD) simulations on the other hand help with the interpretation of the NMR and NS data. Simulations can also supplement the experiments by calculating quantities not easily accessible to experiments. Thus using NMR, NS and MD simulations in conjunction, a complete description of the molecular structure and dynamics of confined geo-fluids can be obtained. In the current review, our aim is to show how a synergistic use of these three techniques has helped shed light on the complex behavior of water, CO2, and low molecular weight hydrocarbons. After summarizing the theoretical backgrounds of the techniques, we will discuss some recent examples of the use of NMR, NS, and MD simulations to the study of confined fluids.

Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter.

PubMed

Gedeon, Patrick C; Thomas, James R; Madura, Jeffry D

2015-01-01

Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis.

Dynamics of the diffusive DM-DE interaction – Dynamical system approach

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

Haba, Zbigniew; Stachowski, Aleksander; Szydłowski, Marek, E-mail: zhab@ift.uni.wroc.pl, E-mail: aleksander.stachowski@uj.edu.pl, E-mail: marek.szydlowski@uj.edu.pl

We discuss dynamics of a model of an energy transfer between dark energy (DE) and dark matter (DM) . The energy transfer is determined by a non-conservation law resulting from a diffusion of dark matter in an environment of dark energy. The relativistic invariance defines the diffusion in a unique way. The system can contain baryonic matter and radiation which do not interact with the dark sector. We treat the Friedman equation and the conservation laws as a closed dynamical system. The dynamics of the model is examined using the dynamical systems methods for demonstration how solutions depend on initialmore » conditions. We also fit the model parameters using astronomical observation: SNIa, H ( z ), BAO and Alcock-Paczynski test. We show that the model with diffuse DM-DE is consistent with the data.« less

Lattice dynamics and metastability of fcc metals in the hcp structure and the crucial role of spin-orbit coupling in platinum

NASA Astrophysics Data System (ADS)

Schönecker, Stephan; Li, Xiaoqing; Richter, Manuel; Vitos, Levente

2018-06-01

We investigate the lattice dynamical properties of Ni, Cu, Rh, Pd, Ag, Ir, Pt, and Au in the nonequilibrium hcp structure by means of density-functional simulations, wherein spin-orbit coupling (SOC) was considered for Ir, Pt, and Au. The determined dynamical properties reveal that all eight elements possess a metastable hcp phase at zero temperature and pressure. The hcp Ni, Cu, Rh, Pd, and Au previously observed in nanostructures support this finding. We make evident that the inclusion of SOC is mandatory for an accurate description of the phonon dispersion relations and dynamical stability of hcp Pt. The underlying sensitivity of the interatomic force constants is ascribed to a SOC-induced splitting of degenerate band states accompanied by a pronounced reduction of electronic density of states at the Fermi level. To give further insight into the importance of SOC in Pt, we (i) focus on phase stability and examine a lattice transformation related to optical phonons in the hcp phase and (ii) focus on the generalized stacking fault energy (GSFE) of the fcc phase pertinent to crystal plasticity. We show that the intrinsic stable and unstable fault energies of the GSFE scale as in other common fcc metals, provided that the spin-orbit interaction is taken into account.

Gravitational Conundrum? Dynamical Mass Segregation versus Disruption of Binary Stars in Dense Stellar Systems

NASA Astrophysics Data System (ADS)

de Grijs, Richard; Li, Chengyuan; Zheng, Yong; Deng, Licai; Hu, Yi; Kouwenhoven, M. B. N.; Wicker, James E.

2013-03-01

Upon their formation, dynamically cool (collapsing) star clusters will, within only a few million years, achieve stellar mass segregation for stars down to a few solar masses, simply because of gravitational two-body encounters. Since binary systems are, on average, more massive than single stars, one would expect them to also rapidly mass segregate dynamically. Contrary to these expectations and based on high-resolution Hubble Space Telescope observations, we show that the compact, 15-30 Myr old Large Magellanic Cloud cluster NGC 1818 exhibits tantalizing hints at the >~ 2σ level of significance (>3σ if we assume a power-law secondary-to-primary mass-ratio distribution) of an increasing fraction of F-star binary systems (with combined masses of 1.3-1.6 M ⊙) with increasing distance from the cluster center, specifically between the inner 10''-20'' (approximately equivalent to the cluster's core and half-mass radii) and the outer 60''-80''. If confirmed, then this will offer support for the theoretically predicted but thus far unobserved dynamical disruption processes of the significant population of "soft" binary systems—with relatively low binding energies compared to the kinetic energy of their stellar members—in star clusters, which we have access to here by virtue of the cluster's unique combination of youth and high stellar density.

Ultrafast direct electron transfer at organic semiconductor and metal interfaces.

PubMed

Xiang, Bo; Li, Yingmin; Pham, C Huy; Paesani, Francesco; Xiong, Wei

2017-11-01

The ability to control direct electron transfer can facilitate the development of new molecular electronics, light-harvesting materials, and photocatalysis. However, control of direct electron transfer has been rarely reported, and the molecular conformation-electron dynamics relationships remain unclear. We describe direct electron transfer at buried interfaces between an organic polymer semiconductor film and a gold substrate by observing the first dynamical electric field-induced vibrational sum frequency generation (VSFG). In transient electric field-induced VSFG measurements on this system, we observe dynamical responses (<150 fs) that depend on photon energy and polarization, demonstrating that electrons are directly transferred from the Fermi level of gold to the lowest unoccupied molecular orbital of organic semiconductor. Transient spectra further reveal that, although the interfaces are prepared without deliberate alignment control, a subensemble of surface molecules can adopt conformations for direct electron transfer. Density functional theory calculations support the experimental results and ascribe the observed electron transfer to a flat-lying polymer configuration in which electronic orbitals are found to be delocalized across the interface. The present observation of direct electron transfer at complex interfaces and the insights gained into the relationship between molecular conformations and electron dynamics will have implications for implementing novel direct electron transfer in energy materials.

A theory for protein dynamics: Global anisotropy and a normal mode approach to local complexity

NASA Astrophysics Data System (ADS)

Copperman, Jeremy; Romano, Pablo; Guenza, Marina

2014-03-01

We propose a novel Langevin equation description for the dynamics of biological macromolecules by projecting the solvent and all atomic degrees of freedom onto a set of coarse-grained sites at the single residue level. We utilize a multi-scale approach where molecular dynamic simulations are performed to obtain equilibrium structural correlations input to a modified Rouse-Zimm description which can be solved analytically. The normal mode solution provides a minimal basis set to account for important properties of biological polymers such as the anisotropic global structure, and internal motion on a complex free-energy surface. This multi-scale modeling method predicts the dynamics of both global rotational diffusion and constrained internal motion from the picosecond to the nanosecond regime, and is quantitative when compared to both simulation trajectory and NMR relaxation times. Utilizing non-equilibrium sampling techniques and an explicit treatment of the free-energy barriers in the mode coordinates, the model is extended to include biologically important fluctuations in the microsecond regime, such as bubble and fork formation in nucleic acids, and protein domain motion. This work supported by the NSF under the Graduate STEM Fellows in K-12 Education (GK-12) program, grant DGE-0742540 and NSF grant DMR-0804145, computational support from XSEDE and ACISS.

A novel laser-collider used to produce monoenergetic 13.3 MeV 7Li (d, n) neutrons

PubMed Central

Zhao, J. R.; Zhang, X. P.; Yuan, D. W.; Li, Y. T.; Li, D. Z.; Rhee, Y. J.; Zhang, Z.; Li, F.; Zhu, B. J.; Li, Yan F.; Han, B.; Liu, C.; Ma, Y.; Li, Yi F.; Tao, M. Z.; Li, M. H.; Guo, X.; Huang, X. G.; Fu, S. Z.; Zhu, J. Q.; Zhao, G.; Chen, L. M.; Fu, C. B.; Zhang, J.

2016-01-01

Neutron energy is directly correlated with the energy of the incident ions in experiments involving laser-driven nuclear reactions. Using high-energy incident ions reduces the energy concentration of the generated neutrons. A novel “laser-collider” method was used at the Shenguang II laser facility to produce monoenergetic neutrons via 7Li (d, n) nuclear reactions. The specially designed K-shaped target significantly increased the numbers of incident d and Li ions at the keV level. Ultimately, 13.3 MeV neutrons were obtained. Considering the time resolution of the neutron detector, we demonstrated that the produced neutrons were monoenergetic. Interferometry and a Multi hydro-dynamics simulation confirmed the monoenergetic nature of these neutrons. PMID:27250660

The North American Energy System: Overview of the 3rd Chapter of SOCCR-2

NASA Astrophysics Data System (ADS)

Marcotullio, P. J.

2016-12-01

North America, including Canada, Mexico and the United States, has a large and complex energy system, which includes the extraction and conversion of primary energy sources and their storage, transmission, distribution and ultimate end use in the building, transportation and industrial sectors. The chapter overviews this system focusing on our understanding of the energy trends and system feedback dynamics, key drivers of change, and subsequent carbon emissions and the basis for carbon management. We also put the carbon emissions from the North American system in global context. Highlights include the changes to the system (sources, fuel mix, drivers, infrastructure, etc.,) over the past decade, and a review of scenarios that provide glimpses into future emissions levels and meeting the requirements for decarbonization in the medium and longer term.

A Hierarchical Approach to Fracture Mechanics

NASA Technical Reports Server (NTRS)

Saether, Erik; Taasan, Shlomo

2004-01-01

Recent research conducted under NASA LaRC's Creativity and Innovation Program has led to the development of an initial approach for a hierarchical fracture mechanics. This methodology unites failure mechanisms occurring at different length scales and provides a framework for a physics-based theory of fracture. At the nanoscale, parametric molecular dynamic simulations are used to compute the energy associated with atomic level failure mechanisms. This information is used in a mesoscale percolation model of defect coalescence to obtain statistics of fracture paths and energies through Monte Carlo simulations. The mathematical structure of predicted crack paths is described using concepts of fractal geometry. The non-integer fractal dimension relates geometric and energy measures between meso- and macroscales. For illustration, a fractal-based continuum strain energy release rate is derived for inter- and transgranular fracture in polycrystalline metals.

Multiscale molecular dynamics simulations of rotary motor proteins.

PubMed

Ekimoto, Toru; Ikeguchi, Mitsunori

2018-04-01

Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

Energy absorption ability of buckyball C720 at low impact speed: a numerical study based on molecular dynamics

PubMed Central

2013-01-01

The dynamic impact response of giant buckyball C720 is investigated by using molecular dynamics simulations. The non-recoverable deformation of C720 makes it an ideal candidate for high-performance energy absorption. Firstly, mechanical behaviors under dynamic impact and low-speed crushing are simulated and modeled, which clarifies the buckling-related energy absorption mechanism. One-dimensional C720 arrays (both vertical and horizontal alignments) are studied at various impact speeds, which show that the energy absorption ability is dominated by the impact energy per buckyball and less sensitive to the number and arrangement direction of buckyballs. Three-dimensional stacking of buckyballs in simple cubic, body-centered cubic, hexagonal, and face-centered cubic forms are investigated. Stacking form with higher occupation density yields higher energy absorption. The present study may shed lights on employing C720 assembly as an advanced energy absorption system against low-speed impacts. PMID:23360618

Understanding self-assembly of charged-neutral block copolymer (BCP) and surfactant complexes using molecular dynamics (MD) simulation

NASA Astrophysics Data System (ADS)

Goswami, Monojoy; Sumpter, Bobby; Kilbey, Michael

Here we report the formation of phase separated BCP-surfactant complexes resulting from the electrostatic self-assembly of charge-neutral block copolymers with oppositely charged surfactants. Complexation behaviors of oppositely charged polyelectrolytes has gained considerable attention in the field of soft condensed matter physics due to their potential application as functional nanomaterials for batteries, wastewater treatment and drug delivery systems. Numerous experiments have examined the self-assembled structures resulting from complexation of charge-neutral BCP and surfactants, however, there is a lack of comprehensive understanding at the fundamental level. To help bridge this gap, we use, MD simulations to study self-assembly and dynamics of the BCP-surfactant complex at the molecular level. Our results show an overcharging effect in BCPs with hydrophobic neutral blocks and a formation of core-shell colloidal structure. Hydrophilic neutral blocks, on the other hand, show stable, hairy colloidal structures with neutral blocks forming a loosely-bound, fuzzy outer layer. Our results qualitatively agree with previous SANS and SAXS experiments. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Materials Science and Engineering Division.

Dynamic Geospatial Modeling of the Building Stock to Project Urban Energy Demand.

PubMed

Breunig, Hanna Marie; Huntington, Tyler; Jin, Ling; Robinson, Alastair; Scown, Corinne Donahue

2018-06-26

In the United States, buildings account for more than 40 percent of total energy consumption, and the evolution of the urban form will impact the effectiveness of strategies to reduce energy use and mitigate emissions. This paper presents a broadly applicable approach for modeling future commercial, residential, and industrial floorspace, thermal consumption (heating and cooling), and associated GHG emissions at the tax assessor land parcel level. The approach accounts for changing building standards and retrofitting, climate change, and trends in housing and industry. We demonstrate the automated workflow for California, and project building stock, thermal energy consumption, and associated GHG emissions out to 2050. Our results suggest that if buildings in California have long lifespans, and minimal energy efficiency improvements compared to building codes reflective of 2008, then the state will face a 20% or higher increase in thermal energy consumption by 2050. Baseline annual GHG emissions associated with thermal energy consumption in the modeled building stock in 2016 is 34% below 1990 levels (110 Mt CO2eq/y).While the 2020 targets for the reduction of GHG emissions set by the California Senate Bill 350 have already been met, none of our scenarios achieve >80% reduction from 1990 levels by 2050, despite assuming an 86% reduction in electricity carbon intensity in our "Low Carbon" scenario. The results highlight the challenge California faces in meeting its new energy efficiency targets unless the State's building stock undergoes timely and strategic turnover, paired with deep retrofitting of existing buildings and natural gas equipment.

Coupled Atmosphere-Surface Modeling of Lake Levels of the North American Great Lakes under Climate Change

NASA Astrophysics Data System (ADS)

Lofgren, B. M.; Xiao, C.

2016-12-01

The influence of projected climate change on the water levels of the Great Lakes is subject to considerable uncertainty, and methods that have long been used to determine this sensitivity have been discredited. A strong candidate, albeit expensive, to replace problematic methods is to use outputs that result from dynamical downscaling of future climate simulations, focused on the hydroclimate of the Great Lakes basin. We have produced initial estimates of Great Lakes water levels in the mid- and late 21st century using the Weather Research and Forecasting (WRF) model, including its lake module, driven by lateral boundary conditions from the Geophysical Fluid Dynamics Lab Climate Model version 3.0 (GFDL CM3), under RCP4.5 and 8.5 scenarios. Future lake levels are influenced by the balance between projected general increases in precipitation and increases in evapotranspiration from both land and lake in the basin, driven primarily by the surface radiative energy budget and secondarily by air temperature. The net result was drops in lake level of up to 15 cm, in contrast to the results from much-used older methods, which often projected drops exceeding 1 m. Future plans include increased detail in the simulation of water flow overland and in river channels using WRF-Hydro, and full coupling of regional atmospheric systems with 3-dimensional dynamical lake implementation of the Finite Volume Community Ocean Model (FVCOM).

Dynamical manifestations of quantum chaos: correlation hole and bulge

NASA Astrophysics Data System (ADS)

Torres-Herrera, E. J.; Santos, Lea F.

2017-10-01

A main feature of a chaotic quantum system is a rigid spectrum where the levels do not cross. We discuss how the presence of level repulsion in lattice many-body quantum systems can be detected from the analysis of their time evolution instead of their energy spectra. This approach is advantageous to experiments that deal with dynamics, but have limited or no direct access to spectroscopy. Dynamical manifestations of avoided crossings occur at long times. They correspond to a drop, referred to as correlation hole, below the asymptotic value of the survival probability and to a bulge above the saturation point of the von Neumann entanglement entropy and the Shannon information entropy. By contrast, the evolution of these quantities at shorter times reflects the level of delocalization of the initial state, but not necessarily a rigid spectrum. The correlation hole is a general indicator of the integrable-chaos transition in disordered and clean models and as such can be used to detect the transition to the many-body localized phase in disordered interacting systems. This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'.

Effect of initial strain and material nonlinearity on the nonlinear static and dynamic response of graphene sheets

NASA Astrophysics Data System (ADS)

Singh, Sandeep; Patel, B. P.

2018-06-01

Computationally efficient multiscale modelling based on Cauchy-Born rule in conjunction with finite element method is employed to study static and dynamic characteristics of graphene sheets, with/without considering initial strain, involving Green-Lagrange geometric and material nonlinearities. The strain energy density function at continuum level is established by coupling the deformation at continuum level to that at atomic level through Cauchy-Born rule. The atomic interactions between carbon atoms are modelled through Tersoff-Brenner potential. The governing equation of motion obtained using Hamilton's principle is solved through standard Newton-Raphson method for nonlinear static response and Newmark's time integration technique to obtain nonlinear transient response characteristics. Effect of initial strain on the linear free vibration frequencies, nonlinear static and dynamic response characteristics is investigated in detail. The present multiscale modelling based results are found to be in good agreement with those obtained through molecular mechanics simulation. Two different types of boundary constraints generally used in MM simulation are explored in detail and few interesting findings are brought out. The effect of initial strain is found to be greater in linear response when compared to that in nonlinear response.

Modulation of ecdysal cyst and toxin dynamics of two Alexandrium (Dinophyceae) species under small-scale turbulence

NASA Astrophysics Data System (ADS)

Bolli, L.; Llaveria, G.; Garcés, E.; Guadayol, Ó.; van Lenning, K.; Peters, F.; Berdalet, E.

2007-03-01

In some dinoflagellate species, physiological processes appear to be altered by exposure to certain turbulent conditions. Here we investigated how two levels of turbulent kinetic energy dissipation rates (ɛ = 0.4 and 27 cm2 s-3) affected the toxin and ecdysal cyst dynamics of two bloom forming species, Alexandrium minutum and A. catenella. The most striking responses were observed at the high ɛ generated by an orbital shaker. In A. catenella, lower cellular toxin content was measured in cultures shaken for more than 4 days. The same trend was observed in A. minutum, although variability masked statistical significance. For the two species, inhibition of ecdysal cyst production occurred immediately and during the period of exposure of the cultures to stirring (4 or more days) at any time during their growth curve. Recovery of cyst abundances was always observed when turbulence stopped. When turbulence persisted for more than 4 days the net growth rate significantly decreased and the final biomass yield was lower than in the unshaken cultures. This study suggests that high levels of small-scale turbulence would contribute to the modulation of the harmful bloom dynamics through the interaction at the level of toxin and encystment processes.

Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals.

PubMed

Ambrosio, Francesco; Miceli, Giacomo; Pasquarello, Alfredo

2015-12-28

We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H(+)/H2 level defining the standard hydrogen electrode, the OH(-)/OH(∗) level corresponding to the oxidation of the hydroxyl ion, and the H2O/OH(∗) level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band-edge positions, and redox levels in overall good agreement with experiment.

Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals

NASA Astrophysics Data System (ADS)

Ambrosio, Francesco; Miceli, Giacomo; Pasquarello, Alfredo

2015-12-01

We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H+/H2 level defining the standard hydrogen electrode, the OH-/OH∗ level corresponding to the oxidation of the hydroxyl ion, and the H2O/OH∗ level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band-edge positions, and redox levels in overall good agreement with experiment.

Keeping returns optimal: gain control exerted through sensitivity adjustments in the harbour porpoise auditory system

PubMed Central

Linnenschmidt, Meike; Beedholm, Kristian; Wahlberg, Magnus; Højer-Kristensen, Jakob; Nachtigall, Paul E.

2012-01-01

Animals that use echolocation (biosonar) listen to acoustic signals with a large range of intensities, because echo levels vary with the fourth power of the animal's distance to the target. In man-made sonar, engineers apply automatic gain control to stabilize the echo energy levels, thereby rendering them independent of distance to the target. Both toothed whales and bats vary the level of their echolocation clicks to compensate for the distance-related energy loss. By monitoring the auditory brainstem response (ABR) during a psychophysical task, we found that a harbour porpoise (Phocoena phocoena), in addition to adjusting the sound level of the outgoing signals up to 5.4 dB, also reduces its ABR threshold by 6 dB when the target distance doubles. This self-induced threshold shift increases the dynamic range of the biosonar system and compensates for half of the variation of energy that is caused by changes in the distance to the target. In combination with an increased source level as a function of target range, this helps the porpoise to maintain a stable echo-evoked ABR amplitude irrespective of target range, and is therefore probably an important tool enabling porpoises to efficiently analyse and classify received echoes. PMID:22279169

Stable schemes for dissipative particle dynamics with conserved energy

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

Stoltz, Gabriel, E-mail: stoltz@cermics.enpc.fr

2017-07-01

This article presents a new numerical scheme for the discretization of dissipative particle dynamics with conserved energy. The key idea is to reduce elementary pairwise stochastic dynamics (either fluctuation/dissipation or thermal conduction) to effective single-variable dynamics, and to approximate the solution of these dynamics with one step of a Metropolis–Hastings algorithm. This ensures by construction that no negative internal energies are encountered during the simulation, and hence allows to increase the admissible timesteps to integrate the dynamics, even for systems with small heat capacities. Stability is only limited by the Hamiltonian part of the dynamics, which suggests resorting to multiplemore » timestep strategies where the stochastic part is integrated less frequently than the Hamiltonian one.« less

Validation of the train energy and dynamics simulator (TEDS).

DOT National Transportation Integrated Search

2015-01-01

FRA has developed Train Energy and Dynamics Simulator (TEDS) based upon a longitudinal train dynamics and operations : simulation model which allows users to conduct safety and risk evaluations, incident investigations, studies of train operations, :...