Discrete kinetic models from funneled energy landscape simulations.
Directory of Open Access Journals (Sweden)
Nicholas P Schafer
Full Text Available A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK. In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.
Research using energy landscape
International Nuclear Information System (INIS)
Kim, Hack Jin
2007-01-01
Energy landscape is a theoretical tool used for the study of systems where cooperative processes occur such as liquid, glass, clusters, and protein. Theoretical and experimental researches related to energy landscape are introduced in this review
Wales, David J.
2018-04-01
Recent advances in the potential energy landscapes approach are highlighted, including both theoretical and computational contributions. Treating the high dimensionality of molecular and condensed matter systems of contemporary interest is important for understanding how emergent properties are encoded in the landscape and for calculating these properties while faithfully representing barriers between different morphologies. The pathways characterized in full dimensionality, which are used to construct kinetic transition networks, may prove useful in guiding such calculations. The energy landscape perspective has also produced new procedures for structure prediction and analysis of thermodynamic properties. Basin-hopping global optimization, with alternative acceptance criteria and generalizations to multiple metric spaces, has been used to treat systems ranging from biomolecules to nanoalloy clusters and condensed matter. This review also illustrates how all this methodology, developed in the context of chemical physics, can be transferred to landscapes defined by cost functions associated with machine learning.
Energy landscape Allgaeu; Energielandschaft Allgaeu
Energy Technology Data Exchange (ETDEWEB)
NONE
2013-04-01
In tandems with questions on the energy policy turnaround, the topics cultural landscape history, morphology, actual land use, tourism, settlement development or infrastructure are summarized in regional concepts and designs to a consistent landscape. Thus, a true integration of renewable energies in the landscape enhances existing or creates completely new landscape qualities. Energy supply shall be understood as a component of the every day life world. The energy supply shall not be hidden any more, but it rather should be communicated as the brand 'Allgaeu'.
Dark energy from discrete spacetime.
Directory of Open Access Journals (Sweden)
Aaron D Trout
Full Text Available Dark energy accounts for most of the matter-energy content of our universe, yet current theories of its origin rely on radical physical assumptions such as the holographic principle or controversial anthropic arguments. We give a better motivated explanation for dark energy, claiming that it arises from a small negative scalar-curvature present even in empty spacetime. The vacuum has this curvature because spacetime is fundamentally discrete and there are more ways for a discrete geometry to have negative curvature than positive. We explicitly compute this effect using a variant of the well known dynamical-triangulations (DT model for quantum gravity. Our model predicts a time-varying non-zero cosmological constant with a current value, [Formula: see text] in natural units, in agreement with observation. This calculation is made possible by a novel characterization of the possible DT action values combined with numerical evidence concerning their degeneracies.
Dark energy from discrete spacetime.
Trout, Aaron D
2013-01-01
Dark energy accounts for most of the matter-energy content of our universe, yet current theories of its origin rely on radical physical assumptions such as the holographic principle or controversial anthropic arguments. We give a better motivated explanation for dark energy, claiming that it arises from a small negative scalar-curvature present even in empty spacetime. The vacuum has this curvature because spacetime is fundamentally discrete and there are more ways for a discrete geometry to have negative curvature than positive. We explicitly compute this effect using a variant of the well known dynamical-triangulations (DT) model for quantum gravity. Our model predicts a time-varying non-zero cosmological constant with a current value, [Formula: see text] in natural units, in agreement with observation. This calculation is made possible by a novel characterization of the possible DT action values combined with numerical evidence concerning their degeneracies.
Discrete symmetries in the heterotic-string landscape
International Nuclear Information System (INIS)
Athanasopoulos, P
2015-01-01
We describe a new type of discrete symmetry that relates heterotic-string models. It is based on the spectral flow operator which normally acts within a general N = (2, 2) model and we use this operator to construct a map between N = (2, 0) models. The landscape of N = (2, 0) models is of particular interest among all heterotic-string models for two important reasons: Firstly, N =1 spacetime SUSY requires (2, 0) superconformal invariance and secondly, models with the well motivated by the Standard Model SO(10) unification structure are of this type. This idea was inspired by a new discrete symmetry in the space of fermionic ℤ 2 × ℤ 2 heterotic-string models that exchanges the spinors and vectors of the SO(10) GUT group, dubbed spinor-vector duality. We will describe how to generalize this to arbitrary internal rational Conformal Field Theories. (paper)
Discrete symmetries in the heterotic-string landscape
Athanasopoulos, P.
2015-07-01
We describe a new type of discrete symmetry that relates heterotic-string models. It is based on the spectral flow operator which normally acts within a general N = (2, 2) model and we use this operator to construct a map between N = (2, 0) models. The landscape of N = (2, 0) models is of particular interest among all heterotic-string models for two important reasons: Firstly, N =1 spacetime SUSY requires (2, 0) superconformal invariance and secondly, models with the well motivated by the Standard Model SO(10) unification structure are of this type. This idea was inspired by a new discrete symmetry in the space of fermionic ℤ2 × ℤ2 heterotic-string models that exchanges the spinors and vectors of the SO(10) GUT group, dubbed spinor-vector duality. We will describe how to generalize this to arbitrary internal rational Conformal Field Theories.
Energy landscapes in a crowded world
Pasqualetti, Martin; Stremke, Sven
2018-01-01
One of the main drivers of landscape transformation has been our demand for energy. We refer to the results of such transformations as "energy landscapes". This paper examines the definition of energy landscapes within a conceptual framework, proposes a classification of energy landscapes, and
Energy Landscape of Social Balance
Marvel, Seth A.; Strogatz, Steven H.; Kleinberg, Jon M.
2009-11-01
We model a close-knit community of friends and enemies as a fully connected network with positive and negative signs on its edges. Theories from social psychology suggest that certain sign patterns are more stable than others. This notion of social “balance” allows us to define an energy landscape for such networks. Its structure is complex: numerical experiments reveal a landscape dimpled with local minima of widely varying energy levels. We derive rigorous bounds on the energies of these local minima and prove that they have a modular structure that can be used to classify them.
Energy landscape of social balance.
Marvel, Seth A; Strogatz, Steven H; Kleinberg, Jon M
2009-11-06
We model a close-knit community of friends and enemies as a fully connected network with positive and negative signs on its edges. Theories from social psychology suggest that certain sign patterns are more stable than others. This notion of social "balance" allows us to define an energy landscape for such networks. Its structure is complex: numerical experiments reveal a landscape dimpled with local minima of widely varying energy levels. We derive rigorous bounds on the energies of these local minima and prove that they have a modular structure that can be used to classify them.
Energy transition: towards landscape devastation?
International Nuclear Information System (INIS)
Posokhow, Andre
2013-09-01
The author criticizes some aspects of the content of the French policy for energy transition. He states that the objective of reduction of greenhouse emissions is unreachable and moreover useless when China keeps on opening new coal-fired power stations. He states that temperatures do not increase any longer and that it is not sure that CO 2 emissions are responsible for past increases. He outlines that the power of wind turbines is only a quarter of their theoretical one, that replacing nuclear energy by wind energy would require the installation of 33.000 wind turbines. He states that objectives of energy saving are not credible, and that the energy mix predictions are fuzzy. He outlines contradictions about the nuclear power station life duration, states that the installation of 210 wind turbines per district would devastate the French landscape
Competing Wind Energy Discourses, Contested Landscapes
Directory of Open Access Journals (Sweden)
Antje Otto
2014-10-01
Full Text Available The impairment of landscapes is a concern constantly raised against wind energy developments in Germany as in other countries. Often, landscapes or landscape types are treated in the literature as essentialist or at least as uncontested categories. We analyse two examples of local controversies about wind energy, in which “landscape” is employed by supporters and opponents alike, from a poststructuralist and discourse theoretical angle. The aim is to identify and compare landscape constructs produced in the micro discourses of wind energy objectors and proponents at local level (a within each case, (b between the two cases and (c with landscape constructs that were previously found in macro discourses. One major finding is that several different landscapes can exist at one and the same place. Furthermore there seems to be a relatively stable set of competing landscape concepts which is reproduced in specific controversies. The paper concludes by highlighting practical consequences and by identifying promising avenues of further research.
Sustainable energy landscapes : designing, planning, and development
Stremke, S.; Dobbelsteen, van den A.
2013-01-01
In the near future the appearance and spatial organization of urban and rural landscapes will be strongly influenced by the generation of renewable energy. One of the critical tasks will be the re-integration of these sustainable energy landscapes into the existing environment—which people value and
Energy forest cultivation and the landscape
International Nuclear Information System (INIS)
Bell, Simon
1994-01-01
The place of energy forestry in the landscape is discussed, principally with reference to Britain and Europe. The importance of design as a means of ensuring an attractive appearance, while meeting functional and economic requirements, is stressed. Simple design principles which help energy forests, mainly short rotation arable coppice, to fit into the landscape are suggested. (author)
International Nuclear Information System (INIS)
2014-06-01
This guide first defines the notion of landscape, outlines what is at stake with decentralised renewable energy production, and presents the various important aspects of a deployment of decentralised renewable energy production. It describes how to define a general strategy for the integration of this production: relationship between energy and landscape, project implementation, partnership, tools to anticipate changes, evolution of social demand through dialogue, conciliation of technical and financial constraints and landscape ambitions. An appendix proposes legal and bibliographical information: legal relationships between energy and landscape, possible arrangements for PLU (plan local d'urbanisme, local urban plan) and SCOT (schema de coherence territoriale, territorial planning document)
Energy-pointwise discrete ordinates transport methods
International Nuclear Information System (INIS)
Williams, M.L.; Asgari, M.; Tashakorri, R.
1997-01-01
A very brief description is given of a one-dimensional code, CENTRM, which computes a detailed, space-dependent flux spectrum in a pointwise-energy representation within the resolved resonance range. The code will become a component in the SCALE system to improve computation of self-shielded cross sections, thereby enhancing the accuracy of codes such as KENO. CENTRM uses discrete-ordinates transport theory with an arbitrary angular quadrature order and a Legendre expansion of scattering anisotropy for moderator materials and heavy nuclides. The CENTRM program provides capability to deterministically compute full energy range, space-dependent angular flux spectra, rigorously accounting for resonance fine-structure and scattering anisotropy effects
Energy landscapes shape animal movement ecology.
Shepard, Emily L C; Wilson, Rory P; Rees, W Gareth; Grundy, Edward; Lambertucci, Sergio A; Vosper, Simon B
2013-09-01
The metabolic costs of animal movement have been studied extensively under laboratory conditions, although frequently these are a poor approximation of the costs of operating in the natural, heterogeneous environment. Construction of "energy landscapes," which relate animal locality to the cost of transport, can clarify whether, to what extent, and how movement properties are attributable to environmental heterogeneity. Although behavioral responses to aspects of the energy landscape are well documented in some fields (notably, the selection of tailwinds by aerial migrants) and scales (typically large), the principles of the energy landscape extend across habitat types and spatial scales. We provide a brief synthesis of the mechanisms by which environmentally driven changes in the cost of transport can modulate the behavioral ecology of animal movement in different media, develop example cost functions for movement in heterogeneous environments, present methods for visualizing these energy landscapes, and derive specific predictions of expected outcomes from individual- to population- and species-level processes. Animals modulate a suite of movement parameters (e.g., route, speed, timing of movement, and tortuosity) in relation to the energy landscape, with the nature of their response being related to the energy savings available. Overall, variation in movement costs influences the quality of habitat patches and causes nonrandom movement of individuals between them. This can provide spatial and/or temporal structure to a range of population- and species-level processes, ultimately including gene flow. Advances in animal-attached technology and geographic information systems are opening up new avenues for measuring and mapping energy landscapes that are likely to provide new insight into their influence in animal ecology.
International Nuclear Information System (INIS)
Ching, J.; Oblow, E.M.; Goldstein, H.
1976-01-01
An algebraic equivalence between the point-energy and multigroup forms of the Boltzmann transport equation is demonstrated that allows the development of a discrete energy, discrete ordinates method for the solution of radiation transport problems. In the discrete energy method, the group averaging required in the cross-section processing for multigroup calculations is replaced by a faster numerical quadrature scheme capable of generating transfer cross sections describing all the physical processes of interest on a fine point-energy grid. Test calculations in which the discrete energy method is compared with the multigroup method show that, for the same energy grid, the discrete energy method is much faster, although somewhat less accurate, than the multigroup method. However, the accuracy of the discrete energy method increases rapidly as the spacing between energy grid points is decreased, approaching that of multigroup calculations. For problems requiring great detail in the energy spectrum, the discrete energy method is therefore expected to be far more economical than the multigroup technique for equivalent accuracy solutions. This advantage of the point method is demonstrated by application to the study of neutron transport in a thick iron slab
The renewable energies: the landscape
International Nuclear Information System (INIS)
Acket, C.; Bacher, P.
2005-03-01
If one takes into account the hydroelectric power, the France is the first european country in the renewable energies domain. The position is also honorable concerning the wood energy. Meanwhile, for the solar and wind energy, France is late. To discuss this debate, the authors bring together today data on the renewable energies, offer some proposals for the next 50 years taking into account the reduction of greenhouse gases emission for 2050. (A.L.B.)
Towards an Integrated Energy Landscape
de Boer, Jessica; Zuidema, Christian
2013-01-01
In this paper, we show that an area-based approach to fostering the ‘energy transition’ has potential to help spatial planners and policy makers understand how innovative sustainable energy initiatives may contribute to the energy transition. On the basis of a desk study of research reports on
Orientational dynamics and energy landscape features of ...
Indian Academy of Sciences (India)
WINTEC
Energy landscape analysis of inherent structures shows that the ... to be strikingly similar to that of supercooled molecular liquids5 .... where eiα is the α-component (in the space-fixed frame) of the unit orientation vector ei along the principal symmetry axis of the ith ellipsoid of revo- ..... understand pathways of protein folding.
Accelerated weight histogram method for exploring free energy landscapes
Energy Technology Data Exchange (ETDEWEB)
Lindahl, V.; Lidmar, J.; Hess, B. [Department of Theoretical Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm (Sweden)
2014-07-28
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies from these simulations remains a major challenge. Fully exploring the free energy landscape of, say, a biological macromolecule typically requires sampling large conformational changes and slow transitions. Often, the only feasible way to study such a system is to simulate it using an enhanced sampling method. The accelerated weight histogram (AWH) method is a new, efficient extended ensemble sampling technique which adaptively biases the simulation to promote exploration of the free energy landscape. The AWH method uses a probability weight histogram which allows for efficient free energy updates and results in an easy discretization procedure. A major advantage of the method is its general formulation, making it a powerful platform for developing further extensions and analyzing its relation to already existing methods. Here, we demonstrate its efficiency and general applicability by calculating the potential of mean force along a reaction coordinate for both a single dimension and multiple dimensions. We make use of a non-uniform, free energy dependent target distribution in reaction coordinate space so that computational efforts are not wasted on physically irrelevant regions. We present numerical results for molecular dynamics simulations of lithium acetate in solution and chignolin, a 10-residue long peptide that folds into a β-hairpin. We further present practical guidelines for setting up and running an AWH simulation.
Exploring the conformational energy landscape of proteins
Energy Technology Data Exchange (ETDEWEB)
Nienhaus, G.U. [Univ. of Illinois, Urbana, IL (United States)]|[Universitaet Ulm (Germany); Mueller, J.D.; McMahon, B.H. [Univ. of Illinois, Urbana, IL (United States)] [and others
1997-04-01
Proteins possess a complex energy landscape with a large number of local minima called conformational substates that are arranged in a hierarchical fashion. Here we discuss experiments aimed at the elucidation of the energy landscape in carbonmonoxy myoglobin (MbCO). In the highest tier of the hierarchy, a few taxonomic substates exist. Because of their small number, these substates are accessible to detailed structural investigations. Spectroscopic experiments are discussed that elucidate the role of protonations of amino acid side chains in creating the substates. The lower tiers of the hierarchy contain a large number of statistical substates. Substate interconversions are observed in the entire temperature range from below 1 K up to the denaturation temperature, indicating a wide spectrum of energy barriers that separate the substates.
The changing geopolitical landscape of energy
International Nuclear Information System (INIS)
Lesourne, Jacques
2011-08-01
The author first discusses the impact of the financial crisis of 2008, and of the large-scale exploitation of shale gases in the USA on energy policies and on the geopolitical landscape of energy. Then, he discusses the influence that events which occurred in 2011 had on these issues: firstly, the Copenhagen and Cancun Conferences, secondly, the Fukushima accident, thirdly, the nuclear phasing-out by Germany and incidentally by Italy, and fourthly, the Arab Spring. In the next parts, he comments the consequences for the European energy policy, and the perspectives for the struggle against climate change
Stremke, S.
2013-01-01
For some time now, the concept of “energy landscape” is discussed in academia while more and more practising landscape architects contribute to the siting, designing, and assessment of renewable energy technologies (see Stremke et al. 2012). Yet, there remains some ambiguity what exactly is meant
New interaction paths in the energy landscape: the role of local energy initiatives
de Boer, Jessica; Zuidema, Christian; Gugerell, Katharina
2018-01-01
Energy transition is an encompassing process which not only involves the energy system but also the landscape in which the energy system is embedded. Renewable energy is triggering new interactions with local landscapes in physical, socio-economic and institutional senses. We capture these interactions using the energy landscape concept, which expresses the interdependence of the energy system with the landscape. We aim to understand whether and how local energy initiatives facilitate this in...
Discrete event simulations for glycolysis pathway and energy balance
Zwieten, van D.A.J.; Rooda, J.E.; Armbruster, H.D.; Nagy, J.D.
2010-01-01
In this report, the biological network of the glycolysis pathway has been modeled using discrete event models (DEMs). The most important feature of this pathway is that energy is released. To create a stable steady-state system an energy molecule equilibrating enzyme and metabolic reactions have
Maximal energy extraction under discrete diffusive exchange
Energy Technology Data Exchange (ETDEWEB)
Hay, M. J., E-mail: hay@princeton.edu [Department of Astrophysical Sciences, Princeton University, Princeton, New Jersey 08544 (United States); Schiff, J. [Department of Mathematics, Bar-Ilan University, Ramat Gan 52900 (Israel); Fisch, N. J. [Department of Astrophysical Sciences, Princeton University, Princeton, New Jersey 08544 (United States); Princeton Plasma Physics Laboratory, Princeton, New Jersey 08543 (United States)
2015-10-15
Waves propagating through a bounded plasma can rearrange the densities of states in the six-dimensional velocity-configuration phase space. Depending on the rearrangement, the wave energy can either increase or decrease, with the difference taken up by the total plasma energy. In the case where the rearrangement is diffusive, only certain plasma states can be reached. It turns out that the set of reachable states through such diffusive rearrangements has been described in very different contexts. Building upon those descriptions, and making use of the fact that the plasma energy is a linear functional of the state densities, the maximal extractable energy under diffusive rearrangement can then be addressed through linear programming.
Potential energy landscapes of elemental and heterogeneous chalcogen clusters
International Nuclear Information System (INIS)
Mauro, John C.; Loucks, Roger J.; Balakrishnan, Jitendra; Varshneya, Arun K.
2006-01-01
We describe the potential energy landscapes of elemental S 8 , Se 8 , and Te 8 clusters using disconnectivity graphs. Inherent structures include both ring and chain configurations, with rings especially dominant in Se 8 . We also map the potential energy landscapes of heterogeneous Se n (S,Te) 8-n clusters, which offer insights into the structure of heterogeneous chalcogen glasses
Mitigation/Adaptation: landscape architecture meets sustainable energy transition
Stremke, S.
2009-01-01
Mitigation of climate change and adaptation to renewable energy sources are among the emerging fields of activity in landscape architecture. If landscape architects recognize the need for sustainable development on the basis of renewable energy sources, then how can we contribute to sustainable and
Testing the discreteness of spacetime at low energies
International Nuclear Information System (INIS)
Chardin, G.
1994-01-01
Expected at the Planck scale, the discreteness of spacetime can hardly be tested at such high energies in a foreseable future. However, the Bekenstein relation suggests another approach, based on the study of time-asymmetry. After a brief introduction to discrete physics, the relation between gravitation and discreteness on the one hand, and between gravitation and time-asymmetry on the other was investigated. These relations have led to reconsider the possibility that CP violation in the neutral kaon system, the only known microscopic 'arrow of time', could be attributed to gravitation. The arguments suggesting that 'antigravity' could occur for antimatter and could even be expected in General Relativity itself are summarized. Experimental tests are proposed. (author). 48 refs
Testing the discreteness of spacetime at low energies
Energy Technology Data Exchange (ETDEWEB)
Chardin, G. [CEA Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France). Dept. d`Astrophysique, de la Physique des Particules, de la Physique Nucleaire et de l`Instrumentation Associee
1994-12-31
Expected at the Planck scale, the discreteness of spacetime can hardly be tested at such high energies in a foreseable future. However, the Bekenstein relation suggests another approach, based on the study of time-asymmetry. After a brief introduction to discrete physics, the relation between gravitation and discreteness on the one hand, and between gravitation and time-asymmetry on the other was investigated. These relations have led to reconsider the possibility that CP violation in the neutral kaon system, the only known microscopic `arrow of time`, could be attributed to gravitation. The arguments suggesting that `antigravity` could occur for antimatter and could even be expected in General Relativity itself are summarized. Experimental tests are proposed. (author). 48 refs.
Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.
Directory of Open Access Journals (Sweden)
Paul C Whitford
Full Text Available Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.
Histogram plots and cutoff energies for nuclear discrete levels
International Nuclear Information System (INIS)
Belgya, T.; Molnar, G.; Fazekas, B.; Oestoer, J.
1997-05-01
Discrete level schemes for 1277 nuclei, from 6 Li through 251 Es, extracted from the Evaluated Nuclear Structure Data File were analyzed. Cutoff energies (U max ), indicating the upper limit of level scheme completeness, were deduced from the inspection of histograms of the cumulative number of levels. Parameters of the constant-temperature level density formula (nuclear temperature T and energy shift U 0 ) were obtained by means of the least square fit of the formula to the known levels below cutoff energy. The results are tabulated for all 1277 nuclei allowing for an easy and reliable application of the constant-temperature level density approach. A complete set of cumulative plots of discrete levels is also provided. (author). 5 figs, 2 tabs
Energy landscapes in proteins and glasses
Singh, Sadanand
Soft materials are ubiquitous in our day-to-day life. They include liquids, colloids, polymers, foams, gels, granular systems, and a number of biological materials. While these materials exhibit a wide range of textures and morphologies, many of their properties have common physicochemical origins. A better understanding of such origins would lead to rational design and engineering of functional soft materials. A common feature of soft materials is the wide range of time and length scales that characterizes their behavior. Unfortunately, available molecular modeling techniques are often ill-suited for problems that exhibit multiple length and time scales. In this thesis, we introduce and implement new simulation methods that have enabled molecular-level studies of soft materials. Such methods permit calculation of free energy surfaces, and we demonstrate their usefulness in the context of proteins and glasses, both of which exhibit rugged free energy landscapes. A first application is concerned with human amylin, a protein associated with Type II diabetes. Patients with Type II diabetes exhibit fibrillar deposits of human amylin protein in the pancreas. By applying the advanced simulation methods and algorithms developed in this work, we investigate the structure and folding dynamics of human amylin. A detailed mechanism is presented at the atomic-level for the nucleation and aggregation of the peptide. The results presented in this work could help in development of therapeutic strategies for Type II diabetes. The second application is concerned with the study of vapor-deposited ultrastable glasses. These stable glasses have, far below the conventional glass transition temperature, the properties expected from the equilibrium supercooled liquid state. Our results indicate that optimal stability is attained when deposition occurs near the Kauzmann temperature. We also show that the extraordinary stability of model vapor deposited glasses is associated with distinct
How animals distribute themselves in space: variable energy landscapes
Masello, Juan F.; Kato, Akiko; Sommerfeld, Julia; Mattern, Thomas; Quillfeldt, Petra
2017-01-01
Background Foraging efficiency determines whether animals will be able to raise healthy broods, maintain their own condition, avoid predators and ultimately increase their fitness. Using accelerometers and GPS loggers, features of the habitat and the way animals deal with variable conditions can be translated into energetic costs of movement, which, in turn, can be translated to energy landscapes.We investigated energy landscapes in Gentoo Penguins Pygoscelis papua from two colonies at New Is...
Ideal glass transitions in thin films: An energy landscape perspective
Truskett, Thomas M.; Ganesan, Venkat
2003-01-01
We introduce a mean-field model for the potential energy landscape of a thin fluid film confined between parallel substrates. The model predicts how the number of accessible basins on the energy landscape and, consequently, the film's ideal glass transition temperature depend on bulk pressure, film thickness, and the strength of the fluid-fluid and fluid-substrate interactions. The predictions are in qualitative agreement with the experimental trends for the kinetic glass transition temperatu...
Ideal glass transitions in thin films: An energy landscape perspective
Truskett, Thomas M.; Ganesan, Venkat
2003-07-01
We introduce a mean-field model for the potential energy landscape of a thin fluid film confined between parallel substrates. The model predicts how the number of accessible basins on the energy landscape and, consequently, the film's ideal glass transition temperature depend on bulk pressure, film thickness, and the strength of the fluid-fluid and fluid-substrate interactions. The predictions are in qualitative agreement with the experimental trends for the kinetic glass transition temperature of thin films, suggesting the utility of landscape-based approaches for studying the behavior of confined fluids.
The effects of landscaping on the residential cooling energy
Misni, A.
2018-02-01
This paper examines the effectiveness of landscaping on the air-conditioning energy saving of houses in a tropical environment. This case study involved looking at the construction and landscaping of three single-family houses in three sections of Shah Alam, Selangor, Malaysia. The houses ranged in age from 5 to 30 years old, which provided different examples of construction and maturity levels of the surrounding landscaping. Landscaping affects the thermal performance as well as on the air-conditioning energy of houses, in how it provides shade, channels wind, and evapotranspiration. While the construction of the three houses was similar, they were different in size and design, including their landscape design. These houses were chosen because they are representative of single-family tropical houses and landscaping styles in Malaysia since 30 years ago. Three houses were chosen; the 30-year-old house, the 10-year-old house, and the 5-year-old house. In a tropical country, landscaping is used to reduce the effects of the hot and humid climate. The houses spent 15-45% of the electricity cost on cooling. These results were influenced by human factors and the surrounding landscaping. Every type of vegetation, such as trees, grass, shrubs, groundcover, and turf, contributes to reducing air temperatures near the house and providing evaporative cooling.
Random versus Deterministic Descent in RNA Energy Landscape Analysis
Directory of Open Access Journals (Sweden)
Luke Day
2016-01-01
Full Text Available Identifying sets of metastable conformations is a major research topic in RNA energy landscape analysis, and recently several methods have been proposed for finding local minima in landscapes spawned by RNA secondary structures. An important and time-critical component of such methods is steepest, or gradient, descent in attraction basins of local minima. We analyse the speed-up achievable by randomised descent in attraction basins in the context of large sample sets where the size has an order of magnitude in the region of ~106. While the gain for each individual sample might be marginal, the overall run-time improvement can be significant. Moreover, for the two nongradient methods we analysed for partial energy landscapes induced by ten different RNA sequences, we obtained that the number of observed local minima is on average larger by 7.3% and 3.5%, respectively. The run-time improvement is approximately 16.6% and 6.8% on average over the ten partial energy landscapes. For the large sample size we selected for descent procedures, the coverage of local minima is very high up to energy values of the region where the samples were randomly selected from the partial energy landscapes; that is, the difference to the total set of local minima is mainly due to the upper area of the energy landscapes.
Potential energy landscape of TIP4P/2005 water
Handle, Philip H.; Sciortino, Francesco
2018-04-01
We report a numerical study of the statistical properties of the potential energy landscape of TIP4P/2005, one of the most accurate rigid water models. We show that, in the region where equilibrated configurations can be generated, a Gaussian landscape description is able to properly describe the model properties. We also find that the volume dependence of the landscape properties is consistent with the existence of a locus of density maxima in the phase diagram. The landscape-based equation of state accurately reproduces the TIP4P/2005 pressure-vs-volume curves, providing a sound extrapolation of the free-energy at low T. A positive-pressure liquid-liquid critical point is predicted by the resulting free-energy.
New interaction paths in the energy landscape: the role of local energy initiatives
de Boer, Jessica; Zuidema, Christian; Gugerell, Katharina
2018-01-01
Energy transition is an encompassing process which not only involves the energy system but also the landscape in which the energy system is embedded. Renewable energy is triggering new interactions with local landscapes in physical, socio-economic and institutional senses. We capture these
International Nuclear Information System (INIS)
Ching, J.T.
1975-01-01
An algebraic equivalence between the point-energy and multigroup forms of the Boltzmann transport equation is demonstrated which allows the development of a discrete-energy, discrete-ordinates method for the solution of radiation transport problems. The method utilizes a modified version of a cross section processing scheme devised for the moments method code BMT and the transport equation solution algorithm from the one-dimensional discrete-ordinates transport code ANISN. The combined system, identified as MOMANS, computes fluxes directly from point cross sections in a single operation. In the cross-section processing, the group averaging required for multigroup calculations is replaced by a fast numerical scheme capable of generating a set of transfer cross sections containing all the physical features of interest, thereby increasing the detail in the calculated results. Test calculations in which the discrete-energy method was compared with the multigroup method have shown that for the same energy grid (number of points = number of groups), the discrete-energy method is faster but somewhat less accurate than the multigroup method. However, the accuracy of the discrete-energy method increases rapidly as the spacing between energy points is decreased, approaching that of multigroup calculations. For problems requiring great detail in the energy spectrum the discrete-energy method has therefore proven to be as accurate as, and more economical than, the multigroup technique. This was demonstrated by the application of the method to the study of the transport of neutrons in an iron sphere. Using the capability of the discrete-energy method for rapidly treating changes in cross-section sets, the propagation of neutrons from a 14 MeV source in a 22 cm radius sphere of iron was analyzed for sensitivity to changes in the microscopic scattering mechanisms
Energy landscapes for a machine learning application to series data
Energy Technology Data Exchange (ETDEWEB)
Ballard, Andrew J.; Stevenson, Jacob D.; Das, Ritankar; Wales, David J., E-mail: dw34@cam.ac.uk [University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW (United Kingdom)
2016-03-28
Methods developed to explore and characterise potential energy landscapes are applied to the corresponding landscapes obtained from optimisation of a cost function in machine learning. We consider neural network predictions for the outcome of local geometry optimisation in a triatomic cluster, where four distinct local minima exist. The accuracy of the predictions is compared for fits using data from single and multiple points in the series of atomic configurations resulting from local geometry optimisation and for alternative neural networks. The machine learning solution landscapes are visualised using disconnectivity graphs, and signatures in the effective heat capacity are analysed in terms of distributions of local minima and their properties.
Energy landscapes for a machine learning application to series data
International Nuclear Information System (INIS)
Ballard, Andrew J.; Stevenson, Jacob D.; Das, Ritankar; Wales, David J.
2016-01-01
Methods developed to explore and characterise potential energy landscapes are applied to the corresponding landscapes obtained from optimisation of a cost function in machine learning. We consider neural network predictions for the outcome of local geometry optimisation in a triatomic cluster, where four distinct local minima exist. The accuracy of the predictions is compared for fits using data from single and multiple points in the series of atomic configurations resulting from local geometry optimisation and for alternative neural networks. The machine learning solution landscapes are visualised using disconnectivity graphs, and signatures in the effective heat capacity are analysed in terms of distributions of local minima and their properties.
Inflation in random landscapes with two energy scales
Blanco-Pillado, Jose J.; Vilenkin, Alexander; Yamada, Masaki
2018-02-01
We investigate inflation in a multi-dimensional landscape with a hierarchy of energy scales, motivated by the string theory, where the energy scale of Kahler moduli is usually assumed to be much lower than that of complex structure moduli and dilaton field. We argue that in such a landscape, the dynamics of slow-roll inflation is governed by the low-energy potential, while the initial condition for inflation are determined by tunneling through high-energy barriers. We then use the scale factor cutoff measure to calculate the probability distribution for the number of inflationary e-folds and the amplitude of density fluctuations Q, assuming that the low-energy landscape is described by a random Gaussian potential with a correlation length much smaller than M pl. We find that the distribution for Q has a unique shape and a preferred domain, which depends on the parameters of the low-energy landscape. We discuss some observational implications of this distribution and the constraints it imposes on the landscape parameters.
Integrated visions (part II): Envisioning Sustainable Energy Landscapes
Stremke, S.; Koh, J.; Neven, C.T.; Boekel, A.
2012-01-01
ABSTRACT Climate change and resource depletion are driving the transition to renewable energy sources. Both the supply of renewables and the demand for energy are influenced by the physical environment and therefore concern spatial planning and landscape design. Envisioning the longterm development
Inflation, Dark Matter, and Dark Energy in the String Landscape
Liddle, Andrew R; Ureña-López, L Arturo
2006-01-01
We consider the conditions needed to unify the description of dark matter, dark energy and inflation in the context of the string landscape. We find that incomplete decay of the inflaton field gives the possibility that a single field is responsible for all three phenomena. By contrast, unifying dark matter and dark energy into a single field, separate from the inflaton, appears rather difficult.
Energy Landscapes for the Self-Assembly of Supramolecular Polyhedra
Russell, Emily R.; Menon, Govind
2016-06-01
We develop a mathematical model for the energy landscape of polyhedral supramolecular cages recently synthesized by self-assembly (Sun et al. in Science 328:1144-1147, 2010). Our model includes two essential features of the experiment: (1) geometry of the organic ligands and metallic ions; and (2) combinatorics. The molecular geometry is used to introduce an energy that favors square-planar vertices (modeling {Pd}^{2+} ions) and bent edges with one of two preferred opening angles (modeling boomerang-shaped ligands of two types). The combinatorics of the model involve two-colorings of edges of polyhedra with four-valent vertices. The set of such two-colorings, quotiented by the octahedral symmetry group, has a natural graph structure and is called the combinatorial configuration space. The energy landscape of our model is the energy of each state in the combinatorial configuration space. The challenge in the computation of the energy landscape is a combinatorial explosion in the number of two-colorings of edges. We describe sampling methods based on the symmetries of the configurations and connectivity of the configuration graph. When the two preferred opening angles encompass the geometrically ideal angle, the energy landscape exhibits a very low-energy minimum for the most symmetric configuration at equal mixing of the two angles, even when the average opening angle does not match the ideal angle.
A Laplace transform method for energy multigroup hybrid discrete ordinates
International Nuclear Information System (INIS)
Segatto, C.F.; Vilhena, M.T.; Barros, R.C.
2010-01-01
In typical lattice cells where a highly absorbing, small fuel element is embedded in the moderator, a large weakly absorbing medium, high-order transport methods become unnecessary. In this work we describe a hybrid discrete ordinates (S N) method for energy multigroup slab lattice calculations. This hybrid S N method combines the convenience of a low-order S N method in the moderator with a high-order S N method in the fuel. The idea is based on the fact that in weakly absorbing media whose physical size is several neutron mean free paths in extent, even the S 2 method (P 1 approximation), leads to an accurate result. We use special fuel-moderator interface conditions and the Laplace transform (LTS N ) analytical numerical method to calculate the two-energy group neutron flux distributions and the thermal disadvantage factor. We present numerical results for a range of typical model problems.
Learning free energy landscapes using artificial neural networks.
Sidky, Hythem; Whitmer, Jonathan K
2018-03-14
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.
Learning free energy landscapes using artificial neural networks
Sidky, Hythem; Whitmer, Jonathan K.
2018-03-01
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.
The German energy landscape in 2015
International Nuclear Information System (INIS)
Lauer, Hartmut
2016-01-01
This article proposes a brief overview of the German energy sector: stagnation of primary energy consumption, shares of the different energy sources (renewable, coal, lignite, oil, gas, nuclear), shares of the different electric power production sources and their recent evolution. It evokes issues related to the objectives defined for energy transition, the high level of renewable energy production and the high level of power exports. It outlines that consumption must be reduced to reach the objectives defined for 2020. It notices a stagnation of the energy system de-carbonation, and comments the evolution of electricity prices
Sustainable energy landscapes: The power of imagination
Stremke, S.
2012-01-01
Resource depletion and climate change motivate a transition to sustainable energy systems that make effective use of renewable sources. Sustainable energy transition necessitates a transformation of large parts of the existing built environment and presents one of the great challenges of present-day
Membranes: A Variety of Energy Landscapes for Many Transfer Opportunities.
Bacchin, Patrice
2018-02-22
A membrane can be represented by an energy landscape that solutes or colloids must cross. A model accounting for the momentum and the mass balances in the membrane energy landscape establishes a new way of writing for the Darcy law. The counter-pressure in the Darcy law is no longer written as the result of an osmotic pressure difference but rather as a function of colloid-membrane interactions. The ability of the model to describe the physics of the filtration is discussed in detail. This model is solved in a simplified energy landscape to derive analytical relationships that describe the selectivity and the counter-pressure from ab initio operating conditions. The model shows that the stiffness of the energy landscape has an impact on the process efficiency: a gradual increase in interactions (such as with hourglass pore shape) can reduce the separation energetic cost. It allows the introduction of a new paradigm to increase membrane efficiency: the accumulation that is inherent to the separation must be distributed across the membrane. Asymmetric interactions thus lead to direction-dependent transfer properties and the membrane exhibits diode behavior. These new transfer opportunities are discussed.
Modeling energy market dynamics using discrete event system simulation
International Nuclear Information System (INIS)
Gutierrez-Alcaraz, G.; Sheble, G.B.
2009-01-01
This paper proposes the use of Discrete Event System Simulation to study the interactions among fuel and electricity markets and consumers, and the decision-making processes of fuel companies (FUELCOs), generation companies (GENCOs), and consumers in a simple artificial energy market. In reality, since markets can reach a stable equilibrium or fail, it is important to observe how they behave in a dynamic framework. We consider a Nash-Cournot model in which marketers are depicted as Nash-Cournot players that determine supply to meet end-use consumption. Detailed engineering considerations such as transportation network flows are omitted, because the focus is upon the selection and use of appropriate market models to provide answers to policy questions. (author)
Evaluating the landscape impact of renewable energy plants
Ioannidis, Romanos; Koutsoyiannis, Demetris
2017-04-01
Different types of renewable energy have been on an ongoing competition with each other. There has been a lot of research comparing the most common types of renewable energy plants in relation with their efficiency, cost and environmental impact. However, few papers so far have attempted to analyse their impact on landscape and there has never been in depth research on which type of renewable energy causes the least impact on the natural, cultural and aesthetic characteristics of a landscape. This seems to be a significant omission given the vast areas of land already covered with renewable energy plants and the worldwide plans for many more renewable energy projects in the future. Meanwhile, the low aesthetic quality of renewable energy plants has already been an obstacle to their further development, with several relevant examples from countries such as Spain and the Netherlands. There have even been cases where aesthetic degradation is the primary or even the single argument of the opposition to proposed plants. In any case, the aesthetic design and the integration of renewable energy plants into the landscape should really be important design parameters if we plan those projects to truly be sustainable and to be considered complete works of engineering. To initiate dialogue over those aspects of renewable energy, we provide a first comparison on hydro, solar and wind energy. To materialize this comparison, we use data from existing dams, photovoltaic and wind farms. Initially, the average area per MW covered by each type of energy plant is calculated and then evaluated qualitatively from a landscape-impact perspective. Although the area affected is comparable in these three cases, the analysis of the data suggests that dams offer a considerable amount of advantages compared to the other two types of plants. This conclusion arises from the fact that dams, whose basic impact to the landscape is the creation of an artificial lake, contribute much less to the
Peptide Free Energy Landscapes Calibrated by Molecular Orbital Calculations
Ono, S.; Kuroda, M.; Higo, J.; Kamiya, N.; Nakajima, N.; Nakamura, H.
2002-01-01
Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was cal...
Free-energy landscape of a hyperstable RNA tetraloop.
Miner, Jacob C; Chen, Alan A; García, Angel E
2016-06-14
We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.
Physics landscape-fixed target energies
International Nuclear Information System (INIS)
Berger, E.L.
1989-10-01
An introductory review is presented of physics issues and opportunities at Fermilab fixed-target energies. Included are discussions of precision electroweak studies; deep inelastic lepton scattering; heavy quark production, spectroscopy, and decays; perturbative QCD; prompt photon production; massive lepton production; and spin dependence. 79 refs., 7 figs
Chen, Huangxin; Sun, Shuyu; Zhang, Tao
2017-01-01
In this paper we consider the energy stability estimates for some fully discrete schemes which both consider time and spatial discretizations for the incompressible Navier–Stokes equations. We focus on three kinds of fully discrete schemes, i
Energy landscapes of resting-state brain networks
Directory of Open Access Journals (Sweden)
Takamitsu eWatanabe
2014-02-01
Full Text Available During rest, the human brain performs essential functions such as memory maintenance, which are associated with resting-state brain networks (RSNs including the default-mode network (DMN and frontoparietal network (FPN. Previous studies based on spiking-neuron network models and their reduced models, as well as those based on imaging data, suggest that resting-state network activity can be captured as attractor dynamics, i.e., dynamics of the brain state toward an attractive state and transitions between different attractors. Here, we analyze the energy landscapes of the RSNs by applying the maximum entropy model, or equivalently the Ising spin model, to human RSN data. We use the previously estimated parameter values to define the energy landscape, and the disconnectivity graph method to estimate the number of local energy minima (equivalent to attractors in attractor dynamics, the basin size, and hierarchical relationships among the different local minima. In both of the DMN and FPN, low-energy local minima tended to have large basins. A majority of the network states belonged to a basin of one of a few local minima. Therefore, a small number of local minima constituted the backbone of each RSN. In the DMN, the energy landscape consisted of two groups of low-energy local minima that are separated by a relatively high energy barrier. Within each group, the activity patterns of the local minima were similar, and different minima were connected by relatively low energy barriers. In the FPN, all dominant energy were separated by relatively low energy barriers such that they formed a single coarse-grained global minimum. Our results indicate that multistable attractor dynamics may underlie the DMN, but not the FPN, and assist memory maintenance with different memory states.
Directory of Open Access Journals (Sweden)
Jean-Philippe Gastellu-Etchegorry
2015-02-01
Full Text Available Satellite and airborne optical sensors are increasingly used by scientists, and policy makers, and managers for studying and managing forests, agriculture crops, and urban areas. Their data acquired with given instrumental specifications (spectral resolution, viewing direction, sensor field-of-view, etc. and for a specific experimental configuration (surface and atmosphere conditions, sun direction, etc. are commonly translated into qualitative and quantitative Earth surface parameters. However, atmosphere properties and Earth surface 3D architecture often confound their interpretation. Radiative transfer models capable of simulating the Earth and atmosphere complexity are, therefore, ideal tools for linking remotely sensed data to the surface parameters. Still, many existing models are oversimplifying the Earth-atmosphere system interactions and their parameterization of sensor specifications is often neglected or poorly considered. The Discrete Anisotropic Radiative Transfer (DART model is one of the most comprehensive physically based 3D models simulating the Earth-atmosphere radiation interaction from visible to thermal infrared wavelengths. It has been developed since 1992. It models optical signals at the entrance of imaging radiometers and laser scanners on board of satellites and airplanes, as well as the 3D radiative budget, of urban and natural landscapes for any experimental configuration and instrumental specification. It is freely distributed for research and teaching activities. This paper presents DART physical bases and its latest functionality for simulating imaging spectroscopy of natural and urban landscapes with atmosphere, including the perspective projection of airborne acquisitions and LIght Detection And Ranging (LIDAR waveform and photon counting signals.
Comparing the Folding and Misfolding Energy Landscapes of Phosphoglycerate Kinase
Agocs, Gergely; Szabo, Bence T.; Koehler, Gottfried; Osvath, Szabolcs
2012-01-01
Partitioning of polypeptides between protein folding and amyloid formation is of outstanding pathophysiological importance. Using yeast phosphoglycerate kinase as model, here we identify the features of the energy landscape that decide the fate of the protein: folding or amyloidogenesis. Structure formation was initiated from the acid-unfolded state, and monitored by fluorescence from 10 ms to 20 days. Solvent conditions were gradually shifted between folding and amyloidogenesis, and the prop...
Polyomaviridae Assembly Polymorphism from an Energy Landscape Perspective
Directory of Open Access Journals (Sweden)
Karim M. ElSawy
2008-01-01
Full Text Available Polyomaviridae assemble in vitro into different aggregates depending on experimental conditions. We use an energy landscape approach using empirical energy calculations to quantify how the formation of these different aggregates depends on pH, the presence of bound calcium ions and disulfide linkages. Computations are carried out for SV40, a member of the Polyomaviridae family and are based on the binding free energy landscape of three distinct trimers of pentamers that correspond to the different bonding configurations between the capsid proteins observed in its crystal structure. Our computational analysis shows that the energetics of one of these environments is pivotal for the polymorphic assembly behaviour of SV40, whilst the binding energy landscapes of the other two environments are broadly funnel-shaped and thus contribute little to the formation of particles other than virus-like particles (VLP. We have quantified how the existence of bound calcium ions in the absence of disulfide linkages enhances the binding free energies of all three environments and hence, favours the assembly of VLPs. Moreover, estimation of the relative binding free energies of the three environments at pH 5 and pH 8 reveals that they are destabilized at pH 5 relative to pH 8. The extent of this destabilization is dependent on the presence of disulfide linkages and bound calcium ions and accounts for the experimentally observed polymorphic behaviour of VP1 proteins at pH 5. Interestingly, concurrent existence of bound calcium ions and disulfide linkages is found to be destabilizing and thus may disrupt the assembly of VLPs at pH 8.
Characterizing structural transitions using localized free energy landscape analysis.
Directory of Open Access Journals (Sweden)
Nilesh K Banavali
Full Text Available Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes.Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom.The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.
Sustainable Energy Landscape: Implementing Energy Transition in the Physical Realm
Stremke, S.
2015-01-01
Since the beginning of the new millennium, the concept of “energy landscape” is being discussed by academia from the environmental design domain while more and more practitioners have been contributing to sustainable energy transition. Yet, there remains some ambiguity as to what exactly is meant
New Energy Landscapes of Pennsylvania: Forests to Farms to Fracking
Johnson, Deborah A.
This dissertation adds to the literature on energy needed by industry, government, and citizens for decision-making. The pursuit to access or create new energy resources spawns new landscapes of energy in the early 21st century. The combination of hydraulic fracturing and horizontal drilling technologies---popularly called "fracking"---enables entry into previously inaccessible natural gas reserves such as the Marcellus shale much of which lies beneath Pennsylvania. Although this unconventional method offers a promising source of domestic energy and job growth, the potential for negative impacts raises concerns and questions. The questions include: What is the controversy about fracking in Pennsylvania? What are the impacts of fracking? What costs is Pennsylvania paying as it shifts to shale gas extraction? Are there activities taking place or material signs that point to the emerging new landscapes? Are the individuals and organizations that resist shale gas extraction---the so-called "Green Forces"---and others who live within the region of development more or less attuned to these costs? A mixed methods approach consists of landscape and stakeholder analyses including visual examination of GIS-generated maps, satellite images, and photos taken in the field specifically from four counties: Washington, Warren, McKean, and Bradford. Research captures stakeholders' voices across the public, government, and private sectors at different scales. A stakeholder matrix facilitates data organization and analysis. Data include 114 individual statements from an EPA Public Meeting, texts from 40 online-newspaper articles or blogs, and face-to-face interviews or focus group participation of 36 individuals. Further data come from a public health conference, industry convention, and public protest. The new energy landscape covers spaces in Pennsylvania where oil and gas development previously had not been present. It obscures as well as exposes the legacy of past energy
Heenan, Patrick R; Yu, Hao; Siewny, Matthew G W; Perkins, Thomas T
2018-03-28
Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG 0 ) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG 0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.
Multiscale coarse-graining of the protein energy landscape.
Directory of Open Access Journals (Sweden)
Ronald D Hills
2010-06-01
Full Text Available A variety of coarse-grained (CG models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop and test a CG interaction potential of general utility for the simulation of proteins of arbitrary sequence. The reduced representation relies on multiple interaction sites to maintain the anisotropic packing and polarity of individual sidechains. CG energy landscapes computed from replica exchange simulations of the folding of Trpzip, Trp-cage and adenylate kinase resemble those of other reduced representations; non-native structures are observed with energies similar to those of the native state. The artifactual stabilization of misfolded states implies that non-native interactions play a deciding role in deviations from ideal funnel-like cooperative folding. The role of surface tension, backbone hydrogen bonding and the smooth pairwise CG landscape is discussed. Ab initio folding aside, the improved treatment of sidechain rotamers results in stability of the native state in constant temperature simulations of Trpzip, Trp-cage, and the open to closed conformational transition of adenylate kinase, illustrating the potential value of the CG force field for simulating protein complexes and transitions between well-defined structural states.
Protein energy landscapes determined by five-dimensional crystallography
International Nuclear Information System (INIS)
Schmidt, Marius; Srajer, Vukica; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh
2013-01-01
Barriers of activation within the photocycle of a photoactive protein were extracted from comprehensive time courses of time resolved crystallographic data collected at multiple temperature settings. Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012 ▶), Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001 ▶), Chem. Rev.101, 1569–1581; Schmidt et al. (2005 ▶), Methods Mol. Biol.305, 115–154; Schmidt (2008 ▶), Ultrashort Laser Pulses in Medicine and Biology] because both can be determined from the same set of X-ray data. Here, it is demonstrated how barriers of activation can be determined solely from five-dimensional crystallography, where in addition to space and time, temperature is a variable as well [Schmidt et al. (2010 ▶), Acta Cryst. A66, 198–206]. Directly linking molecular structures with barriers of activation between them allows insight into the structural nature of the barrier to be gained. Comprehensive time series of crystallographic data at 14 different temperature settings were analyzed and the entropy and enthalpy contributions to the barriers of activation were determined. One hundred years after the discovery of X-ray scattering, these results advance X-ray structure determination to a new frontier: the determination of energy landscapes
Technology assessment in energy landscapes. Agent-based modeling of energy conflicts
International Nuclear Information System (INIS)
Scheffran, Juergen; Link, P. Michael; Shaaban, Mostafa; Suesser, Diana
2017-01-01
The risks and conflicts of the fossil-nuclear age are in contrast to the effects of renewable energies which appear in a largely positive light. However, the transformation towards a low-carbon energy supply creates new energy landscapes with a high demand for suitable land areas - which may also provoke energy conflicts. Technology assessment can contribute to reducing such energy conflicts and increasing public acceptance by using spatial agent-based models that represent dynamic decisions and interactions of stakeholders regarding energy alternatives and land-use options. Northern Germany serves as a case study region where farmers and communities are local actors of the energy transition.
Chen, Huangxin
2017-09-01
In this paper we consider the energy stability estimates for some fully discrete schemes which both consider time and spatial discretizations for the incompressible Navier–Stokes equations. We focus on three kinds of fully discrete schemes, i.e., the linear implicit scheme for time discretization with the finite difference method (FDM) on staggered grids for spatial discretization, pressure-correction schemes for time discretization with the FDM on staggered grids for the solutions of the decoupled velocity and pressure equations, and pressure-stabilization schemes for time discretization with the FDM on staggered grids for the solutions of the decoupled velocity and pressure equations. The energy stability estimates are obtained for the above each fully discrete scheme. The upwind scheme is used in the discretization of the convection term which plays an important role in the design of unconditionally stable discrete schemes. Numerical results are given to verify the theoretical analysis.
Landscape of Future Accelerators at the Energy and Intensity Frontier
Energy Technology Data Exchange (ETDEWEB)
Syphers, M. J. [Northern Illinois U.; Chattopadhyay, S. [Northern Illinois U.
2016-11-21
An overview is provided of the currently envisaged landscape of charged particle accelerators at the energy and intensity frontiers to explore particle physics beyond the standard model via 1-100 TeV-scale lepton and hadron colliders and multi-Megawatt proton accelerators for short- and long- baseline neutrino experiments. The particle beam physics, associated technological challenges and progress to date for these accelerator facilities (LHC, HL-LHC, future 100 TeV p-p colliders, Tev-scale linear and circular electron-positron colliders, high intensity proton accelerator complex PIP-II for DUNE and future upgrade to PIP-III) are outlined. Potential and prospects for advanced “nonlinear dynamic techniques” at the multi-MW level intensity frontier and advanced “plasma- wakefield-based techniques” at the TeV-scale energy frontier and are also described.
Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.
Shaffer, Patrick; Valsson, Omar; Parrinello, Michele
2016-12-13
In recent work, we demonstrated that it is possible to obtain approximate representations of high-dimensional free energy surfaces with variationally enhanced sampling ( Shaffer, P.; Valsson, O.; Parrinello, M. Proc. Natl. Acad. Sci. , 2016 , 113 , 17 ). The high-dimensional spaces considered in that work were the set of backbone dihedral angles of a small peptide, Chignolin, and the high-dimensional free energy surface was approximated as the sum of many two-dimensional terms plus an additional term which represents an initial estimate. In this paper, we build on that work and demonstrate that we can calculate high-dimensional free energy surfaces of very high accuracy by incorporating additional terms. The additional terms apply to a set of collective variables which are more coarse than the base set of collective variables. In this way, it is possible to build hierarchical free energy surfaces, which are composed of terms that act on different length scales. We test the accuracy of these free energy landscapes for the proteins Chignolin and Trp-cage by constructing simple coarse-grained models and comparing results from the coarse-grained model to results from atomistic simulations. The approach described in this paper is ideally suited for problems in which the free energy surface has important features on different length scales or in which there is some natural hierarchy.
Free energy landscape and molecular pathways of gas hydrate nucleation
International Nuclear Information System (INIS)
Bi, Yuanfei; Porras, Anna; Li, Tianshu
2016-01-01
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.
Free energy landscape and molecular pathways of gas hydrate nucleation.
Bi, Yuanfei; Porras, Anna; Li, Tianshu
2016-12-07
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.
Free energy landscape and molecular pathways of gas hydrate nucleation
Energy Technology Data Exchange (ETDEWEB)
Bi, Yuanfei; Porras, Anna; Li, Tianshu, E-mail: tsli@gwu.edu [Department of Civil and Environmental Engineering, George Washington University, Washington DC 20052 (United States)
2016-12-07
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p{sub B} histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p{sub B} histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.
Directory of Open Access Journals (Sweden)
Chellaboina Vijaysekhar
2005-01-01
Full Text Available We develop thermodynamic models for discrete-time large-scale dynamical systems. Specifically, using compartmental dynamical system theory, we develop energy flow models possessing energy conservation, energy equipartition, temperature equipartition, and entropy nonconservation principles for discrete-time, large-scale dynamical systems. Furthermore, we introduce a new and dual notion to entropy; namely, ectropy, as a measure of the tendency of a dynamical system to do useful work and grow more organized, and show that conservation of energy in an isolated thermodynamic system necessarily leads to nonconservation of ectropy and entropy. In addition, using the system ectropy as a Lyapunov function candidate, we show that our discrete-time, large-scale thermodynamic energy flow model has convergent trajectories to Lyapunov stable equilibria determined by the system initial subsystem energies.
Low energy nuclear reactions driven by discrete breathers
Dubinko, Vladimir
2014-01-01
A new mechanism of LENR in solids is proposed, which is based on the large amplitude anharmonic lattice vibrations, a.k.a. intrinsic localized modes or discrete breathers (DBs). In particular, so called gap DBs, which can arise in diatomic crystals such as metal hydrides, are argued to be the LENR catalyzers. The large mass difference between H or D and the metal atoms provides a gap in phonon spectrum, in which DBs can be excited in the H/D sub-lattice resulting in extreme dynamic closing of...
Hof, Bas van ’t; Veldman, Arthur E.P.
2012-01-01
The paper explains a method by which discretizations of the continuity and momentum equations can be designed, such that they can be combined with an equation of state into a discrete energy equation. The resulting 'MaMEC' discretizations conserve mass, momentum as well as energy, although no
Trp-cage: Folding free energy landscape in explicit water
Zhou, Ruhong
2003-11-01
Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å C-RMSD (C-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.
Multivariable extrapolation of grand canonical free energy landscapes
Mahynski, Nathan A.; Errington, Jeffrey R.; Shen, Vincent K.
2017-12-01
We derive an approach for extrapolating the free energy landscape of multicomponent systems in the grand canonical ensemble, obtained from flat-histogram Monte Carlo simulations, from one set of temperature and chemical potentials to another. This is accomplished by expanding the landscape in a Taylor series at each value of the order parameter which defines its macrostate phase space. The coefficients in each Taylor polynomial are known exactly from fluctuation formulas, which may be computed by measuring the appropriate moments of extensive variables that fluctuate in this ensemble. Here we derive the expressions necessary to define these coefficients up to arbitrary order. In principle, this enables a single flat-histogram simulation to provide complete thermodynamic information over a broad range of temperatures and chemical potentials. Using this, we also show how to combine a small number of simulations, each performed at different conditions, in a thermodynamically consistent fashion to accurately compute properties at arbitrary temperatures and chemical potentials. This method may significantly increase the computational efficiency of biased grand canonical Monte Carlo simulations, especially for multicomponent mixtures. Although approximate, this approach is amenable to high-throughput and data-intensive investigations where it is preferable to have a large quantity of reasonably accurate simulation data, rather than a smaller amount with a higher accuracy.
Approximate scaling properties of RNA free energy landscapes
Baskaran, S.; Stadler, P. F.; Schuster, P.
1996-01-01
RNA free energy landscapes are analysed by means of "time-series" that are obtained from random walks restricted to excursion sets. The power spectra, the scaling of the jump size distribution, and the scaling of the curve length measured with different yard stick lengths are used to describe the structure of these "time series". Although they are stationary by construction, we find that their local behavior is consistent with both AR(1) and self-affine processes. Random walks confined to excursion sets (i.e., with the restriction that the fitness value exceeds a certain threshold at each step) exhibit essentially the same statistics as free random walks. We find that an AR(1) time series is in general approximately self-affine on timescales up to approximately the correlation length. We present an empirical relation between the correlation parameter rho of the AR(1) model and the exponents characterizing self-affinity.
Energy transfer, orbital angular momentum, and discrete current in a double-ring fiber array
International Nuclear Information System (INIS)
Alexeyev, C. N.; Volyar, A. V.; Yavorsky, M. A.
2011-01-01
We study energy transfer and orbital angular momentum of supermodes in a double-ring array of evanescently coupled monomode optical fibers. The structure of supermodes and the spectra of their propagation constants are obtained. The geometrical parameters of the array, at which the energy is mostly confined within the layers, are determined. The developed method for finding the supermodes of concentric arrays is generalized for the case of multiring arrays. The orbital angular momentum carried by a supermode of a double-ring array is calculated. The discrete lattice current is introduced. It is shown that the sum of discrete currents over the array is a conserved quantity. The connection of the total discrete current with orbital angular momentum of discrete optical vortices is made.
Energy transfer, orbital angular momentum, and discrete current in a double-ring fiber array
Energy Technology Data Exchange (ETDEWEB)
Alexeyev, C. N.; Volyar, A. V. [Taurida National V.I. Vernadsky University, Vernadsky Prospekt, 4, Simferopol, 95007, Crimea (Ukraine); Yavorsky, M. A. [Taurida National V.I. Vernadsky University, Vernadsky Prospekt, 4, Simferopol, 95007, Crimea (Ukraine); Universite Bordeaux and CNRS, LOMA, UMR 5798, FR-33400 Talence (France)
2011-12-15
We study energy transfer and orbital angular momentum of supermodes in a double-ring array of evanescently coupled monomode optical fibers. The structure of supermodes and the spectra of their propagation constants are obtained. The geometrical parameters of the array, at which the energy is mostly confined within the layers, are determined. The developed method for finding the supermodes of concentric arrays is generalized for the case of multiring arrays. The orbital angular momentum carried by a supermode of a double-ring array is calculated. The discrete lattice current is introduced. It is shown that the sum of discrete currents over the array is a conserved quantity. The connection of the total discrete current with orbital angular momentum of discrete optical vortices is made.
Temporal disconnectivity of the energy landscape in glassy systems
Lempesis, Nikolaos; Boulougouris, Georgios C.; Theodorou, Doros N.
2013-03-01
An alternative graphical representation of the potential energy landscape (PEL) has been developed and applied to a binary Lennard-Jones glassy system, providing insight into the unique topology of the system's potential energy hypersurface. With the help of this representation one is able to monitor the different explored basins of the PEL, as well as how - and mainly when - subsets of basins communicate with each other via transitions in such a way that details of the prior temporal history have been erased, i.e., local equilibration between the basins in each subset has been achieved. In this way, apart from detailed information about the structure of the PEL, the system's temporal evolution on the PEL is described. In order to gather all necessary information about the identities of two or more basins that are connected with each other, we consider two different approaches. The first one is based on consideration of the time needed for two basins to mutually equilibrate their populations according to the transition rate between them, in the absence of any effect induced by the rest of the landscape. The second approach is based on an analytical solution of the master equation that explicitly takes into account the entire explored landscape. It is shown that both approaches lead to the same result concerning the topology of the PEL and dynamical evolution on it. Moreover, a "temporal disconnectivity graph" is introduced to represent a lumped system stemming from the initial one. The lumped system is obtained via a specially designed algorithm [N. Lempesis, D. G. Tsalikis, G. C. Boulougouris, and D. N. Theodorou, J. Chem. Phys. 135, 204507 (2011), 10.1063/1.3663207]. The temporal disconnectivity graph provides useful information about both the lumped and the initial systems, including the definition of "metabasins" as collections of basins that communicate with each other via transitions that are fast relative to the observation time. Finally, the two examined
Discretized energy minimization in a wave guide with point sources
Propst, G.
1994-01-01
An anti-noise problem on a finite time interval is solved by minimization of a quadratic functional on the Hilbert space of square integrable controls. To this end, the one-dimensional wave equation with point sources and pointwise reflecting boundary conditions is decomposed into a system for the two propagating components of waves. Wellposedness of this system is proved for a class of data that includes piecewise linear initial conditions and piecewise constant forcing functions. It is shown that for such data the optimal piecewise constant control is the solution of a sparse linear system. Methods for its computational treatment are presented as well as examples of their applicability. The convergence of discrete approximations to the general optimization problem is demonstrated by finite element methods.
Communication strategies for two models of discrete energy harvesting
DEFF Research Database (Denmark)
Trillingsgaard, Kasper Fløe; Popovski, Petar
2014-01-01
Energy harvesting is becoming a viable option for powering small wireless devices. Energy for data transmission is supplied by the nature, such that when a transmission is about to take place in an arbitrary instant, the amount of available energy is a random quantity. The arrived energy is stored...... in a battery and transmissions are interrupted if the battery runs out of energy. We address communication in slot-based energy harvesting systems, where the transmitter communicates with ON-OFF signaling: in each slot it can either choose to transmit (ON) or stay silent (OFF). Two different models...... strategies and compare the slot- with the frame-based model in the case of an errorless transmission channel. Additionally, for the slot-based model and channel with errors, we provide a new proof of the capacity achieved by the save-and-transmit scheme....
Observations of discrete energy loss effects in spectra of positrons reflected from solid surfaces
International Nuclear Information System (INIS)
Dale, J.M.; Hulett, L.D.; Pendyala, S.
1980-01-01
Surfaces of tungsten and silicon have been bombarded with monoenergetic beams of positrons and electrons. Spectra of reflected particles show energy loss tails with discrete peaks at kinetic energies about 15 eV lower than that of the elastic peaks. In the higher energy loss range for tungsten, positron spectra show fine structure that is not apparent in the electron spectra. This suggests that the positrons are losing energy through mechanisms different from that of the electrons
Free energy landscape of a minimalist salt bridge model.
Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei
2016-01-01
Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.
International Nuclear Information System (INIS)
Henke, Paul S.; Mak, Chi H.
2014-01-01
The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg 2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure
Energy Technology Data Exchange (ETDEWEB)
Henke, Paul S. [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Mak, Chi H., E-mail: cmak@usc.edu [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089 (United States)
2014-08-14
The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg{sup 2+} that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.
Guaranteed Discrete Energy Optimization on Large Protein Design Problems.
Simoncini, David; Allouche, David; de Givry, Simon; Delmas, Céline; Barbe, Sophie; Schiex, Thomas
2015-12-08
In Computational Protein Design (CPD), assuming a rigid backbone and amino-acid rotamer library, the problem of finding a sequence with an optimal conformation is NP-hard. In this paper, using Dunbrack's rotamer library and Talaris2014 decomposable energy function, we use an exact deterministic method combining branch and bound, arc consistency, and tree-decomposition to provenly identify the global minimum energy sequence-conformation on full-redesign problems, defining search spaces of size up to 10(234). This is achieved on a single core of a standard computing server, requiring a maximum of 66GB RAM. A variant of the algorithm is able to exhaustively enumerate all sequence-conformations within an energy threshold of the optimum. These proven optimal solutions are then used to evaluate the frequencies and amplitudes, in energy and sequence, at which an existing CPD-dedicated simulated annealing implementation may miss the optimum on these full redesign problems. The probability of finding an optimum drops close to 0 very quickly. In the worst case, despite 1,000 repeats, the annealing algorithm remained more than 1 Rosetta unit away from the optimum, leading to design sequences that could differ from the optimal sequence by more than 30% of their amino acids.
The Suppression of Energy Discretization Errors in Multigroup Transport Calculations
International Nuclear Information System (INIS)
Larsen, Edward
2013-01-01
The Objective of this project is to develop, implement, and test new deterministric methods to solve, as efficiently as possible, multigroup neutron transport problems having an extremely large number of groups. Our approach was to (i) use the standard CMFD method to 'coarsen' the space-angle grid, yielding a multigroup diffusion equation, and (ii) use a new multigrid-in-space-and-energy technique to efficiently solve the multigroup diffusion problem. The overall strategy of (i) how to coarsen the spatial an energy grids, and (ii) how to navigate through the various grids, has the goal of minimizing the overall computational effort. This approach yields not only the fine-grid solution, but also coarse-group flux-weighted cross sections that can be used for other related problems.
Bayesian energy landscape tilting: towards concordant models of molecular ensembles.
Beauchamp, Kyle A; Pande, Vijay S; Das, Rhiju
2014-03-18
Predicting biological structure has remained challenging for systems such as disordered proteins that take on myriad conformations. Hybrid simulation/experiment strategies have been undermined by difficulties in evaluating errors from computational model inaccuracies and data uncertainties. Building on recent proposals from maximum entropy theory and nonequilibrium thermodynamics, we address these issues through a Bayesian energy landscape tilting (BELT) scheme for computing Bayesian hyperensembles over conformational ensembles. BELT uses Markov chain Monte Carlo to directly sample maximum-entropy conformational ensembles consistent with a set of input experimental observables. To test this framework, we apply BELT to model trialanine, starting from disagreeing simulations with the force fields ff96, ff99, ff99sbnmr-ildn, CHARMM27, and OPLS-AA. BELT incorporation of limited chemical shift and (3)J measurements gives convergent values of the peptide's α, β, and PPII conformational populations in all cases. As a test of predictive power, all five BELT hyperensembles recover set-aside measurements not used in the fitting and report accurate errors, even when starting from highly inaccurate simulations. BELT's principled framework thus enables practical predictions for complex biomolecular systems from discordant simulations and sparse data. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.
Computational design of RNAs with complex energy landscapes.
Höner zu Siederdissen, Christian; Hammer, Stefan; Abfalter, Ingrid; Hofacker, Ivo L; Flamm, Christoph; Stadler, Peter F
2013-12-01
RNA has become an integral building material in synthetic biology. Dominated by their secondary structures, which can be computed efficiently, RNA molecules are amenable not only to in vitro and in vivo selection, but also to rational, computation-based design. While the inverse folding problem of constructing an RNA sequence with a prescribed ground-state structure has received considerable attention for nearly two decades, there have been few efforts to design RNAs that can switch between distinct prescribed conformations. We introduce a user-friendly tool for designing RNA sequences that fold into multiple target structures. The underlying algorithm makes use of a combination of graph coloring and heuristic local optimization to find sequences whose energy landscapes are dominated by the prescribed conformations. A flexible interface allows the specification of a wide range of design goals. We demonstrate that bi- and tri-stable "switches" can be designed easily with moderate computational effort for the vast majority of compatible combinations of desired target structures. RNAdesign is freely available under the GPL-v3 license. Copyright © 2013 Wiley Periodicals, Inc.
Relationship between energy landscape and low-temperature dynamics of ±J spin glasses
International Nuclear Information System (INIS)
Kobe, S.; Krawczyk, J.
2004-01-01
Clusters and valleys in the exact low-energy landscape of finite Edwards-Anderson ±J spin glasses are related to the distribution of spin domains and free spins in the ground states. The time evolution of the spin correlation function reflects a walk through the landscape at a given temperature and shows typical glassy behaviour
Institute of Scientific and Technical Information of China (English)
德克·西蒙斯; 李佳怿(译); 吴晓彤(校)
2016-01-01
research-through-design projects. The Rotterdam case is produced with local stakeholders for the 2014 ‘Landscape and Energy’ book publication. This land-oriented case is complemented by a project on the seascape of the North Sea as a future energy landscape in the IABR-2016 project 2050: An Energetic Odyssey. Especialy the last case not only justifies the conclusion that landscape architecture can play a role but also that research-by-design is a strong instrument to help in policy making.
Energy Minimization of Discrete Protein Titration State Models Using Graph Theory
Purvine, Emilie; Monson, Kyle; Jurrus, Elizabeth; Star, Keith; Baker, Nathan A.
2016-01-01
There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial-time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and uses techniques from discrete mathematics and graph theory to restate the optimization problem in terms of “maximum flow-minimum cut” graph analysis. The interaction energy graph, a graph in which vertices (amino acids) and edges (interactions) are weighted with their respective energies, is transformed into a flow network in which the value of the minimum cut in the network equals the minimum free energy of the protein, and the cut itself encodes the state that achieves the minimum free energy. Because of its deterministic nature and polynomial-time performance, this algorithm has the potential to allow for the ionization state of larger proteins to be discovered. PMID:27089174
Energy Minimization of Discrete Protein Titration State Models Using Graph Theory.
Purvine, Emilie; Monson, Kyle; Jurrus, Elizabeth; Star, Keith; Baker, Nathan A
2016-08-25
There are several applications in computational biophysics that require the optimization of discrete interacting states, for example, amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and uses techniques from discrete mathematics and graph theory to restate the optimization problem in terms of "maximum flow-minimum cut" graph analysis. The interaction energy graph, a graph in which vertices (amino acids) and edges (interactions) are weighted with their respective energies, is transformed into a flow network in which the value of the minimum cut in the network equals the minimum free energy of the protein and the cut itself encodes the state that achieves the minimum free energy. Because of its deterministic nature and polynomial time performance, this algorithm has the potential to allow for the ionization state of larger proteins to be discovered.
Conference on landscape impacts of wind energy and local acceptance: France-Germany crossed views
International Nuclear Information System (INIS)
Bouscatel, Jerome; Olagne, Regis; Derkenne, Chantal; Galiano, Mila; Mayer, Joerg; Ratzbor, Guenter; Laborgne, Pia; Nadai, Alain; Ratouis, Marie-Odile; Schoebel-Rutschmann, Soeren; Petit, Jean-Francois; Guennewig, Dieter; Portales, David
2008-01-01
The French-German office for Renewable energies (OFAEnR) organised a conference on the landscape impacts of wind energy. In the framework of this French-German exchange of experience, more than 100 participants exchanged views on the environmental impact of wind farms and the opinion of residents. This document brings together the available presentations (slides) made during this event: 1 - French people and wind energy (Mila Galiano); 2 - Wind energy acceptance in Germany: an essential factor for the wind industry development (Joerg Mayer); 3 - Taking into account landscapes and residents in the development of wind farms: a France-Germany comparison (Pia Laborgne, Alain Nadai); 3 - Wind energy development supervision thanks to territorial planning in Germany (Guenter Ratzbor); 4 - Landscape challenges in wind energy development: point of view and role of a state decentralised department (Marie-Odile Ratouis); 5 - Park or landscape - Wind turbines as elements of the cultural landscape (Soeren Schoebel-Rutschmann); 6 - How should a developer approach the 'landscape' aspect when foreseeing a wind energy project installation (Jean-Francois Petit); 7 - More consensual wind energy projects along highways, railways and overhead power lines? (Dieter Guennewig); 8 - The 'wings top': un example of participatory and citizen's project (David Portales)
Clarke, Peter; Varghese, Philip; Goldstein, David
2018-01-01
A discrete velocity method is developed for gas mixtures of diatomic molecules with both rotational and vibrational energy states. A full quantized model is described, and rotation-translation and vibration-translation energy exchanges are simulated using a Larsen-Borgnakke exchange model. Elastic and inelastic molecular interactions are modeled during every simulated collision to help produce smooth internal energy distributions. The method is verified by comparing simulations of homogeneous relaxation by our discrete velocity method to numerical solutions of the Jeans and Landau-Teller equations, and to direct simulation Monte Carlo. We compute the structure of a 1D shock using this method, and determine how the rotational energy distribution varies with spatial location in the shock and with position in velocity space.
A discrete-continuous choice model of climate change impacts on energy
International Nuclear Information System (INIS)
Morrison, W.N.; Mendelsohn, R.
1998-01-01
This paper estimates a discrete-continuous fuel choice model in order to explore climate impacts on the energy sector. The model is estimated on a national data set of firms and households. The results reveal that actors switch from oil in cold climates to electricity and natural gas in warm climates and that fuel-specific expenditures follow a U-shaped relationship with respect to temperature. The model implies that warming will increase American energy expenditures, reflecting a sizable welfare damage
The free energy landscape of small molecule unbinding.
Directory of Open Access Journals (Sweden)
Danzhi Huang
2011-02-01
Full Text Available The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide and eleven (5-diethylamino-2-pentanone non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics of ligand unbinding.
Improving Energy Efficiency for the Vehicle Assembly Industry: A Discrete Event Simulation Approach
Oumer, Abduaziz; Mekbib Atnaw, Samson; Kie Cheng, Jack; Singh, Lakveer
2016-11-01
This paper presented a Discrete Event Simulation (DES) model for investigating and improving energy efficiency in vehicle assembly line. The car manufacturing industry is one of the highest energy consuming industries. Using Rockwell Arena DES package; a detailed model was constructed for an actual vehicle assembly plant. 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. Sound energy efficiency model within this industry has two-fold advantage: reducing CO2 emission and cost reduction associated with fuel and electricity consumption. The paper starts with an overview of challenges in energy consumption within the facilities of automotive assembly line and highlights the parameters for energy efficiency. The results of the simulation model indicated improvements for energy saving objectives and reduced costs.
Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function.
Directory of Open Access Journals (Sweden)
Giulio Quarta
Full Text Available Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant "downhill" pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the "new view" of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design.
Numerical evaluation of the statistical properties of a potential energy landscape
International Nuclear Information System (INIS)
Nave, E La; Sciortino, F; Tartaglia, P; Michele, C De; Mossa, S
2003-01-01
The techniques which allow the numerical evaluation of the statistical properties of the potential energy landscape for models of simple liquids are reviewed and critically discussed. Expressions for the liquid free energy and its vibrational and configurational components are reported. Finally, a possible model for the statistical properties of the landscape, which appears to describe correctly fragile liquids in the region where equilibrium simulations are feasible, is discussed
Energy Transition: Missed Opportunities and Emerging Challenges for Landscape Planning and Designing
Directory of Open Access Journals (Sweden)
Renée M. de Waal
2014-07-01
Full Text Available Making the shift from fossil fuels to renewable energy seems inevitable. Because energy transition poses new challenges and opportunities to the discipline of landscape architecture, the questions addressed in this paper are: (1 what landscape architects can learn from successful energy transitions in Güssing, Jühnde and Samsø; and (2 to what extent landscape architecture (or other spatial disciplines contributed to energy transition in the aforementioned cases. An exploratory, comparative case study was conducted to identify differences and similarities among the cases, to answer the research questions, and to formulate recommendations for further research and practice. The comparison indicated that the realized renewable energy systems are context-dependent and, therefore, specifically designed to meet the respective energy demand, making use of the available potentials for renewable energy generation and efficiency. Further success factors seemed to be the presence of (local frontrunners and a certain degree of citizen participation. The relatively smooth implementation of renewable energy technologies in Jühnde and on Samsø may indicate the importance of careful and (partly institutionalized consideration of landscape impact, siting and design. Comparing the cases against the literature demonstrated that landscape architects were not as involved as they, theoretically, could have been. However, particularly when the aim is sustainable development, rather than “merely” renewable energy provision, the integrative concept of “sustainable energy landscapes” can be the arena where landscape architecture and other disciplines meet to pursue global sustainability goals, while empowering local communities and safeguarding landscape quality.
Reliable protein folding on non-funneled energy landscapes: the free energy reaction path
Lois, Gregg; Blawzdziewicz, Jerzy; O'Hern, Corey S.
2008-01-01
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical denaturant or pH, are adjusted to induce folding. A theory based on this insight predicts that (1) proteins with non-funneled energy landscapes can fold reliably to their native state, (2) reliable folding can occur as an equilibrium or out-of-equilibrium pro...
Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding.
Malhotra, Pooja; Jethva, Prashant N; Udgaonkar, Jayant B
2017-08-08
To characterize experimentally the ruggedness of the free energy landscape of protein folding is challenging, because the distributed small free energy barriers are usually dominated by one, or a few, large activation free energy barriers. This study delineates changes in the roughness of the free energy landscape by making use of the observation that a decrease in ruggedness is accompanied invariably by an increase in folding cooperativity. Hydrogen exchange (HX) coupled to mass spectrometry was used to detect transient sampling of local energy minima and the global unfolded state on the free energy landscape of the small protein single-chain monellin. Under native conditions, local noncooperative openings result in interconversions between Boltzmann-distributed intermediate states, populated on an extremely rugged "uphill" energy landscape. The cooperativity of these interconversions was increased by selectively destabilizing the native state via mutations, and further by the addition of a chemical denaturant. The perturbation of stability alone resulted in seven backbone amide sites exchanging cooperatively. The size of the cooperatively exchanging and/or unfolding unit did not depend on the extent of protein destabilization. Only upon the addition of a denaturant to a destabilized mutant variant did seven additional backbone amide sites exchange cooperatively. Segmentwise analysis of the HX kinetics of the mutant variants further confirmed that the observed increase in cooperativity was due to the smoothing of the ruggedness of the free energy landscape of folding of the protein by the chemical denaturant.
Directory of Open Access Journals (Sweden)
Renée M. de Waal
2015-04-01
Full Text Available Energy transition is expected to make an important contribution to sustainable development. Although it is argued that landscape design could foster energy transition, there is scant empirical research on how practitioners approach this new challenge. The research question central to this study is: To what extent and how is renewable energy science incorporated in regional landscape design? To address this knowledge gap, a case study of a regional landscape design competition in the Netherlands, held from 2010–2012, is presented. Its focus was on integral, strategic landscape transformation with energy transition as a major theme. Content analysis of the 36 competition entries was supplemented and triangulated with a survey among the entrants, observation of the process and a study of the competition documents and website. Results indicated insufficient use of key-strategies elaborated by renewable energy science. If landscape design wants to adopt a supportive role towards energy transition, a well-informed and evidence-based approach is highly recommended. Nevertheless, promising strategies for addressing the complex process of ensuring sustainable energy transition also emerged. They include the careful cultivation of public support by developing inclusive and bottom-up processes, and balancing energy-conscious interventions with other land uses and interests.
Zhu, Guangpu
2018-01-26
In this paper, a fully discrete scheme which considers temporal and spatial discretizations is presented for the coupled Cahn-Hilliard equation in conserved form with the dynamic contact line condition and the Navier-Stokes equation with the generalized Navier boundary condition. Variable densities and viscosities are incorporated in this model. A rigorous proof of energy stability is provided for the fully discrete scheme based on a semi-implicit temporal discretization and a finite difference method on the staggered grids for the spatial discretization. A splitting method based on the pressure stabilization is implemented to solve the Navier-Stokes equation, while the stabilization approach is also used for the Cahn-Hilliard equation. Numerical results in both 2-D and 3-D demonstrate the accuracy, efficiency and decaying property of discrete energy of the proposed scheme.
Knowledge network model of the energy consumption in discrete manufacturing system
Xu, Binzi; Wang, Yan; Ji, Zhicheng
2017-07-01
Discrete manufacturing system generates a large amount of data and information because of the development of information technology. Hence, a management mechanism is urgently required. In order to incorporate knowledge generated from manufacturing data and production experience, a knowledge network model of the energy consumption in the discrete manufacturing system was put forward based on knowledge network theory and multi-granularity modular ontology technology. This model could provide a standard representation for concepts, terms and their relationships, which could be understood by both human and computer. Besides, the formal description of energy consumption knowledge elements (ECKEs) in the knowledge network was also given. Finally, an application example was used to verify the feasibility of the proposed method.
Energy Cost of Avoiding Pressure Oscillations in a Discrete Fluid Power Force System
DEFF Research Database (Denmark)
Hansen, Anders Hedegaard; Pedersen, Henrik Clemmensen
2015-01-01
In secondary valve controlled discrete fluid power force systems the valve opening trajectory greatly influences the pressure dynamics in the actuator chambers. For discrete fluid power systems featuring hoses of significant length pressure oscillations due to fast valve switching is well......-known. This paper builds upon theoretical findings on how shaping of the valve opening may reduce the cylinder pressure oscillations. The current paper extents the work by implementing the valve opening characteristics reducing the pressure oscillations on a full scale power take-off test-bench for wave energy...... will present measurements comparing pressure dynamics for two valve opening algorithms. In addition the paper will give a theoretical investigation of the energy loss during valve shifting and finally measurements of average power output from the power take-off system in various sea states are compared...
Energy Optimal Tracking Control with Discrete Fluid Power Systems using Model Predictive Control
DEFF Research Database (Denmark)
Hansen, Anders Hedegaard; Asmussen, Magnus Færing; Bech, Michael Møller
2017-01-01
For Discrete Displacement Cylinder (DDC) drives the control task lies in choosing force level. Hence, which force level to apply and thereby which pressure level each cylinder chambers shall be connected to. The DDC system is inherently a force system why often a force reference is generated...... and compared to a PID like tracking controller combined with a FSA. The results indicate that the energy efficiency of position tracking DDC systems may be improved significantly by using the MPC algorithm....
Roatta , Luca
2017-01-01
Assuming that space and time can only have discrete values, we obtain the expression of the gravitational potential energy that at large distance coincides with the Newtonian. In very precise circumstances it coincides with the relativistic mass-energy relation: this shows that the Universe is a black hole in which all bodies are subjected to an acceleration toward the border of the Universe itself. Since the Universe is a black hole with a fixed radius, we can obtain the density of the Unive...
Directory of Open Access Journals (Sweden)
Xiakun Chu
2014-08-01
Full Text Available Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we meet the challenge by quantifying the intrinsic biomolecular recognition energy landscapes with and without flexibility through the underlying density of states. We quantified the thermodynamic intrinsic specificity by the topography of the intrinsic binding energy landscape and the kinetic specificity by association rate. We found that the thermodynamic and kinetic specificity are strongly correlated. Furthermore, we found that flexibility decreases binding affinity on one hand, but increases binding specificity on the other hand, and the decreasing or increasing proportion of affinity and specificity are strongly correlated with the degree of flexibility. This shows more (less flexibility leads to weaker (stronger coupling between affinity and specificity. Our work provides a theoretical foundation and quantitative explanation of the previous qualitative studies on the relationship among flexibility, affinity and specificity. In addition, we found that the folding energy landscapes are more funneled with binding, indicating that binding helps folding during the recognition. Finally, we demonstrated that the whole binding-folding energy landscapes can be integrated by the rigid binding and isolated folding energy landscapes under weak flexibility. Our results provide a novel way to quantify the affinity and specificity in flexible biomolecular recognition.
Impacts of renewable energy on landscape. Alternative of offshore wind in marine areas
Directory of Open Access Journals (Sweden)
Francesca Moraci
2014-01-01
Full Text Available The effects determined in the landscape by plants powered by renewable sources represent some unresolved issues in terms of visual and landscape impact mitigation in general. These aspects relate to the landscape are recognized in all types of impact with due attention to the various components and dynamics involved identifiable in the landscape of reference.The wind power plants, in particular, while making unquestionable environmental benefits thanks to the production of energy from renewable sources, but imposes a significant cost to the landscape with the installation of wind turbines in contexts necessarily favorable to impact, interrupting the skyline, creating territorial discontinuities, "subtracting" and altering the landscape in the absence of effective mitigation works.The environmental compatibility of the proposed solutions depends primarily on the location of wind farms.Is necessary indicate an overall strategy, a shared model of planning and land management, as in other European countries such as Denmark, Germany, France and the United Kingdom where the choice of locating wind farms has resulted in a new draft territory, construction and redesign of the landscape.
Uzoh, O.G.; Cruz-Cabeza, A.J.; Price, S. L.
2012-01-01
The concept of a polymorphophore was investigated by contrasting the crystal energy landscapes of monomorphic fenamic acid (2-(phenylamino)-benzoic acid, FA) and one of its highly polymorphic derivatives, tolfenamic acid (2-[(3-chloro-2-methylphenyl)amino]-benzoic acid, TA). The crystal energy
Linking habitat selection to fitness-related traits in herbivores: the role of the energy landscape
Ryan A. Long; R. T. Bowyer; Warren P. Porter; Paul Mathewson; Kevin L. Monteith; Scott L. Findholt; Brian L. Dick; John G. Kie
2016-01-01
Animals may partially overcome environmental constraints on fitness by behaviorally adjusting their exposure to costs and supplies of energy. Few studies, however, have linked spatiotemporal variation in the energy landscape to behaviorally mediated measures of performance that ostensibly influence individual fitness. We hypothesized that strength of selection by North...
Zhou, Bingliang; Zhou, Jianbin; Zhang, Qisheng
2017-10-01
This study aims at investigating the pyrolysis behavior of Camellia sinensis branches by the Discrete Distributed Activation Energy Model (DAEM) and thermogravimetric experiments. Then the Discrete DAEM method is used to describe pyrolysis process of Camellia sinensis branches dominated by 12 characterized reactions. The decomposition mechanism of Camellia sinensis branches and interaction with components are observed. And the reaction at 350.77°C is a significant boundary of the first and second reaction range. The pyrolysis process of Camellia sinensis branches at the heating rate of 10,000°C/min is predicted and provides valuable references for gasification or combustion. The relationship and function between four typical indexes and heating rates from 10 to 10,000°C/min are revealed. Copyright © 2017 Elsevier Ltd. All rights reserved.
International Nuclear Information System (INIS)
Hof, Bas van’t; Veldman, Arthur E.P.
2012-01-01
The paper explains a method by which discretizations of the continuity and momentum equations can be designed, such that they can be combined with an equation of state into a discrete energy equation. The resulting ‘MaMEC’ discretizations conserve mass, momentum as well as energy, although no explicit conservation law for the total energy is present. Essential ingredients are (i) discrete convection that leaves the discrete energy invariant, and (ii) discrete consistency between the thermodynamic terms. Of particular relevance is the way in which finite volume fluxes are related to nodal values. The method is an extension of existing methods based on skew-symmetry of discrete operators, because it allows arbitrary equations of state and a larger class of grids than earlier methods. The method is first illustrated with a one-dimensional example on a highly stretched staggered grid, in which the MaMEC method calculates qualitatively correct results and a non-skew-symmetric finite volume method becomes unstable. A further example is a two-dimensional shallow water calculation on a rectilinear grid as well as on an unstructured grid. The conservation of mass, momentum and energy is checked, and losses are found negligible up to machine accuracy.
Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele
2015-10-26
The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.
Control of the Effective Free-Energy Landscape in a Frustrated Magnet by a Field Pulse
Wan, Yuan; Moessner, Roderich
2017-10-01
Thermal fluctuations can lift the degeneracy of a ground state manifold, producing a free-energy landscape without accidentally degenerate minima. In a process known as order by disorder, a subset of states incorporating symmetry breaking may be selected. Here, we show that such a free-energy landscape can be controlled in a nonequilibrium setting as the slow motion within the ground state manifold is governed by the fast modes out of it. For the paradigmatic case of the classical pyrochlore X Y antiferromagnet, we show that a uniform magnetic field pulse can excite these fast modes to generate a tunable effective free-energy landscape with minima at thermodynamically unstable portions of the ground state manifold.
Discrete Displacement Hydraulic Power Take-Off System for the Wavestar Wave Energy Converter
Directory of Open Access Journals (Sweden)
Enrique Vidal
2013-08-01
Full Text Available The Wavestar Wave Energy Converter (WEC is a multiple absorber concept, consisting of 20 hemisphere shaped floats attached to a single platform. The heart of the Wavestar WEC is the Power Take-Off (PTO system, converting the wave induced motion of the floats into a steady power output to the grid. In the present work, a PTO based on a novel discrete displacement fluid power technology is explored for the Wavestar WEC. Absorption of power from the floats is performed by hydraulic cylinders, supplying power to a common fixed pressure system with accumulators for energy smoothing. The stored pressure energy is converted into electricity at a steady pace by hydraulic motors and generators. The storage, thereby, decouples the complicated process of wave power absorption from power generation. The core for enabling this PTO technology is implementing a near loss-free force control of the energy absorbing cylinders. This is achieved by using special multi-chambered cylinders, where the different chambers may be connected to the available system pressures using fast on/off valves. Resultantly, a Discrete Displacement Cylinder (DDC is created, allowing near loss free discrete force control. This paper presents a complete PTO system for a 20 float Wavestar based on the DDC. The WEC and PTO is rigorously modeled from incident waves to the electric output to the grid. The resulting model of +600 states is simulated in different irregular seas, showing that power conversion efficiencies above 70% from input power to electrical power is achievable for all relevant sea conditions.
An energy recondensation method using the discrete generalized multigroup energy expansion theory
International Nuclear Information System (INIS)
Zhu Lei; Forget, Benoit
2011-01-01
Highlights: → Discrete-generalized multigroup method was implemented as a recondensation scheme. → Coarse group cross-sections were recondensed from core-level solution. → Neighboring effect of reflector and MOX bundle was improved. → Methodology was shown to be fully consistent when a flat angular flux approximation is used. - Abstract: In this paper, the discrete generalized multigroup (DGM) method was used to recondense the coarse group cross-sections using the core level solution, thus providing a correction for neighboring effect found at the core level. This approach was tested using a discrete ordinates implementation in both 1-D and 2-D. Results indicate that 2 or 3 iterations can substantially improve the flux and fission density errors associated with strong interfacial spectral changes as found in the presence of strong absorbers, reflector of mixed-oxide fuel. The methodology is also proven to be fully consistent with the multigroup methodology as long as a flat-flux approximation is used spatially.
Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition
Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin
2013-01-01
Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding–folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative “coupled binding–folding” and three-state noncooperative “folding prior to binding” scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding–folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding–folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found “U-shape” temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments. PMID:23754431
Discrete gradients in discrete classical mechanics
International Nuclear Information System (INIS)
Renna, L.
1987-01-01
A simple model of discrete classical mechanics is given where, starting from the continuous Hamilton equations, discrete equations of motion are established together with a proper discrete gradient definition. The conservation laws of the total discrete momentum, angular momentum, and energy are demonstrated
Another possible energy landscape; Un autre paysage energetique possible
Energy Technology Data Exchange (ETDEWEB)
NONE
2002-06-01
This analysis presents the national energy balances from the national energy accounting. The first part presents the accounting analysis on the electric power consumption and production in France. The second part deals with the global energy accounting, for the energy sources and utilization, together. From these analysis the authors show how the global energy efficiency of production and utilization is possible. Solutions allowing the reduction of the non renewable energies consumption and solution for the nuclear power phaseout are also proposed. (A.L.B.)
Exploring the free energy landscape: from dynamics to networks and back.
Directory of Open Access Journals (Sweden)
Diego Prada-Gracia
2009-06-01
Full Text Available Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers there are, what the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times and rate constants, or hierarchical relationships among basins, completes the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.
Energy Technology Data Exchange (ETDEWEB)
Silva, Davi J.M.; Nunes, Carlos E.A.; Alves Filho, Hermes; Barros, Ricardo C., E-mail: davijmsilva@yahoo.com.br, E-mail: ceanunes@yahoo.com.br, E-mail: rcbarros@pq.cnpq.br [Secretaria Municipal de Educacao de Itaborai, RJ (Brazil); Universidade Estacio de Sa (UNESA), Rio de Janeiro, RJ (Brazil); Universidade do Estado do Rio de Janeiro (UERJ), Novra Friburgo, RJ (Brazil). Instituto Politecnico. Departamento de Modelagem Computacional
2017-11-01
Discussed here is the accuracy of approximate albedo boundary conditions for energy multigroup discrete ordinates (S{sub N}) eigenvalue problems in two-dimensional rectangular geometry for criticality calculations in neutron fission reacting systems, such as nuclear reactors. The multigroup (S{sub N}) albedo matrix substitutes approximately the non-multiplying media around the core, e.g., baffle and reflector, as we neglect the transverse leakage terms within these non-multiplying regions. Numerical results to a typical model problem are given to illustrate the accuracy versus the computer running time. (author)
Measurement of discrete energy-level spectra in individual chemically synthesized gold nanoparticles
DEFF Research Database (Denmark)
Kuemmeth, Ferdinand; Bolotin, Kirill I; Shi, Su-Fei
2008-01-01
We form single-electron transistors from individual chemically synthesized gold nanoparticles, 5-15 nm in diameter, with monolayers of organic molecules serving as tunnel barriers. These devices allow us to measure the discrete electronic energy levels of individual gold nanoparticles that are......, by virtue of chemical synthesis, well-defined in their composition, size and shape. We show that the nanoparticles are nonmagnetic and have spectra in good accord with random-matrix-theory predictions taking into account strong spin-orbit coupling....
Minimum Energy Control of 2D Positive Continuous-Discrete Linear Systems
Directory of Open Access Journals (Sweden)
Kaczorek Tadeusz
2014-09-01
Full Text Available The minimum energy control problem for the 2D positive continuous-discrete linear systems is formulated and solved. Necessary and sufficient conditions for the reachability at the point of the systems are given. Sufficient conditions for the existence of solution to the problem are established. It is shown that if the system is reachable then there exists an optimal input that steers the state from zero boundary conditions to given final state and minimizing the performance index for only one step (q = 1. A procedure for solving of the problem is proposed and illustrated by a numerical example.
International Nuclear Information System (INIS)
Bosevski, T.
1971-01-01
The polynomial interpolation of neutron flux between the chosen space and energy variables enabled transformation of the integral transport equation into a system of linear equations with constant coefficients. Solutions of this system are the needed values of flux for chosen values of space and energy variables. The proposed improved method for solving the neutron transport problem including the mathematical formalism is simple and efficient since the number of needed input data is decreased both in treating the spatial and energy variables. Mathematical method based on this approach gives more stable solutions with significantly decreased probability of numerical errors. Computer code based on the proposed method was used for calculations of one heavy water and one light water reactor cell, and the results were compared to results of other very precise calculations. The proposed method was better concerning convergence rate, decreased computing time and needed computer memory. Discretization of variables enabled direct comparison of theoretical and experimental results
Deciphering hierarchical features in the energy landscape of adenylate kinase folding/unfolding
Taylor, J. Nicholas; Pirchi, Menahem; Haran, Gilad; Komatsuzaki, Tamiki
2018-03-01
Hierarchical features of the energy landscape of the folding/unfolding behavior of adenylate kinase, including its dependence on denaturant concentration, are elucidated in terms of single-molecule fluorescence resonance energy transfer (smFRET) measurements in which the proteins are encapsulated in a lipid vesicle. The core in constructing the energy landscape from single-molecule time-series across different denaturant concentrations is the application of rate-distortion theory (RDT), which naturally considers the effects of measurement noise and sampling error, in combination with change-point detection and the quantification of the FRET efficiency-dependent photobleaching behavior. Energy landscapes are constructed as a function of observation time scale, revealing multiple partially folded conformations at small time scales that are situated in a superbasin. As the time scale increases, these denatured states merge into a single basin, demonstrating the coarse-graining of the energy landscape as observation time increases. Because the photobleaching time scale is dependent on the conformational state of the protein, possible nonequilibrium features are discussed, and a statistical test for violation of the detailed balance condition is developed based on the state sequences arising from the RDT framework.
Direct design of an energy landscape with bistable DNA origami mechanisms.
Zhou, Lifeng; Marras, Alexander E; Su, Hai-Jun; Castro, Carlos E
2015-03-11
Structural DNA nanotechnology provides a feasible technique for the design and fabrication of complex geometries even exhibiting controllable dynamic behavior. Recently we have demonstrated the possibility of implementing macroscopic engineering design approaches to construct DNA origami mechanisms (DOM) with programmable motion and tunable flexibility. Here, we implement the design of compliant DNA origami mechanisms to extend from prescribing motion to prescribing an energy landscape. Compliant mechanisms facilitate motion via deformation of components with tunable stiffness resulting in well-defined mechanical energy stored in the structure. We design, fabricate, and characterize a DNA origami nanostructure with an energy landscape defined by two stable states (local energy minima) separated by a designed energy barrier. This nanostructure is a four-bar bistable mechanism with two undeformed states. Traversing between those states requires deformation, and hence mechanical energy storage, in a compliant arm of the linkage. The energy barrier for switching between two states was obtained from the conformational distribution based on a Boltzmann probability function and closely follows a predictive mechanical model. Furthermore, we demonstrated the ability to actuate the mechanism into one stable state via additional DNA inputs and then release the actuation via DNA strand displacement. This controllable multistate system establishes a foundation for direct design of energy landscapes that regulate conformational dynamics similar to biomolecular complexes.
Free-energy landscape of protein oligomerization from atomistic simulations
Barducci, Alessandro; Bonomi, Massimiliano; Prakash, Meher K.; Parrinello, Michele
2013-01-01
In the realm of protein–protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage. PMID:24248370
Designing sustainable energy landscapes : concepts, principles and procedures
Stremke, S.
2010-01-01
The depletion of fossil fuels, in combination with climate change, necessitates a transition to sustainable energy systems. Such systems are characterized by a decreased energy demand and an increase in the use of renewables. The objective of this dissertation is to advance the planning and design
Discrete Energies of a Weakly Outcoupled Atom Laser Beam Outside the Bose–Einstein Condensate Region
Directory of Open Access Journals (Sweden)
Teguh Budi Prayitno
2014-12-01
Full Text Available We consider the possibility of a discrete set of energies of a weakly outcoupled atom laser beam to the homogeneous Schrödinger equation with anisotropic harmonic trap in Cartesian coordinates outside the Bose–Einstein condensate region. This treatment is used because working in the cylindrical coordinates is not really possible, even though we implement the cigar-shaped trap case. The Schrödinger equation appears to replace a set of two-coupled Gross– Pitaevskii equations by enabling the weak-coupling assumption. This atom laser can be produced in a simple way that only involves extracting the atoms in a condensate from by using the radio frequency field. We initially present the relation between condensates as sources and atom laser as an output by exploring the previous work of Riou et al. in the case of theoretical work for the propagation of atom laser beams. We also show that even though the discrete energies are obtained by means of an approaching harmonic oscillator, degeneracy is only available in two states because of the anisotropic external potential
Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.
Iida, Shinji; Nakamura, Haruki; Higo, Junichi
2016-06-15
We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).
Relaxation height in energy landscapes : an application to multiple metastable states
Cirillo, E.N.M.; Nardi, F.R.
2012-01-01
The study of systems with multiple (not necessarily degenerate) metastable states presents subtle difficulties from the mathematical point of view related to the variational problem that has to be solved in these cases. We introduce the notion of relaxation height in a general energy landscape and
Probing the Free Energy Landscape of the FBP28 WW Domain Using Multiple Techniques
Periole, Xavier; Allen, Lucy R.; Tamiola, Kamil; Mark, Alan E.; Paci, Emanuele
The free-energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse-grained to all-atom with either an implicit or explicit treatment of the solvent.
Chowdhary, J; Keyes, T
2002-02-01
Instantaneous normal modes (INM's) are calculated during a conjugate-gradient (CG) descent of the potential energy landscape, starting from an equilibrium configuration of a liquid or crystal. A small number (approximately equal to 4) of CG steps removes all the Im-omega modes in the crystal and leaves the liquid with diffusive Im-omega which accurately represent the self-diffusion constant D. Conjugate gradient filtering appears to be a promising method, applicable to any system, of obtaining diffusive modes and facilitating INM theory of D. The relation of the CG-step dependent INM quantities to the landscape and its saddles is discussed.
The relative importance of physical and biological energy in landscape evolution
Turowski, J. M.; Schwanghart, W.
2017-12-01
Landscapes are formed by the interplay of uplift and geomorphic processes, including interacting and competing physical and biological processes. For example, roots re-inforce soil and thereby stabilize hillslopes and the canopy cover of the forest may mediate the impact of precipitation. Furthermore, plants and animals act as geomorphic agents, directly altering landscape response and dynamics by their actions: tree roots may crack rocks, thus changing subsurface water flows and exposing fresh material for denudation; fungi excrete acids that accelerate rates of chemical weathering, and burrowing animals displace soil and rocks while digging holes for shelter or in search of food. Energetically, landscapes can be viewed as open systems in which topography stores potential energy above a base level. Tectonic processes add energy to the system by uplift and mechanically altering rock properties. Especially in unvegetated regions, erosion and transport by wind can be an important geomorphic process. Advection of atmospheric moisture in high altitudes provides potential energy that is converted by water fluxes through catchments. At the same time, the conversion of solar energy through atmospheric and biological processes drives primary production of living organisms. If we accept that biota influence geomorphic processes, then what is their energetic contribution to landscape evolution relative to physical processes? Using two case studies, we demonstrate that all components of energy input are negligible apart from biological production, quantified by net primary productivity (NPP) and potential energy conversion by water that is placed high up in the landscape as rainfall and leaves it as runoff. Assuming that the former is representative for biological energy and the latter for physical energy, we propose that the ratio of these two values can be used as a proxy for the relative importance of biological and physical processes in landscape evolution. All necessary
The Landscape of Renewable Energies in Europe in 2030
International Nuclear Information System (INIS)
Cruciani, Michel
2017-06-01
The study analyses the European rules designed to promote renewable energy, highlighting their innovations and the difficulties they will raise. The study highlights the consequences of some of the measures envisaged and pays particular attention to the electricity market. On 30 November 2016, the European Commission issued a new set of proposals, the 'Clean Energy Package', covering a wide spectrum of activities. This study analyses the provisions of this package which aim at improving energy efficiency by 30% and giving renewable energy a share of 27% of consumption by 2030. In 2014, Member States had called for these objectives to be assessed for the entire European Union. Nevertheless the Commission wishes to obtain a mandate to check that each State makes an honest contribution to the collective effort. The study stresses that the 30% target for energy efficiency weakens the role of the CO_2 market. The simulations reveal that this weakness will benefit coal, which keeps in 2030 a higher share than it would have occupied with a target of 27%, whereas natural gas is penalized by a low CO_2 price. It also appears that by remaining too low, the price of CO_2 will discourage certain investments in favour of renewable energies that would have naturally emerged with a high price. Therefore it will be necessary to roll out costly public policies to trigger these investments, so that the share of these energies totals 27% by 2030. The simulations also show that the renewable energy target will be largely achieved through very rapid growth of wind and solar power. The proposals of 30 November 2016 hence are drafted to encourage the development of these two sectors by reforming the electricity market so that it establishes a price that is remunerative and reduces the need for public aid, while clearly reflecting the burdens generated by the different actors. It seems unlikely that the Member States will accept such a profound market reform as the Commission envisages
Global optimization of proteins using a dynamical lattice model: Ground states and energy landscapes
Dressel, F.; Kobe, S.
2004-01-01
A simple approach is proposed to investigate the protein structure. Using a low complexity model, a simple pairwise interaction and the concept of global optimization, we are able to calculate ground states of proteins, which are in agreement with experimental data. All possible model structures of small proteins are available below a certain energy threshold. The exact lowenergy landscapes for the trp cage protein (1L2Y) is presented showing the connectivity of all states and energy barriers.
Energy Landscape of Pentapeptides in a Higher-Order (ϕ,ψ Conformational Subspace
Directory of Open Access Journals (Sweden)
Karim M. ElSawy
2016-01-01
Full Text Available The potential energy landscape of pentapeptides was mapped in a collective coordinate principal conformational subspace derived from principal component analysis of a nonredundant representative set of protein structures from the PDB. Three pentapeptide sequences that are known to be distinct in terms of their secondary structure characteristics, (Ala5, (Gly5, and Val.Asn.Thr.Phe.Val, were considered. Partitioning the landscapes into different energy valleys allowed for calculation of the relative propensities of the peptide secondary structures in a statistical mechanical framework. The distribution of the observed conformations of pentapeptide data showed good correspondence to the topology of the energy landscape of the (Ala5 sequence where, in accord with reported trends, the α-helix showed a predominant propensity at 298 K. The topography of the landscapes indicates that the stabilization of the α-helix in the (Ala5 sequence is enthalpic in nature while entropic factors are important for stabilization of the β-sheet in the Val.Asn.Thr.Phe.Val sequence. The results indicate that local interactions within small pentapeptide segments can lead to conformational preference of one secondary structure over the other where account of conformational entropy is important in order to reveal such preference. The method, therefore, can provide critical structural information for ab initio protein folding methods.
Lin, Albert; Fu, Sze-Ming; Chung, Yen-Kai; Lai, Shih-Yun; Tseng, Chi-Wei
2013-01-14
Surface plasmon enhancement has been proposed as a way to achieve higher absorption for thin-film photovoltaics, where surface plasmon polariton(SPP) and localized surface plasmon (LSP) are shown to provide dense near field and far field light scattering. Here it is shown that controlled far-field light scattering can be achieved using successive coupling between surface plasmonic (SP) nano-particles. Through genetic algorithm (GA) optimization, energy transfer between discrete nano-particles (ETDNP) is identified, which enhances solar cell efficiency. The optimized energy transfer structure acts like lumped-element transmission line and can properly alter the direction of photon flow. Increased in-plane component of wavevector is thus achieved and photon path length is extended. In addition, Wood-Rayleigh anomaly, at which transmission minimum occurs, is avoided through GA optimization. Optimized energy transfer structure provides 46.95% improvement over baseline planar cell. It achieves larger angular scattering capability compared to conventional surface plasmon polariton back reflector structure and index-guided structure due to SP energy transfer through mode coupling. Via SP mediated energy transfer, an alternative way to control the light flow inside thin-film is proposed, which can be more efficient than conventional index-guided mode using total internal reflection (TIR).
Chen, Changjun
2016-03-31
The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.
Directory of Open Access Journals (Sweden)
Xinhua Nie
Full Text Available Magnetic anomaly detection (MAD is a passive approach for detection of a ferromagnetic target, and its performance is often limited by external noises. In consideration of one major noise source is the fractal noise (or called 1/f noise with a power spectral density of 1/fa (0energy detection method based on undecimated discrete wavelet transform (UDWT is proposed in this paper. Firstly, the foundations of magnetic anomaly detection and UDWT are introduced in brief, while a possible detection system based on giant magneto-impedance (GMI magnetic sensor is also given out. Then our proposed energy detection based on UDWT is described in detail, and the probabilities of false alarm and detection for given the detection threshold in theory are presented. It is noticeable that no a priori assumptions regarding the ferromagnetic target or the magnetic noise probability are necessary for our method, and different from the discrete wavelet transform (DWT, the UDWT is shift invariant. Finally, some simulations are performed and the results show that the detection performance of our proposed detector is better than that of the conventional energy detector even utilized in the Gaussian white noise, especially when the spectral parameter α is less than 1.0. In addition, a real-world experiment was done to demonstrate the advantages of the proposed method.
Owens, A. R.; Kópházi, J.; Welch, J. A.; Eaton, M. D.
2017-04-01
In this paper a hanging-node, discontinuous Galerkin, isogeometric discretisation of the multigroup, discrete ordinates (SN) equations is presented in which each energy group has its own mesh. The equations are discretised using Non-Uniform Rational B-Splines (NURBS), which allows the coarsest mesh to exactly represent the geometry for a wide range of engineering problems of interest; this would not be the case using straight-sided finite elements. Information is transferred between meshes via the construction of a supermesh. This is a non-trivial task for two arbitrary meshes, but is significantly simplified here by deriving every mesh from a common coarsest initial mesh. In order to take full advantage of this flexible discretisation, goal-based error estimators are derived for the multigroup, discrete ordinates equations with both fixed (extraneous) and fission sources, and these estimators are used to drive an adaptive mesh refinement (AMR) procedure. The method is applied to a variety of test cases for both fixed and fission source problems. The error estimators are found to be extremely accurate for linear NURBS discretisations, with degraded performance for quadratic discretisations owing to a reduction in relative accuracy of the "exact" adjoint solution required to calculate the estimators. Nevertheless, the method seems to produce optimal meshes in the AMR process for both linear and quadratic discretisations, and is ≈×100 more accurate than uniform refinement for the same amount of computational effort for a 67 group deep penetration shielding problem.
Low Energy Supersymmetry from the Heterotic String Landscape
Lebedev, O; Raby, S; Ramos-Sanchez, S; Ratz, M; Vaudrevange, P K S; Wingerter, A; Lebedev, Oleg; Nilles, Hans-Peter; Raby, Stuart; Ramos-Sanchez, Saul; Ratz, Michael; Vaudrevange, Patrick K. S.; Wingerter, Akin
2007-01-01
We study possible correlations between properties of the observable and hidden sectors in heterotic string theory. Specifically, we analyze the case of the Z6-II orbifold compactification which produces a significant number of models with the spectrum of the supersymmetric standard model. We find that requiring realistic features does affect the hidden sector such that hidden sector gauge group factors SU(4) and SO(8) are favoured. In the context of gaugino condensation, this implies low energy supersymmetry breaking.
Landscape management for sustainable supplies of bio energy feedstock and enhanced soil quality
International Nuclear Information System (INIS)
Douglas, K.; Muth, D.
2013-01-01
Agriculture can simultaneously address global food, feed, fiber, and energy challenges provided our soil, water, and air resources are not compromised in doing so. Our objective is to present a landscape management concept as an approach for integrating multiple bio energy feedstock sources into current crop production systems. This is done to show how multiple, increasing global challenges can be met in a sustainable manner. We discuss how collaborative research among Usda-Agricultural Research Service (ARS), US Department of Energy (DOE) Idaho National Laboratory (INL), several university extension and research partners, and industry representatives [known as the Renewable Energy Assessment Project (Reap) team] has led to the development of computer-based decision aids for guiding sustainable bio energy feedstock production. The decision aids, known initially as the Corn Stover Tool and more recently as the Landscape Environmental Assessment Framework (Leaf) are tools designed to recognize the importance of nature s diversity and can therefore be used to guide sustainable feedstock production without having negative impacts on critical ecosystem services. Using a 57 ha farm site in central Iowa, USA, we show how producer decisions regarding corn (Zea mays L.) stover harvest within the US Corn Belt can be made in a more sustainable manner. This example also supports Reap team conclusions that stover should not be harvested if average grain yields are less than 11 Mg ha-1 unless more balanced landscape management practices are implemented. The tools also illustrate the importance of sub-field management and site-specific stover harvest strategies
Directory of Open Access Journals (Sweden)
Cheng Lv
2015-03-01
Full Text Available Quantitatively understanding the robustness, adaptivity and efficiency of cell cycle dynamics under the influence of noise is a fundamental but difficult question to answer for most eukaryotic organisms. Using a simplified budding yeast cell cycle model perturbed by intrinsic noise, we systematically explore these issues from an energy landscape point of view by constructing an energy landscape for the considered system based on large deviation theory. Analysis shows that the cell cycle trajectory is sharply confined by the ambient energy barrier, and the landscape along this trajectory exhibits a generally flat shape. We explain the evolution of the system on this flat path by incorporating its non-gradient nature. Furthermore, we illustrate how this global landscape changes in response to external signals, observing a nice transformation of the landscapes as the excitable system approaches a limit cycle system when nutrients are sufficient, as well as the formation of additional energy wells when the DNA replication checkpoint is activated. By taking into account the finite volume effect, we find additional pits along the flat cycle path in the landscape associated with the checkpoint mechanism of the cell cycle. The difference between the landscapes induced by intrinsic and extrinsic noise is also discussed. In our opinion, this meticulous structure of the energy landscape for our simplified model is of general interest to other cell cycle dynamics, and the proposed methods can be applied to study similar biological systems.
Modeling energy fluxes in heterogeneous landscapes employing a mosaic approach
Klein, Christian; Thieme, Christoph; Priesack, Eckart
2015-04-01
Recent studies show that uncertainties in regional and global climate and weather simulations are partly due to inadequate descriptions of the energy flux exchanges between the land surface and the atmosphere. One major shortcoming is the limitation of the grid-cell resolution, which is recommended to be about at least 3x3 km² in most models due to limitations in the model physics. To represent each individual grid cell most models select one dominant soil type and one dominant land use type. This resolution, however, is often too coarse in regions where the spatial diversity of soil and land use types are high, e.g. in Central Europe. An elegant method to avoid the shortcoming of grid cell resolution is the so called mosaic approach. This approach is part of the recently developed ecosystem model framework Expert-N 5.0. The aim of this study was to analyze the impact of the characteristics of two managed fields, planted with winter wheat and potato, on the near surface soil moistures and on the near surface energy flux exchanges of the soil-plant-atmosphere interface. The simulated energy fluxes were compared with eddy flux tower measurements between the respective fields at the research farm Scheyern, North-West of Munich, Germany. To perform these simulations, we coupled the ecosystem model Expert-N 5.0 to an analytical footprint model. The coupled model system has the ability to calculate the mixing ratio of the surface energy fluxes at a given point within one grid cell (in this case at the flux tower between the two fields). This approach accounts for the differences of the two soil types, of land use managements, and of canopy properties due to footprint size dynamics. Our preliminary simulation results show that a mosaic approach can improve modeling and analyzing energy fluxes when the land surface is heterogeneous. In this case our applied method is a promising approach to extend weather and climate models on the regional and on the global scale.
Model Predictive Control of a Wave Energy Converter with Discrete Fluid Power Power Take-Off System
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Anders Hedegaard Hansen
2018-03-01
Full Text Available Wave power extraction algorithms for wave energy converters are normally designed without taking system losses into account leading to suboptimal power extraction. In the current work, a model predictive power extraction algorithm is designed for a discretized power take of system. It is shown how the quantized nature of a discrete fluid power system may be included in a new model predictive control algorithm leading to a significant increase in the harvested power. A detailed investigation of the influence of the prediction horizon and the time step is reported. Furthermore, it is shown how the inclusion of a loss model may increase the energy output. Based on the presented results it is concluded that power extraction algorithms based on model predictive control principles are both feasible and favorable for use in a discrete fluid power power take-off system for point absorber wave energy converters.
Control of a 420 KN Discrete Displacement Cylinder Drive for the Wavestar Wave Energy Converter
DEFF Research Database (Denmark)
Hansen, Rico H.; Andersen, Torben Ole; Pedersen, Henrik C.
2014-01-01
absorbers. The system is implemented using multi-chambered cylinders, where the different chambers may be switched between three pressure lines using a manifold with fast on/off valves. Resultantly, a Discrete Displacement Cylinder (DDC) is obtained, where force control is implemented by shifting between...... different area/pressure combinations. Currently, a 420 kN DDC prototype has been implemented and tested at the newly commissioned full size wave energy testbench at Aalborg University. The initial design and control of the DDC had poorly damped switching transients. These issues treated in this paper....... This leads to a new control, which gives a smooth operating DDC, while meeting the requirements to the efficiency of the drive....
Manz, Christoph; Kobitski, Andrei Yu.; Samanta, Ayan; Jäschke, Andres; Nienhaus, G. Ulrich
2018-03-01
RNA (ribonucleic acid) molecules are highly flexible biopolymers fluctuating at physiological temperatures among many different conformations that are represented by minima in a hierarchical conformational free energy landscape. Here we have employed single-molecule FRET (smFRET) to explore the energy landscape of the B. subtilis yitJ SAM-I riboswitch (RS). In this small RNA molecule, specific binding of an S-adenosyl-L-methionine (SAM) ligand in the aptamer domain regulates gene expression by inducing structural changes in another domain, the expression platform, causing transcription termination by the RNA polymerase. We have measured smFRET histograms over wide ranges of Mg2+ concentration for three RS variants that were specifically labeled with fluorescent dyes on different sites. In the analysis, different conformations are associated with discrete Gaussian model distributions, which are typically fairly broad on the FRET efficiency scale and thus can be extremely challenging to unravel due to their mutual overlap. Our earlier work on two SAM-I RS variants revealed four major conformations. By introducing a global fitting procedure which models both the Mg2+ concentration dependencies of the fractional populations and the average FRET efficiencies of the individual FRET distributions according to Mg2+ binding isotherms, we were able to consistently describe the histogram data of both variants at all studied Mg2+ concentrations. With the third FRET-labeled variant, however, we found significant deviations when applying the four-state model to the data. This can arise because the different FRET labeling of the new variant allows two states to be distinguished that were previously not separable due to overlap. Indeed, the resulting five-state model presented here consistently describes the smFRET histograms of all three variants as well as their variations with Mg2+ concentration. We also performed a triangulation of the donor position for two of the constructs
Energy landscape of defects in body-centered cubic metals
International Nuclear Information System (INIS)
Alexander, Rebecca
2016-01-01
The structural materials in nuclear reactors are subjected to severe irradiation conditions, leading to changes in their mechanical properties. The aging of these materials raises important issues such as those related to the safety of existing plants and future reactors. In many cases, materials with body-centered cubic bcc crystal structure are used with iron, tungsten, vanadium and tantalum as base metal. Collisions between irradiating particles and atoms constituting materials generate point defects whose migration leads to the formation of clusters responsible for aging. In this thesis, we studied the energetic properties of point defects in the bcc metals mentioned above at the atomic scale. Modeling point defects at the atomic scale can be achieved with different methods that differ only in the quality of the description of the interaction between atoms. Studies using accurate atomic interactions such ab initio calculations are computationally costly making it impossible to directly study clusters of large sizes. The modeling of atomic interactions using semi-empirical potentials reduces the reliability of predictive calculations but allow calculations for large-sized clusters. In this thesis we have developed a unique energy model for dislocation loops as well as for three-dimensional interstitial cluster of type C15. The resulting model has no size limit and can be set entirely by ab initio calculations. To test its robustness for large sizes of clusters we also set this model with semi-empirical potentials calculations and compared the predictions of the model to atomic simulations. With our development we have determined: (i) The relative stability of interstitial dislocation loops according to their Burgers vectors. (ii) The stability of the clusters C15 compared to the type of cluster loop. We showed that the C15 type clusters are more stable when they involve less than 41 interstitials in iron. (iii) In Ta we were able to show the same stability till
Renewable energy policy and landscape management in Andalusia, Spain: The facts
International Nuclear Information System (INIS)
Prados, Maria-Jose
2010-01-01
Renewable energy has developed spectacularly in Spain since the European Union started a process of energy policy reform. A review of Spanish State legislation on renewable energies confirms that the success in installing renewable energy is attributable to public aid. Andalusia is one of the autonomous communities, which has simultaneously developed the legal framework and very successfully implemented the introduction of renewable power. When implementing the central government's policy, the Andalusian regional government prioritised increases in both surface cover by wind and solar plants (thermal and photovoltaic energy) and in the number of companies involved. However, this development of renewable energies took place without any proper integration into regional spatial and landscape planning. This paper explores renewable power implementation in Andalusia through regulatory measures put in place over the last decade to develop renewable energy systems and the way they can be managed alongside planning issues. The location of large-scale renewable plants has had consequences for territory in the socio-political context of renewable energy promotion. The main findings focus on renewable energy plant sprawl throughout rural areas in Andalusia with no clear effect on landscape management and no firm backing from the local population.
Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models.
Nayar, Divya; Chakravarty, Charusita
2015-08-27
Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.
Kim, Tae Heon; Yoon, Jong-Gul; Baek, Seung Hyub; Park, Woong-kyu; Yang, Sang Mo; Yup Jang, Seung; Min, Taeyuun; Chung, Jin-Seok; Eom, Chang-Beom; Noh, Tae Won
2015-07-01
Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields.
Heon Kim, Tae; Yoon, Jong-Gul; Hyub Baek, Seung; Park, Woong-Kyu; Mo Yang, Sang; Yup Jang, Seung; Min, Taeyuun; Chung, Jin-Seok; Eom, Chang-Beom; Won Noh, Tae
2015-07-01
Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields.
Multiple discrete-energy ion features in the inner magnetosphere: 9 February 1998, event
Directory of Open Access Journals (Sweden)
Y. Ebihara
2004-04-01
Full Text Available Multiple discrete-energy ion bands observed by the Polar satellite in the inner magnetosphere on 9 February 1998 were investigated by means of particle simulation with a realistic model of the convection electric field. The multiple bands appeared in the energy vs. L spectrum in the 1–100 keV range when Polar traveled in the heart of the ring current along the outbound and inbound paths. We performed particle tracing, and simulated the energy vs. L spectra of proton fluxes under the dipole magnetic field, the corotation electric field, and the realistic convection electric field model with its parameters depending on the solar wind data. Simulated spectra are shown to agree well with the observed ones. A better agreement is achieved when we rotate the convection electric potential eastward by 2h inMLT and we change the distribution function in time in the near-Earth magnetotail. It is concluded that the multiple bands are likely produced by two processes for this particular event, that is, changes in the convection electric field (for >3keV protons and changes in the distribution function in the near-Earth magnetotail (for <3keV protons. Key words. Magnetospheric physics (energetic particles, trapped; electric field – Space plasma physics (numerical simulation studies
Relationship between energy systems and landscapes. Guidelines and tools for design and management
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Elisabetta Ginelli
2014-10-01
Full Text Available Landscapes undergoing conservation, valorisation, management and reconstruction policies, become a fundamental factor for the local/global development of natural, cultural, human and social potentials of territories. With the contribution of technological design culture, the research, having a strong multidisciplinary character, focuses on managing the relationship between energy systems and landscapes with the general aim of subverting and transforming apparent conflicts in synergies, in order to overcome a sectorial and segmented approach barely based on energy performances. Through the introduction of a complex multidimensional methodology of analysis and evaluation the goal of this work, is to develop standards of acceptability, meta-design criteria and guidelines for design, intro- ducing a methodology for multidimen- sional complex analysis and evaluation, to support Public Authorities.
International Nuclear Information System (INIS)
Bishop, Clare L; Wilson, Mark
2009-01-01
The mechanisms for filling carbon nanotubes with molten salts are investigated using molecular dynamics computer simulation. Inorganic nanotubular structures, whose morphologies can be rationalized in terms of the folding, or the removal of sections from, planes of square nets are found to form. The formation mechanisms are found to follow a 'chain-by-chain' motif in which the structures build systematically from charge neutral M-X-M-Xc chains. The formation mechanisms are rationalized in terms of the ion-ion interactions (intra-chain and inter-chain terms). In addition, the mechanisms of filling are discussed in terms of a 'hopping' between basins on the underlying energy landscape. The role of the carbon nanotube as an energy landscape filter is discussed.
Frustration in the energy landscapes of multidomain protein misfolding.
Zheng, Weihua; Schafer, Nicholas P; Wolynes, Peter G
2013-01-29
Frustration from strong interdomain interactions can make misfolding a more severe problem in multidomain proteins than in single-domain proteins. On the basis of bioinformatic surveys, it has been suggested that lowering the sequence identity between neighboring domains is one of nature's solutions to the multidomain misfolding problem. We investigate folding of multidomain proteins using the associative-memory, water-mediated, structure and energy model (AWSEM), a predictive coarse-grained protein force field. We find that reducing sequence identity not only decreases the formation of domain-swapped contacts but also decreases the formation of strong self-recognition contacts between β-strands with high hydrophobic content. The ensembles of misfolded structures that result from forming these amyloid-like interactions are energetically disfavored compared with the native state, but entropically favored. Therefore, these ensembles are more stable than the native ensemble under denaturing conditions, such as high temperature. Domain-swapped contacts compete with self-recognition contacts in forming various trapped states, and point mutations can shift the balance between the two types of interaction. We predict that multidomain proteins that lack these specific strong interdomain interactions should fold reliably.
Directory of Open Access Journals (Sweden)
Laura E Rosen
Full Text Available An important approach to understanding how a protein sequence encodes its energy landscape is to compare proteins with different sequences that fold to the same general native structure. In this work, we compare E. coli and T. thermophilus homologs of the protein RNase H. Using protein fragments, we create equilibrium mimics of two different potential partially-folded intermediates (I(core and I(core+1 hypothesized to be present on the energy landscapes of these two proteins. We observe that both T. thermophilus RNase H (ttRNH fragments are folded and have distinct stabilities, indicating that both regions are capable of autonomous folding and that both intermediates are present as local minima on the ttRNH energy landscape. In contrast, the two E. coli RNase H (ecRNH fragments have very similar stabilities, suggesting that the presence of additional residues in the I(core+1 fragment does not affect the folding or structure as compared to I(core. NMR experiments provide additional evidence that only the I(core intermediate is populated by ecRNH. This is one of the biggest differences that has been observed between the energy landscapes of these two proteins. Additionally, we used a FRET experiment in the background of full-length ttRNH to specifically monitor the formation of the I(core+1 intermediate. We determine that the ttRNH I(core+1 intermediate is likely the intermediate populated prior to the rate-limiting barrier to global folding, in contrast to E. coli RNase H for which I(core is the folding intermediate. This result provides new insight into the nature of the rate-limiting barrier for the folding of RNase H.
Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch
Cragnolini, Tristan; Chakraborty, Debayan; Šponer, Jiří; Derreumaux, Philippe; Pasquali, Samuela; Wales, David J.
2017-10-01
We explore the energy landscape for a four-fold telomere repeat, obtaining interconversion pathways between six experimentally characterised G-quadruplex topologies. The results reveal a multi-funnel system, with a variety of intermediate configurations and misfolded states. This organisation is identified with the intrinsically multi-functional nature of the system, suggesting a new paradigm for the classification of such biomolecules and clarifying issues regarding apparently conflicting experimental results.
Finite-element discretization of 3D energy-transport equations for semiconductors
Energy Technology Data Exchange (ETDEWEB)
Gadau, Stephan
2007-07-01
In this thesis a mathematical model was derived that describes the charge and energy transport in semiconductor devices like transistors. Moreover, numerical simulations of these physical processes are performed. In order to accomplish this, methods of theoretical physics, functional analysis, numerical mathematics and computer programming are applied. After an introduction to the status quo of semiconductor device simulation methods and a brief review of historical facts up to now, the attention is shifted to the construction of a model, which serves as the basis of the subsequent derivations in the thesis. Thereby the starting point is an important equation of the theory of dilute gases. From this equation the model equations are derived and specified by means of a series expansion method. This is done in a multi-stage derivation process, which is mainly taken from a scientific paper and which does not constitute the focus of this thesis. In the following phase we specify the mathematical setting and make precise the model assumptions. Thereby we make use of methods of functional analysis. Since the equations we deal with are coupled, we are concerned with a nonstandard problem. In contrary, the theory of scalar elliptic equations is established meanwhile. Subsequently, we are preoccupied with the numerical discretization of the equations. A special finite-element method is used for the discretization. This special approach has to be done in order to make the numerical results appropriate for practical application. By a series of transformations from the discrete model we derive a system of algebraic equations that are eligible for numerical evaluation. Using self-made computer programs we solve the equations to get approximate solutions. These programs are based on new and specialized iteration procedures that are developed and thoroughly tested within the frame of this research work. Due to their importance and their novel status, they are explained and
A new approach to quantify semiochemical effects on insects based on energy landscapes.
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Rory P Wilson
Full Text Available Our ability to document insect preference for semiochemicals is pivotal in pest control as these agents can improve monitoring and be deployed within integrated pest management programmes for more efficacious control of pest species. However, methods used to date have drawbacks that limit their utility. We present and test a new concept for determining insect motivation to move towards, or away from, semiochemicals by noting direction and speed of movement as animals work against a defined energy landscape (environmentally dependent variation in the cost of transport requiring different powers to negotiate. We conducted trials with the pine weevils Hylobius abietis and peach-potato aphids Myzus persicae exposed to various attractants and repellents and placed so that they either moved up defined slopes against gravity or had to travel over variously rough surfaces.Linear Mixed Models demonstrated clear reductions in travel speed by insects moving along increasingly energetically taxing energy landscapes but also that responses varied according to different semiochemicals, thus highlighting the value of energy landscapes as a new concept to help measure insect motivation to access or avoid different attractants or repellents across individuals.New sensitive, detailed indicators of insect motivation derived from this approach should prove important in pest control across the world.
Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.
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Kei Moritsugu
2014-10-01
Full Text Available Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.
Landscape encodings enhance optimization.
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Konstantin Klemm
Full Text Available Hard combinatorial optimization problems deal with the search for the minimum cost solutions (ground states of discrete systems under strong constraints. A transformation of state variables may enhance computational tractability. It has been argued that these state encodings are to be chosen invertible to retain the original size of the state space. Here we show how redundant non-invertible encodings enhance optimization by enriching the density of low-energy states. In addition, smooth landscapes may be established on encoded state spaces to guide local search dynamics towards the ground state.
Landscape Encodings Enhance Optimization
Klemm, Konstantin; Mehta, Anita; Stadler, Peter F.
2012-01-01
Hard combinatorial optimization problems deal with the search for the minimum cost solutions (ground states) of discrete systems under strong constraints. A transformation of state variables may enhance computational tractability. It has been argued that these state encodings are to be chosen invertible to retain the original size of the state space. Here we show how redundant non-invertible encodings enhance optimization by enriching the density of low-energy states. In addition, smooth landscapes may be established on encoded state spaces to guide local search dynamics towards the ground state. PMID:22496860
Directory of Open Access Journals (Sweden)
Paul D. Pickell
2014-07-01
Full Text Available The accelerated development of energy resources around the world has substantially increased forest change related to oil and gas activities. In some cases, oil and gas activities are the primary catalyst of land-use change in forested landscapes. We discuss the challenges associated with characterizing ecological change related to energy resource development using North America as an exemplar. We synthesize the major impacts of energy development to forested ecosystems and offer new perspectives on how to detect and monitor anthropogenic disturbance during the Anthropocene. The disturbance of North American forests for energy development has resulted in persistent linear corridors, suppression of historical disturbance regimes, novel ecosystems, and the eradication of ecological memory. Characterizing anthropogenic disturbances using conventional patch-based disturbance measures will tend to underestimate the ecological impacts of energy development. Suitable indicators of anthropogenic impacts in forests should be derived from the integration of multi-scalar Earth observations. Relating these indicators to ecosystem condition will be a capstone in the progress toward monitoring forest change in landscapes undergoing rapid energy development.
The potential energy landscape in the Lennard-Jones binary mixture model
International Nuclear Information System (INIS)
Sampoli, M; Benassi, P; Eramo, R; Angelani, L; Ruocco, G
2003-01-01
The potential energy landscape in the Kob-Andersen Lennard-Jones binary mixture model has been studied carefully from the liquid down to the supercooled regime, from T = 2 down to 0.46. One thousand independent configurations along the time evolution locus have been examined at each temperature investigated. From the starting configuration, we searched for the nearest saddle (or quasi-saddle) and minimum of the potential energy. The vibrational densities of states for the starting and the two derived configurations have been evaluated. Besides the number of negative eigenvalues of the saddles other quantities show some signature of the approach of the dynamical arrest temperature
Model Predictive Control of a Wave Energy Converter with Discrete Fluid Power Power Take-Off System
DEFF Research Database (Denmark)
Hansen, Anders Hedegaard; Asmussen, Magnus Færing; Bech, Michael Møller
2018-01-01
Wave power extraction algorithms for wave energy converters are normally designed without taking system losses into account leading to suboptimal power extraction. In the current work, a model predictive power extraction algorithm is designed for a discretized power take of system. It is shown how...... the quantized nature of a discrete fluid power system may be included in a new model predictive control algorithm leading to a significant increase in the harvested power. A detailed investigation of the influence of the prediction horizon and the time step is reported. Furthermore, it is shown how...
International Nuclear Information System (INIS)
Horne, M.; Jaccard, M.; Tiedemann, K.
2005-01-01
Hybrid energy-economy models combine top-down and bottom-up approaches to explore behaviorally realistic responses to technology-focused policies. This research uses empirically derived discrete choice models to inform key behavioral parameters in CIMS, a hybrid model. The discrete choice models are estimated for vehicle and commuting decisions from a survey of 1150 Canadians. With the choice models integrated into CIMS, we simulate carbon taxes, gasoline vehicle disincentives, and single occupancy vehicle disincentives to show how different policy levers can motivate technological change. We also use the empirical basis for the choice models to portray uncertainty in technological change, costs, and emissions. (author)
Chakraborty, Debayan; Wales, David J
2018-01-04
The recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences and positional contexts could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick (WC) to HG transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape perspective. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of WC and HG base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a challenging target for both simulation and experiment.
Naumis, Gerardo G
2012-06-01
When a liquid melt is cooled, a glass or phase transition can be obtained depending on the cooling rate. Yet, this behavior has not been clearly captured in energy-landscape models. Here, a model is provided in which two key ingredients are considered in the landscape, metastable states and their multiplicity. Metastable states are considered as in two level system models. However, their multiplicity and topology allows a phase transition in the thermodynamic limit for slow cooling, while a transition to the glass is obtained for fast cooling. By solving the corresponding master equation, the minimal speed of cooling required to produce the glass is obtained as a function of the distribution of metastable states.
Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge.
Dahle, Håkon; Økland, Ingeborg; Thorseth, Ingunn H; Pederesen, Rolf B; Steen, Ida H
2015-07-01
Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki's Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition.
An energy landscape based approach for studying supercooled liquid and glassy thin films
Shah, Pooja; Mittal, Jeetain; Truskett, Thomas M.
2004-03-01
Materials in confined spaces are important in science and technology. Examples include biological fluids in membranes, liquids trapped in porous rocks, and thin-film materials used in high-resolution patterning technologies. However, few reliable rules exist to predict how the properties of materials will be affected by thin-film confinement. We have recently shown that the potential energy landscape formalism can be used to study, by both theory [1] and simulation [2], how the behavior of thin-film materials depends on sample dimensions and film-substrate interactions. Our landscape-based mean-field theory [1] can be used to study both the thermodynamic properties and the ideal glass transition of thin films. It predicts that, in the case of neutral or repulsive walls, the ideal glass transition temperature is lowered by decreasing film thickness. This is in qualitative agreement with experimental trends for the kinetic glass transition in confined fluids. Landscape-based approaches are also valuable for understanding the structural and mechanical properties of thin-film glasses. We demonstrate how the concept of an "equation of state of the energy landscape" [3] can be generalized to thin films [1, 2], where it gives insights into potential molecular mechanisms of tensile strength. [1] T. M. Truskett and V. Ganesan, J. Chem. Phys. 119, 1897-1900(2003); J. Mittal, P. Shah and T. M. Truskett, to be submitted to Langmuir. [2] P. Shah and T. M. Truskett, to be submitted to J. Phys. Chem. B. [3] S. Sastry, P. G. Debenedetti and F. H. Stillinger, Phys. Rev. E 56, 5533 (1997)
Vishwakarma, Abhaypratap; Kumari, Aprajita; Mur, Luis A J; Gupta, Kapuganti Jagadis
2018-03-28
Alternative oxidase (AOX) is an integral part of the mitochondrial electron transport and can prevent reactive oxygen species (ROS) and nitric oxide (NO) production under non-stressed, normoxic conditions. Here we assessed the roles of AOX by imposing stress under normoxia in comparison to hypoxic conditions using AOX over expressing (AOX OE) and anti-sense (AOX AS) transgenic Arabidopsis seedlings and roots. Under normoxic conditions stress was induced with the defence elicitor flagellin (flg22). AOX OE reduced NO production whilst this was increased in AOX AS. Moreover AOX AS also exhibited an increase in superoxide and therefore peroxynitrite, tyrosine nitration suggesting that scavenging of NO by AOX can prevent toxic peroxynitrite formation under normoxia. In contrast, during hypoxia interestingly we found that AOX is a generator of NO. Thus, the NO produced during hypoxia, was enhanced in AOX OE and suppressed in AOX AS. Additionally, treatment of WT or AOX OE with the AOX inhibitor SHAM inhibited hypoxic NO production. The enhanced levels of NO correlated with expression of non-symbiotic haemoglobin, increased NR activity and ATP production. The ATP generation was suppressed in nia1,2 mutant and non symbiotic haemoglobin antisense line treated with SHAM. Taken together these results suggest that hypoxic NO generation mediated by AOX has a discrete role by feeding into the haemoglobin-NO cycle to drive energy efficiency under conditions of low oxygen tension. Copyright © 2018 Elsevier Inc. All rights reserved.
International Nuclear Information System (INIS)
Leyendecker, Sigrid; Betsch, Peter; Steinmann, Paul
2008-01-01
In the present work, the unified framework for the computational treatment of rigid bodies and nonlinear beams developed by Betsch and Steinmann (Multibody Syst. Dyn. 8, 367-391, 2002) is extended to the realm of nonlinear shells. In particular, a specific constrained formulation of shells is proposed which leads to the semi-discrete equations of motion characterized by a set of differential-algebraic equations (DAEs). The DAEs provide a uniform description for rigid bodies, semi-discrete beams and shells and, consequently, flexible multibody systems. The constraints may be divided into two classes: (i) internal constraints which are intimately connected with the assumption of rigidity of the bodies, and (ii) external constraints related to the presence of joints in a multibody framework. The present approach thus circumvents the use of rotational variables throughout the whole time discretization, facilitating the design of energy-momentum methods for flexible multibody dynamics. After the discretization has been completed a size-reduction of the discrete system is performed by eliminating the constraint forces. Numerical examples dealing with a spatial slider-crank mechanism and with intersecting shells illustrate the performance of the proposed method
International Nuclear Information System (INIS)
Suzuki, Yohichi; Tanimura, Yoshitaka
2007-01-01
Electron transfer reaction in a polar solvent is modeled by a solute dipole surrounded by dipolar molecules with simple rotational dynamics posted on the three-dimensional distorted lattice sites. The interaction energy between the solute and solvent dipoles as a reaction coordinate is adopted and free energy landscapes are calculated by generating all possible states for a 26 dipolar system and by employing Wang-Landau sampling algorithm for a 92 dipolar system. For temperatures higher than the energy scale of dipole-dipole interactions, the free energy landscapes for the small reaction coordinate region have quadratic shape as predicted by Marcus [Rev. Mod. Phys. 65, 599 (1993)] whereas for the large reaction coordinate region, the landscapes exhibit a nonquadratic shape. When the temperature drops, small notched structures appear on the free energy profiles because of the frustrated interactions among dipoles. The formation of notched structure is analyzed with statistical approach and it is shown that the amplitude of notched structure depend upon the segment size of the reaction coordinate and is characterized by the interaction energy among the dipoles. Using simulated free energy landscapes, the authors calculate the reaction rates as a function of the energy gap for various temperatures. At high temperature, the reactions rates follow a bell shaped (inverted parabolic) energy gap law in the small energy gap regions, while it becomes steeper than the parabolic shape in a large energy gap regions due to the nonquadratic shape of the free energy landscape. The peak position of parabola also changes as the function of temperature. At low temperature, the profile of the reaction rates is no longer smooth because of the many local minima of the free energy landscape
Potential energy landscape and robustness of a gene regulatory network: toggle switch.
Directory of Open Access Journals (Sweden)
Keun-Young Kim
2007-03-01
Full Text Available Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers. It leads to the robustness of the biological basins of the gene switches. The technique used here is general and can be applied to explore the potential energy landscape of the gene networks.
The environmental benefits of cellulosic energy crops at a landscape scale
International Nuclear Information System (INIS)
Graham, R.L.; Liu, W.; English, B.C.
1995-01-01
The objective of this paper is to present a broad overview of the potential environmental impacts of biomass energy from energy crops--particularly the cellulosic energy crops current under development. For this discussion, the term energy crop refers to a crop grown primarily to create feedstock for either making biofuels such as ethanol or burning in a heat or electricity generation facility. Cellulosic energy crops are designed to be used in cellulose-based ethanol conversion processes (as opposed to starch or sugar-based ethanol conversion processes). As more cellulose can be produced per hectare of land than can sugar or starch, the cellulose-based ethanol conversion process is a more efficient sue of land for ethanol production. Assessing the environmental impacts of biomass energy from energy crops is complex because the environmental impact of using biomass for energy must be considered in the context of alternative energy options while the environmental impact of producing biomass from energy crops must be considered in the context of alternative land-uses. Using biomass-derived energy can reduce greenhouse gas emissions or increase them; growing biomass energy crops can enhance soil fertility or degrade it. Without knowing the context of the biomass energy, one can say little about its specific environmental impacts. The primary focus of this paper is an evaluation of the environmental impacts of growing cellulosic energy crops especially at the landscape or regional scale. However, to set the stage for this discussion, the authors begin by comparing the environmental advantages and disadvantages of biomass-derived energy relative to other energy alternatives such as coal, hydropower, nuclear power, oil/gasoline, natural gas and photovoltaics
Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.
Ghaemi, Zhaleh; Guzman, Irisbel; Gnutt, David; Luthey-Schulten, Zaida; Gruebele, Martin
2017-09-14
U1A protein-stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape toward a specific binding site. We show by using molecular dynamics simulations that deletion of two long-range electrostatic interactions (K22Q and K50Q) leads to mutant-specific alternative RNA bound states. One of these states preserves short-range interactions with aromatic residues in the original binding site, while the other one does not. We test the computational prediction with experimental temperature-jump kinetics using a tryptophan probe in the U1A-RNA binding site. The two mutants show the distinct predicted kinetic behaviors. Thus, the stem loop 2 RNA has multiple binding sites on a rough RNA-protein binding landscape. We speculate that the rough protein-RNA binding landscape, when biased to different local minima by electrostatics, could be one way that protein-RNA interactions evolve toward new binding sites and novel function.
Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.
Tsai, Min-Yeh; Zheng, Weihua; Balamurugan, D; Schafer, Nicholas P; Kim, Bobby L; Cheung, Margaret S; Wolynes, Peter G
2016-01-01
While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes. © 2015 The Protein Society.
Pierre, Jon Paul; Young, Michael H.; Wolaver, Brad D.; Andrews, John R.; Breton, Caroline L.
2017-11-01
Spatio-temporal trends in infrastructure footprints, energy production, and landscape alteration were assessed for the Eagle Ford Shale of Texas. The period of analysis was over four 2-year periods (2006-2014). Analyses used high-resolution imagery, as well as pipeline data to map EF infrastructure. Landscape conditions from 2006 were used as baseline. Results indicate that infrastructure footprints varied from 94.5 km2 in 2008 to 225.0 km2 in 2014. By 2014, decreased land-use intensities (ratio of land alteration to energy production) were noted play-wide. Core-area alteration by period was highest (3331.6 km2) in 2008 at the onset of play development, and increased from 582.3 to 3913.9 km2 by 2014, though substantial revegetation of localized core areas was observed throughout the study (i.e., alteration improved in some areas and worsened in others). Land-use intensity in the eastern portion of the play was consistently lower than that in the western portion, while core alteration remained relatively constant east to west. Land alteration from pipeline construction was 65 km2 for all time periods, except in 2010 when alteration was recorded at 47 km2. Percent of total alteration from well-pad construction increased from 27.3% in 2008 to 71.5% in 2014. The average number of wells per pad across all 27 counties increased from 1.15 to 1.7. This study presents a framework for mapping landscape alteration from oil and gas infrastructure development. However, the framework could be applied to other energy development programs, such as wind or solar fields, or any other regional infrastructure development program.
Free energy landscape and cooperatively rearranging region in a hard sphere glass
Yoshidome, Takashi; Yoshimori, Akira; Odagaki, Takashi
2007-08-01
Exploiting the density functional theory, we calculate the free energy landscape (FEL) of the hard sphere glass in three dimensions. From the FEL, we estimate the number of the particles in the cooperatively rearranging region (CRR). We find that the density dependence of the number of the particles in the CRR is expressed as a power law function of the density. Analyzing the relaxation process in the CRR, we also find that the string motion is the elementary process for the structural relaxation, which leads to the natural definition of the simultaneously rearranging region as the particles displaced in the string motion.
Cornil, J; Verlaak, S; Martinelli, N; Mityashin, A; Olivier, Y; Van Regemorter, T; D'Avino, G; Muccioli, L; Zannoni, C; Castet, F; Beljonne, D; Heremans, P
2013-02-19
strongly interacting electron-hole pairs can potentially escape from their Coulomb well, a process that is at the heart of photoconversion or molecular doping. Yet they do, with near-quantitative yield in some cases. Limited screening by the low dielectric medium in organic materials leads to subtle static and dynamic electronic polarization effects that strongly impact the energy landscape for charges, which offers a rationale for this apparent inconsistency. In this Account, we use different theoretical approaches to predict the energy landscape of charge carriers at the molecular level and review a few case studies highlighting the role of electrostatic interactions in conjugated organic molecules. We describe the pros and cons of different theoretical approaches that provide access to the energy landscape defining the motion of charge carriers. We illustrate the applications of these approaches through selected examples involving OFETs, OLEDs, and solar cells. The three selected examples collectively show that energetic disorder governs device performances and highlights the relevance of theoretical tools to probe energy landscapes in molecular assemblies.
Energy landscape for martensitic phase transformation in shape memory NiTi
International Nuclear Information System (INIS)
Kibey, S.; Sehitoglu, H.; Johnson, D.D.
2009-01-01
First-principles calculations are presented for parent B2 phase and martensitic B19 and B19' phases in NiTi. The results indicate that both B19 and B19' are energetically more stable than the parent B2 phase. By means of ab initio density functional theory, the complete distortion-shuffle energy landscape associated with B2 → B19 transformation in NiTi is then determined. In addition to accounting for the Bain-type deformation through the Cauchy-Born rule, the study explicitly accounts for the shuffle displacements experienced by the internal ions in NiTi. The energy landscape allows the energy barrier associated with the B2 → B19 transformation pathway to be identified. The results indicate that a barrier of 0.48 mRyd atom -1 (relative to the B2 phase) must be overcome to transform the parent B2 NiTi to orthorhombic B19 martensite
Quantitative analysis of the publishing landscape in high-energy physics
International Nuclear Information System (INIS)
Mele, Salvatore; Dallman, David; Vigen, Jens; Yeomans, Joanne
2006-01-01
World-wide collaboration in high-energy physics (HEP) is a tradition which dates back several decades, with scientific publications mostly coauthored by scientists from different countries. This coauthorship phenomenon makes it difficult to identify precisely the 'share' of each country in HEP scientific production. One year's worth of HEP scientific articles published in peer-reviewed journals is analysed and their authors are uniquely assigned to countries. This method allows the first correct estimation on a pro rata basis of the share of HEP scientific publishing among several countries and institutions. The results provide an interesting insight into the geographical collaborative patterns of the HEP community. The HEP publishing landscape is further analysed to provide information on the journals favoured by the HEP community and on the geographical variation of their author bases. These results provide quantitative input to the ongoing debate on the possible transition of HEP publishing to an Open Access model. Foreword. This paper reports the results of a recent detailed study of the publishing landscape in high energy physics. We thought that because of its direct relevance to the high energy physics community, this important quantitative input to the debate on the transition to Open Access naturally finds its place in our journal. Marc Henneaux, JHEP Scientific Director
Obsolete or resurgent? The International Energy Agency in a changing global landscape
International Nuclear Information System (INIS)
Van de Graaf, Thijs
2012-01-01
Founded in response to the 1973 oil shock, the International Energy Agency (IEA) is arguably still the most important multilateral organization for energy-importing countries. Yet, the global geopolitical landscape has changed considerably since the IEA's creation. The rise of new energy consumers, new energy-related challenges and new international energy forums prompt a rethink of the agency's current role and institutional design. This article seeks to contribute to the recent debate on the future role of the IEA by examining specific drivers, avenues and constraints for institutional reform. The method used is SWOT analysis, which allows to summarize the key factors emanating from an assessment of an organization's internal characteristics (strengths and weaknesses) and its external environment (opportunities and threats). Building on this SWOT analysis, the article formulates a strategy for the IEA to remain the focal point in global energy governance. Key elements of this strategy include: stronger engagement with new consumers, rapprochement with OPEC, becoming a leading voice in the energy transition, and changing the agency's internal governance practices. - Highlights: ► The IEA is challenged by the rise of new consumers, threats and organizations. ► Assessment of the agency’s internal characteristics and external environment. ► The IEA needs to step up its outreach policy and fully embrace sustainable energy.
Olariu, Victor; Manesso, Erica; Peterson, Carsten
2017-06-01
Depicting developmental processes as movements in free energy genetic landscapes is an illustrative tool. However, exploring such landscapes to obtain quantitative or even qualitative predictions is hampered by the lack of free energy functions corresponding to the biochemical Michaelis-Menten or Hill rate equations for the dynamics. Being armed with energy landscapes defined by a network and its interactions would open up the possibility of swiftly identifying cell states and computing optimal paths, including those of cell reprogramming, thereby avoiding exhaustive trial-and-error simulations with rate equations for different parameter sets. It turns out that sigmoidal rate equations do have approximate free energy associations. With this replacement of rate equations, we develop a deterministic method for estimating the free energy surfaces of systems of interacting genes at different noise levels or temperatures. Once such free energy landscape estimates have been established, we adapt a shortest path algorithm to determine optimal routes in the landscapes. We explore the method on three circuits for haematopoiesis and embryonic stem cell development for commitment and reprogramming scenarios and illustrate how the method can be used to determine sequential steps for onsets of external factors, essential for efficient reprogramming.
Pierre, Jon Paul; Wolaver, Brad D; Labay, Benjamin J; LaDuc, Travis J; Duran, Charles M; Ryberg, Wade A; Hibbitts, Toby J; Andrews, John R
2018-05-01
Recent research assessed how hydrocarbon and wind energy expansion has altered the North American landscape. Less understood, however, is how this energy development compares to other anthropogenic land use changes. Texas leads U.S. hydrocarbon production and wind power generation and has a rapidly expanding population. Thus, for ~47% of Texas (~324,000 km 2 ), we mapped the 2014 footprint of energy activities (~665,000 oil and gas wells, ~5700 wind turbines, ~237,000 km oil and gas pipelines, and ~2000 km electrical transmission lines). We compared the footprint of energy development to non-energy-related activities (agriculture, roads, urbanization) and found direct landscape alteration from all factors affects ~23% of the study area (~76,000 km 2 ), led by agriculture (~16%; ~52,882 km 2 ). Oil and gas activities altered turbine pads and ~10 km 2 from power transmission lines. We found that edge effects of widely-distributed energy infrastructure caused more indirect landscape alteration than larger, more concentrated urbanization and agriculture. This study presents a novel technique to quantify and compare anthropogenic activities causing both direct and indirect landscape alteration. We illustrate this landscape-mapping framework in Texas for the Spot-tailed Earless Lizard (Holbrookia lacerata); however, the approach can be applied to a range of species in developing regions globally.
A Tale of Two Regions: Landscape Ecological Planning for Shale Gas Energy Futures
Murtha, T., Jr.; Schroth, O.; Orland, B.; Goldberg, L.; Mazurczyk, T.
2015-12-01
As we increasingly embrace deep shale gas deposits to meet global energy demands new and dispersed local and regional policy and planning challenges emerge. Even in regions with long histories of energy extraction, such as coal, shale gas and the infrastructure needed to produce the gas and transport it to market offers uniquely complex transformations in land use and landcover not previously experienced. These transformations are fast paced, dispersed and can overwhelm local and regional planning and regulatory processes. Coupled to these transformations is a structural confounding factor. While extraction and testing are carried out locally, regulation and decision-making is multilayered, often influenced by national and international factors. Using a geodesign framework, this paper applies a set of geospatial landscape ecological planning tools in two shale gas settings. First, we describe and detail a series of ongoing studies and tools that we have developed for communities in the Marcellus Shale region of the eastern United States, specifically the northern tier of Pennsylvania. Second, we apply a subset of these tools to potential gas development areas of the Fylde region in Lancashire, United Kingdom. For the past five years we have tested, applied and refined a set of place based and data driven geospatial models for forecasting, envisioning, analyzing and evaluating shale gas activities in northern Pennsylvania. These models are continuously compared to important landscape ecological planning challenges and priorities in the region, e.g. visual and cultural resource preservation. Adapting and applying these tools to a different landscape allow us to not only isolate and define important regulatory and policy exigencies in each specific setting, but also to develop and refine these models for broader application. As we continue to explore increasingly complex energy solutions globally, we need an equally complex comparative set of landscape ecological
Protein Folding Free Energy Landscape along the Committor - the Optimal Folding Coordinate.
Krivov, Sergei V
2018-06-06
Recent advances in simulation and experiment have led to dramatic increases in the quantity and complexity of produced data, which makes the development of automated analysis tools very important. A powerful approach to analyze dynamics contained in such data sets is to describe/approximate it by diffusion on a free energy landscape - free energy as a function of reaction coordinates (RC). For the description to be quantitatively accurate, RCs should be chosen in an optimal way. Recent theoretical results show that such an optimal RC exists; however, determining it for practical systems is a very difficult unsolved problem. Here we describe a solution to this problem. We describe an adaptive nonparametric approach to accurately determine the optimal RC (the committor) for an equilibrium trajectory of a realistic system. In contrast to alternative approaches, which require a functional form with many parameters to approximate an RC and thus extensive expertise with the system, the suggested approach is nonparametric and can approximate any RC with high accuracy without system specific information. To avoid overfitting for a realistically sampled system, the approach performs RC optimization in an adaptive manner by focusing optimization on less optimized spatiotemporal regions of the RC. The power of the approach is illustrated on a long equilibrium atomistic folding simulation of HP35 protein. We have determined the optimal folding RC - the committor, which was confirmed by passing a stringent committor validation test. It allowed us to determine a first quantitatively accurate protein folding free energy landscape. We have confirmed the recent theoretical results that diffusion on such a free energy profile can be used to compute exactly the equilibrium flux, the mean first passage times, and the mean transition path times between any two points on the profile. We have shown that the mean squared displacement along the optimal RC grows linear with time as for
A cavitation transition in the energy landscape of simple cohesive liquids and glasses
International Nuclear Information System (INIS)
Altabet, Y. Elia; Debenedetti, Pablo G.; Stillinger, Frank H.
2016-01-01
In particle systems with cohesive interactions, the pressure-density relationship of the mechanically stable inherent structures sampled along a liquid isotherm (i.e., the equation of state of an energy landscape) will display a minimum at the Sastry density ρ S . The tensile limit at ρ S is due to cavitation that occurs upon energy minimization, and previous characterizations of this behavior suggested that ρ S is a spinodal-like limit that separates all homogeneous and fractured inherent structures. Here, we revisit the phenomenology of Sastry behavior and find that it is subject to considerable finite-size effects, and the development of the inherent structure equation of state with system size is consistent with the finite-size rounding of an athermal phase transition. What appears to be a continuous spinodal-like point at finite system sizes becomes discontinuous in the thermodynamic limit, indicating behavior akin to a phase transition. We also study cavitation in glassy packings subjected to athermal expansion. Many individual expansion trajectories averaged together produce a smooth equation of state, which we find also exhibits features of finite-size rounding, and the examples studied in this work give rise to a larger limiting tension than for the corresponding landscape equation of state.
The energy landscape of glassy dynamics on the amorphous hafnium diboride surface
Nguyen, Duc; Mallek, Justin; Cloud, Andrew N.; Abelson, John R.; Girolami, Gregory S.; Lyding, Joseph; Gruebele, Martin
2014-11-01
Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB2 glass surface, two-state hopping of 1-2 nm diameter cooperatively rearranging regions or "clusters" occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how "mixed" features can show up in surface dynamics of glasses.
Stremke, S.; Picchi, Paolo
2017-01-01
The chapter begins with a literature review of energy potential mapping, ecosystem services (ES) assessment and participatory mapping (PM). PM is a key technique to conduct tradeoff analysis while co-designing sustainable energy landscapes (SEL) with local communities. Stakeholders, among others,
Communication: Theoretical prediction of free-energy landscapes for complex self-assembly
Energy Technology Data Exchange (ETDEWEB)
Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)
2015-01-14
We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.
Kazmier, Kelli; Claxton, Derek P; Mchaourab, Hassane S
2017-08-01
Secondary active transporters couple the uphill translocation of substrates to electrochemical ion gradients. Transporter conformational motion, generically referred to as alternating access, enables a central ligand binding site to change its orientation relative to the membrane. Here we review themes of alternating access and the transduction of ion gradient energy to power this process in the LeuT-fold class of transporters where crystallographic, computational and spectroscopic approaches have converged to yield detailed models of transport cycles. Specifically, we compare findings for the Na + -coupled amino acid transporter LeuT and the Na + -coupled hydantoin transporter Mhp1. Although these studies have illuminated multiple aspects of transporter structures and dynamics, a number of questions remain unresolved that so far hinder understanding transport mechanisms in an energy landscape perspective. Copyright © 2016 Elsevier Ltd. All rights reserved.
3D modeling of satellite spectral images, radiation budget and energy budget of urban landscapes
Gastellu-Etchegorry, J. P.
2008-12-01
DART EB is a model that is being developed for simulating the 3D (3 dimensional) energy budget of urban and natural scenes, possibly with topography and atmosphere. It simulates all non radiative energy mechanisms (heat conduction, turbulent momentum and heat fluxes, water reservoir evolution, etc.). It uses DART model (Discrete Anisotropic Radiative Transfer) for simulating radiative mechanisms: 3D radiative budget of 3D scenes and their remote sensing images expressed in terms of reflectance or brightness temperature values, for any atmosphere, wavelength, sun/view direction, altitude and spatial resolution. It uses an innovative multispectral approach (ray tracing, exact kernel, discrete ordinate techniques) over the whole optical domain. This paper presents two major and recent improvements of DART for adapting it to urban canopies. (1) Simulation of the geometry and optical characteristics of urban elements (houses, etc.). (2) Modeling of thermal infrared emission by vegetation and urban elements. The new DART version was used in the context of the CAPITOUL project. For that, districts of the Toulouse urban data base (Autocad format) were translated into DART scenes. This allowed us to simulate visible, near infrared and thermal infrared satellite images of Toulouse districts. Moreover, the 3D radiation budget was used by DARTEB for simulating the time evolution of a number of geophysical quantities of various surface elements (roads, walls, roofs). Results were successfully compared with ground measurements of the CAPITOUL project.
Discrete Displacement Hydraulic Power Take-Off System for the Wavestar Wave Energy Converter
DEFF Research Database (Denmark)
Hansen, Rico Hjerm; Kramer, Morten; Vidal, Enrique
2013-01-01
. This is achieved by using special multi-chambered cylinders, where the different chambers may be connected to the available system pressures using fast on/off valves. Resultantly, a Discrete Displacement Cylinder (DDC) is created, allowing near loss free discrete force control. This paper presents a complete PTO...... system for a 20 float Wavestar based on the DDC. The WEC and PTO is rigorously modeled from incident waves to the electric output to the grid. The resulting model of +600 states is simulated in different irregular seas, showing that power conversion efficiencies above 70% from input power to electrical...
Multiple coupled landscapes and non-adiabatic dynamics with applications to self-activating genes.
Chen, Cong; Zhang, Kun; Feng, Haidong; Sasai, Masaki; Wang, Jin
2015-11-21
Many physical, chemical and biochemical systems (e.g. electronic dynamics and gene regulatory networks) are governed by continuous stochastic processes (e.g. electron dynamics on a particular electronic energy surface and protein (gene product) synthesis) coupled with discrete processes (e.g. hopping among different electronic energy surfaces and on and off switching of genes). One can also think of the underlying dynamics as the continuous motion on a particular landscape and discrete hoppings among different landscapes. The main difference of such systems from the intra-landscape dynamics alone is the emergence of the timescale involved in transitions among different landscapes in addition to the timescale involved in a particular landscape. The adiabatic limit when inter-landscape hoppings are fast compared to continuous intra-landscape dynamics has been studied both analytically and numerically, but the analytical treatment of the non-adiabatic regime where the inter-landscape hoppings are slow or comparable to continuous intra-landscape dynamics remains challenging. In this study, we show that there exists mathematical mapping of the dynamics on 2(N) discretely coupled N continuous dimensional landscapes onto one single landscape in 2N dimensional extended continuous space. On this 2N dimensional landscape, eddy current emerges as a sign of non-equilibrium non-adiabatic dynamics and plays an important role in system evolution. Many interesting physical effects such as the enhancement of fluctuations, irreversibility, dissipation and optimal kinetics emerge due to non-adiabaticity manifested by the eddy current illustrated for an N = 1 self-activator. We further generalize our theory to the N-gene network with multiple binding sites and multiple synthesis rates for discretely coupled non-equilibrium stochastic physical and biological systems.
Energy Technology Data Exchange (ETDEWEB)
Mansur, Ralph S.; Moura, Carlos A., E-mail: ralph@ime.uerj.br, E-mail: demoura@ime.uerj.br [Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil). Departamento de Engenharia Mecanica; Barros, Ricardo C., E-mail: rcbarros@pq.cnpq.br [Universidade do Estado do Rio de Janeiro (UERJ), Nova Friburgo, RJ (Brazil). Departamento de Modelagem Computacional
2017-07-01
Presented here is an application of the Response Matrix (RM) method for adjoint discrete ordinates (S{sub N}) problems in slab geometry applied to energy-dependent source-detector problems. The adjoint RM method is free from spatial truncation errors, as it generates numerical results for the adjoint angular fluxes in multilayer slabs that agree with the numerical values obtained from the analytical solution of the energy multigroup adjoint SN equations. Numerical results are given for two typical source-detector problems to illustrate the accuracy and the efficiency of the offered RM computer code. (author)
Deshpande, VS; Needleman, A; Van der Giessen, E; Deshpande, V.S.
2005-01-01
The initiation of frictional sliding between a flat-bottomed indenter and a planar single crystal substrate is analyzed using discrete dislocation plasticity. Plastic deformation is modeled through the motion of edge dislocations in an elastic solid with the lattice resistance to dislocation motion,
Investigation of the Structures and Energy Landscapes of Thiocyanate-Water Clusters
Directory of Open Access Journals (Sweden)
Lewis C. Smeeton
2017-03-01
Full Text Available The Basin Hopping search method is used to find the global minima (GM and map the energy landscapes of thiocyanate-water clusters, (SCN−(H2On with 3–50 water molecules, with empirical potentials describing the ion-water and water-water interactions. (It should be noted that beyond n = 23, the lowest energy structures were only found in 1 out of 8 searches so they are unlikely to be the true GM but are indicative low energy structures. As for pure water clusters, the low energy isomers of thiocyanate-water clusters show a preponderance of fused water cubes and pentagonal prisms, with the weakly solvated thiocyanate ion lying on the surface, replacing two water molecules along an edge of a water polyhedron and with the sulfur atom in lower coordinated sites than nitrogen. However, by comparison with Density Functional Theory (DFT calculations, the empirical potential is found to overestimate the strength of the thiocyanate-water interaction, especially O–H⋯S, with low energy DFT structures having lower coordinate N and (especially S atoms than for the empirical potential. In the case of these finite ion-water clusters, the chaotropic (“disorder-making” thiocyanate ion weakens the water cluster structure but the water molecule arrangement is not significantly changed.
Holzinger, Dennis; Koch, Iris; Burgard, Stefan; Ehresmann, Arno
2015-07-28
An approach for a remotely controllable transport of magnetic micro- and/or nanoparticles above a topographically flat exchange-bias (EB) thin film system, magnetically patterned into parallel stripe domains, is presented where the particle manipulation is achieved by sub-mT external magnetic field pulses. Superparamagnetic core-shell particles are moved stepwise by the dynamic transformation of the particles' magnetic potential energy landscape due to the external magnetic field pulses without affecting the magnetic state of the thin film system. The magnetic particle velocity is adjustable in the range of 1-100 μm/s by the design of the substrate's magnetic field landscape (MFL), the particle-substrate distance, and the magnitude of the applied external magnetic field pulses. The agglomeration of magnetic particles is avoided by the intrinsic magnetostatic repulsion of particles due to the parallel alignment of the particles' magnetic moments perpendicular to the transport direction and parallel to the surface normal of the substrate during the particle motion. The transport mechanism is modeled by a quantitative theory based on the precise knowledge of the sample's MFL and the particle-substrate distance.
International Nuclear Information System (INIS)
Pointereau, Ph.; Bochu, J.L.; Couturier, Ch.; Coulon, F.; Arnal, A.; Giorgis, S.
2009-01-01
This study aims at identifying positive and negative impacts of new energy productions implemented in farms on the environment (water, soil, biodiversity, space occupancy) and on landscapes, and at proposing techniques and regulations to strengthen positive consequences and to limit possible problems created by these energy productions. The considered productions are: trees apart from forest (hedges and copses), new farm energetic crops (Miscanthus for example), solar equipment (photovoltaic mounted on buildings or on ground, solar hot water and solar dryers), biogas production equipment, hydraulic micro-plants. The authors addressed the following environmental impacts: water (in quantity and quality), soils (quality, erosion risks), biodiversity, space occupancy (with respect to other activities), and landscape
DEFF Research Database (Denmark)
Stoy, Paul C.; Mauder, Matthias; Foken, Thomas
2013-01-01
approached 1. These results suggest that landscape-level heterogeneity in vegetation and topography cannot be ignored as a contributor to incomplete energy balance closure at the flux network level, although net radiation measurements, biological energy assimilation, unmeasured storage terms......The energy balance at most surface-atmosphere flux research sites remains unclosed. The mechanisms underlying the discrepancy between measured energy inputs and outputs across the global FLUXNET tower network are still under debate. Recent reviews have identified exchange processes and turbulent...... motions at large spatial and temporal scales in heterogeneous landscapes as the primary cause of the lack of energy balance closure at some intensively-researched sites, while unmeasured storage terms cannot be ruled out as a dominant contributor to the lack of energy balance closure at many other sites...
Mainzer, Stephen P.
We are using more energy every year. Between 2001 and 2011, Pennsylvania residential electricity sales increased by two and a half times the number of new customers, accounting for almost one third of the state's total electricity consumption. Our ability to meet demand by acquiring new energy sources faces several challenges. Confusion surrounds the physical and economic accessibility of remaining fossil fuel sources. Immense land use requirements and subsequent environmental impacts challenge a total shift to renewable energy sources. The laws of thermodynamics limit the potential for new technology to efficiently convert raw energy to consumable sources. As a result, any rational strategy to meet future energy demands must involve conservation. Conservation is a pro-environmental behavior, an act intended to benefit the environment surrounding a person. I posit that a transdisciplinary model, the community landscape model of the pro-environmental behavior, unifies the conceptually analogous - yet disparate - fields of landscape, community, and behavior towards explaining residential energy conservation actions. Specifically, the study attempted to describe links between the physical environment, social environment, and conservation behaviors through a mixed-method framework. Two Pennsylvania townships - Spring and East Buffalo townships - were selected from an analysis of housing, electricity consumption, and land cover trends. Key informants from both townships informed the design of a survey instrument that captured the utility consumption, residential conservation actions, energy and environmental values, types and levels of community engagement, perceived barriers, and socio-demographic information from 107 randomly selected households. A mixed-method analysis produced evidence that place-based values and intention to participate in the community were significantly linked to lower utility consumption in households. People who cared deeply about their town
Tantakitti, Faifan
Supramolecular chemistry is a powerful tool to create a material of a defined structure with tunable properties. This strategy has led to catalytically active, bioactive, and environment-responsive materials, among others, that are valuable in applications ranging from sensor technology to energy and medicine. Supramolecular polymers formed by peptide amphiphiles (PAs) have been especially relevant in tissue regeneration due to their ability to form biocompatible structures and mimic many important signaling molecules in biology. These supramolecular polymers can form nanofibers that create networks which mimic natural extracellular matrices. PA materials have been shown to induce growth of blood vessels, bone, cartilage, and nervous tissue, among others. The work described in this thesis not only studied the relationship between molecular structure and functions of PA assemblies, but also uncovered a powerful link between the energy landscape of their supramolecular self-assembly and the ability of PA materials to interact with cells. In chapter 2, it is argued that fabricating fibrous nanostructures with defined mechanical properties and decoration with bioactive molecules is not sufficient to create a material that can effectively communicate with cells. By systemically placing the fibronectin-derived RGDS epitope at increasing distances from the surface of PA nanofibers through a linker of one to five glycine residues, integrin-mediated RGDS signaling was enhanced. The results suggested that the spatial presentation of an epitope on PA nanofibers strongly influences the bioactivity of the PA substrates. In further improving functionality of a PA-based scaffold to effectively direct cell growth and differentiation, chapter 3 explored the use of a cell microcarrier to compartmentalize and simultaneously tune insoluble and soluble signals in a single matrix. PA nanofibers were incorporated at the surface of the microcarrier in order to promote cell adhesion, while
Golf-course and funnel energy landscapes: Protein folding concepts in martensites
Shankaraiah, N.
2017-06-01
We use protein folding energy landscape concepts such as golf course and funnel to study re-equilibration in athermal martensites under systematic temperature quench Monte Carlo simulations. On quenching below a transition temperature, the seeded high-symmetry parent-phase austenite that converts to the low-symmetry product-phase martensite, through autocatalytic twinning or elastic photocopying, has both rapid conversions and incubation delays in the temperature-time-transformation phase diagram. We find the rapid (incubation delays) conversions at low (high) temperatures arises from the presence of large (small) size of golf-course edge that has the funnel inside for negative energy states. In the incubating state, the strain structure factor enters into the Brillouin-zone golf course through searches for finite transitional pathways which close off at the transition temperature with Vogel-Fulcher divergences that are insensitive to Hamiltonian energy scales and log-normal distributions, as signatures of dominant entropy barriers. The crossing of the entropy barrier is identified through energy occupancy distributions, Monte Carlo acceptance fractions, heat emission, and internal work.
PELE: Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique.
Borrelli, Kenneth W; Vitalis, Andreas; Alcantara, Raul; Guallar, Victor
2005-11-01
Combining protein structure prediction algorithms and Metropolis Monte Carlo techniques, we provide a novel method to explore all-atom energy landscapes. The core of the technique is based on a steered localized perturbation followed by side-chain sampling as well as minimization cycles. The algorithm and its application to ligand diffusion are presented here. Ligand exit pathways are successfully modeled for different systems containing ligands of various sizes: carbon monoxide in myoglobin, camphor in cytochrome P450cam, and palmitic acid in the intestinal fatty-acid-binding protein. These initial applications reveal the potential of this new technique in mapping millisecond-time-scale processes. The computational cost associated with the exploration is significantly less than that of conventional MD simulations.
Quantitative analysis of the publishing landscape in High-Energy Physics
Mele, S; Vigen, Jens; Yeomans, Joanne
2006-01-01
World-wide collaboration in high-energy physics (HEP) is a tradition which dates back several decades, with scientific publications mostly coauthored by scientists from different countries. This coauthorship phenomenon makes it difficult to identify precisely the "share" of each country in HEP scientific production. One year's worth of HEP scientific articles published in peer-reviewed journals is analysed and their authors are uniquely assigned to countries. This method allows the first correct estimation on a pro rata basis of the share of HEP scientific publishing among several countries and institutions. The results provide an interesting insight into the geographical collaborative patterns of the HEP community. The HEP publishing landscape is further analysed to provide information on the journals favoured by the HEP community and on the geographical variation of their author bases. These results provide quantitative input to the ongoing debate on the possible transition of HEP publishing to an Open Acce...
Free Energy Landscape of the Dissolution of Gibbsite at High pH
Energy Technology Data Exchange (ETDEWEB)
Shen, Zhizhang; Kerisit, Sebastien N.; Stack, Andrew G.; Rosso, Kevin M.
2018-03-26
The individual elementary reactions involved in the dissolution of a solid into solution remain mostly speculative due to a lack of suitable, direct experimental probes. In this regard, we have applied atomistic simulations to map the free energy landscape of the dissolution of gibbsite from a step edge, as a model of metal hydroxide dissolution. The overall reaction combines kink site formation and kink site propagation. Two individual reactions were found to be rate-limiting for kink site formation, that is, the displacement of Al from a step site to a ledge adatom site and its detachment from ledge/terrace adatom sites into the solution. As a result, a pool of mobile and labile Al adsorbed species, or adatoms, exists before the release of Al into solution. Because of the quasi-hexagonal symmetry of gibbsite, kink site propagation can occur in multiple directions. Overall, the simulation results will enable the development of microscopic mechanistic models of metal oxide dissolution.
The energy landscape of glassy dynamics on the amorphous hafnium diboride surface
International Nuclear Information System (INIS)
Nguyen, Duc; Girolami, Gregory S.; Mallek, Justin; Cloud, Andrew N.; Abelson, John R.; Lyding, Joseph; Gruebele, Martin
2014-01-01
Direct visualization of the dynamics of structural glasses and amorphous solids on the sub-nanometer scale provides rich information unavailable from bulk or conventional single molecule techniques. We study the surface of hafnium diboride, a conductive ultrahigh temperature ceramic material that can be grown in amorphous films. Our scanning tunneling movies have a second-to-hour dynamic range and single-point current measurements extend that to the millisecond-to-minute time scale. On the a-HfB 2 glass surface, two-state hopping of 1–2 nm diameter cooperatively rearranging regions or “clusters” occurs from sub-milliseconds to hours. We characterize individual clusters in detail through high-resolution (<0.5 nm) imaging, scanning tunneling spectroscopy and voltage modulation, ruling out individual atoms, diffusing adsorbates, or pinned charges as the origin of the observed two-state hopping. Smaller clusters are more likely to hop, larger ones are more likely to be immobile. HfB 2 has a very high bulk glass transition temperature T g , and we observe no three-state hopping or sequential two-state hopping previously seen on lower T g glass surfaces. The electronic density of states of clusters does not change when they hop up or down, allowing us to calibrate an accurate relative z-axis scale. By directly measuring and histogramming single cluster vertical displacements, we can reconstruct the local free energy landscape of individual clusters, complete with activation barrier height, a reaction coordinate in nanometers, and the shape of the free energy landscape basins between which hopping occurs. The experimental images are consistent with the compact shape of α-relaxors predicted by random first order transition theory, whereas the rapid hopping rate, even taking less confined motion at the surface into account, is consistent with β-relaxations. We make a proposal of how “mixed” features can show up in surface dynamics of glasses
International Nuclear Information System (INIS)
Salehi, A. A.; Vosoughi, N.; Shahriari, M.
2002-01-01
In reactor core neutronic calculations, we usually choose a control volume and investigate about the input, output, production and absorption inside it. Finally, we derive neutron transport equation. This equation is not easy to solve for simple and symmetrical geometry. The objective of this paper is to introduce a new direct method for neutronic calculations. This method is based on physics of problem and with meshing of the desired geometry, writing the balance equation for each mesh intervals and with notice to the conjunction between these mesh intervals, produce the final discrete equation series without production of neutron transport differential equation and mandatory passing form differential equation bridge. This method, which is named Direct Discrete Method, was applied in static state, for a cylindrical geometry in one group energy. The validity of the results from this new method are tested with MCNP-4B code with a one group energy library. One energy group direct discrete equation produces excellent results, which can be compared with the results of MCNP-4B
Crossover to potential energy landscape dominated dynamics in a model glass-forming liquid
DEFF Research Database (Denmark)
Schrøder, Thomas; Sastry, S.; Dyre, Jeppe
2000-01-01
An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this "inherent dynamics" approach we find direct numerical evidence for the ......An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this "inherent dynamics" approach we find direct numerical evidence...... for the long held view that below a crossover temperature, Tx, the liquid's dynamics can be separated into (i) vibrations around inherent structures and (ii) transitions between inherent structures [M. Goldstein, J. Chem. Phys. 51, 3728 (1969)], i.e., the dynamics become "dominated" by the potential energy...... landscape. In agreement with previous proposals, we find that Tx is within the vicinity of the mode-coupling critical temperature Tc. We further find that near Tx, transitions between inherent structures occur via cooperative, stringlike rearrangements of groups of particles moving distances substantially...
Directory of Open Access Journals (Sweden)
Jason D Tack
Full Text Available Proactive conservation planning for species requires the identification of important spatial attributes across ecologically relevant scales in a model-based framework. However, it is often difficult to develop predictive models, as the explanatory data required for model development across regional management scales is rarely available. Golden eagles are a large-ranging predator of conservation concern in the United States that may be negatively affected by wind energy development. Thus, identifying landscapes least likely to pose conflict between eagles and wind development via shared space prior to development will be critical for conserving populations in the face of imposing development. We used publically available data on golden eagle nests to generate predictive models of golden eagle nesting sites in Wyoming, USA, using a suite of environmental and anthropogenic variables. By overlaying predictive models of golden eagle nesting habitat with wind energy resource maps, we highlight areas of potential conflict among eagle nesting habitat and wind development. However, our results suggest that wind potential and the relative probability of golden eagle nesting are not necessarily spatially correlated. Indeed, the majority of our sample frame includes areas with disparate predictions between suitable nesting habitat and potential for developing wind energy resources. Map predictions cannot replace on-the-ground monitoring for potential risk of wind turbines on wildlife populations, though they provide industry and managers a useful framework to first assess potential development.
Investigation and Optimisation of a Discrete Fluid Power PTO-system for Wave Energy Converters
DEFF Research Database (Denmark)
Hansen, Anders Hedegaard
Patents on ocean wave energy dates back to 1799, however no wave energy converter (WEC) concept have a commercialised device. The cost of energy produced with wave energy converters is very high compared to traditional energy sources. Even when compared to energy from wind turbines wave energy...... investigation show how the wave climate naturally influence the optimal system configuration yielding maximal energy output, and how one may choose the system configuration based on the installation site. The switching manifold is the control element of the secondary controlled force system. The force...... needs cost reductions. Hence, next to political will, the main obstacle for a commercial break through of wave energy technology is the high cost of energy. Initiatives to lower costs are made in areas of minimising structural costs and increasing the energy production per device. Wave Star A/S has...
Seki, Kazuhiko; Bagchi, Kaushik; Bagchi, Biman
2016-05-01
Diffusion in one dimensional rugged energy landscape (REL) is predicted to be pathologically different (from any higher dimension) with a much larger chance of encountering broken ergodicity [D. L. Stein and C. M. Newman, AIP Conf. Proc. 1479, 620 (2012)]. However, no quantitative study of this difference has been reported, despite the prevalence of multidimensional physical models in the literature (like a high dimensional funnel guiding protein folding/unfolding). Paradoxically, some theoretical studies of these phenomena still employ a one dimensional diffusion description for analytical tractability. We explore the dimensionality dependent diffusion on REL by carrying out an effective medium approximation based analytical calculations and compare them with the available computer simulation results. We find that at an intermediate level of ruggedness (assumed to have a Gaussian distribution), where diffusion is well-defined, the value of the effective diffusion coefficient depends on dimensionality and changes (increases) by several factors (˜5-10) in going from 1d to 2d. In contrast, the changes in subsequent transitions (like 2d to 3d and 3d to 4d and so on) are far more modest, of the order of 10-20% only. When ruggedness is given by random traps with an exponential distribution of barrier heights, the mean square displacement (MSD) is sub-diffusive (a well-known result), but the growth of MSD is described by different exponents in one and higher dimensions. The reason for such strong ruggedness induced retardation in the case of one dimensional REL is discussed. We also discuss the special limiting case of infinite dimension (d = ∞) where the effective medium approximation becomes exact and where theoretical results become simple. We discuss, for the first time, the role of spatial correlation in the landscape on diffusion of a random walker.
International Nuclear Information System (INIS)
Guo, Z.; Lin, P.; Lowengrub, J.S.
2014-01-01
In this paper, we investigate numerically a diffuse interface model for the Navier–Stokes equation with fluid–fluid interface when the fluids have different densities [48]. Under minor reformulation of the system, we show that there is a continuous energy law underlying the system, assuming that all variables have reasonable regularities. It is shown in the literature that an energy law preserving method will perform better for multiphase problems. Thus for the reformulated system, we design a C 0 finite element method and a special temporal scheme where the energy law is preserved at the discrete level. Such a discrete energy law (almost the same as the continuous energy law) for this variable density two-phase flow model has never been established before with C 0 finite element. A Newton method is introduced to linearise the highly non-linear system of our discretization scheme. Some numerical experiments are carried out using the adaptive mesh to investigate the scenario of coalescing and rising drops with differing density ratio. The snapshots for the evolution of the interface together with the adaptive mesh at different times are presented to show that the evolution, including the break-up/pinch-off of the drop, can be handled smoothly by our numerical scheme. The discrete energy functional for the system is examined to show that the energy law at the discrete level is preserved by our scheme
Tuning Surface Energy Landscapes in Metallic Quantum Films using Alkali Adsorbates
Khajetoorians, Alexander; Qin, Shengyong; Zhu, Wenguang; Eisele, Holger; Zhang, Zhenyu; Shih, Chih-Kang
2008-03-01
Quantum confinement shows a strong interplay with growth and kinetics in thin metal systems where the Fermi wavelength has a special relationship to the surface normal lattice constant. In the case of Pb/Si(111) systems, this relationship reveals an interesting thickness-dependent bilayer oscillation in the density of states and surface energy up to a phase. In this paper, we report on a novel effect: tuning of the energy landscape of a flat-top quantum Pb mesa using Cs adsorbates. Using STM/STS, we show that depositing Cs adsorbates on a thin Pb mesa promotes quantum stable Pb nanoislands on preferentially unstable thicknesses. Thickness-dependent nanoisland densities show a strong bilayer oscillation correlating with quantum stability. By modifying the Cs coverage on the mesa surface, we can tune the lateral size distribution of the nanoislands and the overall amplitude of the island density oscillation. Nanoisland formation is linked to a step decoration of Cs adatoms along the step edge of the nanoisland.
Hybrid organic–inorganic inks flatten the energy landscape in colloidal quantum dot solids
Liu, Mengxia
2016-11-14
Bandtail states in disordered semiconductor materials result in losses in open-circuit voltage (Voc) and inhibit carrier transport in photovoltaics. For colloidal quantum dot (CQD) films that promise low-cost, large-area, air-stable photovoltaics, bandtails are determined by CQD synthetic polydispersity and inhomogeneous aggregation during the ligand-exchange process. Here we introduce a new method for the synthesis of solution-phase ligand-exchanged CQD inks that enable a flat energy landscape and an advantageously high packing density. In the solid state, these materials exhibit a sharper bandtail and reduced energy funnelling compared with the previous best CQD thin films for photovoltaics. Consequently, we demonstrate solar cells with higher Voc and more efficient charge injection into the electron acceptor, allowing the use of a closer-to-optimum bandgap to absorb more light. These enable the fabrication of CQD solar cells made via a solution-phase ligand exchange, with a certified power conversion efficiency of 11.28%. The devices are stable when stored in air, unencapsulated, for over 1,000 h.
Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead
Directory of Open Access Journals (Sweden)
Fabio Pietrucci
2017-11-01
Full Text Available Computer simulations play an important role in the study of transformation processes of condensed matter, including phase transitions, chemical reactions, and conformational changes of biomolecules. In principle, atomic trajectories, such as those generated using the molecular dynamics approach, contain detailed structural, thermodynamic, and kinetic information about activated processes. In practice, due to free energy barriers, there is often a wide gap between the time scale of the transformation and the time scale accessible with simulations. This review offers a practical guide to the ingenious methods aimed to accelerate the exploration and reconstruction of free energy landscapes of complex systems. The focus is on basic unifying concepts, successful strategies, and pitfalls, illustrated with examples of application to scientific problems from different disciplines. The current challenges in the field consist mainly in the cumbersome identification of optimal reaction coordinates and in the extensive recourse to expert human supervision and fine tuning of the algorithms. The full achievement of wide-spectrum formulations and easy reproducibility of results would constitute the breakthrough necessary to enter the era of routine use of enhanced sampling simulations.
Hybrid organic–inorganic inks flatten the energy landscape in colloidal quantum dot solids
Liu, Mengxia; Voznyy, Oleksandr; Sabatini, Randy; Arquer, F. Pelayo Garcí a de; Munir, Rahim; Balawi, Ahmed Hesham; Lan, Xinzheng; Fan, Fengjia; Walters, Grant; Kirmani, Ahmad R.; Hoogland, Sjoerd; Laquai, Fré dé ric; Amassian, Aram; Sargent, Edward H.
2016-01-01
Bandtail states in disordered semiconductor materials result in losses in open-circuit voltage (Voc) and inhibit carrier transport in photovoltaics. For colloidal quantum dot (CQD) films that promise low-cost, large-area, air-stable photovoltaics, bandtails are determined by CQD synthetic polydispersity and inhomogeneous aggregation during the ligand-exchange process. Here we introduce a new method for the synthesis of solution-phase ligand-exchanged CQD inks that enable a flat energy landscape and an advantageously high packing density. In the solid state, these materials exhibit a sharper bandtail and reduced energy funnelling compared with the previous best CQD thin films for photovoltaics. Consequently, we demonstrate solar cells with higher Voc and more efficient charge injection into the electron acceptor, allowing the use of a closer-to-optimum bandgap to absorb more light. These enable the fabrication of CQD solar cells made via a solution-phase ligand exchange, with a certified power conversion efficiency of 11.28%. The devices are stable when stored in air, unencapsulated, for over 1,000 h.
International Nuclear Information System (INIS)
Chatterjee, A; Bhattacharya, S
2016-01-01
We perform several molecular dynamics (MD) calculations of solvated alanine dipeptide and decalanine in vacuum with temperature as a tunable parameter and in the process, generate Markov state models (MSMs) at each temperature. An interesting observation that the kinetic rates appear to obey the Arrhenius rate law allows us to predict the dynamics of alanine dipeptide at 300 K at the microsecond timescales using the nanoseconds long high temperature calculations without actually performing MD simulations at 300 K. We conclude that the energy landscape of alanine dipeptide contains superbasins deeper than k B T and determine the energy barriers associated with the moves from the Arrhenius rate expression. Similar insights regarding the energy landscape associated with folding/unfolding pathways of a deca-alanine molecule are obtained using kinetic rates calculated at different temperatures. (paper)
International Nuclear Information System (INIS)
Aydin, Alhun; Sisman, Altug
2016-01-01
By considering the quantum-mechanically minimum allowable energy interval, we exactly count number of states (NOS) and introduce discrete density of states (DOS) concept for a particle in a box for various dimensions. Expressions for bounded and unbounded continua are analytically recovered from discrete ones. Even though substantial fluctuations prevail in discrete DOS, they're almost completely flattened out after summation or integration operation. It's seen that relative errors of analytical expressions of bounded/unbounded continua rapidly decrease for high NOS values (weak confinement or high energy conditions), while the proposed analytical expressions based on Weyl's conjecture always preserve their lower error characteristic. - Highlights: • Discrete density of states considering minimum energy difference is proposed. • Analytical DOS and NOS formulas based on Weyl conjecture are given. • Discrete DOS and NOS functions are examined for various dimensions. • Relative errors of analytical formulas are much better than the conventional ones.
Energy Technology Data Exchange (ETDEWEB)
Aydin, Alhun; Sisman, Altug, E-mail: sismanal@itu.edu.tr
2016-03-22
By considering the quantum-mechanically minimum allowable energy interval, we exactly count number of states (NOS) and introduce discrete density of states (DOS) concept for a particle in a box for various dimensions. Expressions for bounded and unbounded continua are analytically recovered from discrete ones. Even though substantial fluctuations prevail in discrete DOS, they're almost completely flattened out after summation or integration operation. It's seen that relative errors of analytical expressions of bounded/unbounded continua rapidly decrease for high NOS values (weak confinement or high energy conditions), while the proposed analytical expressions based on Weyl's conjecture always preserve their lower error characteristic. - Highlights: • Discrete density of states considering minimum energy difference is proposed. • Analytical DOS and NOS formulas based on Weyl conjecture are given. • Discrete DOS and NOS functions are examined for various dimensions. • Relative errors of analytical formulas are much better than the conventional ones.
Do high-energy neutrinos travel faster than photons in a discrete space-time?
Energy Technology Data Exchange (ETDEWEB)
Xue Shesheng, E-mail: xue@icra.it [ICRANeT, Piazzale della Repubblica, 10-65122, Pescara, Physics Department, University of Rome ' ' La Sapienza' ' , Rome (Italy)
2011-12-06
The recent OPERA measurement of high-energy neutrino velocity, once independently verified, implies new physics in the neutrino sector. We revisit the theoretical inconsistency of the fundamental high-energy cutoff attributing to quantum gravity with the parity-violating gauge symmetry of local quantum field theory describing neutrinos. This inconsistency suggests high-dimension operators of neutrino interactions. Based on these studies, we try to view the OPERA result, high-energy neutrino oscillations and indicate to observe the restoration of parity conservation by measuring the asymmetry of high-energy neutrinos colliding with left- and right-handed polarized electrons.
Free energy landscape and multiple folding pathways of an H-type RNA pseudoknot.
Directory of Open Access Journals (Sweden)
Yunqiang Bian
Full Text Available How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA.
Zhu, Guangpu; Chen, Huangxin; Sun, Shuyu; Yao, Jun
2018-01-01
In this paper, a fully discrete scheme which considers temporal and spatial discretizations is presented for the coupled Cahn-Hilliard equation in conserved form with the dynamic contact line condition and the Navier-Stokes equation
Quantum energy teleportation with an electromagnetic field: discrete versus continuous variables
International Nuclear Information System (INIS)
Hotta, Masahiro
2010-01-01
It is well known that usual quantum teleportation protocols cannot transport energy. Recently, new protocols called quantum energy teleportation (QET) have been proposed, which transport energy by local operations and classical communication with the ground states of many-body quantum systems. In this paper, we compare two different QET protocols for transporting energy with the electromagnetic field. In the first protocol, a 1/2 spin (a qubit) is coupled with the quantum fluctuation in the vacuum state and measured in order to obtain one-bit information about the fluctuation for the teleportation. In the second protocol, a harmonic oscillator is coupled with the fluctuation and measured in order to obtain continuous-variable information about the fluctuation. In the spin protocol, the amount of teleported energy is suppressed by an exponential damping factor when the amount of input energy increases. This suppression factor becomes power damping in the case of the harmonic oscillator protocol. Therefore, it is concluded that obtaining more information about the quantum fluctuation leads to teleporting more energy. This result suggests a profound relationship between energy and quantum information.
Optimisation of Working Areas in Discrete Hydraulic Power Take off-system for Wave Energy Converters
DEFF Research Database (Denmark)
Hansen, Anders Hedegaard; Hansen, Rico Hjerm; Pedersen, Henrik C.
2012-01-01
Fluid power is the leading technology in Power Take Off(PTO) systems in Wave Energy Converters(WEC’s), due to the capability of generating high force at low velocity. However, as hydraulic force controlling system may suffer from large energy losses the efficiency of the hydraulic PTO systems may...
Hybrid discrete PSO and OPF approach for optimization of biomass fueled micro-scale energy system
International Nuclear Information System (INIS)
Gómez-González, M.; López, A.; Jurado, F.
2013-01-01
Highlights: ► Method to determine the optimal location and size of biomass power plants. ► The proposed approach is a hybrid of PSO algorithm and optimal power flow. ► Comparison among the proposed algorithm and other methods. ► Computational costs are enough lower than that required for exhaustive search. - Abstract: This paper addresses generation of electricity in the specific aspect of finding the best location and sizing of biomass fueled gas micro-turbine power plants, taking into account the variables involved in the problem, such as the local distribution of biomass resources, biomass transportation and extraction costs, operation and maintenance costs, power losses costs, network operation costs, and technical constraints. In this paper a hybrid method is introduced employing discrete particle swarm optimization and optimal power flow. The approach can be applied to search the best sites and capacities to connect biomass fueled gas micro-turbine power systems in a distribution network among a large number of potential combinations and considering the technical constraints of the network. A fair comparison among the proposed algorithm and other methods is performed.
Machine learning for the structure-energy-property landscapes of molecular crystals.
Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele
2018-02-07
Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.
Chowdhury, Md Mukul
With the increased practice of modularization and prefabrication, the construction industry gained the benefits of quality management, improved completion time, reduced site disruption and vehicular traffic, and improved overall safety and security. Whereas industrialized construction methods, such as modular and manufactured buildings, have evolved over decades, core techniques used in prefabrication plants vary only slightly from those employed in traditional site-built construction. With a focus on energy and cost efficient modular construction, this research presents the development of a simulation, measurement and optimization system for energy consumption in the manufacturing process of modular construction. The system is based on Lean Six Sigma principles and loosely coupled system operation to identify the non-value adding tasks and possible causes of low energy efficiency. The proposed system will also include visualization functions for demonstration of energy consumption in modular construction. The benefits of implementing this system include a reduction in the energy consumption in production cost, decrease of energy cost in the production of lean-modular construction, and increase profit. In addition, the visualization functions will provide detailed information about energy efficiency and operation flexibility in modular construction. A case study is presented to validate the reliability of the system.
Swiecicki, I.; Ulysse, C.; Wolf, T.; Bernard, R.; Bergeal, N.; Briatico, J.; Faini, G.; Lesueur, J.; Villegas, Javier E.
2012-06-01
We have developed a masked ion irradiation technique to engineer the energy landscape for vortices in oxide superconductors. This approach associates the possibility to design the landscape geometry at the nanoscale with the unique capability to adjust the depth of the energy wells for vortices. This enabled us to unveil the key role of vortex channeling in modulating the amplitude of the field matching effects with the artificial energy landscape, and to make the latter govern flux dynamics over an unusually wide range of temperatures and applied fields for high-temperature superconducting films.
Cherenkov detectors for spatial imaging applications using discrete-energy photons
Energy Technology Data Exchange (ETDEWEB)
Rose, Paul B.; Erickson, Anna S., E-mail: erickson@gatech.edu [Georgia Institute of Technology, Nuclear and Radiological Engineering, G.W. Woodruff School of Mechanical Engineering, 770 State St., Atlanta, Georgia 30332 (United States)
2016-08-14
Cherenkov detectors can offer a significant advantage in spatial imaging applications when excellent timing response, low noise and cross talk, large area coverage, and the ability to operate in magnetic fields are required. We show that an array of Cherenkov detectors with crude energy resolution coupled with monochromatic photons resulting from a low-energy nuclear reaction can be used to produce a sharp image of material while providing large and inexpensive detector coverage. The analysis of the detector response to relative transmission of photons with various energies allows for reconstruction of material's effective atomic number further aiding in high-Z material identification.
Meng, Yilin; Roux, Benoît
2015-08-11
The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost.
Shaffer, Patrick; Valsson, Omar; Parrinello, Michele
2016-02-02
The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin.
Shaffer, Patrick; Valsson, Omar; Parrinello, Michele
2016-01-01
The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin. PMID:26787868
Li, Chen; Lu, Jianfeng; Yang, Weitao
2015-12-14
We develop the gentlest ascent dynamics for Kohn-Sham density functional theory to search for the index-1 saddle points on the energy landscape of the Kohn-Sham density functionals. These stationary solutions correspond to excited states in the ground state functionals. As shown by various examples, the first excited states of many chemical systems are given by these index-1 saddle points. Our novel approach provides an alternative, more robust way to obtain these excited states, compared with the widely used ΔSCF approach. The method can be easily generalized to target higher index saddle points. Our results also reveal the physical interest and relevance of studying the Kohn-Sham energy landscape.
Benchmarking of EPRI-cell epithermal methods with the point-energy discrete-ordinates code (OZMA)
International Nuclear Information System (INIS)
Williams, M.L.; Wright, R.Q.; Barhen, J.; Rothenstein, W.
1982-01-01
The purpose of the present study is to benchmark E-C resonance-shielding and cell-averaging methods against a rigorous deterministic solution on a fine-group level (approx. 30 groups between 1 eV and 5.5 keV). The benchmark code used is OZMA, which solves the space-dependent slowing-down equations using continuous-energy discrete ordinates or integral transport theory to produce fine-group cross sections. Results are given for three water-moderated lattices - a mixed oxide, a uranium method, and a tight-pitch high-conversion uranium oxide configuration. The latter two lattices were chosen because of the strong self shielding of the 238 U resonances
Energy landscape, structure and rate effects on strength properties of alpha-helical proteins
International Nuclear Information System (INIS)
Bertaud, Jeremie; Hester, Joshua; Jimenez, Daniel D; Buehler, Markus J
2010-01-01
The strength of protein domains is crucial to identify the mechanical role of protein domains in biological processes such as mechanotransduction, tissue mechanics and tissue remodeling. Whereas the concept of strength has been widely investigated for engineered materials, the strength of fundamental protein material building blocks and how it depends on structural parameters such as the chemical bonding, the protein filament length and the timescale of observation or deformation velocity remains poorly understood. Here we report a systematic analysis of the influence of key parameters that define the energy landscape of the strength properties of alpha-helical protein domains, including energy barriers, unfolding and refolding distances, the locations of folded and unfolded states, as well as variations of the length and pulling velocity of alpha-helical protein filaments. The analysis is facilitated by the development of a double-well mesoscale potential formulation, utilized here to carry out a systematic numerical analysis of the behavior of alpha-helices. We compare the results against widely used protein strength models based on the Bell model, one of the simplest models used to characterize the strength of protein filaments. We find that, whereas Bell-type models are a reasonable approximation to describe the rupture of alpha-helical protein domains for a certain range of pulling speeds and values of energy barriers, the model ceases to hold for very large energy barriers and for very small pulling speeds, in agreement with earlier findings. We conclude with an application of our mesoscale model to investigate the effect of the length of alpha-helices on their mechanical strength. We find a weakening effect as the length of alpha-helical proteins increases, followed by an asymptotic regime in which the strength remains constant. We compare strand lengths found in biological proteins with the scaling law of strength versus alpha-helix filament length. The
International Nuclear Information System (INIS)
Ramanujan, R.V.
2003-01-01
The concept of the dividing surface has been extensively used to define the relationships between thermodynamic quantities at the interface between two phases; it is also useful in calculations of interfacial energy (γ). However, in the original formulation, the two phases are continuum phases, the atomistic nature of the interface was not considered. It is, therefore, useful to examine the use of the dividing surface in the context of atomistic interfacial energy calculations. The case of a planar fcc:hcp interface is considered and the dividing surface positions which are useful in atomistic interfacial energy calculations are stated, one position equates γ to the excess internal energy, the other position allows us to use the Gibbs adsorption equation. An example of a calculation using the convenient dividing surface positions is presented
Determining required valve performance for discrete control of PTO cylinders for wave energy
DEFF Research Database (Denmark)
Hansen, Rico Hjerm; Andersen, Torben Ole; Pedersen, Henrik C.
2012-01-01
investigates the required valve performance to achieve this energy efficient operation, while meeting basic dynamic requirements. The components making up the total energy loss during shifting is identified by analytically expressing the losses from the governing differential equations. From the analysis...... a framework for evaluating the adequacy of a valve’s response is established, and the analysis shows the results may be normalised for a wider range of systems. Finally, the framework is successfully applied to the Wavestar converter....
Statistical topography of fitness landscapes
Franke, Jasper
2011-01-01
Fitness landscapes are generalized energy landscapes that play an important conceptual role in evolutionary biology. These landscapes provide a relation between the genetic configuration of an organism and that organism’s adaptive properties. In this work, global topographical features of these fitness landscapes are investigated using theoretical models. The resulting predictions are compared to empirical landscapes. It is shown that these landscapes allow, at least with respe...
Cuevas-Maraver, Jesús; Kevrekidis, Panayotis G.; Vainchtein, Anna; Xu, Haitao
2017-09-01
In this work, we provide two complementary perspectives for the (spectral) stability of solitary traveling waves in Hamiltonian nonlinear dynamical lattices, of which the Fermi-Pasta-Ulam and the Toda lattice are prototypical examples. One is as an eigenvalue problem for a stationary solution in a cotraveling frame, while the other is as a periodic orbit modulo shifts. We connect the eigenvalues of the former with the Floquet multipliers of the latter and using this formulation derive an energy-based spectral stability criterion. It states that a sufficient (but not necessary) condition for a change in the wave stability occurs when the functional dependence of the energy (Hamiltonian) H of the model on the wave velocity c changes its monotonicity. Moreover, near the critical velocity where the change of stability occurs, we provide an explicit leading-order computation of the unstable eigenvalues, based on the second derivative of the Hamiltonian H''(c0) evaluated at the critical velocity c0. We corroborate this conclusion with a series of analytically and numerically tractable examples and discuss its parallels with a recent energy-based criterion for the stability of discrete breathers.
Interpolation of band-limited discrete-time signals by minimising out-of-band energy
Janssen, A.J.E.M.; Vries, L.B.
1984-01-01
An interpolation method for restoring burst errors in discrete—time, band—limited signals is presented. The restoration is such that the restored signal has minimal out—of—band energy. The filter coefficients depend Only on the burst length and on the size of the band to which the signal is assumed
The effect of tensile stress on the conformational free energy landscape of disulfide bonds.
Directory of Open Access Journals (Sweden)
Padmesh Anjukandi
Full Text Available Disulfide bridges are no longer considered to merely stabilize protein structure, but are increasingly recognized to play a functional role in many regulatory biomolecular processes. Recent studies have uncovered that the redox activity of native disulfides depends on their C-C-S-S dihedrals, χ2 and χ'2. Moreover, the interplay of chemical reactivity and mechanical stress of disulfide switches has been recently elucidated using force-clamp spectroscopy and computer simulation. The χ2 and χ'2 angles have been found to change from conformations that are open to nucleophilic attack to sterically hindered, so-called closed states upon exerting tensile stress. In view of the growing evidence of the importance of C-C-S-S dihedrals in tuning the reactivity of disulfides, here we present a systematic study of the conformational diversity of disulfides as a function of tensile stress. With the help of force-clamp metadynamics simulations, we show that tensile stress brings about a large stabilization of the closed conformers, thereby giving rise to drastic changes in the conformational free energy landscape of disulfides. Statistical analysis shows that native TDi, DO and interchain Ig protein disulfides prefer open conformations, whereas the intrachain disulfide bridges in Ig proteins favor closed conformations. Correlating mechanical stress with the distance between the two a-carbons of the disulfide moiety reveals that the strain of intrachain Ig protein disulfides corresponds to a mechanical activation of about 100 pN. Such mechanical activation leads to a severalfold increase of the rate of the elementary redox S(N2 reaction step. All these findings constitute a step forward towards achieving a full understanding of functional disulfides.
DEFF Research Database (Denmark)
Sørensen, John Aasted
2011-01-01
The objectives of Discrete Mathematics (IDISM2) are: The introduction of the mathematics needed for analysis, design and verification of discrete systems, including the application within programming languages for computer systems. Having passed the IDISM2 course, the student will be able...... to accomplish the following: -Understand and apply formal representations in discrete mathematics. -Understand and apply formal representations in problems within discrete mathematics. -Understand methods for solving problems in discrete mathematics. -Apply methods for solving problems in discrete mathematics......; construct a finite state machine for a given application. Apply these concepts to new problems. The teaching in Discrete Mathematics is a combination of sessions with lectures and students solving problems, either manually or by using Matlab. Furthermore a selection of projects must be solved and handed...
International Nuclear Information System (INIS)
Boeri, Marco; Longo, Alberto
2017-01-01
This study provides a methodologically rigorous attempt to disentangle the impact of various factors – unobserved heterogeneity, information and environmental attitudes – on the inclination of individuals to exhibit either a utility maximization or a regret minimization behaviour in a discrete choice experiment for renewable energy programmes described by four attributes: greenhouse gas emissions, power outages, employment in the energy sector, and electricity bill. We explore the ability of different models – multinomial logit, random parameters logit, and hybrid latent class – and of different choice paradigms – utility maximization and regret minimization – in explaining people's choices for renewable energy programmes. The “pure” random regret random parameters logit model explains the choices of our respondents better than other models, indicating that regret is an important choice paradigm, and that choices for renewable energy programmes are mostly driven by regret, rather than by rejoice. In particular, we find that our respondents' choices are driven more by changes in greenhouse gas emissions than by reductions in power outages. Finally, we find that changing the level of information to one attribute has no effect on choices, and that being a member of an environmental organization makes a respondent more likely to be associated with the utility maximization choice framework. - Highlights: • The first paper to use the Random Regret Minimization choice paradigm in energy economics • With a hybrid latent class model, choices conform to either utility or pure random regret. • The pure random regret random parameters logit model outperforms other models. • Reducing greenhouse gas emissions is more important than reducing power outages.
Akhter, Nasrin; Shehu, Amarda
2018-01-19
Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.
Directory of Open Access Journals (Sweden)
Nasrin Akhter
2018-01-01
Full Text Available Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.
Modeling long-term changes in forested landscapes and their relation to the Earth's energy balance
Shugart, H. H.; Emanuel, W. R.; Solomon, A. M.
1984-01-01
The dynamics of the forested parts of the Earth's surface on time scales from decades to centuries are discussed. A set of computer models developed at Oak Ridge National Laboratory and elsewhere are applied as tools. These models simulate a landscape by duplicating the dynamics of growth, death and birth of each tree living on a 0.10 ha element of the landscape. This spatial unit is generally referred to as a gap in the case of the forest models. The models were tested against and applied to a diverse array of forests and appear to provide a reasonable representation for investigating forest-cover dynamics. Because of the climate linkage, one important test is the reconstruction of paleo-landscapes. Detailed reconstructions of changes in vegetation in response to changes in climate are crucial to understanding the association of the Earth's vegetation and climate and the response of the vegetation to climate change.
Discrete repulsive oscillator wavefunctions
International Nuclear Information System (INIS)
Munoz, Carlos A; Rueda-Paz, Juvenal; Wolf, Kurt Bernardo
2009-01-01
For the study of infinite discrete systems on phase space, the three-dimensional Lorentz algebra and group, so(2,1) and SO(2,1), provide a discrete model of the repulsive oscillator. Its eigenfunctions are found in the principal irreducible representation series, where the compact generator-that we identify with the position operator-has the infinite discrete spectrum of the integers Z, while the spectrum of energies is a double continuum. The right- and left-moving wavefunctions are given by hypergeometric functions that form a Dirac basis for l 2 (Z). Under contraction, the discrete system limits to the well-known quantum repulsive oscillator. Numerical computations of finite approximations raise further questions on the use of Dirac bases for infinite discrete systems.
Krishnasamy, M.; Qian, Feng; Zuo, Lei; Lenka, T. R.
2018-03-01
The charge cancellation due to the change of strain along single continuous piezoelectric layer can remarkably affect the performance of a cantilever based harvester. In this paper, analytical models using distributed parameters are developed with some extent of averting the charge cancellation in cantilever piezoelectric transducer where the piezoelectric layers are segmented at strain nodes of concerned vibration mode. The electrode of piezoelectric segments are parallelly connected with a single external resistive load in the 1st model (Model 1). While each bimorph piezoelectric layers are connected in parallel to a resistor to form an independent circuit in the 2nd model (Model 2). The analytical expressions of the closed-form electromechanical coupling responses in frequency domain under harmonic base excitation are derived based on the Euler-Bernoulli beam assumption for both models. The developed analytical models are validated by COMSOL and experimental results. The results demonstrate that the energy harvesting performance of the developed segmented piezoelectric layer models is better than the traditional model of continuous piezoelectric layer.
Jacobson, Daniel; Stratt, Richard M.
2014-05-01
Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.
International Nuclear Information System (INIS)
Nunes, Carlos Eduardo de Araujo
2011-01-01
As neutron fission events do not take place in the non-multiplying regions of nuclear reactors, e.g., moderator, reflector, and structural core, these regions do not generate power and the computational efficiency of nuclear reactor global calculations can hence be improved by eliminating the explicit numerical calculations within the non-multiplying regions around the active domain. Discussed here is the computational efficiency of approximate discrete ordinates (SN) albedo boundary conditions for two-energy group eigenvalue problems in X, Y geometry. Albedo, the Latin word for w hiteness , was originally defined as the fraction of incident light reflected diffusely by a surface. This Latin word has remained the usual scientific term in astronomy and in this dissertation this concept is extended for the reflection of neutrons. The non-standard SN albedo substitutes approximately the reflector region around the active domain, as we neglect the transverse leakage terms within the non-multiplying reflector. Should the problem have no transverse leakage terms, i.e., one dimensional slab geometry, then the offered albedo boundary conditions are exact. By computational efficiency we mean analyzing the accuracy of the numerical results versus the CPU execution time of each run for a given model problem. Numerical results to two 1/4 symmetric test problems are shown to illustrate this efficiency analysis. (author)
DEFF Research Database (Denmark)
Sørensen, John Aasted
2011-01-01
; construct a finite state machine for a given application. Apply these concepts to new problems. The teaching in Discrete Mathematics is a combination of sessions with lectures and students solving problems, either manually or by using Matlab. Furthermore a selection of projects must be solved and handed...... to accomplish the following: -Understand and apply formal representations in discrete mathematics. -Understand and apply formal representations in problems within discrete mathematics. -Understand methods for solving problems in discrete mathematics. -Apply methods for solving problems in discrete mathematics...... to new problems. Relations and functions: Define a product set; define and apply equivalence relations; construct and apply functions. Apply these concepts to new problems. Natural numbers and induction: Define the natural numbers; apply the principle of induction to verify a selection of properties...
DEFF Research Database (Denmark)
Busch, Peter Andre; Zinner Henriksen, Helle
2018-01-01
discretion is suggested to reduce this footprint by influencing or replacing their discretionary practices using ICT. What is less researched is whether digital discretion can cause changes in public policy outcomes, and under what conditions such changes can occur. Using the concept of public service values......This study reviews 44 peer-reviewed articles on digital discretion published in the period from 1998 to January 2017. Street-level bureaucrats have traditionally had a wide ability to exercise discretion stirring debate since they can add their personal footprint on public policies. Digital......, we suggest that digital discretion can strengthen ethical and democratic values but weaken professional and relational values. Furthermore, we conclude that contextual factors such as considerations made by policy makers on the macro-level and the degree of professionalization of street...
International Nuclear Information System (INIS)
Bewerunge, Jörg; Capellmann, Ronja F.; Platten, Florian; Egelhaaf, Stefan U.; Sengupta, Ankush; Sengupta, Surajit
2016-01-01
Colloidal particles were exposed to a random potential energy landscape that has been created optically via a speckle pattern. The mean particle density as well as the potential roughness, i.e., the disorder strength, were varied. The local probability density of the particles as well as its main characteristics were determined. For the first time, the disorder-averaged pair density correlation function g (1) (r) and an analogue of the Edwards-Anderson order parameter g (2) (r), which quantifies the correlation of the mean local density among disorder realisations, were measured experimentally and shown to be consistent with replica liquid state theory results.
Biewick, Laura
2009-01-01
The purpose of this report is to explore current oil and gas energy development in the area encompassing the Wyoming Landscape Conservation Initiative. The Wyoming Landscape Conservation Initiative is a long-term science-based effort to ensure southwestern Wyoming's wildlife and habitat remain viable in areas facing development pressure. Wyoming encompasses some of the highest quality wildlife habitats in the Intermountain West. At the same time, this region is an important source of natural gas. Using Geographic Information System technology, energy data pertinent to the conservation decision-making process have been assembled to show historical oil and gas exploration and production in southwestern Wyoming. In addition to historical data, estimates of undiscovered oil and gas are included from the 2002 U.S. Geological Survey National Assessment of Oil and Gas in the Southwestern Wyoming Province. This report is meant to facilitate the integration of existing data with new knowledge and technologies to analyze energy resources development and to assist in habitat conservation planning. The well and assessment data can be accessed and shared among many different clients including, but not limited to, an online web-service for scientists and resource managers engaged in the Initiative.
Hyeon, Changbong
2010-01-01
In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule force experiments, quantitative analyses of measurements employing sound theoretical models and molecular simulations play central role more than any other field. With a brief description of basic theories for force mechanics and molecular simulation techniqu...
Passaiacquaa, Paola; Belmont, Patrick; Staley, Dennis M.; Simley, Jeffery; Arrowsmith, J. Ramon; Bode, Collin A.; Crosby, Christopher; DeLong, Stephen; Glenn, Nancy; Kelly, Sara; Lague, Dimitri; Sangireddy, Harish; Schaffrath, Keelin; Tarboton, David; Wasklewicz, Thad; Wheaton, Joseph
2015-01-01
The study of mass and energy transfer across landscapes has recently evolved to comprehensive considerations acknowledging the role of biota and humans as geomorphic agents, as well as the importance of small-scale landscape features. A contributing and supporting factor to this evolution is the emergence over the last two decades of technologies able to acquire high resolution topography (HRT) (meter and sub-meter resolution) data. Landscape features can now be captured at an appropriately fine spatial resolution at which surface processes operate; this has revolutionized the way we study Earth-surface processes. The wealth of information contained in HRT also presents considerable challenges. For example, selection of the most appropriate type of HRT data for a given application is not trivial. No definitive approach exists for identifying and filtering erroneous or unwanted data, yet inappropriate filtering can create artifacts or eliminate/distort critical features. Estimates of errors and uncertainty are often poorly defined and typically fail to represent the spatial heterogeneity of the dataset, which may introduce bias or error for many analyses. For ease of use, gridded products are typically preferred rather than the more information-rich point cloud representations. Thus many users take advantage of only a fraction of the available data, which has furthermore been subjected to a series of operations often not known or investigated by the user. Lastly, standard HRT analysis work-flows are yet to be established for many popular HRT operations, which has contributed to the limited use of point cloud data.In this review, we identify key research questions relevant to the Earth-surface processes community within the theme of mass and energy transfer across landscapes and offer guidance on how to identify the most appropriate topographic data type for the analysis of interest. We describe the operations commonly performed from raw data to raster products and
Kelly, Bryce F. J.; Iverach, Charlotte P.; Lowry, Dave; Fisher, Rebecca E.; France, James L.; Nisbet, Euan G.
2015-04-01
Modern cavity ringdown spectroscopy systems (CRDS) enable the continuous measurement of methane concentration. This allows for improved quantification of greenhouse gas emissions associated with various natural and human landscapes. We present a subset of over 4000 km of continuous methane surveying along the east coast of Australia, made using a Picarro G2301 CRDS, deployed in a utility vehicle with an air inlet above the roof at 2.2 mAGL. Measurements were made every 5 seconds to a precision of cut coal mines, unconventional gas developments (coal seam gas; CSG), and leaks detected in cities and country towns. In areas of dryland crops the median methane concentration was 1.78 ppm, while in the irrigation districts located on vertisol soils the concentration was as low as 1.76 ppm, which may indicate that these soils are a sink for methane. In the Hunter Valley, New South Wales, open-cut coal mining district we mapped a continuous 50 km interval where the concentration of methane exceeded 1.80 ppm. The median concentration in this interval was 2.02 ppm. Peak readings were beyond the range of the reliable measurement (in excess of 3.00 ppm). This extended plume is an amalgamation of plumes from 17 major pits 1 to 10 km in length. Adjacent to CSG developments in the Surat Basin, southeast Queensland, only small anomalies were detected near the well-heads. Throughout the vast majority of the gas fields the concentration of methane was below 1.80 ppm. The largest source of fugitive methane associated with CSG was off-gassing methane from the co-produced water holding ponds. At one location the down wind plume had a cross section of approximately 1 km where the concentration of methane was above 1.80 ppm. The median concentration within this section was 1.82 ppm, with a peak reading of 2.11 ppm. The ambient air methane concentration was always higher in urban environments compared to the surrounding countryside. Along one major road in Sydney we mapped an interval
Directory of Open Access Journals (Sweden)
Diego U Ferreiro
2008-05-01
Full Text Available Repeat-proteins are made up of near repetitions of 20- to 40-amino acid stretches. These polypeptides usually fold up into non-globular, elongated architectures that are stabilized by the interactions within each repeat and those between adjacent repeats, but that lack contacts between residues distant in sequence. The inherent symmetries both in primary sequence and three-dimensional structure are reflected in a folding landscape that may be analyzed as a quasi-one-dimensional problem. We present a general description of repeat-protein energy landscapes based on a formal Ising-like treatment of the elementary interaction energetics in and between foldons, whose collective ensemble are treated as spin variables. The overall folding properties of a complete "domain" (the stability and cooperativity of the repeating array can be derived from this microscopic description. The one-dimensional nature of the model implies there are simple relations for the experimental observables: folding free-energy (DeltaG(water and the cooperativity of denaturation (m-value, which do not ordinarily apply for globular proteins. We show how the parameters for the "coarse-grained" description in terms of foldon spin variables can be extracted from more detailed folding simulations on perfectly funneled landscapes. To illustrate the ideas, we present a case-study of a family of tetratricopeptide (TPR repeat proteins and quantitatively relate the results to the experimentally observed folding transitions. Based on the dramatic effect that single point mutations exert on the experimentally observed folding behavior, we speculate that natural repeat proteins are "poised" at particular ratios of inter- and intra-element interaction energetics that allow them to readily undergo structural transitions in physiologically relevant conditions, which may be intrinsically related to their biological functions.
Clalüna, Aline; Baumgarten, Wibke; García Galindo, Daniel; Lenz, Klaus; Doležal, Jan; De Filippi, Federico; Lorenzo, Joaquín; Montagnoli, Louis
2017-04-01
The project greenGain is looking for solutions to increase the energy production with regional and local biomass from landscape conservation and maintenance work, which is performed in the public interest. The relevant resources analysed in the greenGain model regions are, among others, biomass residues from clearing invasive vegetation in marginal agricultural lands in Spain, and residues from abandoned vineyards and olive groves in landscape protected areas in Italy. The main target groups are regional and local players who are responsible for maintenance and conservation work and for the biomass residue management in their regions. Moreover, the focus will be on service providers - including farmers and forest owners, their associations, NGOs, energy providers and consumers. Local companies, municipalities and public authorities are collaborating to identify the still underutilised non-food biomass resources and to discuss the way to integrate them into the local and regional biomass markets. Since the start of the three year project in January 2015, the partners from Italy, Spain, Czech Republic and Germany analysed, among other, the biomass feedstock potential coming from landscape maintenance work, and assessed various technological options to utilise this type of biomass. Further, political, legal and environmental aspects as well as awareness raising and public acceptance actions regarding the energetic use of biomass from public areas were assessed. greenGain also facilitates the exchange between model regions and other similar relevant players in the EU and shares examples of good practice. General guidelines will be prepared to guarantee a wide dissemination to other regions in the EU. Thus, the project shows how to build-up reliable knowledge on local availability of this feedstock and provides know-how concerning planning, harvesting, pre-treatment, storage and sustainable conversion pathways to a wide range of stakeholders in the EU.
Structure prediction of nanoclusters; a direct or a pre-screened search on the DFT energy landscape?
Farrow, M R; Chow, Y; Woodley, S M
2014-10-21
The atomic structure of inorganic nanoclusters obtained via a search for low lying minima on energy landscapes, or hypersurfaces, is reported for inorganic binary compounds: zinc oxide (ZnO)n, magnesium oxide (MgO)n, cadmium selenide (CdSe)n, and potassium fluoride (KF)n, where n = 1-12 formula units. The computational cost of each search is dominated by the effort to evaluate each sample point on the energy landscape and the number of required sample points. The effect of changing the balance between these two factors on the success of the search is investigated. The choice of sample points will also affect the number of required data points and therefore the efficiency of the search. Monte Carlo based global optimisation routines (evolutionary and stochastic quenching algorithms) within a new software package, viz. Knowledge Led Master Code (KLMC), are employed to search both directly and after pre-screening on the DFT energy landscape. Pre-screening includes structural relaxation to minimise a cheaper energy function - based on interatomic potentials - and is found to improve significantly the search efficiency, and typically reduces the number of DFT calculations required to locate the local minima by more than an order of magnitude. Although the choice of functional form is important, the approach is robust to small changes to the interatomic potential parameters. The computational cost of initial DFT calculations of each structure is reduced by employing Gaussian smearing to the electronic energy levels. Larger (KF)n nanoclusters are predicted to form cuboid cuts from the rock-salt phase, but also share many structural motifs with (MgO)n for smaller clusters. The transition from 2D rings to 3D (bubble, or fullerene-like) structures occur at a larger cluster size for (ZnO)n and (CdSe)n. Differences between the HOMO and LUMO energies, for all the compounds apart from KF, are in the visible region of the optical spectrum (2-3 eV); KF lies deep in the UV region
Using graph approach for managing connectivity in integrative landscape modelling
Rabotin, Michael; Fabre, Jean-Christophe; Libres, Aline; Lagacherie, Philippe; Crevoisier, David; Moussa, Roger
2013-04-01
In cultivated landscapes, a lot of landscape elements such as field boundaries, ditches or banks strongly impact water flows, mass and energy fluxes. At the watershed scale, these impacts are strongly conditionned by the connectivity of these landscape elements. An accurate representation of these elements and of their complex spatial arrangements is therefore of great importance for modelling and predicting these impacts.We developped in the framework of the OpenFLUID platform (Software Environment for Modelling Fluxes in Landscapes) a digital landscape representation that takes into account the spatial variabilities and connectivities of diverse landscape elements through the application of the graph theory concepts. The proposed landscape representation consider spatial units connected together to represent the flux exchanges or any other information exchanges. Each spatial unit of the landscape is represented as a node of a graph and relations between units as graph connections. The connections are of two types - parent-child connection and up/downstream connection - which allows OpenFLUID to handle hierarchical graphs. Connections can also carry informations and graph evolution during simulation is possible (connections or elements modifications). This graph approach allows a better genericity on landscape representation, a management of complex connections and facilitate development of new landscape representation algorithms. Graph management is fully operational in OpenFLUID for developers or modelers ; and several graph tools are available such as graph traversal algorithms or graph displays. Graph representation can be managed i) manually by the user (for example in simple catchments) through XML-based files in easily editable and readable format or ii) by using methods of the OpenFLUID-landr library which is an OpenFLUID library relying on common open-source spatial libraries (ogr vector, geos topologic vector and gdal raster libraries). Open
Yang, Changwon; Kim, Eunae; Pak, Youngshang
2015-01-01
Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116
Yang, Changwon; Kim, Eunae; Pak, Youngshang
2015-09-18
Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
DEFF Research Database (Denmark)
Sørensen, John Aasted
2010-01-01
The introduction of the mathematics needed for analysis, design and verification of discrete systems, including applications within programming languages for computer systems. Course sessions and project work. Semester: Spring 2010 Ectent: 5 ects Class size: 18......The introduction of the mathematics needed for analysis, design and verification of discrete systems, including applications within programming languages for computer systems. Course sessions and project work. Semester: Spring 2010 Ectent: 5 ects Class size: 18...
DEFF Research Database (Denmark)
Sørensen, John Aasted
2010-01-01
The introduction of the mathematics needed for analysis, design and verification of discrete systems, including applications within programming languages for computer systems. Course sessions and project work. Semester: Autumn 2010 Ectent: 5 ects Class size: 15......The introduction of the mathematics needed for analysis, design and verification of discrete systems, including applications within programming languages for computer systems. Course sessions and project work. Semester: Autumn 2010 Ectent: 5 ects Class size: 15...
DEFF Research Database (Denmark)
Ruggiero, Michael T; Krynski, Marcin; Kissi, Eric Ofosu
2017-01-01
clear experimental and computational evidence in support of a theory that proposes that the shape and structure of the potential-energy surface (PES) is the fundamental factor underlying the glass-transition processes, regardless of the frequency that experimental methods probe. Whilst this has been....... Combined, these findings provide compelling evidence that the PES landscape, and the corresponding energy barriers, are the ultimate controlling feature behind the atomic and molecular dynamics of disordered solids, regardless of the frequency at which they occur....... proposed previously, we demonstrate, using ab initio molecular-dynamics (AIMD) simulations, that it is of critical importance to carefully consider the complete PES - both the intra-molecular and inter-molecular features - in order to fully understand the entire range of atomic-dynamical processes...
Energy Technology Data Exchange (ETDEWEB)
Van Ewijk, S. [Innovatie Attache Netwerk, Ambassad Berlijn, Berlin (Netherlands)
2012-08-15
An overview is given of innovation in the Swiss energy sector and the following research question will be answered: what are the characteristics of the Swiss innovation landscape in the energy sector and what opportunities are there for the Dutch energy sector? The emphasis is on themes that occur in the Dutch top sector policy, such as natural gas and energy conservation. The aim is to encourage cooperation between the Netherlands and Switzerland in the field of energy and provide inspiration for investment, policy solutions and markets in the field of energy. Each chapter contains references to Swiss authorities for more information and further steps [Dutch] Een overzicht wordt gegeven van innovatie in de Zwitserse energiesector en probeert de volgende onderzoeksvraag te beantwoorden: wat zijn de kenmerken van het Zwitserse innovatielandschap in de energiesector en welke kansen zijn er voor de Nederlandse energiesector? De nadruk ligt daarbij op thema's die ook in het Nederlandse topsectorbeleid voorkomen, zoals aardgas en energiebesparing. Het doel is om de samenwerking tussen Nederland en Zwitserland op energiegebied te stimuleren en informatie te bieden als inspiratie voor investeringen, beleidsoplossingen en afzetmarkten op energiegebied. Ieder hoofdstuk bevat verwijzingen naar Zwitserse instanties voor meer informatie en verdere stappen.
International Nuclear Information System (INIS)
Yan Han; Wang Jin; Zhang Kun
2016-01-01
Cognitive behaviors are determined by underlying neural networks. Many brain functions, such as learning and memory, have been successfully described by attractor dynamics. For decision making in the brain, a quantitative description of global attractor landscapes has not yet been completely given. Here, we developed a theoretical framework to quantify the landscape associated with the steady state probability distributions and associated steady state curl flux, measuring the degree of non-equilibrium through the degree of detailed balance breaking for decision making. We quantified the decision-making processes with optimal paths from the undecided attractor states to the decided attractor states, which are identified as basins of attractions, on the landscape. Both landscape and flux determine the kinetic paths and speed. The kinetics and global stability of decision making are explored by quantifying the landscape topography through the barrier heights and the mean first passage time. Our theoretical predictions are in agreement with experimental observations: more errors occur under time pressure. We quantitatively explored two mechanisms of the speed-accuracy tradeoff with speed emphasis and further uncovered the tradeoffs among speed, accuracy, and energy cost. Our results imply that there is an optimal balance among speed, accuracy, and the energy cost in decision making. We uncovered the possible mechanisms of changes of mind and how mind changes improve performance in decision processes. Our landscape approach can help facilitate an understanding of the underlying physical mechanisms of cognitive processes and identify the key factors in the corresponding neural networks. (paper)
Directory of Open Access Journals (Sweden)
Frantál Bohumil
2017-12-01
Full Text Available Using a case study of the Búrfell wind farm project, a large wind farm proposed in the Central Highlands of Iceland, the authors attempt to provide new insights into the factors shaping subjective landscape perceptions and attitudes to renewable energy developments, and into alternative methods that may be used for their assessment. The research was based on an on-site visit and actual experience of the place, investigated using a combination of mental mapping, the technique of the semantic differential and a questionnaire survey. The results show that participants visiting a landscape and using all sensory organs in combination with mental mapping, can reveal more important information than using only ‘laboratory’ methods with static photographs. The results suggest that the perception of landscape is highly subjective. Those perceiving the landscape as more open, homogenous, industrial, unfamiliar and resilient also consider it more compatible with wind turbines. The perception of the landscape’s compatibility with wind turbines proved to be a dominant factor shaping attitudes towards the project. The acceptance of wind turbines is not, however, inconsistent with the perception of landscape as beautiful, wild and unique. Participants from more densely populated countries and countries with a developed wind energy industry were more tolerant of wind turbines in the Icelandic landscape.
McDonough, J M
2009-06-01
Outline of the derivation and mathematical and physical interpretations are presented for a discrete dynamical system known as the "poor man's Navier-Stokes equation." Numerical studies demonstrate that velocity fields produced by this dynamical system are similar to those seen in laboratory experiments and in detailed simulations, and they lead to scaling for the turbulence kinetic energy spectrum in accord with Kolmogorov K41 theory.
Nonat, Aline; Regueiro-Figueroa, Martín; Esteban-Gómez, David; de Blas, Andrés; Rodríguez-Blas, Teresa; Platas-Iglesias, Carlos; Charbonnière, Loïc J
2012-06-25
-to-Eu energy-transfer process. A mathematical model was developed to interpret the experimental data, leading to energy-transfer rates of 0.98 ms(-1) for the transfer from the site with q=0 to that with q=2 and vice versa. Hartree-Fock (HF) and density functional theory (DFT) calculations performed at the B3LYP level were used to investigate the conformation of the complex in solution, and to estimate the intermetallic distance, which provided Förster radii (R(0)) values of 8.1 Å for the energy transfer from site I to site II, and 6.8 Å for the reverse energy transfer. These results represent the first evidence of an intramolecular energy-transfer equilibrium between two identical lanthanide cations within a discrete molecular complex in solution. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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 (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 (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.
Process Modeling for Energy Usage in “Smart House” System with a Help of Markov Discrete Chain
Directory of Open Access Journals (Sweden)
Victor Kravets
2016-05-01
Full Text Available Method for evaluating economic efficiency of technical systems using discrete Markov chains modelling illustrated by the system of “Smart house”, consisting, for example, of the three independently functioning elements. Dynamic model of a random power consumption process in the form of a symmetrical state graph of heterogeneous discrete Markov chain is built. The corresponding mathematical model of a random Markov process of power consumption in the “smart house” system in recurrent matrix form is being developed. Technique of statistical determination of probability of random transition elements of the system and the corresponding to the transition probability matrix of the discrete inhomogeneous Markov chain are developed. Statistically determined random transitions of system elements power consumption and the corresponding distribution laws are introduced. The matrix of transition prices, expectations for the possible states of a system price transition and, eventually, the cost of Markov process of power consumption throughout the day.
DEFF Research Database (Denmark)
Hansen, Peter Lundsgaard
2017-01-01
Landscape studio documents is the biography of the method 'design conversation' and contributes to the way we work with landscapes. The blog communicates renewed landscape didactics and leads to the innovation of design practices.......Landscape studio documents is the biography of the method 'design conversation' and contributes to the way we work with landscapes. The blog communicates renewed landscape didactics and leads to the innovation of design practices....
Precision cosmology and the landscape
International Nuclear Information System (INIS)
Bousso, Raphael; Bousso, Raphael
2006-01-01
After reviewing the cosmological constant problem--why is Lambda not huge?--I outline the two basic approaches that had emerged by the late 1980s, and note that each made a clear prediction. Precision cosmological experiments now indicate that the cosmological constant is nonzero. This result strongly favors the environmental approach, in which vacuum energy can vary discretely among widely separated regions in the universe. The need to explain this variation from first principles constitutes an observational constraint on fundamental theory. I review arguments that string theory satisfies this constraint, as it contains a dense discretuum of metastable vacua. The enormous landscape of vacua calls for novel, statistical methods of deriving predictions, and it prompts us to reexamine our description of spacetime on the largest scales. I discuss the effects of cosmological dynamics, and I speculate that weighting vacua by their entropy production may allow for prior-free predictions that do not resort to explicitly anthropic arguments
The Energy Footprint on the Landscape and What this Means for Plants, Animals, and Ecosystems
Belnap, Jayne
2012-01-01
Dryland regions of the western U.S. contain abundant energy resources, whether they are traditional oil/gas or alternative sources such as solar or wind. With energy exploration and development comes surface disturbance and other impacts. The impact of energy exploration, such as running seismic lines, is associated with soil surface disruption that can be quite severe at a local level. Energy development brings a host of other concerns that need to be considered and likely mitigated. All ene...
Monkelbaan, Joachim
2014-01-01
We have arrived at a critical juncture when it comes to understanding the numerous ways in which trade interacts with climate change and energy (trade-climate-energy nexus). Trade remains crucial for the sustainable development of the world's greatest trading nation: China. After clarifying the linkages within the trade, climate change and energy nexus, this article delves into China's specific needs and interests related to trade, climate change and energy. Then it explores the ways in which...
Caltagirone, Jean-Paul
2014-01-01
This book presents the fundamental principles of mechanics to re-establish the equations of Discrete Mechanics. It introduces physics and thermodynamics associated to the physical modeling. The development and the complementarity of sciences lead to review today the old concepts that were the basis for the development of continuum mechanics. The differential geometry is used to review the conservation laws of mechanics. For instance, this formalism requires a different location of vector and scalar quantities in space. The equations of Discrete Mechanics form a system of equations where the H
International Nuclear Information System (INIS)
Lee, T.D.
1985-01-01
This paper reviews the role of time throughout all phases of mechanics: classical mechanics, non-relativistic quantum mechanics, and relativistic quantum theory. As an example of the relativistic quantum field theory, the case of a massless scalar field interacting with an arbitrary external current is discussed. The comparison between the new discrete theory and the usual continuum formalism is presented. An example is given of a two-dimensional random lattice and its duel. The author notes that there is no evidence that the discrete mechanics is more appropriate than the usual continuum mechanics
Wlazło, M.; Majewski, J. A.
2018-03-01
We study the dissociative adsorption of methane at the surface of graphene. Free energy profiles, which include activation energies for different steps of the reaction, are computed from constrained ab initio molecular dynamics. At 300 K, the reaction barriers are much lower than experimental bond dissociation energies of gaseous methane, strongly indicating that the graphene surface acts as a catalyst of methane decomposition. On the other hand, the barriers are still much higher than on the nickel surface. Methane dissociation therefore occurs at a higher rate on nickel than on graphene. This reaction is a prerequisite for graphene growth from a precursor gas. Thus, the growth of the first monolayer should be a fast and efficient process while subsequent layers grow at a diminished rate and in a more controllable manner. Defects may also influence reaction energetics. This is evident from our results, in which simple defects (Stone-Wales defect and nitrogen substitution) lead to different free energy landscapes at both dissociation and adsorption steps of the process.
Krivov, Sergei V
2011-07-01
Dimensionality reduction is ubiquitous in the analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed low-dimensional space does not provide a complete and accurate description of the dynamics. Here I describe how to perform dimensionality reduction while preserving the essential properties of the dynamics. The approach is illustrated by analyzing the chess game--the archetype of complex dynamics. A variable that provides complete and accurate description of chess dynamics is constructed. The winning probability is predicted by describing the game as a random walk on the free-energy landscape associated with the variable. The approach suggests a possible way of obtaining a simple yet accurate description of many important complex phenomena. The analysis of the chess game shows that the approach can quantitatively describe the dynamics of processes where human decision-making plays a central role, e.g., financial and social dynamics.
Carichino, Lucia; Guidoboni, Giovanna; Szopos, Marcela
2018-07-01
The goal of this work is to develop a novel splitting approach for the numerical solution of multiscale problems involving the coupling between Stokes equations and ODE systems, as often encountered in blood flow modeling applications. The proposed algorithm is based on a semi-discretization in time based on operator splitting, whose design is guided by the rationale of ensuring that the physical energy balance is maintained at the discrete level. As a result, unconditional stability with respect to the time step choice is ensured by the implicit treatment of interface conditions within the Stokes substeps, whereas the coupling between Stokes and ODE substeps is enforced via appropriate initial conditions for each substep. Notably, unconditional stability is attained without the need of subiterating between Stokes and ODE substeps. Stability and convergence properties of the proposed algorithm are tested on three specific examples for which analytical solutions are derived.
Discrete Exterior Calculus Discretization of Incompressible Navier-Stokes Equations
Mohamed, Mamdouh S.
2017-05-23
A conservative discretization of incompressible Navier-Stokes equations over surface simplicial meshes is developed using discrete exterior calculus (DEC). Numerical experiments for flows over surfaces reveal a second order accuracy for the developed scheme when using structured-triangular meshes, and first order accuracy otherwise. The mimetic character of many of the DEC operators provides exact conservation of both mass and vorticity, in addition to superior kinetic energy conservation. The employment of barycentric Hodge star allows the discretization to admit arbitrary simplicial meshes. The discretization scheme is presented along with various numerical test cases demonstrating its main characteristics.
Directory of Open Access Journals (Sweden)
Gianvito Grasso
Full Text Available The success of medical threatments with DNA and silencing interference RNA is strongly related to the design of efficient delivery technologies. Cationic polymers represent an attractive strategy to serve as nucleic-acid carriers with the envisioned advantages of efficient complexation, low cost, ease of production, well-defined size, and low polydispersity index. However, the balance between efficacy and toxicity (safety of these polymers is a challenge and in need of improvement. With the aim of designing more effective polycationic-based gene carriers, many parameters such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity ratio need to be taken into consideration. In the present work, the binding mechanism of three cationic polymers (polyarginine, polylysine and polyethyleneimine to a model siRNA target is computationally investigated at the atomistic level. In order to better understand the polycationic carrier-siRNA interactions, replica exchange molecular dynamic simulations were carried out to provide an exhaustive exploration of all the possible binding sites, taking fully into account the siRNA flexibility together with the presence of explicit solvent and ions. Moreover, well-tempered metadynamics simulations were employed to elucidate how molecular geometry, polycation flexibility, and charge neutralization affect the siRNA-polycations free energy landscape in term of low-energy binding modes and unbinding free energy barriers. Significant differences among polymer binding modes have been detected, revealing the advantageous binding properties of polyarginine and polylysine compared to polyethyleneimine.
Energy Technology Data Exchange (ETDEWEB)
Yang, Y. Isaac [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871 (China); Zhang, Jun; Che, Xing; Yang, Lijiang; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871 (China); Biodynamic Optical Imaging Center, Peking University, Beijing 100871 (China)
2016-03-07
In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ − ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.
Cellular network entropy as the energy potential in Waddington's differentiation landscape
Banerji, Christopher R. S.; Miranda-Saavedra, Diego; Severini, Simone; Widschwendter, Martin; Enver, Tariq; Zhou, Joseph X.; Teschendorff, Andrew E.
2013-01-01
Differentiation is a key cellular process in normal tissue development that is significantly altered in cancer. Although molecular signatures characterising pluripotency and multipotency exist, there is, as yet, no single quantitative mark of a cellular sample's position in the global differentiation hierarchy. Here we adopt a systems view and consider the sample's network entropy, a measure of signaling pathway promiscuity, computable from a sample's genome-wide expression profile. We demonstrate that network entropy provides a quantitative, in-silico, readout of the average undifferentiated state of the profiled cells, recapitulating the known hierarchy of pluripotent, multipotent and differentiated cell types. Network entropy further exhibits dynamic changes in time course differentiation data, and in line with a sample's differentiation stage. In disease, network entropy predicts a higher level of cellular plasticity in cancer stem cell populations compared to ordinary cancer cells. Importantly, network entropy also allows identification of key differentiation pathways. Our results are consistent with the view that pluripotency is a statistical property defined at the cellular population level, correlating with intra-sample heterogeneity, and driven by the degree of signaling promiscuity in cells. In summary, network entropy provides a quantitative measure of a cell's undifferentiated state, defining its elevation in Waddington's landscape. PMID:24154593
Integration of ecological and thermodynamic concepts in the design of sustainable energy landscapes
Stremke, S.; Koh, J.
2011-01-01
Resource depletion and climate change motivate a transition to sustainable energy systems that make effective use of renewable sources. Whereas nature presents strategies to sustain on the basis of renewables, the Laws of Thermodynamics can help to increase efficiency in energy use. In previous
Peter J. Daugherty; Jeremy S. Fried
2007-01-01
Landscape-scale fuel treatments for forest fire hazard reduction potentially produce large quantities of material suitable for biomass energy production. The analytic framework FIA BioSum addresses this situation by developing detailed data on forest conditions and production under alternative fuel treatment prescriptions, and computes haul costs to alternative sites...
Kirol, Christopher P; Beck, Jeffrey L; Huzurbazar, Snehalata V; Holloran, Matthew J; Miller, Scott N
2015-06-01
Conserving a declining species that is facing many threats, including overlap of its habitats with energy extraction activities, depends upon identifying and prioritizing the value of the habitats that remain. In addition, habitat quality is often compromised when source habitats are lost or fragmented due to anthropogenic development. Our objective was to build an ecological model to classify and map habitat quality in terms of source or sink dynamics for Greater Sage-Grouse (Centrocercus urophasianus) in the Atlantic Rim Project Area (ARPA), a developing coalbed natural gas field in south-central Wyoming, USA. We used occurrence and survival modeling to evaluate relationships between environmental and anthropogenic variables at multiple spatial scales and for all female summer life stages, including nesting, brood-rearing, and non-brooding females. For each life stage, we created resource selection functions (RSFs). We weighted the RSFs and combined them to form a female summer occurrence map. We modeled survival also as a function of spatial variables for nest, brood, and adult female summer survival. Our survival-models were mapped as survival probability functions individually and then combined with fixed vital rates in a fitness metric model that, when mapped, predicted habitat productivity (productivity map). Our results demonstrate a suite of environmental and anthropogenic variables at multiple scales that were predictive of occurrence and survival. We created a source-sink map by overlaying our female summer occurrence map and productivity map to predict habitats contributing to population surpluses (source habitats) or deficits (sink habitat) and low-occurrence habitats on the landscape. The source-sink map predicted that of the Sage-Grouse habitat within the ARPA, 30% was primary source, 29% was secondary source, 4% was primary sink, 6% was secondary sink, and 31% was low occurrence. Our results provide evidence that energy development and avoidance of
Swart, M.; Sola, M.; Bickelhaupt, F.M.
2007-01-01
We have carried out a detailed evaluation of the performance of all classes of density functional theory (DFT) for describing the potential energy surface (PES) of a wide range of nucleophilic substitution (S
Structural and kinetic mapping of side-chain exposure onto the protein energy landscape.
Bernstein, Rachel; Schmidt, Kierstin L; Harbury, Pehr B; Marqusee, Susan
2011-06-28
Identification and characterization of structural fluctuations that occur under native conditions is crucial for understanding protein folding and function, but such fluctuations are often rare and transient, making them difficult to study. Native-state hydrogen exchange (NSHX) has been a powerful tool for identifying such rarely populated conformations, but it generally reveals no information about the placement of these species along the folding reaction coordinate or the barriers separating them from the folded state and provides little insight into side-chain packing. To complement such studies, we have performed native-state alkyl-proton exchange, a method analogous to NSHX that monitors cysteine modification rather than backbone amide exchange, to examine the folding landscape of Escherichia coli ribonuclease H, a protein well characterized by hydrogen exchange. We have chosen experimental conditions such that the rate-limiting barrier acts as a kinetic partition: residues that become exposed only upon crossing the unfolding barrier are modified in the EX1 regime (alkylation rates report on the rate of unfolding), while those exposed on the native side of the barrier are modified predominantly in the EX2 regime (alkylation rates report on equilibrium populations). This kinetic partitioning allows for identification and placement of partially unfolded forms along the reaction coordinate. Using this approach we detect previously unidentified, rarely populated conformations residing on the native side of the barrier and identify side chains that are modified only upon crossing the unfolding barrier. Thus, in a single experiment under native conditions, both sides of the rate-limiting barrier are investigated.
Competitive landscape of the EU’s insulation materials industry for energy-efficient buildings
PAVEL CLAUDIU; BLAGOEVA DARINA
2017-01-01
Insulation materials could contribute significantly to improving the overall energy efficiency and sustainability of the buildings, especially by reducing the energy losses through the building envelope (walls, roofs, floors, etc.). The global demand for thermal insulation materials in building applications is projected to increase at a CAGR of 4.5 % between 2016 and 2027. In the EU the demand for thermal insulation materials is estimated at 3.48 % (2015-2027). Wool minerals (glass and stone ...
International Nuclear Information System (INIS)
von Haeften, K.; von Pietrowski, R.; Moeller, T.; Joppien, M.; Moussavizadeh, L.; de Castro, A.R.
1997-01-01
Discrete visible and near-infrared luminescence of a beam of photoexcited helium clusters is reported. The emission lines are attributed to free helium atoms and molecules desorbing from clusters in electronically excited states. Depending on the excitation energy, various atomic and molecular singlet and triplet states are involved in the relaxation process. With increasing cluster size the intensity of molecular transitions becomes dominant. The temperature of ejected molecules could be estimated to T vib ∼2500 K and T rot ∼450 K and is much higher than that of the cluster itself. copyright 1997 The American Physical Society
Martin, J. I.; Alija, A.; Sobrado, I.; Perez-Junquera, A.; Rodriguez-Rodriguez, G.; Velez, M.; Alameda, J. M.; Marconi, V. I.; Kolton, A. B.; Parrondo, J. M. R.
2009-03-01
The driven motion of domain walls in extended magnetic films patterned with 2D arrays of asymmetric holes has been found to be subject to two different crossed ratchet effects [1] which results in an inversion of the sign of domain wall motion rectification as a function of the applied magnetic field. This effect can be understood in terms of the competition between drive, elasticity and asymmetric pinning as revealed by a simple 4̂-model. In order to optimize the asymmetric hole design, the relevant energy landscapes for domain wall motion across the array of asymmetric holes have been calculated by micromagnetic simulations as a function of array geometrical characteristics. The effects of a transverse magnetic field on these two crossed ratchet effects will also be discussed in terms of the decrease in domain wall energy per unit area and of the modifications in the magnetostatic barriers for domain wall pinning at the asymmetric inclusions. Work supported by Spanish MICINN.[1] A. Perez-Junquera et al, Phys. Rev. Lett. 100 (2008) 037203
Discrete dynamics versus analytic dynamics
DEFF Research Database (Denmark)
Toxværd, Søren
2014-01-01
For discrete classical Molecular dynamics obtained by the “Verlet” algorithm (VA) with the time increment h there exists a shadow Hamiltonian H˜ with energy E˜(h) , for which the discrete particle positions lie on the analytic trajectories for H˜ . Here, we proof that there, independent...... of such an analytic analogy, exists an exact hidden energy invariance E * for VA dynamics. The fact that the discrete VA dynamics has the same invariances as Newtonian dynamics raises the question, which of the formulations that are correct, or alternatively, the most appropriate formulation of classical dynamics....... In this context the relation between the discrete VA dynamics and the (general) discrete dynamics investigated by Lee [Phys. Lett. B122, 217 (1983)] is presented and discussed....
Sub-seasonal thaw slump mass wasting is not consistently energy limited at the landscape scale
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S. Zwieback
2018-02-01
Full Text Available Predicting future thaw slump activity requires a sound understanding of the atmospheric drivers and geomorphic controls on mass wasting across a range of timescales. On sub-seasonal timescales, sparse measurements indicate that mass wasting at active slumps is often limited by the energy available for melting ground ice, but other factors such as rainfall or the formation of an insulating veneer may also be relevant. To study the sub-seasonal drivers, we derive topographic changes from single-pass radar interferometric data acquired by the TanDEM-X satellites. The estimated elevation changes at 12 m resolution complement the commonly observed planimetric retreat rates by providing information on volume losses. Their high vertical precision (around 30 cm, frequent observations (11 days and large coverage (5000 km2 allow us to track mass wasting as drivers such as the available energy change during the summer of 2015 in two study regions. We find that thaw slumps in the Tuktoyaktuk coastlands, Canada, are not energy limited in June, as they undergo limited mass wasting (height loss of around 0 cm day−1 despite the ample available energy, suggesting the widespread presence of early season insulating snow or debris veneer. Later in summer, height losses generally increase (around 3 cm day−1, but they do so in distinct ways. For many slumps, mass wasting tracks the available energy, a temporal pattern that is also observed at coastal yedoma cliffs on the Bykovsky Peninsula, Russia. However, the other two common temporal trajectories are asynchronous with the available energy, as they track strong precipitation events or show a sudden speed-up in late August respectively. The observed temporal patterns are poorly related to slump characteristics like the headwall height. The contrasting temporal behaviour of nearby thaw slumps highlights the importance of complex local and temporally varying controls on mass wasting.
Shiflett, S. A.; Anderson, R. G.; Jenerette, D.
2014-12-01
Urbanization substantially affects energy, surface and air temperature, and hydrology due to extensive modifications in land surface properties such as vegetation, albedo, thermal capacity and soil moisture. The magnitude and direction of these alterations depends heavily on the type of urbanization that occurs. We investigated energy balance variation in a local network of agricultural and urban ecosystems using the eddy covariance method to better understand how vegetation fraction and degree of urbanization affects energy exchanges between the land surface and the atmosphere. We deployed eddy flux systems within a well-irrigated, agricultural citrus orchard, a moderately developed urban zone with a substantial amount of local vegetative cover, and an intensely developed urban zone with minimal vegetative cover and increased impervious surfaces relative to the other two sites. Latent energy (LE) fluxes in the agricultural area ranged from 7.9 ± 1.4 W m-2 (nighttime) to 168.7 ± 6.2 W m-2 (daytime) compared to 10.2 ± 3.5 W m-2 and 40.6 ± 4.1 W m-2, respectively, for the moderately developed urban area. Sensible energy (H) fluxes ranged from -9.1 ± 1.0 W m-2 (nighttime) to 119 ± 7.0 W m-2 (daytime) in the agricultural area compared to 9.6 ± 2.6 W m-2 and 134 ± 6.0 W m-2, respectively, for the moderately developed urban zone. Daytime LE is reduced with increasing urbanization; however, daily cycles of LE are less recognizable in urban areas compared to distinct daily cycles obtained above a mature citrus crop. In contrast, both daytime and nighttime H increases with increasing degree of urbanization. Reduction in vegetation and increases in impervious surfaces along an urbanization gradient leads to alterations in energy balance, which are associated with microclimate and water use changes.
Navigating the new deregulated landscape: Opportunities and risks for wind energy
Energy Technology Data Exchange (ETDEWEB)
Fossum, D.J.; Hill, D.R. [Wiley, Rein & Fielding, Washington, DC (United States)
1997-12-31
Major changes in the law governing the electric industry are underway, fundamentally altering how the generation and sale of electric power is regulated and how electric power is marketed in the United States. Legislative and regulatory initiatives promoting competition will create a variety of opportunities, and commensurate risks, for power generators, marketers, brokers, sellers, and purchasers. To succeed in the new marketplace, suppliers of renewable energy must understand the changes occurring on the state and federal levels, and position themselves to take advantage of the opportunities available. In this environment, monitoring and participating in state and federal legislative and regulatory efforts will be crucial for maximizing opportunities for wind energy.
Charting the energy landscape of metal/organic interfaces via machine learning
Scherbela, Michael; Hörmann, Lukas; Jeindl, Andreas; Obersteiner, Veronika; Hofmann, Oliver T.
2018-04-01
The rich polymorphism exhibited by inorganic/organic interfaces is a major challenge for materials design. In this work, we present a method to efficiently explore the potential energy surface and predict the formation energies of polymorphs and defects. This is achieved by training a machine learning model on a list of only 100 candidate structures that are evaluated via dispersion-corrected density functional theory (DFT) calculations. We demonstrate the power of this approach for tetracyanoethylene on Ag(100) and explain the anisotropic ordering that is observed experimentally.
Dissipation of solar energy in landscape - controlled by management of water and vegetation
Czech Academy of Sciences Publication Activity Database
Pokorný, Jan
2001-01-01
Roč. 24, - (2001), s. 641-645 ISSN 0960-1481 R&D Projects: GA AV ČR KSK6005114 Institutional research plan: CEZ:AV0Z6005908 Keywords : Solar energy dissipation * vegetation * production -evapotranspiration Subject RIV: DA - Hydrology ; Limnology Impact factor: 0.224, year: 2001
Potential energy landscape signatures of slow dynamics in glass forming liquids
DEFF Research Database (Denmark)
Sastry, S.; Debenedetti, P. G.; Stillinger, F. H.
1999-01-01
We study the properties of local potential energy minima (inherent structures) sampled by liquids at low temperatures as an approach to elucidating the mechanisms of the observed dynamical slowing down observed as the glass transition temperature is approached. This onset of slow dynamics...
Directory of Open Access Journals (Sweden)
Joachim Monkelbaan
2014-12-01
As a way forward, different approaches towards the governance of trade and climate change will be highlighted. Besides discussing the specific aspects of Chinese participation in global trade and climate change governance, this paper aims at offering broader insights into the nexus between trade, energy and climate governance in China.
East, J. A., II
2016-12-01
The U.S. Geological Survey's (USGS) Eastern Energy Resources Science Center (EERSC) has an ongoing project which has mapped coal chemistry and stratigraphy since 1977. Over the years, the USGS has collected various forms of coal data and archived that data into the National Coal Resources Data System (NCRDS) database. NCRDS is a repository that houses data from the major coal basins in the United States and includes information on location, seam thickness, coal rank, geologic age, geographic region, geologic province, coalfield, and characteristics of the coal or lithology for that data point. These data points can be linked to the US Coal Quality Database (COALQUAL) to include ultimate, proximate, major, minor and trace-element data. Although coal is an inexpensive energy provider, the United States has shifted away from coal usage recently and branched out into other forms of non-renewable and renewable energy because of environmental concerns. NCRDS's primary method of data capture has been USGS field work coupled with cooperative agreements with state geological agencies and universities doing coal-related research. These agreements are on competitive five-year cycles that have evolved into larger scope research efforts including solid fuel resources such as coal-bed methane, shale gas and oil. Recently these efforts have expanded to include environmental impacts of the use of fossil fuels, which has allowed the USGS to enter into agreements with states for the Geologic CO2 Storage Resources Assessment as required by the Energy Independence and Security Act. In 2016 they expanded into research areas to include geothermal, conventional and unconventional oil and gas. The NCRDS and COALQUAL databases are now online for the public to use, and are in the process of being updated to include new data for other energy resources. Along with this expansion of scope, the database name will change to the National Energy Resources Data System (NERDS) in FY 2017.
Directory of Open Access Journals (Sweden)
M. Christobel
2015-01-01
Full Text Available One of the most significant and the topmost parameters in the real world computing environment is energy. Minimizing energy imposes benefits like reduction in power consumption, decrease in cooling rates of the computing processors, provision of a green environment, and so forth. In fact, computation time and energy are directly proportional to each other and the minimization of computation time may yield a cost effective energy consumption. Proficient scheduling of Bag-of-Tasks in the grid environment ravages in minimum computation time. In this paper, a novel discrete particle swarm optimization (DPSO algorithm based on the particle’s best position (pbDPSO and global best position (gbDPSO is adopted to find the global optimal solution for higher dimensions. This novel DPSO yields better schedule with minimum computation time compared to Earliest Deadline First (EDF and First Come First Serve (FCFS algorithms which comparably reduces energy. Other scheduling parameters, such as job completion ratio and lateness, are also calculated and compared with EDF and FCFS. An energy improvement of up to 28% was obtained when Makespan Conservative Energy Reduction (MCER and Dynamic Voltage Scaling (DVS were used in the proposed DPSO algorithm.
Christobel, M.; Tamil Selvi, S.; Benedict, Shajulin
2015-01-01
One of the most significant and the topmost parameters in the real world computing environment is energy. Minimizing energy imposes benefits like reduction in power consumption, decrease in cooling rates of the computing processors, provision of a green environment, and so forth. In fact, computation time and energy are directly proportional to each other and the minimization of computation time may yield a cost effective energy consumption. Proficient scheduling of Bag-of-Tasks in the grid environment ravages in minimum computation time. In this paper, a novel discrete particle swarm optimization (DPSO) algorithm based on the particle's best position (pbDPSO) and global best position (gbDPSO) is adopted to find the global optimal solution for higher dimensions. This novel DPSO yields better schedule with minimum computation time compared to Earliest Deadline First (EDF) and First Come First Serve (FCFS) algorithms which comparably reduces energy. Other scheduling parameters, such as job completion ratio and lateness, are also calculated and compared with EDF and FCFS. An energy improvement of up to 28% was obtained when Makespan Conservative Energy Reduction (MCER) and Dynamic Voltage Scaling (DVS) were used in the proposed DPSO algorithm. PMID:26075296
Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge
Dahle, H?kon; ?kland, Ingeborg; Thorseth, Ingunn H; Pederesen, Rolf B; Steen, Ida H
2015-01-01
Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent f...
Landscapes of lost energy: counterfactual geographical imaginary for a more sustainable society
Czech Academy of Sciences Publication Activity Database
Van der Horst, Dan
2014-01-01
Roč. 22, č. 2 (2014), s. 66-72 ISSN 1210-8812 R&D Projects: GA MŠk EE2.3.20.0025 Institutional support: RVO:68145535 Keywords : counterfactual * imagery * imagination * energy literacy Subject RIV: DE - Earth Magnetism, Geodesy, Geography Impact factor: 0.872, year: 2014 http://www.geonika.cz/EN/research/ENMgr/MGR_2014_02.pdf
Landscapes of Lost Energy: Counterfactual Geographical Imaginary for A More Sustainable Society
Directory of Open Access Journals (Sweden)
van der Horst Dan
2014-07-01
Full Text Available The quest for sustainable energy, one of the greatest challenges of the 21st century, calls for more input from academics than 'simply' producing good science. Geographical imaginations are as old as storytelling and mapmaking, but this essay is neither about 'long ago and far away', nor about utopian energy futures. This is a call to geographers to engage with 'alternative present' energy scenarios, using the full range of analytical and discursive tools at our disposal. Drawing on a diverse tradition of imagined spaces and the awareness of absences (material, relational or otherwise, geographers should be able to contribute to the quest for a more sustainable society by assessing, envisaging, and communicating a counterfactual 'here and now', based on good practices existing right now, but not (yet right here. We need to understand how much more sustainable our bit of the planet would be if we could just, environmentally speaking, 'keep up' with the best of our neighbours. This counterfactual present should be seen as neither radical nor utopian, because it only assumes the historic adoption of best practices which we now know to be feasible and successful. And if thi alternative current scenario looks radically different from the 'real' state we are in, then this goes to show how radically unsustainable our business-as-usual approach has been.
Parker, R Gary
1988-01-01
This book treats the fundamental issues and algorithmic strategies emerging as the core of the discipline of discrete optimization in a comprehensive and rigorous fashion. Following an introductory chapter on computational complexity, the basic algorithmic results for the two major models of polynomial algorithms are introduced--models using matroids and linear programming. Further chapters treat the major non-polynomial algorithms: branch-and-bound and cutting planes. The text concludes with a chapter on heuristic algorithms.Several appendixes are included which review the fundamental ideas o
Directory of Open Access Journals (Sweden)
Simone R Caljouw
Full Text Available An earlier study suggested that the activity-inviting office landscape called "The End of Sitting", designed by Rietveld Architecture Art Affordances (RAAAF, should be considered as an alternative working environment to prevent sedentary behavior. The End of Sitting lacks chairs and tables but consists instead of a myriad of sloped surfaces at different heights that afford workers to stand, lean or recline at different locations. In this study, we assessed the impact of four of its workspaces on physical intensity, temporary comfort and productivity of office work and compared the outcomes with sitting and standing behind a desk. Twenty-four participants worked for 10 minutes in each of the six test conditions. Energy expenditure, measured by indirect calorimetry, and heart rate were recorded. Questionnaires were used to assess the perceived comfort. The number of words found in the word search test was counted as a measure of productivity. The majority of The End of Sitting workspaces led to a significant increase in energy expenditure compared with sitting behind a desk (ps < .05. Average MET values ranged from 1.40 to 1.58 which is a modest rise in energy expenditure compared to sitting (1.32 METs and not significantly different from standing (1.47 METs. The scores on the general comfort scale indicated that some workspaces were less comfortable than sitting (ps < .05, but the vast majority of participants reported that at least one of The End of Sitting workspaces was equally or more comfortable than sitting. No differences in productivity between the test conditions were found. Further long-term studies are required to assess the behavioral adaptations, productivity and the level of comfort when using The End of Sitting as a permanent office.
Directory of Open Access Journals (Sweden)
Bhattacharyya Moitrayee
2010-08-01
Full Text Available Abstract Background One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results In this study, we have explored the ligand induced conformational changes in H.pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H.pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co-operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in
Effective lagrangian description on discrete gauge symmetries
International Nuclear Information System (INIS)
Banks, T.
1989-01-01
We exhibit a simple low-energy lagrangian which describes a system with a discrete remnant of a spontaneously broken continuous gauge symmetry. The lagrangian gives a simple description of the effects ascribed to such systems by Krauss and Wilczek: black holes carry discrete hair and interact with cosmic strings, and wormholes cannot lead to violation of discrete gauge symmetries. (orig.)
Wiens, J. David; Schumaker, Nathan H.; Inman, Richard D.; Esque, Todd C.; Longshore, Kathleen M.; Nussear, Kenneth E
2017-01-01
Spatial demographic models can help guide monitoring and management activities targeting at-risk species, even in cases where baseline data are lacking. Here, we provide an example of how site-specific changes in land use and anthropogenic stressors can be incorporated into a spatial demographic model to investigate effects on population dynamics of Golden Eagles (Aquila chrysaetos). Our study focused on a population of Golden Eagles exposed to risks associated with rapid increases in renewable energy development in southern California, U.S.A. We developed a spatially explicit, individual-based simulation model that integrated empirical data on demography of Golden Eagles with spatial data on the arrangement of nesting habitats, prey resources, and planned renewable energy development sites. Our model permitted simulated eagles of different stage-classes to disperse, establish home ranges, acquire prey resources, prospect for breeding sites, and reproduce. The distribution of nesting habitats, prey resources, and threats within each individual's home range influenced movement, reproduction, and survival. We used our model to explore potential effects of alternative disturbance scenarios, and proposed conservation strategies, on the future distribution and abundance of Golden Eagles in the study region. Results from our simulations suggest that probable increases in mortality associated with renewable energy infrastructure (e.g., collisions with wind turbines and vehicles, electrocution on power poles) could have negative consequences for population trajectories, but that site-specific conservation actions could reduce the magnitude of negative effects. Our study demonstrates the use of a flexible and expandable modeling framework to incorporate spatially dependent processes when determining relative effects of proposed management options to Golden Eagles and their habitats.
Canvassing the Cyber Security Landscape: Why Energy Companies Need to Pay Attention
Averill, B.; Luiijf, H.A.M.
2010-01-01
Recent news of a “highly sophisticated and targeted” cyber attack on Google, Yahoo, and perhaps on as many as a dozen other companies has once again brought the issue of cyber security to the top of the news. Internet companies, however, are not the only ones vulnerable to such attacks. Over the past decade, a series of events has highlighted the vulnerability of the electric grid and other energy infrastructures to both cyber disruptions (due, e.g., to malware) and from outside attacks using...
International Nuclear Information System (INIS)
2013-01-01
Within a context of lack of regulatory framework, of existence of technological deadlocks, and of absence of any defined business model, this publication reports a study of the emerging market of energy storage. It examines the role public authorities can play to promote investments in this sector, what are the opportunities for operators, and which are the perspectives on the middle term for the French market. In order to highlight recent and future evolutions of stationary and embarked storage, the authors propose an analysis of the main market growth drivers and brakes, a focus on the impact of regulatory, legal, economic, tax-related, technological, and social-cultural factors on sector stakeholders. They also propose an overview of the market status for the cases of stationary and embarked storage, and of the main challenges for these both segments. A panorama of existing actors is given with an analysis of their position, strengths and weaknesses, and of the main axis of development for 4 categories of actors (industries, battery manufacturers, energy operators, and start ups)
Energy landscape and dynamics of brain activity during human bistable perception.
Watanabe, Takamitsu; Masuda, Naoki; Megumi, Fukuda; Kanai, Ryota; Rees, Geraint
2014-08-28
Individual differences in the structure of parietal and prefrontal cortex predict the stability of bistable visual perception. However, the mechanisms linking such individual differences in brain structures to behaviour remain elusive. Here we demonstrate a systematic relationship between the dynamics of brain activity, cortical structure and behaviour underpinning bistable perception. Using fMRI in humans, we find that the activity dynamics during bistable perception are well described as fluctuating between three spatially distributed energy minimums: visual-area-dominant, frontal-area-dominant and intermediate states. Transitions between these energy minimums predicted behaviour, with participants whose brain activity tend to reflect the visual-area-dominant state exhibiting more stable perception and those whose activity transits to frontal-area-dominant states reporting more frequent perceptual switches. Critically, these brain activity dynamics are correlated with individual differences in grey matter volume of the corresponding brain areas. Thus, individual differences in the large-scale dynamics of brain activity link focal brain structure with bistable perception.
Classification of the visual landscape for transmission planning
Curtis Miller; Nargis Jetha; Rod MacDonald
1979-01-01
The Visual Landscape Type Classification method of the Route and Site Selection Division, Ontario Hydro, defines and delineates the landscape into discrete visual units using parametric and judgmental data. This qualitative and quantitative information is documented in a prescribed format to give each of the approximately 1100 Landscape Types a unique description....
Energy Technology Data Exchange (ETDEWEB)
Ruehmkorf, Hilke
2011-07-01
In its effort to implement new climate and energy policies, Germany has been heavily promoting the adoption of renewable energies. This has brought about a dramatic change in the use of arable land during the last years. The primary objective of this study was therefore to assess the effect of energy cropping on existing landscape structures in intensively cultivated regions in the course of the year. According to the available structural parameters an investigation was conducted to ascertain the fallout of energy plant cultivation on both migratory and overwintering birds. The period covered entailed the winter months. Both the advent of the energy crops as well as the associated biogas facilities that sprang up outside built-in areas seem to have reshaped the existing agricultural landscape. Hence, an additional aim of this study was to identify birds that use biogas plants for breeding or as a feeding habitat in winter. In conclusion, it can be asserted that energy crops can definitely contribute to the expansion of structural diversity in the agricultural landscape provided those energy crops were not cultivated on a large scale prior to the advent of the biogas facilities. Hence, there is still room for further energy crop diversification as its potential has not been exhausted. During the winter months mostly common species such as the carrion crow or the wood pigeon consider the maize fields as a viable source of nutrition. Cranes are seen as newcomers, as they probably started resting in the 'Boerde' precisely due to the advent of energy maize cultivation. And more availability of nourishment when the ground is covered by snow is another benefit the avifauna reaps from biogas plants. However, for endangered farmland birds this type of nutrition is a rarely used source, as it runs counter to their escape strategies and food preferences. For these species the habitat function and the food availability depends especially on how the land is managed (e
Gentil-Beccot, Anne; Mele, Salvatore; Holtkamp, Annette; O'Connell, Heath B; Brooks, Travis C
2009-01-01
Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the field of information management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the field reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the field. The survey offers an insight into the most importan...
Photovoltaic performance and the energy landscape of CH3NH3PbI3.
Zhou, Yecheng; Huang, Fuzhi; Cheng, Yi-Bing; Gray-Weale, Angus
2015-09-21
Photovoltaic cells with absorbing layers of certain perovskites have power conversion efficiencies up to 20%. Among these materials, CH3NH3PbI3 is widely used. Here we use density-functional theory to calculate the energies and rotational energy barriers of a methylammonium ion in the α or β phase of CH3NH3PbI3 with differently oriented neighbouring methylammonium ions. Our results suggest the methylammonium ions in CH3NH3PbI3 prefer to rotate collectively, and to be parallel to their neighbours. Changes in polarization on rotation of methylammonium ions are two to three times larger than those on relaxation of the lead ion from the centre of its coordination shell. The preferences for parallel configuration and concerted rotation, with the polarisation changes, are consistent with ferroelectricity in the material, and indicate that this polarisation is governed by methylammonium orientational correlations. We show that the field due to this polarisation is strong enough to screen the field hindering charge transport, and find this screening field in agreement with experiment. We examine two possible mechanisms for the effect of methylammonium ion rotation on photovoltaic performance. One is that rearrangement of methylammoniums promotes the creation and transport of charge carriers. Some effective masses change greatly, but changes in band structure with methylammonium rotation are not large enough to explain current-voltage hysteresis behaviour. The second possible mechanism is that polarization screens the hindering electric field, which arises from charge accumulation in the transport layers. Polarization changes on methylammonium rotation favour this second mechanism, suggesting that collective reorientation of methylammonium ions in the bulk crystal are in significant part responsible for the hysteresis and power conversion characteristics of CH3NH3PbI3 photovoltaic cells.
Griffith, J.A.; Trettin, C.C.; O'Neill, R. V.
2002-01-01
Geographic information systems (GIS) are increasingly being used in environmental impact assessments (EIA) because GIS is useful for analysing spatial impacts of various development scenarios. Spatially representing these impacts provides another tool for landscape ecology in environmental and geographical investigations by facilitating analysis of the effects of landscape patterns on ecological processes and examining change over time. Landscape ecological principles are applied in this study to a hypothetical geothermal development project on the Island of Hawaii. Some common landscape pattern metrics were used to analyse dispersed versus condensed development scenarios and their effect on landscape pattern. Indices of fragmentation and patch shape did not appreciably change with additional development. The amount of forest to open edge, however, greatly increased with the dispersed development scenario. In addition, landscape metrics showed that a human disturbance had a greater simplifying effect on patch shape and also increased fragmentation than a natural disturbance. The use of these landscape pattern metrics can advance the methodology of applying GIS to EIA.
Ruggiero, Michael T; Krynski, Marcin; Kissi, Eric Ofosu; Sibik, Juraj; Markl, Daniel; Tan, Nicholas Y; Arslanov, Denis; van der Zande, Wim; Redlich, Britta; Korter, Timothy M; Grohganz, Holger; Löbmann, Korbinian; Rades, Thomas; Elliott, Stephen R; Zeitler, J Axel
2017-11-15
The fundamental origins surrounding the dynamics of disordered solids near their characteristic glass transitions continue to be fiercely debated, even though a vast number of materials can form amorphous solids, including small-molecule organic, inorganic, covalent, metallic, and even large biological systems. The glass-transition temperature, T g , can be readily detected by a diverse set of techniques, but given that these measurement modalities probe vastly different processes, there has been significant debate regarding the question of why T g can be detected across all of them. Here we show clear experimental and computational evidence in support of a theory that proposes that the shape and structure of the potential-energy surface (PES) is the fundamental factor underlying the glass-transition processes, regardless of the frequency that experimental methods probe. Whilst this has been proposed previously, we demonstrate, using ab initio molecular-dynamics (AIMD) simulations, that it is of critical importance to carefully consider the complete PES - both the intra-molecular and inter-molecular features - in order to fully understand the entire range of atomic-dynamical processes in disordered solids. Finally, we show that it is possible to utilise this dependence to directly manipulate and harness amorphous dynamics in order to control the behaviour of such solids by using high-powered terahertz pulses to induce crystallisation and preferential crystal-polymorph growth in glasses. Combined, these findings provide compelling evidence that the PES landscape, and the corresponding energy barriers, are the ultimate controlling feature behind the atomic and molecular dynamics of disordered solids, regardless of the frequency at which they occur.
DEFF Research Database (Denmark)
Christensen, Andreas Aagaard; Brandt, Jesper; Svenningsen, Stig Roar
2017-01-01
Landscape ecology is an interdisciplinary field of research and practice that deals with the mutual association between the spatial configuration and ecological functioning of landscapes, exploring and describing processes involved in the differentiation of spaces within landscapes......, and the ecological significance of the patterns which are generated by such processes. In landscape ecology, perspectives drawn from existing academic disciplines are integrated based on a common, spatially explicit mode of analysis developed from classical holistic geography, emphasizing spatial and landscape...... pattern analysis and ecological interaction of land units. The landscape is seen as a holon: an assemblage of interrelated phenomena, both cultural and biophysical, that together form a complex whole. Enduring challenges to landscape ecology include the need to develop a systematic approach able...
Firth, Jean M
1992-01-01
The analysis of signals and systems using transform methods is a very important aspect of the examination of processes and problems in an increasingly wide range of applications. Whereas the initial impetus in the development of methods appropriate for handling discrete sets of data occurred mainly in an electrical engineering context (for example in the design of digital filters), the same techniques are in use in such disciplines as cardiology, optics, speech analysis and management, as well as in other branches of science and engineering. This text is aimed at a readership whose mathematical background includes some acquaintance with complex numbers, linear differen tial equations, matrix algebra, and series. Specifically, a familiarity with Fourier series (in trigonometric and exponential forms) is assumed, and an exposure to the concept of a continuous integral transform is desirable. Such a background can be expected, for example, on completion of the first year of a science or engineering degree cour...
Energy Technology Data Exchange (ETDEWEB)
Gentil-Beccot, A.; Mele, S. [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Holtkamp, A. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); O' Connell, H.B. [Fermi National Accelerator Lab., Batavia, IL (United States); Brooks, T.C. [Stanford Linear Accelerator Center, Menlo Park, CA (United States)
2008-04-15
Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the eld of infor- mation management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the eld reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the eld. The survey o ers an in- sight into the most important features that users require to optimize their research workflow. These results inform the future evolution of information management in HEP and, as these researchers are traditionally 'early adopters' of innovation in scholarly communication, can inspire developments of disciplinary repositories serving other communities. (orig.)
Tailoring the Energy Landscape in Quasi-2D Halide Perovskites Enables Efficient Green-Light Emission
Quan, Li Na; Zhao, Yongbiao; Garcí a de Arquer, F. Pelayo; Sabatini, Randy; Walters, Grant; Voznyy, Oleksandr; Comin, Riccardo; Li, Yiying; Fan, James Z.; Tan, Hairen; Pan, Jun; Yuan, Mingjian; Bakr, Osman; Lu, Zhenghong; Kim, Dong Ha; Sargent, Edward H.
2017-01-01
Organo-metal halide perovskites are a promising platform for optoelectronic applications in view of their excellent charge-transport and bandgap tunability. However, their low photoluminescence quantum efficiencies, especially in low-excitation regimes, limit their efficiency for light emission. Consequently, perovskite light-emitting devices are operated under high injection, a regime under which the materials have so far been unstable. Here we show that, by concentrating photoexcited states into a small subpopulation of radiative domains, one can achieve a high quantum yield, even at low excitation intensities. We tailor the composition of quasi-2D perovskites to direct the energy transfer into the lowest-bandgap minority phase and to do so faster than it is lost to nonradiative centers. The new material exhibits 60% photoluminescence quantum yield at excitation intensities as low as 1.8 mW/cm2, yielding a ratio of quantum yield to excitation intensity of 0.3 cm2/mW; this represents a decrease of 2 orders of magnitude in the excitation power required to reach high efficiency compared with the best prior reports. Using this strategy, we report light-emitting diodes with external quantum efficiencies of 7.4% and a high luminescence of 8400 cd/m2.
Ionic Strength Modulation of the Free Energy Landscape of Aβ40 Peptide Fibril Formation.
Abelein, Axel; Jarvet, Jüri; Barth, Andreas; Gräslund, Astrid; Danielsson, Jens
2016-06-01
Protein misfolding and formation of cross-β structured amyloid fibrils are linked to many neurodegenerative disorders. Although recently developed quantitative approaches have started to reveal the molecular nature of self-assembly and fibril formation of proteins and peptides, it is yet unclear how these self-organization events are precisely modulated by microenvironmental factors, which are known to strongly affect the macroscopic aggregation properties. Here, we characterize the explicit effect of ionic strength on the microscopic aggregation rates of amyloid β peptide (Aβ40) self-association, implicated in Alzheimer's disease. We found that physiological ionic strength accelerates Aβ40 aggregation kinetics by promoting surface-catalyzed secondary nucleation reactions. This promoted catalytic effect can be assigned to shielding of electrostatic repulsion between monomers on the fibril surface or between the fibril surface itself and monomeric peptides. Furthermore, we observe the formation of two different β-structured states with similar but distinct spectroscopic features, which can be assigned to an off-pathway immature state (Fβ*) and a mature stable state (Fβ), where salt favors formation of the Fβ fibril morphology. Addition of salt to preformed Fβ* accelerates transition to Fβ, underlining the dynamic nature of Aβ40 fibrils in solution. On the basis of these results we suggest a model where salt decreases the free-energy barrier for Aβ40 folding to the Fβ state, favoring the buildup of the mature fibril morphology while omitting competing, energetically less favorable structural states.
International Nuclear Information System (INIS)
Gentil-Beccot, A.; Mele, S.; Holtkamp, A.; O'Connell, H.B.; Brooks, T.C.
2008-04-01
Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the eld of infor- mation management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the eld reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the eld. The survey o ers an in- sight into the most important features that users require to optimize their research workflow. These results inform the future evolution of information management in HEP and, as these researchers are traditionally ''early adopters'' of innovation in scholarly communication, can inspire developments of disciplinary repositories serving other communities. (orig.)
Energy Technology Data Exchange (ETDEWEB)
Gentil-Beccot, A; Mele, S [European Organization for Nuclear Research (CERN), Geneva (Switzerland); Holtkamp, A [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); O' Connell, H B [Fermi National Accelerator Lab., Batavia, IL (United States); Brooks, T C [Stanford Linear Accelerator Center, Menlo Park, CA (United States)
2008-04-15
Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the eld of infor- mation management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the eld reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the eld. The survey o ers an in- sight into the most important features that users require to optimize their research workflow. These results inform the future evolution of information management in HEP and, as these researchers are traditionally 'early adopters' of innovation in scholarly communication, can inspire developments of disciplinary repositories serving other communities. (orig.)
Energy Technology Data Exchange (ETDEWEB)
Gentil-Beccot, Anne; Mele, Salvatore; Holtkamp, Annette; O' Connell, Heath B.; Brooks, Travis C.
2008-04-22
Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the field of information management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the field reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the field. The survey offers an insight into the most important features that users require to optimize their research workflow. These results inform the future evolution of information management in HEP and, as these researchers are traditionally 'early adopters' of innovation in scholarly communication, can inspire developments of disciplinary repositories serving other communities.
Tailoring the Energy Landscape in Quasi-2D Halide Perovskites Enables Efficient Green-Light Emission
Quan, Li Na
2017-05-10
Organo-metal halide perovskites are a promising platform for optoelectronic applications in view of their excellent charge-transport and bandgap tunability. However, their low photoluminescence quantum efficiencies, especially in low-excitation regimes, limit their efficiency for light emission. Consequently, perovskite light-emitting devices are operated under high injection, a regime under which the materials have so far been unstable. Here we show that, by concentrating photoexcited states into a small subpopulation of radiative domains, one can achieve a high quantum yield, even at low excitation intensities. We tailor the composition of quasi-2D perovskites to direct the energy transfer into the lowest-bandgap minority phase and to do so faster than it is lost to nonradiative centers. The new material exhibits 60% photoluminescence quantum yield at excitation intensities as low as 1.8 mW/cm2, yielding a ratio of quantum yield to excitation intensity of 0.3 cm2/mW; this represents a decrease of 2 orders of magnitude in the excitation power required to reach high efficiency compared with the best prior reports. Using this strategy, we report light-emitting diodes with external quantum efficiencies of 7.4% and a high luminescence of 8400 cd/m2.
International Nuclear Information System (INIS)
Gentil-Beccot, Anne; Mele, Salvatore; Holtkamp, Annette; O'Connell, Heath B.; Brooks, Travis C.
2008-01-01
Access to previous results is of paramount importance in the scientific process. Recent progress in information management focuses on building e-infrastructures for the optimization of the research workflow, through both policy-driven and user-pulled dynamics. For decades, High-Energy Physics (HEP) has pioneered innovative solutions in the field of information management and dissemination. In light of a transforming information environment, it is important to assess the current usage of information resources by researchers and HEP provides a unique test-bed for this assessment. A survey of about 10% of practitioners in the field reveals usage trends and information needs. Community-based services, such as the pioneering arXiv and SPIRES systems, largely answer the need of the scientists, with a limited but increasing fraction of younger users relying on Google. Commercial services offered by publishers or database vendors are essentially unused in the field. The survey offers an insight into the most important features that users require to optimize their research workflow. These results inform the future evolution of information management in HEP and, as these researchers are traditionally 'early adopters' of innovation in scholarly communication, can inspire developments of disciplinary repositories serving other communities
Czech Academy of Sciences Publication Activity Database
Frantál, Bohumil; Bevk, T.; van Veelen, B.; Hărmănescu, M.; Benediktsson, K.
2017-01-01
Roč. 25, č. 4 (2017), s. 234-247 ISSN 1210-8812 R&D Projects: GA ČR GA16-04483S Institutional support: RVO:68145535 Keywords : wind energy * landscape perception * Iceland Subject RIV: DE - Earth Magnetism, Geodesy, Geography OBOR OECD: Environmental sciences (social aspects) Impact factor: 2.149, year: 2016 http://www.geonika.cz/EN/research/ENMGRClanky/2017_4_FRANT%C3%81L.pdf
Thermal Characteristics of Urban Landscapes
Luvall, Jeffrey C.; Quattrochi, Dale A.
1998-01-01
Although satellite data are very useful for analysis of the urban heat island effect at a coarse scale, they do not lend themselves to developing a better understanding of which surfaces across the city contribute or drive the development of the urban heat island effect. Analysis of thermal energy responses for specific or discrete surfaces typical of the urban landscape (e.g., asphalt, building rooftops, vegetation) requires measurements at a very fine spatial scale (i.e., less than 15 m) to adequately resolve these surfaces and their attendant thermal energy regimes. Additionally, very fine scale spatial resolution thermal infrared data, such as that obtained from aircraft, are very useful for demonstrating to planning officials, policy makers, and the general populace the benefits of the urban forest. These benefits include mitigating the urban heat island effect, making cities more aesthetically pleasing and more habitable environments, and aid in overall cooling of the community. High spatial resolution thermal data are required to quantify how artificial surfaces within the city contribute to an increase in urban heating and the benefit of cool surfaces (e.g., surface coatings that reflect much of the incoming solar radiation as opposed to absorbing it thereby lowering urban temperatures). The TRN (thermal response number) is a technique using aircraft remotely sensed surface temperatures to quantify the thermal response of urban surfaces. The TRN was used to quantify the thermal response of various urban surface types ranging from completely vegetated surfaces to asphalt and concrete parking lots for Huntsville, AL.
Discrete Curvatures and Discrete Minimal Surfaces
Sun, Xiang
2012-01-01
This thesis presents an overview of some approaches to compute Gaussian and mean curvature on discrete surfaces and discusses discrete minimal surfaces. The variety of applications of differential geometry in visualization and shape design leads
DEFF Research Database (Denmark)
Christensen, Andreas Aagaard; Brandt, Jesper; Svenningsen, Stig Roar
2017-01-01
, and the ecological significance of the patterns which are generated by such processes. In landscape ecology, perspectives drawn from existing academic disciplines are integrated based on a common, spatially explicit mode of analysis developed from classical holistic geography, emphasizing spatial and landscape...... to translate positivist readings of the environment and hermeneutical perspectives on socioecological interaction into a common framework or terminology....
Discrete Curvatures and Discrete Minimal Surfaces
Sun, Xiang
2012-06-01
This thesis presents an overview of some approaches to compute Gaussian and mean curvature on discrete surfaces and discusses discrete minimal surfaces. The variety of applications of differential geometry in visualization and shape design leads to great interest in studying discrete surfaces. With the rich smooth surface theory in hand, one would hope that this elegant theory can still be applied to the discrete counter part. Such a generalization, however, is not always successful. While discrete surfaces have the advantage of being finite dimensional, thus easier to treat, their geometric properties such as curvatures are not well defined in the classical sense. Furthermore, the powerful calculus tool can hardly be applied. The methods in this thesis, including angular defect formula, cotangent formula, parallel meshes, relative geometry etc. are approaches based on offset meshes or generalized offset meshes. As an important application, we discuss discrete minimal surfaces and discrete Koenigs meshes.
Hoffacker, Madison K; Allen, Michael F; Hernandez, Rebecca R
2017-12-19
Land-cover change from energy development, including solar energy, presents trade-offs for land used for the production of food and the conservation of ecosystems. Solar energy plays a critical role in contributing to the alternative energy mix to mitigate climate change and meet policy milestones; however, the extent that solar energy development on nonconventional surfaces can mitigate land scarcity is understudied. Here, we evaluate the land sparing potential of solar energy development across four nonconventional land-cover types: the built environment, salt-affected land, contaminated land, and water reservoirs (as floatovoltaics), within the Great Central Valley (CV, CA), a globally significant agricultural region where land for food production, urban development, and conservation collide. Furthermore, we calculate the technical potential (TWh year -1 ) of these land sparing sites and test the degree to which projected electricity needs for the state of California can be met therein. In total, the CV encompasses 15% of CA, 8415 km 2 of which was identified as potentially land-sparing for solar energy development. These areas comprise a capacity-based energy potential of at least 17 348 TWh year -1 for photovoltaic (PV) and 2213 TWh year -1 for concentrating solar power (CSP). Accounting for technology efficiencies, this exceeds California's 2025 projected electricity demands up to 13 and 2 times for PV and CSP, respectively. Our study underscores the potential of strategic renewable energy siting to mitigate environmental trade-offs typically coupled with energy sprawl in agricultural landscapes.
Caljouw, Simone R.; de Vries, Rutger; Withagen, Rob
2017-01-01
An earlier study suggested that the activity-inviting office landscape called "The End of Sitting", designed by Rietveld Architecture Art Affordances (RAAAF), should be considered as an alternative working environment to prevent sedentary behavior. The End of Sitting lacks chairs and tables but
Energy Technology Data Exchange (ETDEWEB)
None
2015-05-27
This presentation provides a high-level overview of the current U.S. shared solar landscape, the impact that a given shared solar program's structure has on requiring federal securities oversight, as well as an estimate of market potential for U.S. shared solar deployment.
Landscape characterization and biodiversity research
Energy Technology Data Exchange (ETDEWEB)
Dale, V.H. [Oak Ridge National Lab., TN (United States); Offerman, H. [Univ. of Maryland, College Park, MD (United States). Geography Dept.; Frohn, R. [Univ. of California, Santa Barbara, CA (United States); Gardner, R.H. [Appalachian Environmental Lab., Frostburg, MD (United States)
1995-03-01
Rapid deforestation often produces landscape-level changes in forest characteristics and structure, including area, distribution, and forest habitat types. Changes in landscape pattern through fragmentation or aggregation of natural habitats can alter patterns of abundance for single species and entire communities. Examples of single-species effects include increased predation along the forest edge, the decline in the number of species with poor dispersal mechanisms, and the spread of exotic species that have deleterious effects (e.g., gypsy moth). A decrease in the size and number of natural habitat patches increases the probability of local extirpation and loss of diversity of native species, whereas a decline in connectivity between habitat patches can negatively affect species persistence. Thus, there is empirical justification for managing entire landscapes, not just individual habitat types, in order to insure that native plant and animal diversity is maintained. A landscape is defined as an area composed of a mosaic of interacting ecosystems, or patches, with the heterogeneity among the patches significantly affecting biotic and abiotic processes in the landscape. Patches comprising a landscape are usually composed of discrete areas of relatively homogeneous environmental conditions and must be defined in terms of the organisms of interest. A large body of theoretical work in landscape ecology has provided a wealth of methods for quantifying spatial characteristics of landscapes. Recent advances in remote sensing and geographic information systems allow these methods to be applied over large areas. The objectives of this paper are to present a brief overview of common measures of landscape characteristics, to explore the new technology available for their calculation, to provide examples of their application, and to call attention to the need for collection of spatially-explicit field data.
DEFF Research Database (Denmark)
Brichet, Nathalia Sofie; Hastrup, Frida
2018-01-01
This article has a twofold ambition. It offers a history of landscaping at Søby brown coal beds—a former mining site in western Denmark—and a methodological discussion of how to write such a study. Exploring this specific industrial landscape through a series of projects that have made different...... natural resources appear, we show that even what is recognized as resources shifts over time according to radically different and unpredictable agendas. This indicates that the Søby landscape is fundamentally volatile, as its resourcefulness has been seen interchangeably to shift between the brown coal...... business, inexpensive estates for practically savvy people, pasture for grazing, and recreational forest, among other things. We discuss these rifts in landscape history, motivated by what we refer to as industriousness, to show that, at sites such as Søby, both natural resources and historical...
DEFF Research Database (Denmark)
Cermak, Daniel; Okutsu, Ayaka; Jørgensen, Stina Marie Hasse
2015-01-01
Daniel Cermak-Sassenrath, Ayaka Okutsu, Stina Hasse. Electromagnetic Landscape - In-between Signal, Noise and Environment. Installation and artist talk. 21th International Symposium on Electronic Art (ISEA) 2015, Vancouver, CAN, Aug 14-18, 2015.......Daniel Cermak-Sassenrath, Ayaka Okutsu, Stina Hasse. Electromagnetic Landscape - In-between Signal, Noise and Environment. Installation and artist talk. 21th International Symposium on Electronic Art (ISEA) 2015, Vancouver, CAN, Aug 14-18, 2015....
DEFF Research Database (Denmark)
Hjortshøj, Rasmus
2017-01-01
This Box Set NORDIC LANDSCAPE presents Nordic Territories, a project by Rasmus Hjortshøj, exploring the man-made landscapes of the coastal territories and the entanglement of society and nature in times where it is no longer merely mankind subjected to nature, but where nature is equally being...... territories is not only their transient nature, but also the warm currents of the Gulf Stream making these northern shorelines habitable for human settlements....
Changing Landscapes, Changing Landscape's Story
Czech Academy of Sciences Publication Activity Database
Lapka, Miloslav; Cudlínová, Eva
2003-01-01
Roč. 28, č. 3 (2003), s. 323-328 ISSN 0142-6397. [Symposium on Sustainable Landscapes in an Enlarged Europe. Nové Hrady, 12.09.2001-14.09.2001] R&D Projects: GA MŠk ME 530 Grant - others:GA-(XE) QLK5-CT-2000-01211-SPRITE Institutional research plan: CEZ:AV0Z5039906 Keywords : Landscape stability * narrative approach * socio-economic typology Subject RIV: DO - Wilderness Conservation
Trammel, E. Jamie; Carter, Sarah; Haby, Travis S.; Taylor, Jason J.
2018-01-01
Enhancing natural resource management has been a focus of landscape ecology since its inception, but numerous authors argue that landscape ecology has not yet been effective in achieving the underlying goal of planning and designing sustainable landscapes. We developed nine questions reflecting the application of fundamental research topics in landscape ecology to the landscape planning process and reviewed two recent landscape-scale plans in western North America for evidence of these concepts in plan decisions. Both plans considered multiple resources, uses, and values, including energy development, recreation, conservation, and protection of cultural and historic resources. We found that land use change and multiscale perspectives of resource uses and values were very often apparent in planning decisions. Pattern-process relationships, connectivity and fragmentation, ecosystem services, landscape history, and climate change were reflected less frequently. Landscape sustainability was considered only once in the 295 decisions reviewed, and outputs of landscape models were not referenced. We suggest six actionable opportunities for further integrating landscape ecology concepts into landscape planning efforts: 1) use landscape sustainability as an overarching goal, 2) adopt a broad ecosystem services framework, 3) explore the role of landscape history more comprehensively, 4) regularly consider and accommodate potential effects of climate change, 5) use landscape models to support plan decisions, and 6) promote a greater presence of landscape ecologists within agencies that manage large land bases and encourage active involvement in agency planning efforts. Together these actions may improve the defensibility, durability, and sustainability of landscape plan decisions.
Mimetic discretization methods
Castillo, Jose E
2013-01-01
To help solve physical and engineering problems, mimetic or compatible algebraic discretization methods employ discrete constructs to mimic the continuous identities and theorems found in vector calculus. Mimetic Discretization Methods focuses on the recent mimetic discretization method co-developed by the first author. Based on the Castillo-Grone operators, this simple mimetic discretization method is invariably valid for spatial dimensions no greater than three. The book also presents a numerical method for obtaining corresponding discrete operators that mimic the continuum differential and
Ensemble simulations with discrete classical dynamics
DEFF Research Database (Denmark)
Toxværd, Søren
2013-01-01
For discrete classical Molecular dynamics (MD) obtained by the "Verlet" algorithm (VA) with the time increment $h$ there exist a shadow Hamiltonian $\\tilde{H}$ with energy $\\tilde{E}(h)$, for which the discrete particle positions lie on the analytic trajectories for $\\tilde{H}$. $\\tilde......{E}(h)$ is employed to determine the relation with the corresponding energy, $E$ for the analytic dynamics with $h=0$ and the zero-order estimate $E_0(h)$ of the energy for discrete dynamics, appearing in the literature for MD with VA. We derive a corresponding time reversible VA algorithm for canonical dynamics...
Empirical methods for modeling landscape change, ecosystem services, and biodiversity
David Lewis; Ralph. Alig
2009-01-01
The purpose of this paper is to synthesize recent economics research aimed at integrating discrete-choice econometric models of land-use change with spatially-explicit landscape simulations and quantitative ecology. This research explicitly models changes in the spatial pattern of landscapes in two steps: 1) econometric estimation of parcel-scale transition...
Exploiting Elementary Landscapes for TSP, Vehicle Routing and Scheduling
2015-09-03
similar mathematical foundation to enable gradient descent methods for discrete combinatorial optimization problems. We are also generalizing our prior...research has exploited statistical and mathematical properties of elementary landscapes to develop new gradient methods for combinatorial optimization... mathematically methods to more automatically identify elementary landscapes. If a combinatorial optimization problem is a superposition of elemen
Time Discretization Techniques
Gottlieb, S.; Ketcheson, David I.
2016-01-01
The time discretization of hyperbolic partial differential equations is typically the evolution of a system of ordinary differential equations obtained by spatial discretization of the original problem. Methods for this time evolution include
Discrete Curvature Theories and Applications
Sun, Xiang
2016-08-25
Discrete Di erential Geometry (DDG) concerns discrete counterparts of notions and methods in di erential geometry. This thesis deals with a core subject in DDG, discrete curvature theories on various types of polyhedral surfaces that are practically important for free-form architecture, sunlight-redirecting shading systems, and face recognition. Modeled as polyhedral surfaces, the shapes of free-form structures may have to satisfy di erent geometric or physical constraints. We study a combination of geometry and physics { the discrete surfaces that can stand on their own, as well as having proper shapes for the manufacture. These proper shapes, known as circular and conical meshes, are closely related to discrete principal curvatures. We study curvature theories that make such surfaces possible. Shading systems of freeform building skins are new types of energy-saving structures that can re-direct the sunlight. From these systems, discrete line congruences across polyhedral surfaces can be abstracted. We develop a new curvature theory for polyhedral surfaces equipped with normal congruences { a particular type of congruences de ned by linear interpolation of vertex normals. The main results are a discussion of various de nitions of normality, a detailed study of the geometry of such congruences, and a concept of curvatures and shape operators associated with the faces of a triangle mesh. These curvatures are compatible with both normal congruences and the Steiner formula. In addition to architecture, we consider the role of discrete curvatures in face recognition. We use geometric measure theory to introduce the notion of asymptotic cones associated with a singular subspace of a Riemannian manifold, which is an extension of the classical notion of asymptotic directions. We get a simple expression of these cones for polyhedral surfaces, as well as convergence and approximation theorems. We use the asymptotic cones as facial descriptors and demonstrate the
Discrete symmetries and their stringy origin
International Nuclear Information System (INIS)
Mayorga Pena, Damian Kaloni
2014-05-01
Discrete symmetries have proven to be very useful in controlling the phenomenology of theories beyond the standard model. In this work we explore how these symmetries emerge from string compactifications. Our approach is twofold: On the one hand, we consider the heterotic string on orbifold backgrounds. In this case the discrete symmetries can be derived from the orbifold conformal field theory, and it can be shown that they are in close relation with the orbifold geometry. We devote special attention to R-symmetries, which arise from discrete remnants of the Lorentz group in compact space. Further we discuss the physical implications of these symmetries both in the heterotic mini-landscape and in newly constructed models based on the Z 2 x Z 4 orbifold. In both cases we observe that the discrete symmetries favor particular locations in the orbifold where the particles of standard model should live. On the other hand we consider a class of F-theory models exhibiting an SU(5) gauge group, times additional U(1) symmetries. In this case, the smooth compactification background does not permit us to track the discrete symmetries as transparently as in orbifold models. Hence, we follow a different approach and search for discrete subgroups emerging after the U(1)s are broken. We observe that in this approach it is possible to obtain the standard Z 2 matter parity of the MSSM.
Ishida, Hisashi; Matsumoto, Atsushi
2014-01-01
To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA. PMID:24999999
Directory of Open Access Journals (Sweden)
Hisashi Ishida
Full Text Available To understand the mechanism of reverse tRNA translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-tRNAs-mRNA-EFG complex were performed. The complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-EM density maps. Between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. Multistep structural changes, such as a ratchet-like motion and rotation of the head of the small subunit were observed. The free-energy landscape showed that there were two main free-energy barriers: one between the post-translocational and intermediate states, and the other between the pre-translocational and intermediate states. The former corresponded to a clockwise rotation, which was coupled to the movement of P-tRNA over the P/E-gate made of G1338, A1339 and A790 in the small subunit. The latter corresponded to an anticlockwise rotation of the head, which was coupled to the location of the two tRNAs in the hybrid state. This indicates that the coupled motion of the head rotation and tRNA translocation plays an important role in opening and closing of the P/E-gate during the ratchet-like movement in the ribosome. Conformational change of EF-G was interpreted to be the result of the combination of the external motion by L12 around an axis passing near the sarcin-ricin loop, and internal hinge-bending motion. These motions contributed to the movement of domain IV of EF-G to maintain its interaction with A/P-tRNA.
Contemporary danish landscape research
DEFF Research Database (Denmark)
Vejre, H.; Brandt, J.
2004-01-01
Danish landscape research blossomed during the 1990ies thanks to several transdisciplinary research programmes involving several institutions. The main themes of the programmes encompassed Landscape change, landscape and biological diversity, nature and landscape management, use and monitoring...
International Nuclear Information System (INIS)
Noyes, H.P.; Starson, S.
1991-03-01
Discrete physics, because it replaces time evolution generated by the energy operator with a global bit-string generator (program universe) and replaces ''fields'' with the relativistic Wheeler-Feynman ''action at a distance,'' allows the consistent formulation of the concept of signed gravitational charge for massive particles. The resulting prediction made by this version of the theory is that free anti-particles near the surface of the earth will ''fall'' up with the same acceleration that the corresponding particles fall down. So far as we can see, no current experimental information is in conflict with this prediction of our theory. The experiment crusis will be one of the anti-proton or anti-hydrogen experiments at CERN. Our prediction should be much easier to test than the small effects which those experiments are currently designed to detect or bound. 23 refs
DEFF Research Database (Denmark)
Cermak, Daniel; Okutsu, Ayaka; Hasse, Stina
2015-01-01
Electromagnetic Landscape demonstrates in direct, tangible and immediate ways effects of the disruption of the familiar. An ubiquitous technological medium, FM radio, is turned into an alien and unfamiliar one. Audience participation, the environment, radio signals and noise create a site...
DEFF Research Database (Denmark)
Tunby Gulbrandsen, Ib; Kamstrup, Andreas; Koed Madsen, Anders
with an analysis of the changing organizational landscape created by new ICT’s like Google, Facebook, Wikipedia, iPods, smart phones and Wi-Fi. Based on five netno- and ethno-graphic investigations of the intertwinement of ICT’s and organizational work, we point to three features that have changed the scene: new...
Kevin T. Smith
2008-01-01
Whether we are a traditionalist or on the cutting edge of landscape care, we need to take a deep breath and think about what we are trying to achieve, before we select a specific treatment or practice for tree care. We should measure that treatment or practice against what we know about the tree system. I say "system" because the recent years of Modern...
Discrete Bose-Einstein spectra
International Nuclear Information System (INIS)
Vlad, Valentin I.; Ionescu-Pallas, Nicholas
2001-03-01
The Bose-Einstein energy spectrum of a quantum gas, confined in a rigid cubic box, is shown to become discrete and strongly dependent on the box geometry (size L), temperature, T and atomic mass number, A at , in the region of small γ=A at TV 1/3 . This behavior is the consequence of the random state degeneracy in the box. Furthermore, we demonstrate that the total energy does not obey the conventional law any longer, but a new law, which depends on γ and on the quantum gas fugacity. This energy law imposes a faster decrease to zero than it is classically expected, for γ→0. The lighter the gas atoms, the higher the temperatures or the box size, for the same effects in the discrete Bose-Einstein regime. (author)
Measuring Thermal Characteristics of Urban Landscapes
Luvall, Jeffrey C.; Quattrochi, Dale A.; Rickman, Doug L.
1999-01-01
The additional heating of the air over the city is the result of the replacement of naturally vegetated surfaces with those composed of asphalt, concrete, rooftops and other man-made materials. The temperatures of these artificial surfaces can be 20 to 40 C higher than vegetated surfaces. Materials such as asphalt store much of the sun's energy and remains hot long after sunset. This produces a dome of elevated air temperatures 5 to 8 C greater over the city, compared to the air temperatures over adjacent rural areas. This effect is called the "urban heat island". Urban landscapes are a complex mixture of vegetated and nonvegetated surfaces. It is difficult to take enough temperature measurements over a large city area to characterize the complexity of urban radiant surface temperature variability. However, the use of remotely sensed thermal data from airborne scanners are ideal for the task. In a study funded by NASA, a series of flights over Huntsville, Alabama were performed in September 1994 and over Atlanta, Georgia in May 1997. Analysis of thermal energy responses for specific or discrete surfaces typical of the urban landscape (e.g., asphalt, building rooftops, vegetation) requires measurements at a very fine spatial scale (i.e., energy regimes. Additionally, very fine scale spatial resolution thermal infrared data, such as that obtained from aircraft, are very useful for demonstrating to planning officials, policy makers, and the general populace, what the benefits are of the urban forest in both mitigating the urban heat island effect, in making cities more aesthetically pleasing and more habitable environments, and in overall cooling of the community. In this presentation we will examine the techniques of analyzing remotely sensed data for measuring the effect of various urban surfaces on their contribution to the urban heat island effect.
International Nuclear Information System (INIS)
Vlad, Valentin I.; Ionescu-Pallas, Nicholas
2000-10-01
The Planck radiation spectrum of ideal cubic and spherical cavities, in the region of small adiabatic invariance, γ = TV 1/3 , is shown to be discrete and strongly dependent on the cavity geometry and temperature. This behavior is the consequence of the random distribution of the state weights in the cubic cavity and of the random overlapping of the successive multiplet components, for the spherical cavity. The total energy (obtained by summing up the exact contributions of the eigenvalues and their weights, for low values of the adiabatic invariance) does not obey any longer Stefan-Boltzmann law. The new law includes a corrective factor depending on γ and imposes a faster decrease of the total energy to zero, for γ → 0. We have defined the double quantized regime both for cubic and spherical cavities by the superior and inferior limits put on the principal quantum numbers or the adiabatic invariance. The total energy of the double quantized cavities shows large differences from the classical calculations over unexpected large intervals, which are measurable and put in evidence important macroscopic quantum effects. (author)
Ecological Functions of Landscapes
Kiryushin, V. I.
2018-01-01
Ecological functions of landscapes are considered a system of processes ensuring the development, preservation, and evolution of ecosystems and the biosphere as a whole. The concept of biogeocenosis can be considered a model that integrates biotic and environmental functions. The most general biogeocenotic functions specify the biodiversity, biotic links, self-organization, and evolution of ecosystems. Close interaction between biocenosis and the biotope (ecotope) is ensured by the continuous exchange of matter, energy, and information. Ecotope determines the biocenosis. The group of ecotopic functions includes atmospheric (gas exchange, heat exchange, hydroatmospheric, climate-forming), lithospheric (geodynamic, geophysical, and geochemical), hydrologic and hydrogeologic functions of landscape and ecotopic functions of soils. Bioecological functions emerge as a result of the biotope and ecotope interaction; these are the bioproductive, destructive, organoaccumulative, biochemical (gas, concentration, redox, biochemical, biopedological), pedogenetic, and energy functions
International Nuclear Information System (INIS)
2010-11-01
This article presents the content of a market study which aimed at providing an overview of the development of wind energy in France after market lift-off, at assessing the influence of Grenelle II on this sector, at assessing the competitiveness of wind energy with respect to other production sources, and at analysing strategies of equipment manufacturers and operators on a market where competitive positions are from being fixed. The report proposes an overview of the French wind energy market (legal context, growth dynamics, market valorisation, cost structure and profitability, support measures), analyses the positions and challenges of wind turbine manufacturers (the front end of the sector) and of wind farm developers and operators (the back end of the sector). Several manufacturers (Areva, Enercon, Gamesa, GE Energy, Nordex, REpower, Siemens and Vestas) and developers and operators (Boralex, EDF Energies Nouvelles, EDP Renovavels, Eolfi, GDF Suez, Iberdrola Renovables, Poweo, Theolia) have been analysed
Measuring Thermal Characteristics of Urban Landscapes
Luvall, Jeffrey C.; Quattrochi, Dale A.; Rickman, Doug L.
1999-01-01
The additional heating of the air over the city is the result of the replacement of naturally vegetated surfaces with those composed of asphalt, concrete, rooftops and other man-made materials. The temperatures of these artificial surfaces can be 20 to 40 C higher than vegetated surfaces. Materials such as asphalt store much of the sun's energy and remains hot long after sunset. This produces a dome of elevated air temperatures 5 to 8 C greater over the city, compared to the air temperatures over adjacent rural areas. This effect is called the "urban heat island". Urban landscapes are a complex mixture of vegetated and nonvegetated surfaces. It is difficult to take enough temperature measurements over a large city area to characterize the complexity of urban radiant surface temperature variability. However, the use of remotely sensed thermal data from airborne scanners are ideal for the task. In a study funded by NASA, a series of flights over Huntsville, Alabama were performed in September 1994 and over Atlanta, Georgia in May 1997. Analysis of thermal energy responses for specific or discrete surfaces typical of the urban landscape (e.g., asphalt, building rooftops, vegetation) requires measurements at a very fine spatial scale (i.e., urban forest in both mitigating the urban heat island effect, in making cities more aesthetically pleasing and more habitable environments, and in overall cooling of the community. In this presentation we will examine the techniques of analyzing remotely sensed data for measuring the effect of various urban surfaces on their contribution to the urban heat island effect.
Discrete breathers in graphane: Effect of temperature
Energy Technology Data Exchange (ETDEWEB)
Baimova, J. A., E-mail: julia.a.baimova@gmail.com [Russian Academy of Sciences, Institute of Metal Physics, Ural Branch (Russian Federation); Murzaev, R. T.; Lobzenko, I. P.; Dmitriev, S. V. [Russian Academy of Sciences, Institute for Metals Superplasticity Problems (Russian Federation); Zhou, Kun [Nanyang Technological University, School of Mechanical and Aerospace Engineering (Singapore)
2016-05-15
The discrete breathers in graphane in thermodynamic equilibrium in the temperature range 50–600 K are studied by molecular dynamics simulation. A discrete breather is a hydrogen atom vibrating along the normal to a sheet of graphane at a high amplitude. As was found earlier, the lifetime of a discrete breather at zero temperature corresponds to several tens of thousands of vibrations. The effect of temperature on the decay time of discrete breathers and the probability of their detachment from a sheet of graphane are studied in this work. It is shown that closely spaced breathers can exchange energy with each other at zero temperature. The data obtained suggest that thermally activated discrete breathers can be involved in the dehydrogenation of graphane, which is important for hydrogen energetics.
Mohamed, Mamdouh S.
2016-02-11
A conservative discretization of incompressible Navier–Stokes equations is developed based on discrete exterior calculus (DEC). A distinguishing feature of our method is the use of an algebraic discretization of the interior product operator and a combinatorial discretization of the wedge product. The governing equations are first rewritten using the exterior calculus notation, replacing vector calculus differential operators by the exterior derivative, Hodge star and wedge product operators. The discretization is then carried out by substituting with the corresponding discrete operators based on the DEC framework. Numerical experiments for flows over surfaces reveal a second order accuracy for the developed scheme when using structured-triangular meshes, and first order accuracy for otherwise unstructured meshes. By construction, the method is conservative in that both mass and vorticity are conserved up to machine precision. The relative error in kinetic energy for inviscid flow test cases converges in a second order fashion with both the mesh size and the time step.
Mohamed, Mamdouh S.; Hirani, Anil N.; Samtaney, Ravi
2016-05-01
A conservative discretization of incompressible Navier-Stokes equations is developed based on discrete exterior calculus (DEC). A distinguishing feature of our method is the use of an algebraic discretization of the interior product operator and a combinatorial discretization of the wedge product. The governing equations are first rewritten using the exterior calculus notation, replacing vector calculus differential operators by the exterior derivative, Hodge star and wedge product operators. The discretization is then carried out by substituting with the corresponding discrete operators based on the DEC framework. Numerical experiments for flows over surfaces reveal a second order accuracy for the developed scheme when using structured-triangular meshes, and first order accuracy for otherwise unstructured meshes. By construction, the method is conservative in that both mass and vorticity are conserved up to machine precision. The relative error in kinetic energy for inviscid flow test cases converges in a second order fashion with both the mesh size and the time step.
International Nuclear Information System (INIS)
Bercu, V; Martinelli, M; Massa, C A; Pardi, L A; Leporini, D
2004-01-01
The reorientation of one small paramagnetic molecule (spin probe) in glassy polystyrene (PS) is studied by high-field electron spin resonance spectroscopy at two different Larmor frequencies (190 and 285 GHz). The exponential distribution of the energy barriers for the rotational motion of the spin probe is unambiguously evidenced at both 240 and 270 K. The same shape for the distribution of the energy barriers of PS was evidenced by the master curves provided by previous mechanical and light scattering studies. The breadth of the energy barrier distribution of the spin probe is in the range of the estimates of the breadth of the PS energy barrier distribution. The evidence that the deep structure of the energy landscape of PS exhibits the exponential shape of the energy barrier distribution agrees with the results from extreme-value statistics (Bouchaud and Mezard 1997 J. Phys. A: Math. Gen. 30 7997) and the trap model by Bouchaud and co-workers (1996 J. Phys. A: Math. Gen. 29 3847, 2001 Phys. Rev. B 64 104417). (letter to the editor)
Geometry and Hamiltonian mechanics on discrete spaces
International Nuclear Information System (INIS)
Talasila, V; Clemente-Gallardo, J; Schaft, A J van der
2004-01-01
Numerical simulation is often crucial for analysing the behaviour of many complex systems which do not admit analytic solutions. To this end, one either converts a 'smooth' model into a discrete (in space and time) model, or models systems directly at a discrete level. The goal of this paper is to provide a discrete analogue of differential geometry, and to define on these discrete models a formal discrete Hamiltonian structure-in doing so we try to bring together various fundamental concepts from numerical analysis, differential geometry, algebraic geometry, simplicial homology and classical Hamiltonian mechanics. For example, the concept of a twisted derivation is borrowed from algebraic geometry for developing a discrete calculus. The theory is applied to a nonlinear pendulum and we compare the dynamics obtained through a discrete modelling approach with the dynamics obtained via the usual discretization procedures. Also an example of an energy-conserving algorithm on a simple harmonic oscillator is presented, and its effect on the Poisson structure is discussed
International Nuclear Information System (INIS)
Gleicher, Frederick; Prinja, Anil K.
2001-01-01
An efficient multigroup model that accurately describes electronic energy loss straggling was recently presented for use in multigroup Monte Carlo and deterministic high-energy ion transport codes. The model preserves the mean energy loss per path length, using the continuous slowing down (CSD) approximation, and mean-squared energy loss per path length, using strictly down-scatter multigroup cross sections, and accurately captures the energy spectrum of an initially monoenergetic ion beam. However, the dominant CSD energy loss process coupled with the small (but non-negligible) straggling poses a significant challenge for deterministic numerical solution when incident beams are monoenergetic or have discontinuous energy spectra. Such spectra broaden very slowly with depth into the target material, and thus, the interior distributions display sharpness and discontinuities. Advanced space-energy discretization methods are consequently necessary to achieve numerical robustness. In this paper, we investigate finite element solutions to this problem using two general families of discontinuous trial functions, one linear and the other nonlinear. The two families have been numerically tested, and we show results for 1.7-GeV protons incident on a tungsten target. For benchmarking purposes, we have also performed Monte Carlo (MC) simulations. Figure 1 displays the spatially converged energy spectrum with 200 groups after the beam has penetrated two-thirds of the ion range (85 cm). We contrast results from linear (LD), bilinear (BLD), and quadratic (QD) discontinuous trail functions against those from exponential-linear (LE), exponential-bilinear (BLE), and exponential-quadratic (QE) discontinuous trail functions. It is clear that the linear and bilinear results from both families are grossly inaccurate, both showing unacceptably high numerical straggling when compared against the MC results. The nonlinear results are everywhere positive while the linear schemes display
Energy Technology Data Exchange (ETDEWEB)
Arbat, G.; Pujol, J.; Pelegri, M.; Puig-Bargues, J.; Duran-Ros, M.; Ramirez de Cartagena, F.
2013-05-01
The number of private gardens has increased in recent years, creating a more pleasant urban model, but not without having an environmental impact, including increased energy consumption, which is the focus of this study. The estimation of costs and energy consumption for the generic typology of private urban gardens is based on two simplifying assumptions: square geometry with surface areas from 25 to 500 m{sup 2} and hydraulic design with a single pipe. In total, eight sprinkler models have been considered, along with their possible working pressures, and 31 pumping units grouped into 5 series that adequately cover the range of required flow rates and pressures, resulting in 495 hydraulic designs repeated for two climatically different locations in the Spanish Mediterranean area (Girona and Elche). Mean total irrigation costs for the locality with lower water needs (Girona) and greater needs (Elche) were {epsilon} 2,974 ha{sup -}1 yr-1 and {epsilon}3,383 ha{sup -}1 yr{sup -}1, respectively. Energy costs accounted for 11.4% of the total cost for the first location, and 23.0% for the second. While a suitable choice of the hydraulic elements of the setup is essential, as it may provide average energy savings of 77%, due to the low energy cost in relation to the cost of installation, the potential energy savings do not constitute a significant incentive for the irrigation system design. The low efficiency of the pumping units used in this type of garden is the biggest obstacle and constraint to achieving a high quality energy solution. (Author) 32 refs.
Directory of Open Access Journals (Sweden)
G. Arbat
2013-02-01
Full Text Available The number of private gardens has increased in recent years, creating a more pleasant urban model, but not without having an environmental impact, including increased energy consumption, which is the focus of this study. The estimation of costs and energy consumption for the generic typology of private urban gardens is based on two simplifying assumptions: square geometry with surface areas from 25 to 500 m2 and hydraulic design with a single pipe. In total, eight sprinkler models have been considered, along with their possible working pressures, and 31 pumping units grouped into 5 series that adequately cover the range of required flow rates and pressures, resulting in 495 hydraulic designs repeated for two climatically different locations in the Spanish Mediterranean area (Girona and Elche. Mean total irrigation costs for the locality with lower water needs (Girona and greater needs (Elche were € 2,974 ha-1 yr-1 and € 3,383 ha-1 yr-1, respectively. Energy costs accounted for 11.4% of the total cost for the first location, and 23.0% for the second. While a suitable choice of the hydraulic elements of the setup is essential, as it may provide average energy savings of 77%, due to the low energy cost in relation to the cost of installation, the potential energy savings do not constitute a significant incentive for the irrigation system design. The low efficiency of the pumping units used in this type of garden is the biggest obstacle and constraint to achieving a high quality energy solution.
Giovambattista, N.; Sciortino, F.; Starr, F. W.; Poole, P. H.
The potential energy landscape (PEL) formalism is a valuable approach within statistical mechanics for describing supercooled liquids and glasses. We use the PEL formalism and computer simulations to study the transformation between low-density (LDL) and high-density liquid (HDL) water, and between low-density (LDA) and high-density amorphous ice (HDA). We employ the ST2 water model that exhibits a LDL-HDL first-order phase transition and a sharp LDA-HDA transformation, as observed in experiments. Our results are consistent with the view that LDA and HDA configurations are associated with two distinct regions (megabasins) of the PEL that are separated by a potential energy barrier. At higher temperature, we find that LDL configurations are located in the same megabasin as LDA, and that HDL configurations are located in the same megabasin as HDA. We show that the pressure-induced LDL-HDL and LDA-HDA transformations occur along paths that interconnect these two megabasins, but that the path followed by the liquid and the amorphous ice differ. We also study the liquid-to-ice-VII first-order phase transition. The PEL properties across this transition are qualitatively similar to the changes found during the LDA-HDA transformation, supporting the interpretation that the LDA-HDA transformation is a first-order-like phase transition between out-of-equilibrium states.
Giovambattista, Nicolas; Starr, Francis W.; Poole, Peter H.
2017-07-01
Experiments and computer simulations of the transformations of amorphous ices display different behaviors depending on sample preparation methods and on the rates of change of temperature and pressure to which samples are subjected. In addition to these factors, simulation results also depend strongly on the chosen water model. Using computer simulations of the ST2 water model, we study how the sharpness of the compression-induced transition from low-density amorphous ice (LDA) to high-density amorphous ice (HDA) is influenced by the preparation of LDA. By studying LDA samples prepared using widely different procedures, we find that the sharpness of the LDA-to-HDA transformation is correlated with the depth of the initial LDA sample in the potential energy landscape (PEL), as characterized by the inherent structure energy. Our results show that the complex phenomenology of the amorphous ices reported in experiments and computer simulations can be understood and predicted in a unified way from knowledge of the PEL of the system.
储能技术研究景观辨识及演化探析%Identifying the Landscape and Its Evolution in Energy Storage Research
Institute of Scientific and Technical Information of China (English)
刘娜; 孙静林; 毛荐其
2017-01-01
This study seeks to integrate statistics, text mining, burst detecting and co-occurrence network visualiza-tion to identify the landscape and its evolution of energy storage research from a holistic perspective based on ar-ticles on physical, chemical, electromagnetic and phase change energy storage extracted from SCI-E and SSCI data-base between 1991 and 2015. A stability coefficient and an innovation coefficient are also defined to measure the stability evolution and innovation evolution of keywords co-occurrence networks in energy storage respectively. Our results indicate that the research in energy storage is highly-concentrated in key issues, hot topics are fly-wheel, lithium ion batteries, supercapacitors and phase change materials, and frontier topics are compressed air energy storage, energy storage, lithium ion batteries, thermal conductivity and thermal energy storage. We also find keywords co-occurrence networks expand significantly, knowledge structures evolve constantly and energy storage research is still in its innovation phase.%基于SCI-E及SSCI数据库,检索并提取1991—2015年间物理储能、化学储能、电磁储能和相变储能4大技术领域的论文数据,试图整合统计分析、文本挖掘、突现检测算法和共现网络可视化方法,旨在从整体视角实现对4大储能技术领域科学研究景观的辨识及演化探析.此外,还定义了稳定系数和创新系数,以测度储能关键词共现网络的稳定性演化和创新性演化.研究发现:储能领域的研究问题是高度集中的,"飞轮"、"锂离子电池"、"超级电容器"和"相变材料"是研究热点,"压缩空气储能"、"能源存储"、"锂离子电池"、"导热性"和"热发电"是研究前沿;储能关键词共现网络扩张明显,知识结构也不断演化,储能研究仍处于创新热络期.
DEFF Research Database (Denmark)
Scarpaci, Joseph L.; Portela, Armando
This accessible book offers a vivid geographic portrait of Cuba, exploring the island’s streetscapes, sugar cane fields, beaches, and rural settlements; its billboards, government buildings, and national landmarks. The authors illuminate how natural and built landscapes have shaped Cuban identity...... (cubanidad), and vice versa. They provide a unique perspective on Cuba’s distinct historical periods and political economies, from the colonial period through republicanism and today’s socialist era. Compelling topics include the legacies of slavery and the sugar industry, the past and future of urban...
Baecklund transformations for discrete Painleve equations: Discrete PII-PV
International Nuclear Information System (INIS)
Sakka, A.; Mugan, U.
2006-01-01
Transformation properties of discrete Painleve equations are investigated by using an algorithmic method. This method yields explicit transformations which relates the solutions of discrete Painleve equations, discrete P II -P V , with different values of parameters. The particular solutions which are expressible in terms of the discrete analogue of the classical special functions of discrete Painleve equations can also be obtained from these transformations
Sweetnam, Sean
2014-10-08
Theoretical and experimental studies suggest that energetic offsets between the charge transport energy levels in different morphological phases of polymer:fullerene bulk heterojunctions may improve charge separation and reduce recombination in polymer solar cells (PSCs). In this work, we use cyclic voltammetry, UV-vis absorption, and ultraviolet photoelectron spectroscopy to characterize hole energy levels in the polymer phases of polymer:fullerene bulk heterojunctions. We observe an energetic offset of up to 150 meV between amorphous and crystalline polymer due to bandgap widening associated primarily with changes in polymer conjugation length. We also observe an energetic offset of up to 350 meV associated with polymer:fullerene intermolecular interactions. The first effect has been widely observed, but the second effect is not always considered despite being larger in magnitude for some systems. These energy level shifts may play a major role in PSC performance and must be thoroughly characterized for a complete understanding of PSC function.
Discrete Gabor transform and discrete Zak transform
Bastiaans, M.J.; Namazi, N.M.; Matthews, K.
1996-01-01
Gabor's expansion of a discrete-time signal into a set of shifted and modulated versions of an elementary signal or synthesis window is introduced, along with the inverse operation, i.e. the Gabor transform, which uses an analysis window that is related to the synthesis window and with the help of
Erin L. Landguth; Michael K. Schwartz
2014-01-01
One of the most pressing issues in spatial genetics concerns sampling. Traditionally, substructure and gene flow are estimated for individuals sampled within discrete populations. Because many species may be continuously distributed across a landscape without discrete boundaries, understanding sampling issues becomes paramount. Given large-scale, geographically broad...
Discrete Mathematics Re "Tooled."
Grassl, Richard M.; Mingus, Tabitha T. Y.
1999-01-01
Indicates the importance of teaching discrete mathematics. Describes how the use of technology can enhance the teaching and learning of discrete mathematics. Explorations using Excel, Derive, and the TI-92 proved how preservice and inservice teachers experienced a new dimension in problem solving and discovery. (ASK)
Discrete Tomography and Imaging of Polycrystalline Structures
DEFF Research Database (Denmark)
Alpers, Andreas
High resolution transmission electron microscopy is commonly considered as the standard application for discrete tomography. While this has yet to be technically realized, new applications with a similar flavor have emerged in materials science. In our group at Ris� DTU (Denmark's National...... Laboratory for Sustainable Energy), for instance, we study polycrystalline materials via synchrotron X-ray diffraction. Several reconstruction problems arise, most of them exhibit inherently discrete aspects. In this talk I want to give a concise mathematical introduction to some of these reconstruction...... problems. Special focus is on their relationship to classical discrete tomography. Several open mathematical questions will be mentioned along the way....
AN EVALUATION OF THE SPATIAL DIMENSION OF LANDSCAPE ...
African Journals Online (AJOL)
Osondu
2012-03-30
Mar 30, 2012 ... with adequate landscaping, - using landscape elements, to create a ... air, water and energy cycles that replenish and rejuvenate ... First, using the street map of. Ogbomoso ... swimming pools, etc, were regarded as conscious.
Homogenization of discrete media
International Nuclear Information System (INIS)
Pradel, F.; Sab, K.
1998-01-01
Material such as granular media, beam assembly are easily seen as discrete media. They look like geometrical points linked together thanks to energetic expressions. Our purpose is to extend discrete kinematics to the one of an equivalent continuous material. First we explain how we build the localisation tool for periodic materials according to estimated continuum medium type (classical Cauchy, and Cosserat media). Once the bridge built between discrete and continuum media, we exhibit its application over two bidimensional beam assembly structures : the honey comb and a structural reinforced variation. The new behavior is then applied for the simple plan shear problem in a Cosserat continuum and compared with the real discrete solution. By the mean of this example, we establish the agreement of our new model with real structures. The exposed method has a longer range than mechanics and can be applied to every discrete problems like electromagnetism in which relationship between geometrical points can be summed up by an energetic function. (orig.)
Okuyama, Yoshifumi
2014-01-01
Discrete Control Systems establishes a basis for the analysis and design of discretized/quantized control systemsfor continuous physical systems. Beginning with the necessary mathematical foundations and system-model descriptions, the text moves on to derive a robust stability condition. To keep a practical perspective on the uncertain physical systems considered, most of the methods treated are carried out in the frequency domain. As part of the design procedure, modified Nyquist–Hall and Nichols diagrams are presented and discretized proportional–integral–derivative control schemes are reconsidered. Schemes for model-reference feedback and discrete-type observers are proposed. Although single-loop feedback systems form the core of the text, some consideration is given to multiple loops and nonlinearities. The robust control performance and stability of interval systems (with multiple uncertainties) are outlined. Finally, the monograph describes the relationship between feedback-control and discrete ev...
Energy Technology Data Exchange (ETDEWEB)
Morris, J; Johnson, S
2007-12-03
The Distinct Element Method (also frequently referred to as the Discrete Element Method) (DEM) is a Lagrangian numerical technique where the computational domain consists of discrete solid elements which interact via compliant contacts. This can be contrasted with Finite Element Methods where the computational domain is assumed to represent a continuum (although many modern implementations of the FEM can accommodate some Distinct Element capabilities). Often the terms Discrete Element Method and Distinct Element Method are used interchangeably in the literature, although Cundall and Hart (1992) suggested that Discrete Element Methods should be a more inclusive term covering Distinct Element Methods, Displacement Discontinuity Analysis and Modal Methods. In this work, DEM specifically refers to the Distinct Element Method, where the discrete elements interact via compliant contacts, in contrast with Displacement Discontinuity Analysis where the contacts are rigid and all compliance is taken up by the adjacent intact material.
Landscaping practices can positively or negatively affect local environments and human health. The Landscaping Initiative seeks to enhance benefits of landscaping while reducing need for pesticides, fertilizers, etc., by working with partners.
DEFF Research Database (Denmark)
Dyre, Jeppe; Jacobsen, Jacob M.
1995-01-01
This paper presents a calculation of the time dependence of the mean-square displacement for symmetric random energy barrier hopping models at low temperatures, where the frequency dependence of the normalized diffusion constant D-tilde becomes universal, i.e., independent of the energy barrier...... probability distribution [J. C. Dyre, Phys. Rev. B 49, 11 709 (1994)]. The universal time dependence of the mean-square displacement is calculated from the effective medium approximation (EMA) universality equation, D-tilde lnD-tilde=s-tilde, where s-tilde is the dimensionless imaginary frequency, as well...... as for the approximation to the EMA universality equation D-tilde~=s-tilde/ln(1+s-tilde). At long times the universal mean-square displacement is linear in time, corresponding to ordinary diffusion, whereas the mean-square displacement at short times t in dimensionless units varies as 2/ln(t-1)....
International Nuclear Information System (INIS)
Buchwald, K.
1977-01-01
The environmental agreeability examination through landscape planning in connection with the finding of sites for power stations and their integration into area planning is explained. The procedure of landscape planning for the assessment of power station sites is also presented. (RW) [de
Faraldo-Gómez, José D.; Roux, Benoît
2007-01-01
Regulation of signaling pathways in the cell often involves multidomain allosteric enzymes that are able to adopt alternate active or inactive conformations in response to specific stimuli. It is therefore of great interest to elucidate the energetic and structural determinants that govern the conformational plasticity of these proteins. In this study, free-energy computations have been used to address this fundamental question, focusing on one important family of signaling enzymes, the Src t...
Senay, Gabriel B.; Budde, Michael E.; Verdin, James P.
2011-01-01
Evapotranspiration (ET) can be derived from satellite data using surface energy balance principles. METRIC (Mapping EvapoTranspiration at high Resolution with Internalized Calibration) is one of the most widely used models available in the literature to estimate ET from satellite imagery. The Simplified Surface Energy Balance (SSEB) model is much easier and less expensive to implement. The main purpose of this research was to present an enhanced version of the Simplified Surface Energy Balance (SSEB) model and to evaluate its performance using the established METRIC model. In this study, SSEB and METRIC ET fractions were compared using 7 Landsat images acquired for south central Idaho during the 2003 growing season. The enhanced SSEB model compared well with the METRIC model output exhibiting an r2 improvement from 0.83 to 0.90 in less complex topography (elevation less than 2000 m) and with an improvement of r2 from 0.27 to 0.38 in more complex (mountain) areas with elevation greater than 2000 m. Independent evaluation showed that both models exhibited higher variation in complex topographic regions, although more with SSEB than with METRIC. The higher ET fraction variation in the complex mountainous regions highlighted the difficulty of capturing the radiation and heat transfer physics on steep slopes having variable aspect with the simple index model, and the need to conduct more research. However, the temporal consistency of the results suggests that the SSEB model can be used on a wide range of elevation (more successfully up 2000 m) to detect anomalies in space and time for water resources management and monitoring such as for drought early warning systems in data scarce regions. SSEB has a potential for operational agro-hydrologic applications to estimate ET with inputs of surface temperature, NDVI, DEM and reference ET.
Energy Technology Data Exchange (ETDEWEB)
Roon, Serafin von [Forschungsstelle fuer Energiewirtschaft e.V., Muenchen (Germany)
2009-07-01
Combined heat and power generation is an established technology. With micro-size cogeneration units, the technology is now available to private single or multiple dwellings and for decentral power supply of residential blocks. With the right political boundary conditions and integrated into virtual power stations, this is an option for enhanced use of renewable energy sources and for decentral, flexible and climate-friendly heat and power generation in buildings. Economic efficiency analyses by experts, high utilisation rates, innovative developments of the manufacturers and a positive public image are all in favour of a great future for micro-size cogeneration units. (orig.)
Izadi, F A; Bagirov, G
2009-01-01
With its origins stretching back several centuries, discrete calculus is now an increasingly central methodology for many problems related to discrete systems and algorithms. The topics covered here usually arise in many branches of science and technology, especially in discrete mathematics, numerical analysis, statistics and probability theory as well as in electrical engineering, but our viewpoint here is that these topics belong to a much more general realm of mathematics; namely calculus and differential equations because of the remarkable analogy of the subject to this branch of mathemati
Faraldo-Gómez, José D; Roux, Benoît
2007-08-21
Regulation of signaling pathways in the cell often involves multidomain allosteric enzymes that are able to adopt alternate active or inactive conformations in response to specific stimuli. It is therefore of great interest to elucidate the energetic and structural determinants that govern the conformational plasticity of these proteins. In this study, free-energy computations have been used to address this fundamental question, focusing on one important family of signaling enzymes, the Src tyrosine kinases. Inactivation of these enzymes depends on the formation of an assembly comprising a tandem of SH3 and SH2 modules alongside a catalytic domain. Activation results from the release of the SH3 and SH2 domains, which are then believed to be structurally uncoupled by virtue of a flexible peptide link. In contrast to this view, this analysis shows that inactivation depends critically on the intrinsic propensity of the SH3-SH2 tandem to adopt conformations that are conducive to the assembled inactive state, even when no interactions with the rest of the kinase are possible. This funneling of the available conformational space is encoded within the SH3-SH2 connector, which appears to have evolved to modulate the flexibility of the tandem in solution. To further substantiate this notion, we show how constitutively activating mutations in the SH3-SH2 connector shift the assembly equilibrium toward the disassembled, active state. Based on a similar analysis of several constructs of the kinase complex, we propose that assembly is characterized by the progressive optimization of the protein's conformational energy, with little or no energetic frustration.
Komianos, James E.; Papoian, Garegin A.
2018-04-01
Current understanding of how contractility emerges in disordered actomyosin networks of nonmuscle cells is still largely based on the intuition derived from earlier works on muscle contractility. In addition, in disordered networks, passive cross-linkers have been hypothesized to percolate force chains in the network, hence, establishing large-scale connectivity between local contractile clusters. This view, however, largely overlooks the free energy of cross-linker binding at the microscale, which, even in the absence of active fluctuations, provides a thermodynamic drive towards highly overlapping filamentous states. In this work, we use stochastic simulations and mean-field theory to shed light on the dynamics of a single actomyosin force dipole—a pair of antiparallel actin filaments interacting with active myosin II motors and passive cross-linkers. We first show that while passive cross-linking without motor activity can produce significant contraction between a pair of actin filaments, driven by thermodynamic favorability of cross-linker binding, a sharp onset of kinetic arrest exists at large cross-link binding energies, greatly diminishing the effectiveness of this contractility mechanism. Then, when considering an active force dipole containing nonmuscle myosin II, we find that cross-linkers can also serve as a structural ratchet when the motor dissociates stochastically from the actin filaments, resulting in significant force amplification when both molecules are present. Our results provide predictions of how actomyosin force dipoles behave at the molecular level with respect to filament boundary conditions, passive cross-linking, and motor activity, which can explicitly be tested using an optical trapping experiment.
Directory of Open Access Journals (Sweden)
James E. Komianos
2018-04-01
Full Text Available Current understanding of how contractility emerges in disordered actomyosin networks of nonmuscle cells is still largely based on the intuition derived from earlier works on muscle contractility. In addition, in disordered networks, passive cross-linkers have been hypothesized to percolate force chains in the network, hence, establishing large-scale connectivity between local contractile clusters. This view, however, largely overlooks the free energy of cross-linker binding at the microscale, which, even in the absence of active fluctuations, provides a thermodynamic drive towards highly overlapping filamentous states. In this work, we use stochastic simulations and mean-field theory to shed light on the dynamics of a single actomyosin force dipole—a pair of antiparallel actin filaments interacting with active myosin II motors and passive cross-linkers. We first show that while passive cross-linking without motor activity can produce significant contraction between a pair of actin filaments, driven by thermodynamic favorability of cross-linker binding, a sharp onset of kinetic arrest exists at large cross-link binding energies, greatly diminishing the effectiveness of this contractility mechanism. Then, when considering an active force dipole containing nonmuscle myosin II, we find that cross-linkers can also serve as a structural ratchet when the motor dissociates stochastically from the actin filaments, resulting in significant force amplification when both molecules are present. Our results provide predictions of how actomyosin force dipoles behave at the molecular level with respect to filament boundary conditions, passive cross-linking, and motor activity, which can explicitly be tested using an optical trapping experiment.
Finite Discrete Gabor Analysis
DEFF Research Database (Denmark)
Søndergaard, Peter Lempel
2007-01-01
frequency bands at certain times. Gabor theory can be formulated for both functions on the real line and for discrete signals of finite length. The two theories are largely the same because many aspects come from the same underlying theory of locally compact Abelian groups. The two types of Gabor systems...... can also be related by sampling and periodization. This thesis extends on this theory by showing new results for window construction. It also provides a discussion of the problems associated to discrete Gabor bases. The sampling and periodization connection is handy because it allows Gabor systems...... on the real line to be well approximated by finite and discrete Gabor frames. This method of approximation is especially attractive because efficient numerical methods exists for doing computations with finite, discrete Gabor systems. This thesis presents new algorithms for the efficient computation of finite...
Adaptive Discrete Hypergraph Matching.
Yan, Junchi; Li, Changsheng; Li, Yin; Cao, Guitao
2018-02-01
This paper addresses the problem of hypergraph matching using higher-order affinity information. We propose a solver that iteratively updates the solution in the discrete domain by linear assignment approximation. The proposed method is guaranteed to converge to a stationary discrete solution and avoids the annealing procedure and ad-hoc post binarization step that are required in several previous methods. Specifically, we start with a simple iterative discrete gradient assignment solver. This solver can be trapped in an -circle sequence under moderate conditions, where is the order of the graph matching problem. We then devise an adaptive relaxation mechanism to jump out this degenerating case and show that the resulting new path will converge to a fixed solution in the discrete domain. The proposed method is tested on both synthetic and real-world benchmarks. The experimental results corroborate the efficacy of our method.
Goodrich, Christopher
2015-01-01
This text provides the first comprehensive treatment of the discrete fractional calculus. Experienced researchers will find the text useful as a reference for discrete fractional calculus and topics of current interest. Students who are interested in learning about discrete fractional calculus will find this text to provide a useful starting point. Several exercises are offered at the end of each chapter and select answers have been provided at the end of the book. The presentation of the content is designed to give ample flexibility for potential use in a myriad of courses and for independent study. The novel approach taken by the authors includes a simultaneous treatment of the fractional- and integer-order difference calculus (on a variety of time scales, including both the usual forward and backwards difference operators). The reader will acquire a solid foundation in the classical topics of the discrete calculus while being introduced to exciting recent developments, bringing them to the frontiers of the...
International Nuclear Information System (INIS)
Williams, Ruth M
2006-01-01
A review is given of a number of approaches to discrete quantum gravity, with a restriction to those likely to be relevant in four dimensions. This paper is dedicated to Rafael Sorkin on the occasion of his sixtieth birthday
Discrete computational structures
Korfhage, Robert R
1974-01-01
Discrete Computational Structures describes discrete mathematical concepts that are important to computing, covering necessary mathematical fundamentals, computer representation of sets, graph theory, storage minimization, and bandwidth. The book also explains conceptual framework (Gorn trees, searching, subroutines) and directed graphs (flowcharts, critical paths, information network). The text discusses algebra particularly as it applies to concentrates on semigroups, groups, lattices, propositional calculus, including a new tabular method of Boolean function minimization. The text emphasize
A study of discrete nonlinear systems
International Nuclear Information System (INIS)
Dhillon, H.S.
2001-04-01
An investigation of various spatially discrete time-independent nonlinear models was undertaken. These models are generically applicable to many different physical systems including electron-phonon interactions in solids, magnetic multilayers, layered superconductors and classical lattice systems. To characterise the possible magnetic structures created on magnetic multilayers a model has been formulated and studied. The Euler-Lagrange equation for this model is a discrete version of the Sine-Gordon equation. Solutions of this equation are generated by applying the methods of Chaotic Dynamics - treating the space variable associated with the layer number as a discrete time variable. The states found indicate periodic, quasiperiodic and chaotic structures. Analytic solutions to the discrete nonlinear Schroedinger Equation (DNSE) with cubic nonlinearity are presented in the strong coupling limit. Using these as a starting point, a procedure is developed to determine the wave function and the energy eigenvalue for moderate coupling. The energy eigenvalues of the different structures of the wave function are found to be in excellent agreement with the exact strong coupling result. The solutions to the DNSE indicate commensurate and incommensurate spatial structures associated with different localisation patterns of the wave function. The states which arise may be fractal, periodic, quasiperiodic or chaotic. This work is then extended to solve a first order discrete nonlinear equation. The exact solutions for both the first and second order discrete nonlinear equations with cubic nonlinearity suggests that this method of studying discrete nonlinear equations may be applied to solve discrete equations with any order difference and cubic nonlinearity. (author)
Homogenization of discrete media
Energy Technology Data Exchange (ETDEWEB)
Pradel, F.; Sab, K. [CERAM-ENPC, Marne-la-Vallee (France)
1998-11-01
Material such as granular media, beam assembly are easily seen as discrete media. They look like geometrical points linked together thanks to energetic expressions. Our purpose is to extend discrete kinematics to the one of an equivalent continuous material. First we explain how we build the localisation tool for periodic materials according to estimated continuum medium type (classical Cauchy, and Cosserat media). Once the bridge built between discrete and continuum media, we exhibit its application over two bidimensional beam assembly structures : the honey comb and a structural reinforced variation. The new behavior is then applied for the simple plan shear problem in a Cosserat continuum and compared with the real discrete solution. By the mean of this example, we establish the agreement of our new model with real structures. The exposed method has a longer range than mechanics and can be applied to every discrete problems like electromagnetism in which relationship between geometrical points can be summed up by an energetic function. (orig.) 7 refs.
International Nuclear Information System (INIS)
Pejcha, Ondřej; Thompson, Todd A.
2015-01-01
If the neutrino luminosity from the proto-neutron star formed during a massive star core collapse exceeds a critical threshold, a supernova (SN) results. Using spherical quasi-static evolutionary sequences for hundreds of progenitors over a range of metallicities, we study how the explosion threshold maps onto observables, including the fraction of successful explosions, the neutron star (NS) and black hole (BH) mass functions, the explosion energies (E SN ) and nickel yields (M Ni ), and their mutual correlations. Successful explosions are intertwined with failures in a complex pattern that is not simply related to initial progenitor mass or compactness. We predict that progenitors with initial masses of 15 ± 1, 19 ± 1, and ∼21-26 M ☉ are most likely to form BHs, that the BH formation probability is non-zero at solar-metallicity and increases significantly at low metallicity, and that low luminosity, low Ni-yield SNe come from progenitors close to success/failure interfaces. We qualitatively reproduce the observed E SN -M Ni correlation, we predict a correlation between the mean and width of the NS mass and E SN distributions, and that the means of the NS and BH mass distributions are correlated. We show that the observed mean NS mass of ≅ 1.33 M ☉ implies that the successful explosion fraction is higher than 0.35. Overall, we show that the neutrino mechanism can in principle explain the observed properties of SNe and their compact objects. We argue that the rugged landscape of progenitors and outcomes mandates that SN theory should focus on reproducing the wide ranging distributions of observed SN properties
DISCRETE MATHEMATICS/NUMBER THEORY
Mrs. Manju Devi*
2017-01-01
Discrete mathematics is the study of mathematical structures that are fundamentally discrete rather than continuous. In contrast to real numbers that have the property of varying "smoothly", the objects studied in discrete mathematics such as integers, graphs, and statements do not vary smoothly in this way, but have distinct, separated values. Discrete mathematics therefore excludes topics in "continuous mathematics" such as calculus and analysis. Discrete objects can often be enumerated by ...
Directory of Open Access Journals (Sweden)
Prateek Sharma
2015-04-01
Full Text Available Abstract Simulation can be regarded as the emulation of the behavior of a real-world system over an interval of time. The process of simulation relies upon the generation of the history of a system and then analyzing that history to predict the outcome and improve the working of real systems. Simulations can be of various kinds but the topic of interest here is one of the most important kind of simulation which is Discrete-Event Simulation which models the system as a discrete sequence of events in time. So this paper aims at introducing about Discrete-Event Simulation and analyzing how it is beneficial to the real world systems.
Discrete systems and integrability
Hietarinta, J; Nijhoff, F W
2016-01-01
This first introductory text to discrete integrable systems introduces key notions of integrability from the vantage point of discrete systems, also making connections with the continuous theory where relevant. While treating the material at an elementary level, the book also highlights many recent developments. Topics include: Darboux and Bäcklund transformations; difference equations and special functions; multidimensional consistency of integrable lattice equations; associated linear problems (Lax pairs); connections with Padé approximants and convergence algorithms; singularities and geometry; Hirota's bilinear formalism for lattices; intriguing properties of discrete Painlevé equations; and the novel theory of Lagrangian multiforms. The book builds the material in an organic way, emphasizing interconnections between the various approaches, while the exposition is mostly done through explicit computations on key examples. Written by respected experts in the field, the numerous exercises and the thoroug...
Exarchakis, Georgios; Lücke, Jörg
2017-11-01
Sparse coding algorithms with continuous latent variables have been the subject of a large number of studies. However, discrete latent spaces for sparse coding have been largely ignored. In this work, we study sparse coding with latents described by discrete instead of continuous prior distributions. We consider the general case in which the latents (while being sparse) can take on any value of a finite set of possible values and in which we learn the prior probability of any value from data. This approach can be applied to any data generated by discrete causes, and it can be applied as an approximation of continuous causes. As the prior probabilities are learned, the approach then allows for estimating the prior shape without assuming specific functional forms. To efficiently train the parameters of our probabilistic generative model, we apply a truncated expectation-maximization approach (expectation truncation) that we modify to work with a general discrete prior. We evaluate the performance of the algorithm by applying it to a variety of tasks: (1) we use artificial data to verify that the algorithm can recover the generating parameters from a random initialization, (2) use image patches of natural images and discuss the role of the prior for the extraction of image components, (3) use extracellular recordings of neurons to present a novel method of analysis for spiking neurons that includes an intuitive discretization strategy, and (4) apply the algorithm on the task of encoding audio waveforms of human speech. The diverse set of numerical experiments presented in this letter suggests that discrete sparse coding algorithms can scale efficiently to work with realistic data sets and provide novel statistical quantities to describe the structure of the data.
Sputtering calculations with the discrete ordinated method
International Nuclear Information System (INIS)
Hoffman, T.J.; Dodds, H.L. Jr.; Robinson, M.T.; Holmes, D.K.
1977-01-01
The purpose of this work is to investigate the applicability of the discrete ordinates (S/sub N/) method to light ion sputtering problems. In particular, the neutral particle discrete ordinates computer code, ANISN, was used to calculate sputtering yields. No modifications to this code were necessary to treat charged particle transport. However, a cross section processing code was written for the generation of multigroup cross sections; these cross sections include a modification to the total macroscopic cross section to account for electronic interactions and small-scattering-angle elastic interactions. The discrete ordinates approach enables calculation of the sputtering yield as functions of incident energy and angle and of many related quantities such as ion reflection coefficients, angular and energy distributions of sputtering particles, the behavior of beams penetrating thin foils, etc. The results of several sputtering problems as calculated with ANISN are presented
Characterizing European cultural landscapes
DEFF Research Database (Denmark)
Tieskens, Koen F.; Schulp, Catharina J E; Levers, Christian
2017-01-01
intensification and land abandonment. To prevent the loss of cultural landscapes, knowledge on the location of different types of cultural landscapes is needed. In this paper, we present a characterization of European cultural landscapes based on the prevalence of three key dimensions of cultural landscapes......Almost all rural areas in Europe have been shaped or altered by humans and can be considered cultural landscapes, many of which now are considered to entail valuable cultural heritage. Current dynamics in land management have put cultural landscapes under a huge pressure of agricultural...... the three dimensions into a continuous “cultural landscape index” that allows for a characterization of Europe's rural landscapes. The characterization identifies hotspots of cultural landscapes, where all three dimensions are present, such as in the Mediterranean. On the other hand, Eastern and Northern...
Landscape moderation of biodiversity patterns and processes - eight hypotheses.
Tscharntke, Teja; Tylianakis, Jason M; Rand, Tatyana A; Didham, Raphael K; Fahrig, Lenore; Batáry, Péter; Bengtsson, Janne; Clough, Yann; Crist, Thomas O; Dormann, Carsten F; Ewers, Robert M; Fründ, Jochen; Holt, Robert D; Holzschuh, Andrea; Klein, Alexandra M; Kleijn, David; Kremen, Claire; Landis, Doug A; Laurance, William; Lindenmayer, David; Scherber, Christoph; Sodhi, Navjot; Steffan-Dewenter, Ingolf; Thies, Carsten; van der Putten, Wim H; Westphal, Catrin
2012-08-01
Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human-modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services. We organize the eight hypotheses under four overarching themes. Section A: 'landscape moderation of biodiversity patterns' includes (1) the landscape species pool hypothesis-the size of the landscape-wide species pool moderates local (alpha) biodiversity, and (2) the dominance of beta diversity hypothesis-landscape-moderated dissimilarity of local communities determines landscape-wide biodiversity and overrides negative local effects of habitat fragmentation on biodiversity. Section B: 'landscape moderation of population dynamics' includes (3) the cross-habitat spillover hypothesis-landscape-moderated spillover of energy, resources and organisms across habitats, including between managed and natural ecosystems, influences landscape-wide community structure and associated processes and (4) the landscape-moderated concentration and dilution hypothesis-spatial and temporal changes in landscape composition can cause transient concentration or dilution of populations with functional consequences. Section C: 'landscape moderation of functional trait selection' includes (5) the landscape-moderated functional trait selection hypothesis-landscape moderation of species trait selection shapes the functional role and trajectory of community assembly, and (6) the landscape-moderated insurance hypothesis-landscape complexity provides spatial and temporal insurance, i.e. high resilience and stability of ecological processes in changing environments. Section D: 'landscape constraints on
Introductory discrete mathematics
Balakrishnan, V K
2010-01-01
This concise text offers an introduction to discrete mathematics for undergraduate students in computer science and mathematics. Mathematics educators consider it vital that their students be exposed to a course in discrete methods that introduces them to combinatorial mathematics and to algebraic and logical structures focusing on the interplay between computer science and mathematics. The present volume emphasizes combinatorics, graph theory with applications to some stand network optimization problems, and algorithms to solve these problems.Chapters 0-3 cover fundamental operations involv
Prateek Sharma
2015-01-01
Abstract Simulation can be regarded as the emulation of the behavior of a real-world system over an interval of time. The process of simulation relies upon the generation of the history of a system and then analyzing that history to predict the outcome and improve the working of real systems. Simulations can be of various kinds but the topic of interest here is one of the most important kind of simulation which is Discrete-Event Simulation which models the system as a discrete sequence of ev...
Directory of Open Access Journals (Sweden)
Adrien Nicolaï
Full Text Available ATP regulates the function of many proteins in the cell by transducing its binding and hydrolysis energies into protein conformational changes by mechanisms which are challenging to identify at the atomic scale. Based on molecular dynamics (MD simulations, a method is proposed to analyze the structural changes induced by ATP binding to a protein by computing the effective free-energy landscape (FEL of a subset of its coordinates along its amino-acid sequence. The method is applied to characterize the mechanism by which the binding of ATP to the nucleotide-binding domain (NBD of Hsp70 propagates a signal to its substrate-binding domain (SBD. Unbiased MD simulations were performed for Hsp70-DnaK chaperone in nucleotide-free, ADP-bound and ATP-bound states. The simulations revealed that the SBD does not interact with the NBD for DnaK in its nucleotide-free and ADP-bound states whereas the docking of the SBD was found in the ATP-bound state. The docked state induced by ATP binding found in MD is an intermediate state between the initial nucleotide-free and final ATP-bound states of Hsp70. The analysis of the FEL projected along the amino-acid sequence permitted to identify a subset of 27 protein internal coordinates corresponding to a network of 91 key residues involved in the conformational change induced by ATP binding. Among the 91 residues, 26 are identified for the first time, whereas the others were shown relevant for the allosteric communication of Hsp70 s in several experiments and bioinformatics analysis. The FEL analysis revealed also the origin of the ATP-induced structural modifications of the SBD recently measured by Electron Paramagnetic Resonance. The pathway between the nucleotide-free and the intermediate state of DnaK was extracted by applying principal component analysis to the subset of internal coordinates describing the transition. The methodology proposed is general and could be applied to analyze allosteric communication in
Gueto-Tettay, Carlos; Martinez-Consuegra, Alejandro; Zuchniarz, Joshua; Gueto-Tettay, Luis Roberto; Drosos-Ramírez, Juan Carlos
2017-09-01
BACE1 is an enzyme of scientific interest because it participates in the progression of Alzheimer's disease. Hydroxyethylamines (HEAs) are a family of compounds which exhibit inhibitory activity toward BACE1 at a nanomolar level, favorable pharmacokinetic properties and oral bioavailability. The first step in the inhibition of BACE1 by HEAs consists of their entrance into the protease active site and the resultant conformational change in the protein, from Apo to closed form. These two conformations differ in the position of an antiparallel loop (called the flap) which covers the entrance to the catalytic site. For BACE1, closure of this flap is vital to its catalytic activity and to inhibition of the enzyme due to the new interactions thereby formed with the ligand. In the present study a dynamic energy landscape of residue-ligand interaction energies (ReLIE) measured for 112 amino acids in the BACE1 active site and its immediate vicinity during the closure of the flap induced by 8 HEAs of different inhibitory power is presented. A total of 6.272 million ReLIE calculations, based on the PM7 semiempirical method, provided a deep and quantitative view of the first step in the inhibition of the aspartyl protease. The information suggests that residues Asp93, Asp289, Thr292, Thr293, Asn294 and Arg296 are anchor points for the ligand, accounting for approximately 45% of the total protein-ligand interaction. Additionally, flap closure improved the BACE1-HEA interaction by around 25%. Furthermore, the inhibitory activity of HEAs could be related to the capacity of these ligands to form said anchor point interactions and maintain them over time: the lack of some of these anchor interactions delayed flap closure or impeded it completely, or even caused the flap to reopen. The methodology employed here could be used as a tool to evaluate future structural modifications which lead to improvements in the favorability and stability of BACE1-HEA ReLIEs, aiding in the design of
Buildings Interoperability Landscape
Energy Technology Data Exchange (ETDEWEB)
Hardin, Dave [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Stephan, Eric G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Wang, Weimin [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Corbin, Charles D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Widergren, Steven E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
2015-12-31
Through its Building Technologies Office (BTO), the United States Department of Energy’s Office of Energy Efficiency and Renewable Energy (DOE-EERE) is sponsoring an effort to advance interoperability for the integration of intelligent buildings equipment and automation systems, understanding the importance of integration frameworks and product ecosystems to this cause. This is important to BTO’s mission to enhance energy efficiency and save energy for economic and environmental purposes. For connected buildings ecosystems of products and services from various manufacturers to flourish, the ICT aspects of the equipment need to integrate and operate simply and reliably. Within the concepts of interoperability lie the specification, development, and certification of equipment with standards-based interfaces that connect and work. Beyond this, a healthy community of stakeholders that contribute to and use interoperability work products must be developed. On May 1, 2014, the DOE convened a technical meeting to take stock of the current state of interoperability of connected equipment and systems in buildings. Several insights from that meeting helped facilitate a draft description of the landscape of interoperability for connected buildings, which focuses mainly on small and medium commercial buildings. This document revises the February 2015 landscape document to address reviewer comments, incorporate important insights from the Buildings Interoperability Vision technical meeting, and capture thoughts from that meeting about the topics to be addressed in a buildings interoperability vision. In particular, greater attention is paid to the state of information modeling in buildings and the great potential for near-term benefits in this area from progress and community alignment.
Energy Landscapes of Folding Chromosomes
Zhang, Bin
The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.
Indian Academy of Sciences (India)
We also describe discrete-time systems in terms of difference ... A more modern alternative, especially for larger systems, is to convert ... In other words, ..... picture?) State-variable equations are also called state-space equations because the ...
Discrete Lorentzian quantum gravity
Loll, R.
2000-01-01
Just as for non-abelian gauge theories at strong coupling, discrete lattice methods are a natural tool in the study of non-perturbative quantum gravity. They have to reflect the fact that the geometric degrees of freedom are dynamical, and that therefore also the lattice theory must be formulated
Sharp, Karen Tobey
This paper cites information received from a number of sources, e.g., mathematics teachers in two-year colleges, publishers, and convention speakers, about the nature of discrete mathematics and about what topics a course in this subject should contain. Note is taken of the book edited by Ralston and Young which discusses the future of college…
Fishkova, T. Ya.
2018-01-01
An optimal set of geometric and electrical parameters of a high-aperture electrostatic charged-particle spectrograph with a range of simultaneously recorded energies of E/ E min = 1-50 has been found by computer simulation, which is especially important for the energy analysis of charged particles during fast processes in various materials. The spectrograph consists of two coaxial electrodes with end faces closed by flat electrodes. The external electrode with a conical-cylindrical form is cut into parts with potentials that increase linearly, except for the last cylindrical part, which is electrically connected to the rear end electrode. The internal cylindrical electrode and the front end electrode are grounded. In the entire energy range, the system is sharply focused on the internal cylindrical electrode, which provides an energy resolution of no worse than 3 × 10-3.
DEFF Research Database (Denmark)
Hansen, Anders Hedegaard; Pedersen, Henrik C.; Andersen, Torben Ole
2014-01-01
Fluid power systems are the leading technology for power take off systems in ocean wave energy converters. However, fluid power systems often suffer from poor efficiency, especially in part loads. This degrades the PTO system efficiency and therefore lowers the energy production. To overcome......, the choice of pilot valve, structural mechanical issues and modelling and simulation of various valve configurations. Hence, a mechatronic design process is utilised to choose the best valve configuration....
DEFF Research Database (Denmark)
Hansen, Anders Hedegaard; Pedersen, Henrik C.
2014-01-01
Discrete fluid power technology attracts great attention because it enables energy efficiency and robust system architectures. However, the discrete nature of this technology naturally brings shifting phenomenons into the picture. For fluid power system the relative high inductance of fluid...
Discrete Exterior Calculus Discretization of Incompressible Navier-Stokes Equations
Mohamed, Mamdouh S.; Hirani, Anil N.; Samtaney, Ravi
2017-01-01
A conservative discretization of incompressible Navier-Stokes equations over surface simplicial meshes is developed using discrete exterior calculus (DEC). Numerical experiments for flows over surfaces reveal a second order accuracy
International Nuclear Information System (INIS)
Dine, Michael; O'Neil, Deva; Sun Zheng
2005-01-01
With respect to the question of supersymmetry breaking, there are three branches of the flux landscape. On one of these, if one requires small cosmological constant, supersymmetry breaking is predominantly at the fundamental scale; on another, the distribution is roughly flat on a logarithmic scale; on the third, the preponderance of vacua are at very low scale. A priori, as we will explain, one can say little about the first branch. The vast majority of these states are not accessible even to crude, approximate analysis. On the other two branches one can hope to do better. But as a result of the lack of access to branch one, and our poor understanding of cosmology, we can at best conjecture about whether string theory predicts low energy supersymmetry or not. If we hypothesize that are on branch two or three, distinctive predictions may be possible. We comment of the status of naturalness within the landscape, deriving, for example, the statistics of the first branch from simple effective field theory reasoning
Meshes optimized for discrete exterior calculus (DEC).
Energy Technology Data Exchange (ETDEWEB)
Mousley, Sarah C. [Univ. of Illinois, Urbana-Champaign, IL (United States); Deakin, Michael [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Knupp, Patrick [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mitchell, Scott A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2017-12-01
We study the optimization of an energy function used by the meshing community to measure and improve mesh quality. This energy is non-traditional because it is dependent on both the primal triangulation and its dual Voronoi (power) diagram. The energy is a measure of the mesh's quality for usage in Discrete Exterior Calculus (DEC), a method for numerically solving PDEs. In DEC, the PDE domain is triangulated and this mesh is used to obtain discrete approximations of the continuous operators in the PDE. The energy of a mesh gives an upper bound on the error of the discrete diagonal approximation of the Hodge star operator. In practice, one begins with an initial mesh and then makes adjustments to produce a mesh of lower energy. However, we have discovered several shortcomings in directly optimizing this energy, e.g. its non-convexity, and we show that the search for an optimized mesh may lead to mesh inversion (malformed triangles). We propose a new energy function to address some of these issues.
Discrete mKdV and discrete sine-Gordon flows on discrete space curves
International Nuclear Information System (INIS)
Inoguchi, Jun-ichi; Kajiwara, Kenji; Matsuura, Nozomu; Ohta, Yasuhiro
2014-01-01
In this paper, we consider the discrete deformation of the discrete space curves with constant torsion described by the discrete mKdV or the discrete sine-Gordon equations, and show that it is formulated as the torsion-preserving equidistant deformation on the osculating plane which satisfies the isoperimetric condition. The curve is reconstructed from the deformation data by using the Sym–Tafel formula. The isoperimetric equidistant deformation of the space curves does not preserve the torsion in general. However, it is possible to construct the torsion-preserving deformation by tuning the deformation parameters. Further, it is also possible to make an arbitrary choice of the deformation described by the discrete mKdV equation or by the discrete sine-Gordon equation at each step. We finally show that the discrete deformation of discrete space curves yields the discrete K-surfaces. (paper)
Lines of landscape organisation
DEFF Research Database (Denmark)
Løvschal, Mette
2015-01-01
This paper offers a landscape analysis of the earliest linear landscape boundaries on Skovbjerg Moraine, Denmark, during the first millennium BC. Using Delaunay triangulation as well as classic distribution analyses, it demonstrates that landscape boundaries articulated already established use-pa...
Nijhuis, S.; Jauslin, D.; De Vries, C.
2012-01-01
Flowscapes explores infrastructure as a type of landscape and landscape as a type of infrastructure, and is focused on landscape architectonic design of transportation-, green- and water infrastructures. These landscape infrastructures are considered armatures for urban and rural development. With
Discrete mathematics with applications
Koshy, Thomas
2003-01-01
This approachable text studies discrete objects and the relationsips that bind them. It helps students understand and apply the power of discrete math to digital computer systems and other modern applications. It provides excellent preparation for courses in linear algebra, number theory, and modern/abstract algebra and for computer science courses in data structures, algorithms, programming languages, compilers, databases, and computation.* Covers all recommended topics in a self-contained, comprehensive, and understandable format for students and new professionals * Emphasizes problem-solving techniques, pattern recognition, conjecturing, induction, applications of varying nature, proof techniques, algorithm development and correctness, and numeric computations* Weaves numerous applications into the text* Helps students learn by doing with a wealth of examples and exercises: - 560 examples worked out in detail - More than 3,700 exercises - More than 150 computer assignments - More than 600 writing projects*...
Discrete and computational geometry
Devadoss, Satyan L
2011-01-01
Discrete geometry is a relatively new development in pure mathematics, while computational geometry is an emerging area in applications-driven computer science. Their intermingling has yielded exciting advances in recent years, yet what has been lacking until now is an undergraduate textbook that bridges the gap between the two. Discrete and Computational Geometry offers a comprehensive yet accessible introduction to this cutting-edge frontier of mathematics and computer science. This book covers traditional topics such as convex hulls, triangulations, and Voronoi diagrams, as well as more recent subjects like pseudotriangulations, curve reconstruction, and locked chains. It also touches on more advanced material, including Dehn invariants, associahedra, quasigeodesics, Morse theory, and the recent resolution of the Poincaré conjecture. Connections to real-world applications are made throughout, and algorithms are presented independently of any programming language. This richly illustrated textbook also fe...
2002-01-01
Discrete geometry investigates combinatorial properties of configurations of geometric objects. To a working mathematician or computer scientist, it offers sophisticated results and techniques of great diversity and it is a foundation for fields such as computational geometry or combinatorial optimization. This book is primarily a textbook introduction to various areas of discrete geometry. In each area, it explains several key results and methods, in an accessible and concrete manner. It also contains more advanced material in separate sections and thus it can serve as a collection of surveys in several narrower subfields. The main topics include: basics on convex sets, convex polytopes, and hyperplane arrangements; combinatorial complexity of geometric configurations; intersection patterns and transversals of convex sets; geometric Ramsey-type results; polyhedral combinatorics and high-dimensional convexity; and lastly, embeddings of finite metric spaces into normed spaces. Jiri Matousek is Professor of Com...
Time Discretization Techniques
Gottlieb, S.
2016-10-12
The time discretization of hyperbolic partial differential equations is typically the evolution of a system of ordinary differential equations obtained by spatial discretization of the original problem. Methods for this time evolution include multistep, multistage, or multiderivative methods, as well as a combination of these approaches. The time step constraint is mainly a result of the absolute stability requirement, as well as additional conditions that mimic physical properties of the solution, such as positivity or total variation stability. These conditions may be required for stability when the solution develops shocks or sharp gradients. This chapter contains a review of some of the methods historically used for the evolution of hyperbolic PDEs, as well as cutting edge methods that are now commonly used.
Direct Discrete Method for Neutronic Calculations
International Nuclear Information System (INIS)
Vosoughi, Naser; Akbar Salehi, Ali; Shahriari, Majid
2002-01-01
The objective of this paper is to introduce a new direct method for neutronic calculations. This method which is named Direct Discrete Method, is simpler than the neutron Transport equation and also more compatible with physical meaning of problems. This method is based on physic of problem and with meshing of the desired geometry, writing the balance equation for each mesh intervals and with notice to the conjunction between these mesh intervals, produce the final discrete equations series without production of neutron transport differential equation and mandatory passing from differential equation bridge. We have produced neutron discrete equations for a cylindrical shape with two boundary conditions in one group energy. The correction of the results from this method are tested with MCNP-4B code execution. (authors)
Czech Academy of Sciences Publication Activity Database
Mesiar, Radko; Li, J.; Pap, E.
2013-01-01
Roč. 54, č. 3 (2013), s. 357-364 ISSN 0888-613X R&D Projects: GA ČR GAP402/11/0378 Institutional support: RVO:67985556 Keywords : concave integral * pseudo-addition * pseudo-multiplication Subject RIV: BA - General Mathematics Impact factor: 1.977, year: 2013 http://library.utia.cas.cz/separaty/2013/E/mesiar-discrete pseudo-integrals.pdf
Discrete variational Hamiltonian mechanics
International Nuclear Information System (INIS)
Lall, S; West, M
2006-01-01
The main contribution of this paper is to present a canonical choice of a Hamiltonian theory corresponding to the theory of discrete Lagrangian mechanics. We make use of Lagrange duality and follow a path parallel to that used for construction of the Pontryagin principle in optimal control theory. We use duality results regarding sensitivity and separability to show the relationship between generating functions and symplectic integrators. We also discuss connections to optimal control theory and numerical algorithms
International Nuclear Information System (INIS)
Jalnapurkar, Sameer M; Leok, Melvin; Marsden, Jerrold E; West, Matthew
2006-01-01
This paper develops the theory of Abelian Routh reduction for discrete mechanical systems and applies it to the variational integration of mechanical systems with Abelian symmetry. The reduction of variational Runge-Kutta discretizations is considered, as well as the extent to which symmetry reduction and discretization commute. These reduced methods allow the direct simulation of dynamical features such as relative equilibria and relative periodic orbits that can be obscured or difficult to identify in the unreduced dynamics. The methods are demonstrated for the dynamics of an Earth orbiting satellite with a non-spherical J 2 correction, as well as the double spherical pendulum. The J 2 problem is interesting because in the unreduced picture, geometric phases inherent in the model and those due to numerical discretization can be hard to distinguish, but this issue does not appear in the reduced algorithm, where one can directly observe interesting dynamical structures in the reduced phase space (the cotangent bundle of shape space), in which the geometric phases have been removed. The main feature of the double spherical pendulum example is that it has a non-trivial magnetic term in its reduced symplectic form. Our method is still efficient as it can directly handle the essential non-canonical nature of the symplectic structure. In contrast, a traditional symplectic method for canonical systems could require repeated coordinate changes if one is evoking Darboux' theorem to transform the symplectic structure into canonical form, thereby incurring additional computational cost. Our method allows one to design reduced symplectic integrators in a natural way, despite the non-canonical nature of the symplectic structure
Discrete port-Hamiltonian systems
Talasila, V.; Clemente-Gallardo, J.; Schaft, A.J. van der
2006-01-01
Either from a control theoretic viewpoint or from an analysis viewpoint it is necessary to convert smooth systems to discrete systems, which can then be implemented on computers for numerical simulations. Discrete models can be obtained either by discretizing a smooth model, or by directly modeling
A paradigm for discrete physics
International Nuclear Information System (INIS)
Noyes, H.P.; McGoveran, D.; Etter, T.; Manthey, M.J.; Gefwert, C.
1987-01-01
An example is outlined for constructing a discrete physics using as a starting point the insight from quantum physics that events are discrete, indivisible and non-local. Initial postulates are finiteness, discreteness, finite computability, absolute nonuniqueness (i.e., homogeneity in the absence of specific cause) and additivity
International Nuclear Information System (INIS)
Dickens, J.K.; Todd, J.H.; Larson, D.C.
1990-09-01
Inelastic and nonelastic neutron interactions with 56 Fe have been studied for incident neutron energies between 0.8 and 41 MeV. An iron sample isotopically enriched in the mass 56 isotope was used. Gamma rays representing 70 transitions among levels in residual nuclei were identified, and production cross sections were deduced. The reactions studied were 56 Fe(n,n') 56 Fe, 56 Fe(n,p) 56 Mn, 56 Fe(n,2n) 55 Fe, 56 Fe(n,d + n,np) 55 Mn, 56 Fe(n,t + n,nd + n,2np) 54 Mn, 56 Fe(n,α) 53 Cr, 56 Fe(n,nα) 52 Cr, and 56 Fe(n,3n) 54 Fe. Values obtained for production cross sections as functions of incident neutron energy are presented in tabular form. 38 refs., 7 figs., 12 tabs
Discrete quantum geometries and their effective dimension
International Nuclear Information System (INIS)
Thuerigen, Johannes
2015-01-01
In several approaches towards a quantum theory of gravity, such as group field theory and loop quantum gravity, quantum states and histories of the geometric degrees of freedom turn out to be based on discrete spacetime. The most pressing issue is then how the smooth geometries of general relativity, expressed in terms of suitable geometric observables, arise from such discrete quantum geometries in some semiclassical and continuum limit. In this thesis I tackle the question of suitable observables focusing on the effective dimension of discrete quantum geometries. For this purpose I give a purely combinatorial description of the discrete structures which these geometries have support on. As a side topic, this allows to present an extension of group field theory to cover the combinatorially larger kinematical state space of loop quantum gravity. Moreover, I introduce a discrete calculus for fields on such fundamentally discrete geometries with a particular focus on the Laplacian. This permits to define the effective-dimension observables for quantum geometries. Analysing various classes of quantum geometries, I find as a general result that the spectral dimension is more sensitive to the underlying combinatorial structure than to the details of the additional geometric data thereon. Semiclassical states in loop quantum gravity approximate the classical geometries they are peaking on rather well and there are no indications for stronger quantum effects. On the other hand, in the context of a more general model of states which are superposition over a large number of complexes, based on analytic solutions, there is a flow of the spectral dimension from the topological dimension d on low energy scales to a real number between 0 and d on high energy scales. In the particular case of 1 these results allow to understand the quantum geometry as effectively fractal.
How wind power landscapes change
DEFF Research Database (Denmark)
Möller, Bernd
2006-01-01
Following 25 years of continuous development, Danish wind energy landscapes are going to face changes. Ceased on-shore construction, unresolved re-powering and stalled regional planning characterize the situation overshadowed by off-shore development. One of the factors inhibiting development...... in general. However, the pattern of visibility will become askew, and the present homogenous distribution of visibility will disappear. This skewness, together with changing ownership and receding local involvement, could eventually lead to lower popular acceptance of wind power....
Two new discrete integrable systems
International Nuclear Information System (INIS)
Chen Xiao-Hong; Zhang Hong-Qing
2013-01-01
In this paper, we focus on the construction of new (1+1)-dimensional discrete integrable systems according to a subalgebra of loop algebra Ã 1 . By designing two new (1+1)-dimensional discrete spectral problems, two new discrete integrable systems are obtained, namely, a 2-field lattice hierarchy and a 3-field lattice hierarchy. When deriving the two new discrete integrable systems, we find the generalized relativistic Toda lattice hierarchy and the generalized modified Toda lattice hierarchy. Moreover, we also obtain the Hamiltonian structures of the two lattice hierarchies by means of the discrete trace identity
Discrete Event Simulation Computers can be used to simulate the ...
Indian Academy of Sciences (India)
IAS Admin
people who use computers every moment of their waking lives, others even ... How is discrete event simulation different from other kinds of simulation? ... time, energy consumption .... Schedule the CustomerDeparture event for this customer.
Do geographically isolated wetlands influence landscape functions?
Cohen, Matthew J.; Creed, Irena F.; Alexander, Laurie; Basu, Nandita B.; Calhoun, Aram J. K.; Craft, Christopher; D’Amico, Ellen; DeKeyser, Edward; Fowler, Laurie; Golden, Heather E.; Jawitz, James W.; Kalla, Peter; Kirkman, L. Katherine; Lane, Charles R.; Lang, Megan
2016-01-01
Geographically isolated wetlands (GIWs), those surrounded by uplands, exchange materials, energy, and organisms with other elements in hydrological and habitat networks, contributing to landscape functions, such as flow generation, nutrient and sediment retention, and biodiversity support. GIWs constitute most of the wetlands in many North American landscapes, provide a disproportionately large fraction of wetland edges where many functions are enhanced, and form complexes with other water bo...
Reducing pressure oscillations in discrete fluid power systems
DEFF Research Database (Denmark)
Hansen, Anders Hedegaard; Pedersen, Henrik Clemmensen
2016-01-01
Discrete fluid power systems featuring transmission lines inherently include pressure oscillations. Experimental verification of a discrete fluid power power take off system for wave energy converters has shown the cylinder pressure to oscillate as force shifts are performed. This article investi...... investigates how cylinder pressure oscillations may be reduced by shaping the valve opening trajectory without the need for closed loop pressure feedback. Furthermore the energy costs of reducing pressure oscillations are investigated....
Nonequilibrium landscape theory of neural networks.
Yan, Han; Zhao, Lei; Hu, Liang; Wang, Xidi; Wang, Erkang; Wang, Jin
2013-11-05
The brain map project aims to map out the neuron connections of the human brain. Even with all of the wirings mapped out, the global and physical understandings of the function and behavior are still challenging. Hopfield quantified the learning and memory process of symmetrically connected neural networks globally through equilibrium energy. The energy basins of attractions represent memories, and the memory retrieval dynamics is determined by the energy gradient. However, the realistic neural networks are asymmetrically connected, and oscillations cannot emerge from symmetric neural networks. Here, we developed a nonequilibrium landscape-flux theory for realistic asymmetrically connected neural networks. We uncovered the underlying potential landscape and the associated Lyapunov function for quantifying the global stability and function. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. We applied our theory to rapid-eye movement sleep cycle. We identified the key regulation factors for function through global sensitivity analysis of landscape topography against wirings, which are in good agreements with experiments.
Hirsch, M; Peinado, E; Valle, J W F
2010-01-01
We propose a new motivation for the stability of dark matter (DM). We suggest that the same non-abelian discrete flavor symmetry which accounts for the observed pattern of neutrino oscillations, spontaneously breaks to a Z2 subgroup which renders DM stable. The simplest scheme leads to a scalar doublet DM potentially detectable in nuclear recoil experiments, inverse neutrino mass hierarchy, hence a neutrinoless double beta decay rate accessible to upcoming searches, while reactor angle equal to zero gives no CP violation in neutrino oscillations.
Wuensche, Andrew
DDLab is interactive graphics software for creating, visualizing, and analyzing many aspects of Cellular Automata, Random Boolean Networks, and Discrete Dynamical Networks in general and studying their behavior, both from the time-series perspective — space-time patterns, and from the state-space perspective — attractor basins. DDLab is relevant to research, applications, and education in the fields of complexity, self-organization, emergent phenomena, chaos, collision-based computing, neural networks, content addressable memory, genetic regulatory networks, dynamical encryption, generative art and music, and the study of the abstract mathematical/physical/dynamical phenomena in their own right.
Rosen, Elias P.; Bokhart, Mark T.; Ghashghaei, H. Troy; Muddiman, David C.
2015-06-01
Analyte signal in a laser desorption/postionization scheme such as infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is strongly coupled to the degree of overlap between the desorbed plume of neutral material from a sample and an orthogonal electrospray. In this work, we systematically examine the effect of desorption conditions on IR-MALDESI response to pharmaceutical drugs and endogenous lipids in biological tissue using a design of experiments approach. Optimized desorption conditions have then been used to conduct an untargeted lipidomic analysis of whole body sagittal sections of neonate mouse. IR-MALDESI response to a wide range of lipid classes has been demonstrated, with enhanced lipid coverage received by varying the laser wavelength used for mass spectrometry imaging (MSI). Targeted MS2 imaging (MS2I) of an analyte, cocaine, deposited beneath whole body sections allowed determination of tissue-specific ion response factors, and CID fragments of cocaine were monitored to comment on wavelength-dependent internal energy deposition based on the "survival yield" method.
Directory of Open Access Journals (Sweden)
Angelika Krebs
2014-11-01
Full Text Available This philosophical paper explores the aesthetic argument for landscape conservation. The main claim is that the experience of beautiful landscapes is an essential part of the good human life. Beautiful landscapes make us feel at home in the world. Their great and irreplaceable value lies therein. To establish this claim, the concepts of landscape and “Stimmung” are clarified. It is shown how “Stimmung” (in the sense of mood is infused into landscape (as atmosphere and how we respond to it aesthetically. We respond by resonating or feeling at home. The paper ends by indicating how art can help us to better appreciate landscape beauty. This is done by way of an example from contemporary nature poetry, Michael Donhauser’s Variationen in Prosa, which begins with “Und was da war, es nahm uns an” (“And what was there accepted us”.
Energy Saver: Tips on Saving Money & Energy at Home
Energy Technology Data Exchange (ETDEWEB)
None
2017-09-01
Provides consumers with home energy and money savings tips such as insulation, weatherization, heating, cooling, water heating, energy efficient windows, landscaping, lighting, and energy efficient appliances.
Energy Savers Tips on Saving Energy& Money at Home
Energy Technology Data Exchange (ETDEWEB)
2003-06-01
Provides consumers with home energy and money savings tips such as insulation, weatherization, heating, cooling, water heating, energy efficient windows, landscaping, lighting, and energy efficient appliances
Energy Savers: Tips on Saving Money & Energy at Home
Energy Technology Data Exchange (ETDEWEB)
None
2011-12-01
Provides consumers with home energy and money savings tips such as insulation, weatherization, heating, cooling, water heating, energy efficient windows, landscaping, lighting, and energy efficient appliances.
Energy Savers: Tips on Saving Money & Energy at Home
Energy Technology Data Exchange (ETDEWEB)
None
2014-05-01
Provides consumers with home energy and money savings tips such as insulation, weatherization, heating, cooling, water heating, energy efficient windows, landscaping, lighting, and energy efficient appliances.
International Nuclear Information System (INIS)
Souza, Manoelito M. de
1997-01-01
We discuss the physical meaning and the geometric interpretation of implementation in classical field theories. The origin of infinities and other inconsistencies in field theories is traced to fields defined with support on the light cone; a finite and consistent field theory requires a light-cone generator as the field support. Then, we introduce a classical field theory with support on the light cone generators. It results on a description of discrete (point-like) interactions in terms of localized particle-like fields. We find the propagators of these particle-like fields and discuss their physical meaning, properties and consequences. They are conformally invariant, singularity-free, and describing a manifestly covariant (1 + 1)-dimensional dynamics in a (3 = 1) spacetime. Remarkably this conformal symmetry remains even for the propagation of a massive field in four spacetime dimensions. We apply this formalism to Classical electrodynamics and to the General Relativity Theory. The standard formalism with its distributed fields is retrieved in terms of spacetime average of the discrete field. Singularities are the by-products of the averaging process. This new formalism enlighten the meaning and the problem of field theory, and may allow a softer transition to a quantum theory. (author)
Do geographically isolated wetlands influence landscape functions?
Cohen, Matthew J.; Creed, Irena F.; Alexander, Laurie C.; Basu, Nandita; Calhoun, Aram J.K.; Craft, Christopher; D’Amico, Ellen; DeKeyser, Edward S.; Fowler, Laurie; Golden, Heather E.; Jawitz, James W.; Kalla, Peter; Kirkman, L. Katherine; Lane, Charles R.; Lang, Megan; Leibowitz, Scott G.; Lewis, David Bruce; Marton, John; McLaughlin, Daniel L.; Mushet, David M.; Raanan-Kiperwas, Hadas; Rains, Mark C.; Smith, Lora; Walls, Susan C.
2015-01-01
Geographically isolated wetlands (GIWs), those surrounded by uplands, exchange materials, energy, and organisms with other elements in hydrological and habitat networks, contributing to landscape functions, such as flow generation, nutrient and sediment retention, and biodiversity support. GIWs constitute most of the wetlands in many North American landscapes, provide a disproportionately large fraction of wetland edges where many functions are enhanced, and form complexes with other water bodies to create spatial and temporal heterogeneity in the timing, flow paths, and magnitude of network connectivity. These attributes signal a critical role for GIWs in sustaining a portfolio of landscape functions, but legal protections remain weak despite preferential loss from many landscapes. GIWs lack persistent surface water connections, but this condition does not imply the absence of hydrological, biogeochemical, and biological exchanges with nearby and downstream waters. Although hydrological and biogeochemical connectivity is often episodic or slow (e.g., via groundwater), hydrologic continuity and limited evaporative solute enrichment suggest both flow generation and solute and sediment retention. Similarly, whereas biological connectivity usually requires overland dispersal, numerous organisms, including many rare or threatened species, use both GIWs and downstream waters at different times or life stages, suggesting that GIWs are critical elements of landscape habitat mosaics. Indeed, weaker hydrologic connectivity with downstream waters and constrained biological connectivity with other landscape elements are precisely what enhances some GIW functions and enables others. Based on analysis of wetland geography and synthesis of wetland functions, we argue that sustaining landscape functions requires conserving the entire continuum of wetland connectivity, including GIWs.
Landscape equivalent of the shoving model
DEFF Research Database (Denmark)
Dyre, Jeppe; Olsen, Niels Boye
2004-01-01
It is shown that the shoving model expression for the average relaxation time of viscous liquids, according to which the activation energy is proportional to the instantaneous shear modulus, follows largely from a classical "landscape" estimation of barrier heights from curvature at energy minima...
Condensed landscape experience
DEFF Research Database (Denmark)
Earon, Ofri
2011-01-01
‘Re-thinking interaction between landscape and urban buildings’ participates in an interdisciplinary discourse about the theoretical and practical advantages of openly juxtaposing landscape and architecture without having one more advanced in importance. Recently, the greenification of buildings...... demands, quality of space, mixture of functions, urban complexity, public life and cultural heritage. In order to launch such an approach, an understanding of the spatial, social and environmental significance of a radical re-thinking of relationships between architecture and landscape is necessary...
The shifting beverage landscape.
Storey, Maureen
2010-04-26
STOREY, M.L. The shifting beverage landscape. PHYSIOL BEHAV, 2010. - Simultaneous lifestyle changes have occurred in the last few decades, creating an imbalance in energy intake and energy expenditure that has led to overweight and obesity. Trends in the food supply show that total daily calories available per capita increased 28% since 1970. Total energy intake among men and women has also increased dramatically since that time. Some have suggested that intake of beverages has had a disproportional impact on obesity. Data collected by the Beverage Marketing Corporation between 1988-2008 demonstrate that, in reality, fewer calories per ounce are being produced by the beverage industry. Moreover, data from the National Cancer Institute show that soft drink intake represents 5.5% of daily calories. Data from NHANES 1999-2003 vs. 2003-06 may demonstrate a shift in beverage consumption for age/gender groups, ages 6 to>60years. The beverages provided in schools have significantly changed since 2006 when the beverage industry implemented School Beverage Guidelines. This voluntary action has removed full-calorie soft drinks from participating schools across the country. This shift to lower-calorie and smaller-portion beverages in school has led to a significant decrease in total beverage calories in schools. These data support the concept that to prevent and treat obesity, public health efforts should focus on energy balance and that a narrow focus on sweetened beverages is unlikely to have any meaningful impact on this complex problem. Copyright 2010 Elsevier Inc. All rights reserved.
Discrete gradient methods for solving variational image regularisation models
International Nuclear Information System (INIS)
Grimm, V; McLachlan, Robert I; McLaren, David I; Quispel, G R W; Schönlieb, C-B
2017-01-01
Discrete gradient methods are well-known methods of geometric numerical integration, which preserve the dissipation of gradient systems. In this paper we show that this property of discrete gradient methods can be interesting in the context of variational models for image processing, that is where the processed image is computed as a minimiser of an energy functional. Numerical schemes for computing minimisers of such energies are desired to inherit the dissipative property of the gradient system associated to the energy and consequently guarantee a monotonic decrease of the energy along iterations, avoiding situations in which more computational work might lead to less optimal solutions. Under appropriate smoothness assumptions on the energy functional we prove that discrete gradient methods guarantee a monotonic decrease of the energy towards stationary states, and we promote their use in image processing by exhibiting experiments with convex and non-convex variational models for image deblurring, denoising, and inpainting. (paper)
Advances in discrete differential geometry
2016-01-01
This is one of the first books on a newly emerging field of discrete differential geometry and an excellent way to access this exciting area. It surveys the fascinating connections between discrete models in differential geometry and complex analysis, integrable systems and applications in computer graphics. The authors take a closer look at discrete models in differential geometry and dynamical systems. Their curves are polygonal, surfaces are made from triangles and quadrilaterals, and time is discrete. Nevertheless, the difference between the corresponding smooth curves, surfaces and classical dynamical systems with continuous time can hardly be seen. This is the paradigm of structure-preserving discretizations. Current advances in this field are stimulated to a large extent by its relevance for computer graphics and mathematical physics. This book is written by specialists working together on a common research project. It is about differential geometry and dynamical systems, smooth and discrete theories, ...
Poisson hierarchy of discrete strings
International Nuclear Information System (INIS)
Ioannidou, Theodora; Niemi, Antti J.
2016-01-01
The Poisson geometry of a discrete string in three dimensional Euclidean space is investigated. For this the Frenet frames are converted into a spinorial representation, the discrete spinor Frenet equation is interpreted in terms of a transfer matrix formalism, and Poisson brackets are introduced in terms of the spinor components. The construction is then generalised, in a self-similar manner, into an infinite hierarchy of Poisson algebras. As an example, the classical Virasoro (Witt) algebra that determines reparametrisation diffeomorphism along a continuous string, is identified as a particular sub-algebra, in the hierarchy of the discrete string Poisson algebra. - Highlights: • Witt (classical Virasoro) algebra is derived in the case of discrete string. • Infinite dimensional hierarchy of Poisson bracket algebras is constructed for discrete strings. • Spinor representation of discrete Frenet equations is developed.
Poisson hierarchy of discrete strings
Energy Technology Data Exchange (ETDEWEB)
Ioannidou, Theodora, E-mail: ti3@auth.gr [Faculty of Civil Engineering, School of Engineering, Aristotle University of Thessaloniki, 54249, Thessaloniki (Greece); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108, Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200, Tours (France); Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)
2016-01-28
The Poisson geometry of a discrete string in three dimensional Euclidean space is investigated. For this the Frenet frames are converted into a spinorial representation, the discrete spinor Frenet equation is interpreted in terms of a transfer matrix formalism, and Poisson brackets are introduced in terms of the spinor components. The construction is then generalised, in a self-similar manner, into an infinite hierarchy of Poisson algebras. As an example, the classical Virasoro (Witt) algebra that determines reparametrisation diffeomorphism along a continuous string, is identified as a particular sub-algebra, in the hierarchy of the discrete string Poisson algebra. - Highlights: • Witt (classical Virasoro) algebra is derived in the case of discrete string. • Infinite dimensional hierarchy of Poisson bracket algebras is constructed for discrete strings. • Spinor representation of discrete Frenet equations is developed.
Discretized representations of harmonic variables by bilateral Jacobi operators
Directory of Open Access Journals (Sweden)
Andreas Ruffing
2000-01-01
Full Text Available Starting from a discrete Heisenberg algebra we solve several representation problems for a discretized quantum oscillator in a weighted sequence space. The Schrödinger operator for a discrete harmonic oscillator is derived. The representation problem for a q-oscillator algebra is studied in detail. The main result of the article is the fact that the energy representation for the discretized momentum operator can be interpreted as follows: It allows to calculate quantum properties of a large number of non-interacting harmonic oscillators at the same time. The results can be directly related to current research on squeezed laser states in quantum optics. They reveal and confirm the observation that discrete versions of continuum Schrodinger operators allow more structural freedom than their continuum analogs do.
Our Common Landscapes For The Future
DEFF Research Database (Denmark)
Brandt, Jesper
2017-01-01
Foreword for Marc Antrop and Veerle van Eetvelde: Landscape Perspectives – The Holistic Nature of Landscapes Our common landscapes for the future by Jesper Brandt The solution of the ecological crisis through a transformation towards sustainable development is the most urgent challenge in our time....... It is not just a question of CO2 and conversion toward renewable energy. The reestablishment and conscious development of our common landscapes at all spatial scales for the combined benefits of biodiversity, our cultural heritage and the preservation and development of ecosystem services will probably...... be the most comprehensive and necessary social task in the future, if a conversion towards a sustainable development shall succeed in due time. This is so because it will be necessary to ensure that the potential material wealth of modern society will be transformed into a good, fruitful and healthy life...
Aritz Ruiz-Gonzalez; Samuel A. Cushman; Maria Jose Madeira; Ettore Randi; Benjamin J. Gomez-Moliner
2015-01-01
Landscape genetics provides a valuable framework to understand how landscape features influence gene flow and to disentangle the factors that lead to discrete and/or clinal population structure. Here, we attempt to differentiate between these processes in a forest-dwelling small carnivore [European pine marten (Martes martes)]. Specifically, we used...
Principles of discrete time mechanics
Jaroszkiewicz, George
2014-01-01
Could time be discrete on some unimaginably small scale? Exploring the idea in depth, this unique introduction to discrete time mechanics systematically builds the theory up from scratch, beginning with the historical, physical and mathematical background to the chronon hypothesis. Covering classical and quantum discrete time mechanics, this book presents all the tools needed to formulate and develop applications of discrete time mechanics in a number of areas, including spreadsheet mechanics, classical and quantum register mechanics, and classical and quantum mechanics and field theories. A consistent emphasis on contextuality and the observer-system relationship is maintained throughout.
Dark discrete gauge symmetries
International Nuclear Information System (INIS)
Batell, Brian
2011-01-01
We investigate scenarios in which dark matter is stabilized by an Abelian Z N discrete gauge symmetry. Models are surveyed according to symmetries and matter content. Multicomponent dark matter arises when N is not prime and Z N contains one or more subgroups. The dark sector interacts with the visible sector through the renormalizable kinetic mixing and Higgs portal operators, and we highlight the basic phenomenology in these scenarios. In particular, multiple species of dark matter can lead to an unconventional nuclear recoil spectrum in direct detection experiments, while the presence of new light states in the dark sector can dramatically affect the decays of the Higgs at the Tevatron and LHC, thus providing a window into the gauge origin of the stability of dark matter.
Fanta, J.; Siepel, H.
2010-01-01
Man has had a complex relationship with inland drift sands through the ages. For some centuries these landscapes were seen as a threat to society, especially agriculture and housing. At present we conserve these landscapes as important Natura 2000 priority habitats. In this book you may find these
Principles of landscape architecture
Nijhuis, S.
2013-01-01
The Department of Urbanism at the Faculty of Architecture and Built Environment, TU Delft considers urbanism as a planning and design oriented activity towards urban and rural landscapes. It aims to enhance, restore or create landscapes from a perspective of sustainable development, so as to guide,
Nature and landscape protection
International Nuclear Information System (INIS)
Klinda, J.; Lieskovska, Z.
1998-01-01
In accordance with National Council of the Slovak Republic Act N. 287/1994 Coll. on Nature and Landscape Protection, the system of complex nature landscape protection has been designed based on five levels of protection. Categories of protected areas as well as cultural monuments in the Slovak Republic are reviewed.Slovak contribution to the world heritage is included
Globalization and Landscape Architecture
Robert R. Hewitt
2014-01-01
The literature review examines globalization and landscape architecture as discourse, samples its various meanings, and proposes methods to identify and contextualize its specific literature. Methodologically, the review surveys published articles and books by leading authors and within the WorldCat.org Database associated with landscape architecture and globalization, analyzing survey results for comprehensive concept...
Glossary on agricultural landscapes.
Kruse, A.; Centeri, C.; Renes, J.; Roth, M.; Printsman, A.; Palang, H.; Benito Jorda, M.-D.; Verlarde, M.D.; Kruckenberg, H.
2010-01-01
T he following glossary of terms related to the European agricultural landscape shall serve as a common basis for all parties, working in or on agricultural landscapes. Some of the terms are quite common and sometimes used in our every day language, but they often have different meanings in
Directory of Open Access Journals (Sweden)
Frederick Steiner
2014-03-01
Full Text Available Cities present significant opportunities for new landscape perspectives that can help inform conservation and development decisions. Early in the twenty-first century, the majority of the planet’s population became urban as more people lived in city-regions for the first time in our history. As the global population increases, so does this urbanization. The environmental challenges of population and urban growth are profound. Landscapes represent a synthesis of natural and cultural processes. Cities are certainly cultural phenomena. Historically, cities provided refuge from nature. The expanding field of urban ecology, coupled with landscape ecology, can enhance how the dual natural and cultural dimensions of landscapes in cities are understood. Furthermore, concepts such as ecosystem services and green infrastructure are proving useful for urban landscape planning and design. Examples from Dayton, Ohio; Brooklyn, New York; and Austin, Texas are presented.
An extended discrete gradient formula for oscillatory Hamiltonian systems
International Nuclear Information System (INIS)
Liu Kai; Shi Wei; Wu Xinyuan
2013-01-01
In this paper, incorporating the idea of the discrete gradient method into the extended Runge–Kutta–Nyström integrator, we derive and analyze an extended discrete gradient formula for the oscillatory Hamiltonian system with the Hamiltonian H(p,q)= 1/2 p T p+ 1/2 q T Mq+U(q), where q:R→R d represents generalized positions, p:R→R d represents generalized momenta and M is an element of R dxd is a symmetric and positive semi-definite matrix. The solution of this system is a nonlinear oscillator. Basically, many nonlinear oscillatory mechanical systems with a partitioned Hamiltonian function lend themselves to this approach. The extended discrete gradient formula presented in this paper exactly preserves the energy H(p, q). We derive some properties of the new formula. The convergence is analyzed for the implicit schemes based on the discrete gradient formula, and it turns out that the convergence of the implicit schemes based on the extended discrete gradient formula is independent of ‖M‖, which is a significant property for the oscillatory Hamiltonian system. Thus, it transpires that a larger step size can be chosen for the new energy-preserving schemes than that for the traditional discrete gradient methods when applied to the oscillatory Hamiltonian system. Illustrative examples show the competence and efficiency of the new schemes in comparison with the traditional discrete gradient methods in the scientific literature. (paper)
Nonequilibrium landscape theory of neural networks
Yan, Han; Zhao, Lei; Hu, Liang; Wang, Xidi; Wang, Erkang; Wang, Jin
2013-01-01
The brain map project aims to map out the neuron connections of the human brain. Even with all of the wirings mapped out, the global and physical understandings of the function and behavior are still challenging. Hopfield quantified the learning and memory process of symmetrically connected neural networks globally through equilibrium energy. The energy basins of attractions represent memories, and the memory retrieval dynamics is determined by the energy gradient. However, the realistic neural networks are asymmetrically connected, and oscillations cannot emerge from symmetric neural networks. Here, we developed a nonequilibrium landscape–flux theory for realistic asymmetrically connected neural networks. We uncovered the underlying potential landscape and the associated Lyapunov function for quantifying the global stability and function. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. We applied our theory to rapid-eye movement sleep cycle. We identified the key regulation factors for function through global sensitivity analysis of landscape topography against wirings, which are in good agreements with experiments. PMID:24145451
Control of Discrete Event Systems
Smedinga, Rein
1989-01-01
Systemen met discrete gebeurtenissen spelen in vele gebieden een rol. In dit proefschrift staat de volgorde van gebeurtenissen centraal en worden tijdsaspecten buiten beschouwing gelaten. In dat geval kunnen systemen met discrete gebeurtenissen goed worden gemodelleerd door gebruik te maken van
Discrete Mathematics and Its Applications
Oxley, Alan
2010-01-01
The article gives ideas that lecturers of undergraduate Discrete Mathematics courses can use in order to make the subject more interesting for students and encourage them to undertake further studies in the subject. It is possible to teach Discrete Mathematics with little or no reference to computing. However, students are more likely to be…
Discrete Mathematics and Curriculum Reform.
Kenney, Margaret J.
1996-01-01
Defines discrete mathematics as the mathematics necessary to effect reasoned decision making in finite situations and explains how its use supports the current view of mathematics education. Discrete mathematics can be used by curriculum developers to improve the curriculum for students of all ages and abilities. (SLD)
Connections on discrete fibre bundles
International Nuclear Information System (INIS)
Manton, N.S.; Cambridge Univ.
1987-01-01
A new approach to gauge fields on a discrete space-time is proposed, in which the fundamental object is a discrete version of a principal fibre bundle. If the bundle is twisted, the gauge fields are topologically non-trivial automatically. (orig.)
Hargitai, H.
INTRODUCTION Landscape is one of the most often used category in physical ge- ography. The term "landshap" was introduced by Dutch painters in the 15-16th cen- tury. [1] The elements that build up a landscape (or environment) on Earth consists of natural (biogenic and abiogenic - lithologic, atmospheric, hydrologic) and artificial (antropogenic) factors. Landscape is a complex system of these different elements. The same lithology makes different landscapes under different climatic conditions. If the same conditions are present, the same landscape type will appear. Landscapes build up a hierarchic system and cover the whole surface. On Earth, landscapes can be classified and qualified according to their characteristics: relief forms (morphology), and its potential economic value. Aesthetic and subjective parameters can also be considered. Using the data from landers and data from orbiters we can now classify planetary landscapes (these can be used as geologic mapping units as well). By looking at a unknown landscape, we can determine the processes that created it and its development history. This was the case in the Pathfinder/Sojourner panoramas. [2]. DISCUSSION Planetary landscape evolution. We can draw a raw landscape develop- ment history by adding the different landscape building elements to each other. This has a strong connection with the planet's thermal evolution (age of the planet or the present surface materials) and with orbital parameters (distance from the central star, orbit excentricity etc). This way we can build a complex system in which we use differ- ent evolutional stages of lithologic, atmospheric, hydrologic and biogenic conditions which determine the given - Solar System or exoplanetary - landscape. Landscape elements. "Simple" landscapes can be found on asteroids: no linear horizon is present (not differentiated body, only impact structures), no atmosphere (therefore no atmospheric scattering - black sky as part of the landscape) and no