Specificity and affinity quantification of flexible recognition from underlying energy landscape topography.

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.

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

Science.gov (United States)

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.

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.

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.

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.

Surfing the free energy landscape of flavodoxin folding

NARCIS (Netherlands)

Bollen, Y.J.M.

2004-01-01

The research described in this thesis has been carried out to obtain a better understanding of the fundamental rules describing protein folding. Protein folding is the process in which a linear chain of amino acids contracts to a compact state in which it is active. Flavodoxin from Azotobacter

Visualization of protein folding funnels in lattice models.

Directory of Open Access Journals (Sweden)

Antonio B Oliveira

Full Text Available Protein folding occurs in a very high dimensional phase space with an exponentially large number of states, and according to the energy landscape theory it exhibits a topology resembling a funnel. In this statistical approach, the folding mechanism is unveiled by describing the local minima in an effective one-dimensional representation. Other approaches based on potential energy landscapes address the hierarchical structure of local energy minima through disconnectivity graphs. In this paper, we introduce a metric to describe the distance between any two conformations, which also allows us to go beyond the one-dimensional representation and visualize the folding funnel in 2D and 3D. In this way it is possible to assess the folding process in detail, e.g., by identifying the connectivity between conformations and establishing the paths to reach the native state, in addition to regions where trapping may occur. Unlike the disconnectivity maps method, which is based on the kinetic connections between states, our methodology is based on structural similarities inferred from the new metric. The method was developed in a 27-mer protein lattice model, folded into a 3×3×3 cube. Five sequences were studied and distinct funnels were generated in an analysis restricted to conformations from the transition-state to the native configuration. Consistent with the expected results from the energy landscape theory, folding routes can be visualized to probe different regions of the phase space, as well as determine the difficulty in folding of the distinct sequences. Changes in the landscape due to mutations were visualized, with the comparison between wild and mutated local minima in a single map, which serves to identify different trapping regions. The extension of this approach to more realistic models and its use in combination with other approaches are discussed.

Energy landscapes in a crowded world

NARCIS (Netherlands)

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 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'.

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

Energy Landscapes: From Protein Folding to Molecular Assembly

Science.gov (United States)

Databases National Security Education Center (NSEC) Center for Nonlinear Studies Engineering Institute assembly is very common in biology and in nanotechnology. Simple examples of self-assembly are the folding efflux pump machinery, ATP synthase, the ribosome, and many others. In nanotechnology, self-assembly has

Self-folding origami at any energy scale

Science.gov (United States)

Pinson, Matthew B.; Stern, Menachem; Carruthers Ferrero, Alexandra; Witten, Thomas A.; Chen, Elizabeth; Murugan, Arvind

2017-05-01

Programmable stiff sheets with a single low-energy folding motion have been sought in fields ranging from the ancient art of origami to modern meta-materials research. Despite such attention, only two extreme classes of crease patterns are usually studied; special Miura-Ori-based zero-energy patterns, in which crease folding requires no sheet bending, and random patterns with high-energy folding, in which the sheet bends as much as creases fold. We present a physical approach that allows systematic exploration of the entire space of crease patterns as a function of the folding energy. Consequently, we uncover statistical results in origami, finding the entropy of crease patterns of given folding energy. Notably, we identify three classes of Mountain-Valley choices that have widely varying `typical' folding energies. Our work opens up a wealth of experimentally relevant self-folding origami designs not reliant on Miura-Ori, the Kawasaki condition or any special symmetry in space.

Exploring Energy Landscapes

Science.gov (United States)

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.

Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures

International Nuclear Information System (INIS)

Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor; Onuchic, José N.; Schug, Alexander

2015-01-01

The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimal frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism

Energy landscapes, landscapes in transition. How to prepare one's territory to the deployment of renewable energies

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)

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.

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.

Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch

Science.gov (United States)

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.

Recent developments in the theory of protein folding: searching for the global energy minimum.

Science.gov (United States)

Scheraga, H A

1996-04-16

Statistical mechanical theories and computer simulation are being used to gain an understanding of the fundamental features of protein folding. A major obstacle in the computation of protein structures is the multiple-minima problem arising from the existence of many local minima in the multidimensional energy landscape of the protein. This problem has been surmounted for small open-chain and cyclic peptides, and for regular-repeating sequences of models of fibrous proteins. Progress is being made in resolving this problem for globular proteins.

An expanded view of the protein folding landscape of PDZ domains

DEFF Research Database (Denmark)

Hultqvist, Greta; Pedersen, Søren W; Chi, Celestine N.

2012-01-01

state. In light of these results, we have re-analyzed previous folding data on PDZ domains and present a unified folding mechanism with three distinct transition states separated by two high-energy intermediates. Our data show that sequence composition tunes the relative stabilities of folding...

New interaction paths in the energy landscape: the role of local energy initiatives

OpenAIRE

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...

Energy landscapes shape animal movement ecology.

Science.gov (United States)

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.

The mechanisms for filling carbon nanotubes with molten salts: carbon nanotubes as energy landscape filters

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.

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.

Discriminating trpzip2 and trpzip4 peptides’ folding landscape using the two-dimensional infrared spectroscopy: A simulation study

International Nuclear Information System (INIS)

Wu, Tianmin; Zhang, Ruiting; Li, Huanhuan; Zhuang, Wei; Yang, Lijiang

2014-01-01

We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two β-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB OBC implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors

Computational design of RNAs with complex energy landscapes.

Science.gov (United States)

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.

Energy landscape of social balance.

Science.gov (United States)

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 Landscape of Social Balance

Science.gov (United States)

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 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)

Sustainable energy landscapes : designing, planning, and development

NARCIS (Netherlands)

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 landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

Directory of Open Access Journals (Sweden)

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.

Probing the energy landscape of alanine dipeptide and decalanine using temperature as a tunable parameter in molecular dynamics

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)

Learning free energy landscapes using artificial neural networks.

Science.gov (United States)

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

Science.gov (United States)

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.

Single-molecule studies of the Im7 folding landscape.

Science.gov (United States)

Pugh, Sara D; Gell, Christopher; Smith, D Alastair; Radford, Sheena E; Brockwell, David J

2010-04-23

Under appropriate conditions, the four-helical Im7 (immunity protein 7) folds from an ensemble of unfolded conformers to a highly compact native state via an on-pathway intermediate. Here, we investigate the unfolded, intermediate, and native states populated during folding using diffusion single-pair fluorescence resonance energy transfer by measuring the efficiency of energy transfer (or proximity or P ratio) between pairs of fluorophores introduced into the side chains of cysteine residues placed in the center of helices 1 and 4, 1 and 3, or 2 and 4. We show that while the native states of each variant give rise to a single narrow distribution with high P values, the distributions of the intermediates trapped at equilibrium (denoted I(eqm)) are fitted by two Gaussian distributions. Modulation of the folding conditions from those that stabilize the intermediate to those that destabilize the intermediate enabled the distribution of lower P value to be assigned to the population of the unfolded ensemble in equilibrium with the intermediate state. The reduced stability of the I(eqm) variants allowed analysis of the effect of denaturant concentration on the compaction and breadth of the unfolded state ensemble to be quantified from 0 to 6 M urea. Significant compaction is observed as the concentration of urea is decreased in both the presence and absence of sodium sulfate, as previously reported for a variety of proteins. In the presence of Na(2)SO(4) in 0 M urea, the P value of the unfolded state ensemble approaches that of the native state. Concurrent with compaction, the ensemble displays increased peak width of P values, possibly reflecting a reduction in the rate of conformational exchange among iso-energetic unfolded, but compact conformations. The results provide new insights into the initial stages of folding of Im7 and suggest that the unfolded state is highly conformationally constrained at the outset of folding. (c) 2010 Elsevier Ltd. All rights reserved.

New interaction paths in the energy landscape: the role of local energy initiatives

NARCIS (Netherlands)

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

Impact of hydrodynamic interactions on protein folding rates depends on temperature

Science.gov (United States)

Zegarra, Fabio C.; Homouz, Dirar; Eliaz, Yossi; Gasic, Andrei G.; Cheung, Margaret S.

2018-03-01

We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collective motion with a single reaction coordinate across a folding barrier, we compared the kinetic effects of HI on the folding rates of two protein models that use a chain of single beads with distinctive topologies: a 64-residue α /β chymotrypsin inhibitor 2 (CI2) protein, and a 57-residue β -barrel α -spectrin Src-homology 3 domain (SH3) protein. When comparing the protein folding kinetics simulated with Brownian dynamics in the presence of HI to that in the absence of HI, we find that the effect of HI on protein folding appears to have a "crossover" behavior about the folding temperature. This means that at a temperature greater than the folding temperature, the enhanced friction from the hydrodynamic solvents between the beads in an unfolded configuration results in lowered folding rate; conversely, at a temperature lower than the folding temperature, HI accelerates folding by the backflow of solvent toward the folded configuration of a protein. Additionally, the extent of acceleration depends on the topology of a protein: for a protein like CI2, where its folding nucleus is rather diffuse in a transition state, HI channels the formation of contacts by favoring a major folding pathway in a complex free energy landscape, thus accelerating folding. For a protein like SH3, where its folding nucleus is already specific and less diffuse, HI matters less at a temperature lower than the folding temperature. Our findings provide further theoretical insight to protein folding kinetic experiments and simulations.

Energy-landscape Nexus: Advancing a conceptual framework for the design of sustainable energy landscapes

NARCIS (Netherlands)

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

Examining a Thermodynamic Order Parameter of Protein Folding.

Science.gov (United States)

Chong, Song-Ho; Ham, Sihyun

2018-05-08

Dimensionality reduction with a suitable choice of order parameters or reaction coordinates is commonly used for analyzing high-dimensional time-series data generated by atomistic biomolecular simulations. So far, geometric order parameters, such as the root mean square deviation, fraction of native amino acid contacts, and collective coordinates that best characterize rare or large conformational transitions, have been prevailing in protein folding studies. Here, we show that the solvent-averaged effective energy, which is a thermodynamic quantity but unambiguously defined for individual protein conformations, serves as a good order parameter of protein folding. This is illustrated through the application to the folding-unfolding simulation trajectory of villin headpiece subdomain. We rationalize the suitability of the effective energy as an order parameter by the funneledness of the underlying protein free energy landscape. We also demonstrate that an improved conformational space discretization is achieved by incorporating the effective energy. The most distinctive feature of this thermodynamic order parameter is that it works in pointing to near-native folded structures even when the knowledge of the native structure is lacking, and the use of the effective energy will also find applications in combination with methods of protein structure prediction.

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

Science.gov (United States)

2015-01-01

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

Mitigation/Adaptation: landscape architecture meets sustainable energy transition

NARCIS (Netherlands)

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

Guiding the folding pathway of DNA origami.

Science.gov (United States)

Dunn, Katherine E; Dannenberg, Frits; Ouldridge, Thomas E; Kwiatkowska, Marta; Turberfield, Andrew J; Bath, Jonathan

2015-09-03

DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

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

Science.gov (United States)

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.

Two states or not two states: Single-molecule folding studies of protein L

Science.gov (United States)

Aviram, Haim Yuval; Pirchi, Menahem; Barak, Yoav; Riven, Inbal; Haran, Gilad

2018-03-01

Experimental tools of increasing sophistication have been employed in recent years to study protein folding and misfolding. Folding is considered a complex process, and one way to address it is by studying small proteins, which seemingly possess a simple energy landscape with essentially only two stable states, either folded or unfolded. The B1-IgG binding domain of protein L (PL) is considered a model two-state folder, based on measurements using a wide range of experimental techniques. We applied single-molecule fluorescence resonance energy transfer (FRET) spectroscopy in conjunction with a hidden Markov model analysis to fully characterize the energy landscape of PL and to extract the kinetic properties of individual molecules of the protein. Surprisingly, our studies revealed the existence of a third state, hidden under the two-state behavior of PL due to its small population, ˜7%. We propose that this minority intermediate involves partial unfolding of the two C-terminal β strands of PL. Our work demonstrates that single-molecule FRET spectroscopy can be a powerful tool for a comprehensive description of the folding dynamics of proteins, capable of detecting and characterizing relatively rare metastable states that are difficult to observe in ensemble studies.

Evaluating the landscape impact of renewable energy plants

Science.gov (United States)

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

Kinetic partitioning mechanism of HDV ribozyme folding

Energy Technology Data Exchange (ETDEWEB)

Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: wbzhang@whu.edu.cn [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

2014-01-14

RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

Energy Landscapes for the Self-Assembly of Supramolecular Polyhedra

Science.gov (United States)

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.

The effects of landscaping on the residential cooling energy

Science.gov (United States)

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.

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.

Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry

Science.gov (United States)

Vander Meulen, Kirk A.; Butcher, Samuel E.

2012-01-01

A novel isothermal titration calorimetry (ITC) method was applied to investigate RNA helical packing driven by the GAAA tetraloop–receptor interaction in magnesium and potassium solutions. Both the kinetics and thermodynamics were obtained in individual ITC experiments, and analysis of the kinetic data over a range of temperatures provided Arrhenius activation energies (ΔH‡) and Eyring transition state entropies (ΔS‡). The resulting rich dataset reveals strongly contrasting kinetic and thermodynamic profiles for this RNA folding system when stabilized by potassium versus magnesium. In potassium, association is highly exothermic (ΔH25°C = −41.6 ± 1.2 kcal/mol in 150 mM KCl) and the transition state is enthalpically barrierless (ΔH‡ = −0.6 ± 0.5). These parameters are sigificantly positively shifted in magnesium (ΔH25°C = −20.5 ± 2.1 kcal/mol, ΔH‡ = 7.3 ± 2.2 kcal/mol in 0.5 mM MgCl2). Mixed salt solutions approximating physiological conditions exhibit an intermediate thermodynamic character. The cation-dependent thermodynamic landscape may reflect either a salt-dependent unbound receptor conformation, or alternatively and more generally, it may reflect a small per-cation enthalpic penalty associated with folding-coupled magnesium uptake. PMID:22058128

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

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.

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.

Combinatorial pattern discovery approach for the folding trajectory analysis of a beta-hairpin.

Directory of Open Access Journals (Sweden)

Laxmi Parida

2005-06-01

Full Text Available The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity c in RO((N + nm log n, where N is the size of the output patterns and (n x m is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1 The method recovers states previously obtained by visually analyzing free energy surfaces. (2 It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3 The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the

Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a beta-Hairpin.

Directory of Open Access Journals (Sweden)

2005-06-01

Full Text Available The study of protein folding mechanisms continues to be one of the most challenging problems in computational biology. Currently, the protein folding mechanism is often characterized by calculating the free energy landscape versus various reaction coordinates, such as the fraction of native contacts, the radius of gyration, RMSD from the native structure, and so on. In this paper, we present a combinatorial pattern discovery approach toward understanding the global state changes during the folding process. This is a first step toward an unsupervised (and perhaps eventually automated approach toward identification of global states. The approach is based on computing biclusters (or patterned clusters-each cluster is a combination of various reaction coordinates, and its signature pattern facilitates the computation of the Z-score for the cluster. For this discovery process, we present an algorithm of time complexity cinRO((N + nm log n, where N is the size of the output patterns and (n x m is the size of the input with n time frames and m reaction coordinates. To date, this is the best time complexity for this problem. We next apply this to a beta-hairpin folding trajectory and demonstrate that this approach extracts crucial information about protein folding intermediate states and mechanism. We make three observations about the approach: (1 The method recovers states previously obtained by visually analyzing free energy surfaces. (2 It also succeeds in extracting meaningful patterns and structures that had been overlooked in previous works, which provides a better understanding of the folding mechanism of the beta-hairpin. These new patterns also interconnect various states in existing free energy surfaces versus different reaction coordinates. (3 The approach does not require calculating the free energy values, yet it offers an analysis comparable to, and sometimes better than, the methods that use free energy landscapes, thus validating the

Ideal glass transitions in thin films: An energy landscape perspective

Science.gov (United States)

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.

How animals distribute themselves in space: variable energy landscapes

OpenAIRE

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...

Sparse RNA folding revisited: space-efficient minimum free energy structure prediction.

Science.gov (United States)

Will, Sebastian; Jabbari, Hosna

2016-01-01

RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space efficiency is of even greater concern, particularly for long RNA sequences. So far, space-efficient sparsified RNA folding with fold reconstruction was solved only for simple base-pair-based pseudo-energy models. Here, we revisit the problem of space-efficient free energy minimization. Whereas the space-efficient minimization of the free energy has been sketched before, the reconstruction of the optimum structure has not even been discussed. We show that this reconstruction is not possible in trivial extension of the method for simple energy models. Then, we present the time- and space-efficient sparsified free energy minimization algorithm SparseMFEFold that guarantees MFE structure prediction. In particular, this novel algorithm provides efficient fold reconstruction based on dynamically garbage-collected trace arrows. The complexity of our algorithm depends on two parameters, the number of candidates Z and the number of trace arrows T; both are bounded by [Formula: see text], but are typically much smaller. The time complexity of RNA folding is reduced from [Formula: see text] to [Formula: see text]; the space complexity, from [Formula: see text] to [Formula: see text]. Our empirical results show more than 80 % space savings over RNAfold [Vienna RNA package] on the long RNAs from the RNA STRAND database (≥2500 bases). The presented technique is intentionally generalizable to complex prediction algorithms; due to their high space demands, algorithms like pseudoknot prediction and RNA-RNA-interaction prediction are expected to profit even stronger than "standard" MFE folding. SparseMFEFold is free

Analysis of the free-energy surface of proteins from reversible folding simulations.

Directory of Open Access Journals (Sweden)

Lucy R Allen

2009-07-01

Full Text Available Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

Membranes: A Variety of Energy Landscapes for Many Transfer Opportunities.

Science.gov (United States)

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.

Transferable coarse-grained potential for de novo protein folding and design.

Directory of Open Access Journals (Sweden)

Ivan Coluzza

Full Text Available Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here we provide evidence of how a novel parametrization of the Caterpillar model may be used for both quantitative protein design and folding. With computer simulations it is shown that, for a large set of real protein structures, the model produces designed sequences with similar physical properties to the corresponding natural occurring sequences. The designed sequences require further experimental testing. For an independent set of proteins, previously used as benchmark, the correct folded structure of both the designed and the natural sequences is also demonstrated. The equilibrium folding properties are characterized by free energy calculations. The resulting free energy profiles not only are consistent among natural and designed proteins, but also show a remarkable precision when the folded structures are compared to the experimentally determined ones. Ultimately, the updated Caterpillar model is unique in the combination of its fundamental three features: its simplicity, its ability to produce natural foldable designed sequences, and its structure prediction precision. It is also remarkable that low frustration sequences can be obtained with such a simple and universal design procedure, and that the folding of natural proteins shows funnelled free energy landscapes without the need of any potentials based on the native structure.

Integrated visions (part II): Envisioning Sustainable Energy Landscapes

NARCIS (Netherlands)

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

Shedding Light on Protein Folding, Structural and Functional Dynamics by Single Molecule Studies

Directory of Open Access Journals (Sweden)

Krutika Bavishi

2014-11-01

Full Text Available The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.

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

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)

Ideal glass transitions in thin films: An energy landscape perspective

OpenAIRE

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...

Energy landscapes in proteins and glasses

Science.gov (United States)

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

Pharmacological chaperone reshapes the energy landscape for folding and aggregation of the prion protein

Science.gov (United States)

Gupta, Amar Nath; Neupane, Krishna; Rezajooei, Negar; Cortez, Leonardo M.; Sim, Valerie L.; Woodside, Michael T.

2016-06-01

The development of small-molecule pharmacological chaperones as therapeutics for protein misfolding diseases has proven challenging, partly because their mechanism of action remains unclear. Here we study Fe-TMPyP, a tetrapyrrole that binds to the prion protein PrP and inhibits misfolding, examining its effects on PrP folding at the single-molecule level with force spectroscopy. Single PrP molecules are unfolded with and without Fe-TMPyP present using optical tweezers. Ligand binding to the native structure increases the unfolding force significantly and alters the transition state for unfolding, making it more brittle and raising the barrier height. Fe-TMPyP also binds the unfolded state, delaying native refolding. Furthermore, Fe-TMPyP binding blocks the formation of a stable misfolded dimer by interfering with intermolecular interactions, acting in a similar manner to some molecular chaperones. The ligand thus promotes native folding by stabilizing the native state while also suppressing interactions driving aggregation.

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.

The relative importance of physical and biological energy in landscape evolution

Science.gov (United States)

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

RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry.

Science.gov (United States)

Horesh, Yair; Wexler, Ydo; Lebenthal, Ilana; Ziv-Ukelson, Michal; Unger, Ron

2009-03-04

Scanning large genomes with a sliding window in search of locally stable RNA structures is a well motivated problem in bioinformatics. Given a predefined window size L and an RNA sequence S of size N (L free energy (MFE) for the folding of each of the L-sized substrings of S. The consecutive windows folding problem can be naively solved in O(NL3) by applying any of the classical cubic-time RNA folding algorithms to each of the N-L windows of size L. Recently an O(NL2) solution for this problem has been described. Here, we describe and implement an O(NLpsi(L)) engine for the consecutive windows folding problem, where psi(L) is shown to converge to O(1) under the assumption of a standard probabilistic polymer folding model, yielding an O(L) speedup which is experimentally confirmed. Using this tool, we note an intriguing directionality (5'-3' vs. 3'-5') folding bias, i.e. that the minimal free energy (MFE) of folding is higher in the native direction of the DNA than in the reverse direction of various genomic regions in several organisms including regions of the genomes that do not encode proteins or ncRNA. This bias largely emerges from the genomic dinucleotide bias which affects the MFE, however we see some variations in the folding bias in the different genomic regions when normalized to the dinucleotide bias. We also present results from calculating the MFE landscape of a mouse chromosome 1, characterizing the MFE of the long ncRNA molecules that reside in this chromosome. The efficient consecutive windows folding engine described in this paper allows for genome wide scans for ncRNA molecules as well as large-scale statistics. This is implemented here as a software tool, called RNAslider, and applied to the scanning of long chromosomes, leading to the observation of features that are visible only on a large scale.

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

Energy Landscapes of Folding Chromosomes

Science.gov (United States)

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.

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.

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.

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

Force generation by titin folding.

Science.gov (United States)

Mártonfalvi, Zsolt; Bianco, Pasquale; Naftz, Katalin; Ferenczy, György G; Kellermayer, Miklós

2017-07-01

Titin is a giant protein that provides elasticity to muscle. As the sarcomere is stretched, titin extends hierarchically according to the mechanics of its segments. Whether titin's globular domains unfold during this process and how such unfolded domains might contribute to muscle contractility are strongly debated. To explore the force-dependent folding mechanisms, here we manipulated skeletal-muscle titin molecules with high-resolution optical tweezers. In force-clamp mode, after quenching the force (force trace contained rapid fluctuations and a gradual increase of average force, indicating that titin can develop force via dynamic transitions between its structural states en route to the native conformation. In 4 M urea, which destabilizes H-bonds hence the consolidated native domain structure, the net force increase disappeared but the fluctuations persisted. Thus, whereas net force generation is caused by the ensemble folding of the elastically-coupled domains, force fluctuations arise due to a dynamic equilibrium between unfolded and molten-globule states. Monte-Carlo simulations incorporating a compact molten-globule intermediate in the folding landscape recovered all features of our nanomechanics results. The ensemble molten-globule dynamics delivers significant added contractility that may assist sarcomere mechanics, and it may reduce the dissipative energy loss associated with titin unfolding/refolding during muscle contraction/relaxation cycles. © 2017 The Protein Society.

Cache and energy efficient algorithms for Nussinov's RNA Folding.

Science.gov (United States)

Zhao, Chunchun; Sahni, Sartaj

2017-12-06

An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implementations of Nussinov's classical RNA folding algorithm have been proposed. Our focus is to obtain run time and energy efficiency by reducing the number of cache misses. Three cache-efficient algorithms, ByRow, ByRowSegment and ByBox, for Nussinov's RNA folding are developed. Using a simple LRU cache model, we show that the Classical algorithm of Nussinov has the highest number of cache misses followed by the algorithms Transpose (Li et al.), ByRow, ByRowSegment, and ByBox (in this order). Extensive experiments conducted on four computational platforms-Xeon E5, AMD Athlon 64 X2, Intel I7 and PowerPC A2-using two programming languages-C and Java-show that our cache efficient algorithms are also efficient in terms of run time and energy. Our benchmarking shows that, depending on the computational platform and programming language, either ByRow or ByBox give best run time and energy performance. The C version of these algorithms reduce run time by as much as 97.2% and energy consumption by as much as 88.8% relative to Classical and by as much as 56.3% and 57.8% relative to Transpose. The Java versions reduce run time by as much as 98.3% relative to Classical and by as much as 75.2% relative to Transpose. Transpose achieves run time and energy efficiency at the expense of memory as it takes twice the memory required by Classical. The memory required by ByRow, ByRowSegment, and ByBox is the same as that of Classical. As a result, using the same amount of memory, the algorithms proposed by us can solve problems up to 40% larger than those solvable by Transpose.

Direct design of an energy landscape with bistable DNA origami mechanisms.

Science.gov (United States)

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.

Incorporating Renewable Energy Science in Regional Landscape Design: Results from a Competition in The Netherlands

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.

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.

Energy Savers: Cool Summer Tips

International Nuclear Information System (INIS)

Miller, M.

2001-01-01

A tri-fold brochure addressing energy-saving tips for homeowners ranging from low- or no-cost suggestions to higher cost suggestions for longer-term savings. Cooling, windows, weatherizing, and landscaping are addressed

Insights into the fold organization of TIM barrel from interaction energy based structure networks.

Science.gov (United States)

Vijayabaskar, M S; Vishveshwara, Saraswathi

2012-01-01

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or "sequence conservation" as the basis for their understanding. Recently "interaction energy" based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the "interaction conservation" viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

Adaptive local learning in sampling based motion planning for protein folding.

Science.gov (United States)

Ekenna, Chinwe; Thomas, Shawna; Amato, Nancy M

2016-08-01

Simulating protein folding motions is an important problem in computational biology. Motion planning algorithms, such as Probabilistic Roadmap Methods, have been successful in modeling the folding landscape. Probabilistic Roadmap Methods and variants contain several phases (i.e., sampling, connection, and path extraction). Most of the time is spent in the connection phase and selecting which variant to employ is a difficult task. Global machine learning has been applied to the connection phase but is inefficient in situations with varying topology, such as those typical of folding landscapes. We develop a local learning algorithm that exploits the past performance of methods within the neighborhood of the current connection attempts as a basis for learning. It is sensitive not only to different types of landscapes but also to differing regions in the landscape itself, removing the need to explicitly partition the landscape. We perform experiments on 23 proteins of varying secondary structure makeup with 52-114 residues. We compare the success rate when using our methods and other methods. We demonstrate a clear need for learning (i.e., only learning methods were able to validate against all available experimental data) and show that local learning is superior to global learning producing, in many cases, significantly higher quality results than the other methods. We present an algorithm that uses local learning to select appropriate connection methods in the context of roadmap construction for protein folding. Our method removes the burden of deciding which method to use, leverages the strengths of the individual input methods, and it is extendable to include other future connection methods.

When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches.

Science.gov (United States)

Muñoz, Victor; Cerminara, Michele

2016-09-01

Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats. © 2016 The Author(s).

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.

Multi-stability in folded shells: non-Euclidean origami

Science.gov (United States)

Evans, Arthur

2015-03-01

Both natural and man-made structures benefit from having multiple mechanically stable states, from the quick snapping motion of hummingbird beaks to micro-textured surfaces with tunable roughness. Rather than discuss special fabrication techniques for creating bi-stability through material anisotropy, in this talk I will present several examples of how folding a structure can modify the energy landscape and thus lead to multiple stable states. Using ideas from origami and differential geometry, I will discuss how deforming a non-Euclidean surface can be done either continuously or discontinuously, and explore the effects that global constraints have on the ultimate stability of the surface.

RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry

Directory of Open Access Journals (Sweden)

Ziv-Ukelson Michal

2009-03-01

Full Text Available Abstract Background Scanning large genomes with a sliding window in search of locally stable RNA structures is a well motivated problem in bioinformatics. Given a predefined window size L and an RNA sequence S of size N (L 3 by applying any of the classical cubic-time RNA folding algorithms to each of the N-L windows of size L. Recently an O(NL2 solution for this problem has been described. Results Here, we describe and implement an O(NLψ(L engine for the consecutive windows folding problem, where ψ(L is shown to converge to O(1 under the assumption of a standard probabilistic polymer folding model, yielding an O(L speedup which is experimentally confirmed. Using this tool, we note an intriguing directionality (5'-3' vs. 3'-5' folding bias, i.e. that the minimal free energy (MFE of folding is higher in the native direction of the DNA than in the reverse direction of various genomic regions in several organisms including regions of the genomes that do not encode proteins or ncRNA. This bias largely emerges from the genomic dinucleotide bias which affects the MFE, however we see some variations in the folding bias in the different genomic regions when normalized to the dinucleotide bias. We also present results from calculating the MFE landscape of a mouse chromosome 1, characterizing the MFE of the long ncRNA molecules that reside in this chromosome. Conclusion The efficient consecutive windows folding engine described in this paper allows for genome wide scans for ncRNA molecules as well as large-scale statistics. This is implemented here as a software tool, called RNAslider, and applied to the scanning of long chromosomes, leading to the observation of features that are visible only on a large scale.

Probing Free-Energy Surfaces with Differential Scanning Calorimetry

Science.gov (United States)

Sanchez-Ruiz, Jose M.

2011-05-01

Many aspects of protein folding can be understood in terms of projections of the highly dimensional energy landscape onto a few (or even only one) particularly relevant coordinates. These free-energy surfaces can be probed conveniently from experimental differential scanning calorimetry (DSC) thermograms, as DSC provides a direct relation with the protein partition function. Free-energy surfaces thus obtained are consistent with two fundamental scenarios predicted by the energy-landscape perspective: (a) well-defined macrostates separated by significant free-energy barriers, in some cases, and, in many other cases, (b) marginal or even vanishingly small barriers, which furthermore show a good correlation with kinetics for fast- and ultrafast-folding proteins. Overall, the potential of DSC to assess free-energy surfaces for a wide variety of proteins makes it possible to address fundamental issues, such as the molecular basis of the barrier modulations produced by natural selection in response to functional requirements or to ensure kinetic stability.

Peptide Free Energy Landscapes Calibrated by Molecular Orbital Calculations

OpenAIRE

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...

Energy landscape reveals that the budding yeast cell cycle is a robust and adaptive multi-stage process.

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.

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.

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.

Free energy landscapes of electron transfer system in dipolar environment below and above the rotational freezing temperature

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

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

Science.gov (United States)

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).

Multiple routes and milestones in the folding of HIV-1 protease monomer.

Directory of Open Access Journals (Sweden)

Massimiliano Bonomi

Full Text Available Proteins fold on a time scale incompatible with a mechanism of random search in conformational space thus indicating that somehow they are guided to the native state through a funneled energetic landscape. At the same time the heterogeneous kinetics suggests the existence of several different folding routes. Here we propose a scenario for the folding mechanism of the monomer of HIV-1 protease in which multiple pathways and milestone events coexist. A variety of computational approaches supports this picture. These include very long all-atom molecular dynamics simulations in explicit solvent, an analysis of the network of clusters found in multiple high-temperature unfolding simulations and a complete characterization of free-energy surfaces carried out using a structure-based potential at atomistic resolution and a combination of metadynamics and parallel tempering. Our results confirm that the monomer in solution is stable toward unfolding and show that at least two unfolding pathways exist. In our scenario, the formation of a hydrophobic core is a milestone in the folding process which must occur along all the routes that lead this protein towards its native state. Furthermore, the ensemble of folding pathways proposed here substantiates a rational drug design strategy based on inhibiting the folding of HIV-1 protease.

Control of the Effective Free-Energy Landscape in a Frustrated Magnet by a Field Pulse

Science.gov (United States)

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.

New Energy Landscapes of Pennsylvania: Forests to Farms to Fracking

Science.gov (United States)

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

Exploring the energy landscape of biopolymers using single molecule force spectroscopy and molecular simulations

OpenAIRE

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...

Inflation, Dark Matter, and Dark Energy in the String Landscape

OpenAIRE

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.

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

A deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths.

Science.gov (United States)

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.

Modeling and experimental verification of a fan-folded vibration energy harvester for leadless pacemakers

Science.gov (United States)

Ansari, M. H.; Karami, M. Amin

2016-03-01

This paper studies energy harvesting from heartbeat vibrations for powering leadless pacemakers. Unlike traditional pacemakers, leadless pacemakers are implanted inside the heart and the pacemaker is in direct contact with the myocardium. A leadless pacemaker is in the shape of a cylinder. Thus, in order to utilize the available 3-dimensional space for the energy harvester, we choose a fan-folded 3D energy harvester. The proposed device consists of several piezoelectric beams stacked on top of each other. The volume of the energy harvester is 1 cm3 and its dimensions are 2 cm × 0.5 cm × 1 cm. Although high natural frequency is generally a major concern with micro-scale energy harvesters, by utilizing the fan-folded geometry and adding tip mass and link mass to the configuration, we reduced the natural frequency to the desired range. This fan-folded design makes it possible to generate more than 10 μ W of power per cubic centimeter. The proposed device is compatible with Magnetic Resonance Imaging. Although the proposed device is a linear energy harvester, it is relatively insensitive to the heart rate. The natural frequencies and the mode shapes of the device are calculated analytically. The accuracy of the analytical model is verified by experimental investigations. We use a closed loop shaker system to precisely replicate heartbeat vibrations in vitro.

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.

Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models.

Science.gov (United States)

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.

What determines the structures of native folds of proteins?

International Nuclear Information System (INIS)

Trovato, Antonio; Hoang, Trinh X; Banavar, Jayanth R; Maritan, Amos; Seno, Flavio

2005-01-01

We review a simple physical model (Hoang et al 2004 Proc. Natl Acad. Sci. USA 101 7960, Banavar et al 2004 Phys. Rev. E at press) which captures the essential physico-chemical ingredients that determine protein structure, such as the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by hydrogen bonds, sterics, and hydrophobicity. Within this framework, marginally compact conformations resembling the native state folds of proteins emerge as competing minima in the free energy landscape. Here we demonstrate that a hydrophobic-polar (HP) sequence composed of regularly repeated patterns has as its ground state a β-helical structure remarkably similar to a known architecture in the Protein Data Bank

Prediction of the optimal set of contacts to fold the smallest knotted protein

International Nuclear Information System (INIS)

Dabrowski-Tumanski, P; Jarmolinska, A I; Sulkowska, J I

2015-01-01

Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map. (paper)

Prediction of the optimal set of contacts to fold the smallest knotted protein

Science.gov (United States)

Dabrowski-Tumanski, P.; Jarmolinska, A. I.; Sulkowska, J. I.

2015-09-01

Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map.

Multi-scaled explorations of binding-induced folding of intrinsically disordered protein inhibitor IA3 to its target enzyme.

Directory of Open Access Journals (Sweden)

Jin Wang

2011-04-01

Full Text Available Biomolecular function is realized by recognition, and increasing evidence shows that recognition is determined not only by structure but also by flexibility and dynamics. We explored a biomolecular recognition process that involves a major conformational change - protein folding. In particular, we explore the binding-induced folding of IA3, an intrinsically disordered protein that blocks the active site cleft of the yeast aspartic proteinase saccharopepsin (YPrA by folding its own N-terminal residues into an amphipathic alpha helix. We developed a multi-scaled approach that explores the underlying mechanism by combining structure-based molecular dynamics simulations at the residue level with a stochastic path method at the atomic level. Both the free energy profile and the associated kinetic paths reveal a common scheme whereby IA3 binds to its target enzyme prior to folding itself into a helix. This theoretical result is consistent with recent time-resolved experiments. Furthermore, exploration of the detailed trajectories reveals the important roles of non-native interactions in the initial binding that occurs prior to IA3 folding. In contrast to the common view that non-native interactions contribute only to the roughness of landscapes and impede binding, the non-native interactions here facilitate binding by reducing significantly the entropic search space in the landscape. The information gained from multi-scaled simulations of the folding of this intrinsically disordered protein in the presence of its binding target may prove useful in the design of novel inhibitors of aspartic proteinases.

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

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations

Directory of Open Access Journals (Sweden)

Moye Wang

2016-04-01

Full Text Available As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5–10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.

Comparison of Recent Oil and Gas, Wind Energy, and Other Anthropogenic Landscape Alteration Factors in Texas Through 2014.

Science.gov (United States)

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.

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape

OpenAIRE

Ferreon, Allan Chris M.; Moosa, Mahdi Muhammad; Gambin, Yann; Deniz, Ashok A.

2012-01-01

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster reson...

Energy landscape scheme for an intuitive understanding of complex domain dynamics in ferroelectric thin films

Science.gov (United States)

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.

Energy landscape scheme for an intuitive understanding of complex domain dynamics in ferroelectric thin films.

Science.gov (United States)

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.

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

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.

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

Simulation of fluorescence resonance energy transfer experiments: effect of the dyes on protein folding

International Nuclear Information System (INIS)

Allen, Lucy R; Paci, Emanuele

2010-01-01

Fluorescence resonance energy transfer is a powerful technique which is often used to probe the properties of proteins and complex macromolecules. The technique relies on relatively large fluorescent dyes which are engineered into the molecule of interest. In the case of small proteins, these dyes may affect the stability of the protein, and modify the folding kinetics and the folding mechanisms which are being probed. Here we use atomistic simulation to investigate the effect that commonly used fluorescent dyes have on the folding of a four-helix bundle protein. We show that, depending on where the dyes are attached, their effect on the kinetic and thermodynamic properties of the protein may be significant. We find that, while the overall folding mechanism is not affected by the dyes, they can destabilize, or even stabilize, intermediate states.

Calculation of the Local Free Energy Landscape in the Restricted Region by the Modified Tomographic Method.

Science.gov (United States)

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.

A new approach to quantify semiochemical effects on insects based on energy landscapes.

Directory of Open Access Journals (Sweden)

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.

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

Relaxation height in energy landscapes : an application to multiple metastable states

NARCIS (Netherlands)

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

Peculiarities of high-altitude landscapes formation in the Small Caucasus mountains

Science.gov (United States)

Trifonova, Tatiana

2014-05-01

Various mountain systems differ in character of landscapes and soil. Basic problem of present research: conditions and parameters determining the development of various landscapes and soils in mountain areas. Our research object is the area of Armenia where Small Caucasus, a part of Armenian upland is located. The specific character of the area is defined by the whole variety of all mountain structures like fold, block folding mountain ridges, volcanic upland, individual volcanoes, and intermountain depressions. As for the climate, the area belongs to dry subtropics. We have studied the peculiarities of high-altitude landscapes formation and mountain river basins development. We have used remote sensing data and statistic database of climatic parameters in this research. Field observations and landscape pictures analysis of space images allow distinguishing three types of mountain geosystems clearly: volcanic massifs, fold mountainous structures and closed high mountain basins - area of the lakes. The distribution of precipitation according to altitude shows some peculiarities. It has been found that due to this factor the investigated mountain area may be divided into three regions: storage (fold) mountainous area; Ararat volcanic area (southern macro exposure); closed high mountainous basin-area of the lake Sevan. The mountainous nature-climatic vertical landscapes appear to be horizontally oriented and they are more or less equilibrium (stable) geosystems, where the stable functional relationship between the landscape components is formed. Within their limits, definite bioclimatic structure of soil is developed. Along the slopes of fold mountains specific landscape shapes like litho-drainage basins are formed. They are intensively developing like relatively independent vertical geosystems. Mechanism of basin formation is versatile resulting in formation of the polychronous soil mantle structure. Landscapes and soils within the basin are of a different age, since

Relationship between energy systems and landscapes. Guidelines and tools for design and management

Directory of Open Access Journals (Sweden)

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.

Monitoring Forest Change in Landscapes Under-Going Rapid Energy Development: Challenges and New Perspectives

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.

Structural and kinetic mapping of side-chain exposure onto the protein energy landscape.

Science.gov (United States)

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.

Statistical topography of fitness landscapes

OpenAIRE

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...

SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach.

Science.gov (United States)

Getov, Ivan; Petukh, Marharyta; Alexov, Emil

2016-04-07

Folding free energy is an important biophysical characteristic of proteins that reflects the overall stability of the 3D structure of macromolecules. Changes in the amino acid sequence, naturally occurring or made in vitro, may affect the stability of the corresponding protein and thus could be associated with disease. Several approaches that predict the changes of the folding free energy caused by mutations have been proposed, but there is no method that is clearly superior to the others. The optimal goal is not only to accurately predict the folding free energy changes, but also to characterize the structural changes induced by mutations and the physical nature of the predicted folding free energy changes. Here we report a new method to predict the Single Amino Acid Folding free Energy Changes (SAAFEC) based on a knowledge-modified Molecular Mechanics Poisson-Boltzmann (MM/PBSA) approach. The method is comprised of two main components: a MM/PBSA component and a set of knowledge based terms delivered from a statistical study of the biophysical characteristics of proteins. The predictor utilizes a multiple linear regression model with weighted coefficients of various terms optimized against a set of experimental data. The aforementioned approach yields a correlation coefficient of 0.65 when benchmarked against 983 cases from 42 proteins in the ProTherm database. the webserver can be accessed via http://compbio.clemson.edu/SAAFEC/.

Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.

Directory of Open Access Journals (Sweden)

Yunxiang Sun

Full Text Available Energetic frustration is becoming an important topic for understanding the mechanisms of protein folding, which is a long-standing big biological problem usually investigated by the free energy landscape theory. Despite the significant advances in probing the effects of folding frustrations on the overall features of protein folding pathways and folding intermediates, detailed characterizations of folding frustrations at an atomic or residue level are still lacking. In addition, how and to what extent folding frustrations interact with protein topology in determining folding mechanisms remains unclear. In this paper, we tried to understand energetic frustrations in the context of protein topology structures or native-contact networks by comparing the energetic frustrations of five homologous Im9 alpha-helix proteins that share very similar topology structures but have a single hydrophilic-to-hydrophobic mutual mutation. The folding simulations were performed using a coarse-grained Gō-like model, while non-native hydrophobic interactions were introduced as energetic frustrations using a Lennard-Jones potential function. Energetic frustrations were then examined at residue level based on φ-value analyses of the transition state ensemble structures and mapped back to native-contact networks. Our calculations show that energetic frustrations have highly heterogeneous influences on the folding of the four helices of the examined structures depending on the local environment of the frustration centers. Also, the closer the introduced frustration is to the center of the native-contact network, the larger the changes in the protein folding. Our findings add a new dimension to the understanding of protein folding the topology determination in that energetic frustrations works closely with native-contact networks to affect the protein folding.

An energy landscape based approach for studying supercooled liquid and glassy thin films

Science.gov (United States)

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)

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

Anomalous dimensionality dependence of diffusion in a rugged energy landscape: How pathological is one dimension?

Science.gov (United States)

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.

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

Science.gov (United States)

Song, Yong-Shun; Zhou, Xin; Zheng, Wei-Mou; Wang, Yan-Ting

2017-07-01

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics (MD) simulation in aqueous solution four fragments cut out of a protein G, including one α-helix (seqB: KVFKQYAN), two β-turns (seqA: LNGKTLKG and seqC: YDDATKTF), and one β-strand (seqD: DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics. Supported by the National Basic Research Program of China under Grant No. 2013CB932804, the National Natural Science Foundation of China under Grant No. 11421063, and the CAS Biophysics Interdisciplinary Innovation Team Project

Multivariable extrapolation of grand canonical free energy landscapes

Science.gov (United States)

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.

Linking habitat selection to fitness-related traits in herbivores: the role of the energy landscape

Science.gov (United States)

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...

A Tale of Two Regions: Landscape Ecological Planning for Shale Gas Energy Futures

Science.gov (United States)

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

A data-driven analysis of energy balance closure across FLUXNET research sites: The role of landscape scale heterogeneity

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...

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.

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.

Science.gov (United States)

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.

Is the fenamate group a polymorphophore?: contrasting the crystal energy landscapes of fenamic and tolfenamic acids

NARCIS (Netherlands)

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

Strong field-matching effects in superconducting YBa2Cu3O7-δ films with vortex energy landscapes engineered via masked ion irradiation

Science.gov (United States)

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.

Temporal disconnectivity of the energy landscape in glassy systems

Science.gov (United States)

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

Development and application of a free energy force field for all atom protein folding

International Nuclear Information System (INIS)

Verma, A.

2007-11-01

Proteins are the workhorses of all cellular life. They constitute the building blocks and the machinery of all cells and typically function in specific three-dimensional conformations into which each protein folds. Currently over one million protein sequences are known, compared to about 40,000 structures deposited in the Protein Data Bank (the world-wide database of protein structures). Reliable theoretical methods for protein structure prediction could help to reduce the gap between sequence and structural databases and elucidate the biological information in structurally unresolved sequences. In this thesis we explore an approach for protein structure prediction and folding that is based on the Anfinsen's hypothesis that most proteins in their native state are in thermodynamic equilibrium with their environment. We have developed a free energy forcefield (PFF02) that locates the native conformation of many proteins from all structural classes at the global minimum of the free-energy model. We have validated the forcefield against a large decoy set (Rosetta). The average root mean square deviation (RMSD) for the lowest energy structure for the 32 proteins of the decoy set was only 2.14 Aa from the experimental conformation. We have successfully implemented and used stochastic optimization methods, such as the basin hopping technique and evolutionary algorithms for all atom protein structure prediction. The evolutionary algorithm performs exceptionally well on large supercomputational architectures, such as BlueGene and MareNostrum. Using the PFF02 forcefield, we were able to fold 13 proteins (12-56 amino acids), which include helix, sheet and mixed secondary structure. On average the predicted structure of these proteins deviated from their experimental conformation by only 2.89 Aa RMSD. (orig.)

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge.

Science.gov (United States)

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.

The elastic free energy of a tandem modular protein under force.

Science.gov (United States)

Valle-Orero, Jessica; Eckels, Edward C; Stirnemann, Guillaume; Popa, Ionel; Berkovich, Ronen; Fernandez, Julio M

2015-05-01

Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins. Copyright © 2015. Published by Elsevier Inc.

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

No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution

DEFF Research Database (Denmark)

Workman, Christopher; Krogh, Anders Stærmose

1999-01-01

This work investigates whether mRNA has a lower estimated folding free energy than random sequences. The free energy estimates are calculated by the mfold program for prediction of RNA secondary structures. For a set of 46 mRNAs it is shown that the predicted free energy is not significantly diff...

Microfabrication and integration of a sol-gel PZT folded spring energy harvester.

Science.gov (United States)

Lueke, Jonathan; Badr, Ahmed; Lou, Edmond; Moussa, Walied A

2015-05-26

This paper presents the methodology and challenges experienced in the microfabrication, packaging, and integration of a fixed-fixed folded spring piezoelectric energy harvester. A variety of challenges were overcome in the fabrication of the energy harvesters, such as the diagnosis and rectification of sol-gel PZT film quality and adhesion issues. A packaging and integration methodology was developed to allow for the characterizing the harvesters under a base vibration. The conditioning circuitry developed allowed for a complete energy harvesting system, consisting a harvester, a voltage doubler, a voltage regulator and a NiMH battery. A feasibility study was undertaken with the designed conditioning circuitry to determine the effect of the input parameters on the overall performance of the circuit. It was found that the maximum efficiency does not correlate to the maximum charging current supplied to the battery. The efficiency and charging current must be balanced to achieve a high output and a reasonable output current. The development of the complete energy harvesting system allows for the direct integration of the energy harvesting technology into existing power management schemes for wireless sensing.

Evaluating realized seed dispersal across fragmented tropical landscapes : a two-fold approach using parentage analysis and the neighbourhood model

NARCIS (Netherlands)

Ismail, Sascha A.; Ghazoul, Jaboury; Ravikanth, Gudasalamani; Kushalappa, Cheppudira G.; Uma Shaanker, Ramanan; Kettle, Chris J.

2017-01-01

Despite the importance of seed dispersal for survival of plant species in fragmented landscapes, data on seed dispersal at landscape scales remain sparse. Effective seed dispersal among fragments determines recolonization and plant species persistence in such landscapes. We present the first

Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.

Science.gov (United States)

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.

RNAiFold: a web server for RNA inverse folding and molecular design.

Science.gov (United States)

Garcia-Martin, Juan Antonio; Clote, Peter; Dotu, Ivan

2013-07-01

Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.

A comparison of RNA folding measures

Directory of Open Access Journals (Sweden)

Gardner Paul P

2005-10-01

Full Text Available Abstract Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. Results Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE than random sequences with the same dinucleotide frequency. Moreover, even when the MFE is significant, many ncRNAs appear to not have a unique fold, but rather several alternative folds, at least when folded in silico. Furthermore, we find that the six investigated measures are correlated to varying degrees. Conclusion Due to the correlations between the different measures we find that it is sufficient to use only two of them in RNA folding studies, one to test if the sequence in question has lower energy than a random sequence with the same dinucleotide frequency (the Z-score and the other to see if the sequence has a unique fold (the average base-pair distance, D.

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.

Initial conditions for slow-roll inflation in a random Gaussian landscape

Energy Technology Data Exchange (ETDEWEB)

Masoumi, Ali; Vilenkin, Alexander; Yamada, Masaki, E-mail: ali@cosmos.phy.tufts.edu, E-mail: vilenkin@cosmos.phy.tufts.edu, E-mail: Masaki.Yamada@tufts.edu [Institute of Cosmology, Department of Physics and Astronomy, Tufts University, Medford, MA 02155 (United States)

2017-07-01

In the landscape perspective, our Universe begins with a quantum tunneling from an eternally-inflating parent vacuum, followed by a period of slow-roll inflation. We investigate the tunneling process and calculate the probability distribution for the initial conditions and for the number of e-folds of slow-roll inflation, modeling the landscape by a small-field one-dimensional random Gaussian potential. We find that such a landscape is fully consistent with observations, but the probability for future detection of spatial curvature is rather low, P ∼ 10{sup −3}.

Metal cofactor modulated folding and target recognition of HIV-1 NCp7.

Science.gov (United States)

Ren, Weitong; Ji, Dongqing; Xu, Xiulian

2018-01-01

The HIV-1 nucleocapsid 7 (NCp7) plays crucial roles in multiple stages of HIV-1 life cycle, and its biological functions rely on the binding of zinc ions. Understanding the molecular mechanism of how the zinc ions modulate the conformational dynamics and functions of the NCp7 is essential for the drug development and HIV-1 treatment. In this work, using a structure-based coarse-grained model, we studied the effects of zinc cofactors on the folding and target RNA(SL3) recognition of the NCp7 by molecular dynamics simulations. After reproducing some key properties of the zinc binding and folding of the NCp7 observed in previous experiments, our simulations revealed several interesting features in the metal ion modulated folding and target recognition. Firstly, we showed that the zinc binding makes the folding transition states of the two zinc fingers less structured, which is in line with the Hammond effect observed typically in mutation, temperature or denaturant induced perturbations to protein structure and stability. Secondly, We showed that there exists mutual interplay between the zinc ion binding and NCp7-target recognition. Binding of zinc ions enhances the affinity between the NCp7 and the target RNA, whereas the formation of the NCp7-RNA complex reshapes the intrinsic energy landscape of the NCp7 and increases the stability and zinc affinity of the two zinc fingers. Thirdly, by characterizing the effects of salt concentrations on the target RNA recognition, we showed that the NCp7 achieves optimal balance between the affinity and binding kinetics near the physiologically relevant salt concentrations. In addition, the effects of zinc binding on the inter-domain conformational flexibility and folding cooperativity of the NCp7 were also discussed.

Metal cofactor modulated folding and target recognition of HIV-1 NCp7.

Directory of Open Access Journals (Sweden)

Weitong Ren

Full Text Available The HIV-1 nucleocapsid 7 (NCp7 plays crucial roles in multiple stages of HIV-1 life cycle, and its biological functions rely on the binding of zinc ions. Understanding the molecular mechanism of how the zinc ions modulate the conformational dynamics and functions of the NCp7 is essential for the drug development and HIV-1 treatment. In this work, using a structure-based coarse-grained model, we studied the effects of zinc cofactors on the folding and target RNA(SL3 recognition of the NCp7 by molecular dynamics simulations. After reproducing some key properties of the zinc binding and folding of the NCp7 observed in previous experiments, our simulations revealed several interesting features in the metal ion modulated folding and target recognition. Firstly, we showed that the zinc binding makes the folding transition states of the two zinc fingers less structured, which is in line with the Hammond effect observed typically in mutation, temperature or denaturant induced perturbations to protein structure and stability. Secondly, We showed that there exists mutual interplay between the zinc ion binding and NCp7-target recognition. Binding of zinc ions enhances the affinity between the NCp7 and the target RNA, whereas the formation of the NCp7-RNA complex reshapes the intrinsic energy landscape of the NCp7 and increases the stability and zinc affinity of the two zinc fingers. Thirdly, by characterizing the effects of salt concentrations on the target RNA recognition, we showed that the NCp7 achieves optimal balance between the affinity and binding kinetics near the physiologically relevant salt concentrations. In addition, the effects of zinc binding on the inter-domain conformational flexibility and folding cooperativity of the NCp7 were also discussed.

Amino acid empirical contact energy definitions for fold recognition in the space of contact maps

Directory of Open Access Journals (Sweden)

Fogolari Federico

2003-02-01

Full Text Available Abstract Background Contradicting evidence has been presented in the literature concerning the effectiveness of empirical contact energies for fold recognition. Empirical contact energies are calculated on the basis of information available from selected protein structures, with respect to a defined reference state, according to the quasi-chemical approximation. Protein-solvent interactions are estimated from residue solvent accessibility. Results In the approach presented here, contact energies are derived from the potential of mean force theory, several definitions of contact are examined and their performance in fold recognition is evaluated on sets of decoy structures. The best definition of contact is tested, on a more realistic scenario, on all predictions including sidechains accepted in the CASP4 experiment. In 30 out of 35 cases the native structure is correctly recognized and best predictions are usually found among the 10 lowest energy predictions. Conclusion The definition of contact based on van der Waals radii of alpha carbon and side chain heavy atoms is seen to perform better than other definitions involving only alpha carbons, only beta carbons, all heavy atoms or only backbone atoms. An important prerequisite for the applicability of the approach is that the protein structure under study should not exhibit anomalous solvent accessibility, compared to soluble proteins whose structure is deposited in the Protein Data Bank. The combined evaluation of a solvent accessibility parameter and contact energy allows for an effective gross screening of predictive models.

Probing the Free Energy Landscape of the FBP28 WW Domain Using Multiple Techniques

NARCIS (Netherlands)

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.

Impacts on the environment and landscape of new energy productions on farm parcels and buildings, Final report

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

Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals.

Science.gov (United States)

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.

Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space

OpenAIRE

Parra, R. Gonzalo; Espada, Rocío; Sánchez, Ignacio E.; Sippl, Manfred J.; Ferreiro, Diego U.

2013-01-01

The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy landscape theory indicates that it is much easier to find sequences that satisfy the “Principle of Minimal Frustration” when the folded structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14249–14255). Similarly, repeats and structural mosaics may be fundamentally related to landscape...

Microfabrication and Integration of a Sol-Gel PZT Folded Spring Energy Harvester

Directory of Open Access Journals (Sweden)

Jonathan Lueke

2015-05-01

Full Text Available This paper presents the methodology and challenges experienced in the microfabrication, packaging, and integration of a fixed-fixed folded spring piezoelectric energy harvester. A variety of challenges were overcome in the fabrication of the energy harvesters, such as the diagnosis and rectification of sol-gel PZT film quality and adhesion issues. A packaging and integration methodology was developed to allow for the characterizing the harvesters under a base vibration. The conditioning circuitry developed allowed for a complete energy harvesting system, consisting a harvester, a voltage doubler, a voltage regulator and a NiMH battery. A feasibility study was undertaken with the designed conditioning circuitry to determine the effect of the input parameters on the overall performance of the circuit. It was found that the maximum efficiency does not correlate to the maximum charging current supplied to the battery. The efficiency and charging current must be balanced to achieve a high output and a reasonable output current. The development of the complete energy harvesting system allows for the direct integration of the energy harvesting technology into existing power management schemes for wireless sensing.

Inflation in random Gaussian landscapes

Energy Technology Data Exchange (ETDEWEB)

Masoumi, Ali; Vilenkin, Alexander; Yamada, Masaki, E-mail: ali@cosmos.phy.tufts.edu, E-mail: vilenkin@cosmos.phy.tufts.edu, E-mail: Masaki.Yamada@tufts.edu [Institute of Cosmology, Department of Physics and Astronomy, Tufts University, Medford, MA 02155 (United States)

2017-05-01

We develop analytic and numerical techniques for studying the statistics of slow-roll inflation in random Gaussian landscapes. As an illustration of these techniques, we analyze small-field inflation in a one-dimensional landscape. We calculate the probability distributions for the maximal number of e-folds and for the spectral index of density fluctuations n {sub s} and its running α {sub s} . These distributions have a universal form, insensitive to the correlation function of the Gaussian ensemble. We outline possible extensions of our methods to a large number of fields and to models of large-field inflation. These methods do not suffer from potential inconsistencies inherent in the Brownian motion technique, which has been used in most of the earlier treatments.

A Community Landscape Model of Pro-Environmental Behavior: The Effects of Landscape and Community Interaction on Residential Energy Behaviors in Two Pennsylvania Towns

Science.gov (United States)

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

Global optimization of proteins using a dynamical lattice model: Ground states and energy landscapes

OpenAIRE

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.

Folding and Boudinage As the Same Fundamental Energy Bifurcation in Elasto-Visco-Plastic Rocks

Science.gov (United States)

Peters, M.; Paesold, M.; Veveakis, M.; Poulet, T.; Herwegh, M.; Regenauer-Lieb, K.

2014-12-01

Folding or boudinage are commonly thought to develop due to viscosity contrasts induced by either geometric interactions or material imperfections. However, there exists an additional localization phenomenon, i.e. strain localization out of steady state in homogeneous materials at a critical material parameter (set) or deformation rate. This study focuses on imperfections in terms of grain size variations, using the paleowattmeter relationship [Austin and Evans, 2007; 2009, Herwegh et al., 2014]. We identify the parameters for bifurcation, which is the critical amount of dissipation, expressed by the Gruntfest number [Gruntfest, 1963], incorporating flow stress, the Arrhenius number (Q/RT) and the layer dimensions. We verify the robustness of the solution through a method, developed to analyze such material instabilities [Rudnicki and Rice, 1975]. The second step is to identify the natural mode shapes and frequencies of the geometric structure and material parameters, including geometric imperfections. In a third step, the eigenmodes are perturbed and superposed to the initial conditions. We then subject the composite structure to natural deformation conditions. Grain sizes within the layer relatively quickly equilibrate to a homogeneous state, which is in response to energy optimization following the paleowattmeterrelationship. Upon continued loading, localization in terms of a necking or folding instability consequently arises out of this steady state. We obtain the criteria for the onset of localization from theory and numerical simulation, i.e. the critical Gruntfest number. Boudinage and folding instabilities occur when heat produced by dissipative work overcomes the diffusive capacity of the system. Both instabilities develop for the exact same Arrhenius and Gruntfestnumbers. Consequently, folding and boudinage instabilities can be seen as the same energy bifurcation triggered by dissipative work out of homogeneous state. Austin, N.J. and Evans, B. (2007

The energy landscape of glassy dynamics on the amorphous hafnium diboride surface

Science.gov (United States)

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.

A comparison of RNA folding measures

DEFF Research Database (Denmark)

Freyhult, E.; Gardner, P. P.; Moulton, V.

2005-01-01

the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. Results Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE) than....... Conclusion Due to the correlations between the different measures we find that it is sufficient to use only two of them in RNA folding studies, one to test if the sequence in question has lower energy than a random sequence with the same dinucleotide frequency (the Z-score) and the other to see......Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare...

Single-molecule folding mechanisms of the apo- and Mg2+-bound states of human neuronal calcium sensor-1

DEFF Research Database (Denmark)

Naqvi, Mohsin M; Heiðarsson, Pétur Orri; Otazo, Mariela R

2015-01-01

, at least transiently, at resting Ca(2+) conditions. Here, we used optical tweezers to study the folding behavior of individual NCS-1 molecules in the presence of Mg(2+) and in the absence of divalent ions. Under tension, the Mg(2+)-bound state of NCS-1 unfolds and refolds in a three-state process...... in a variety of cellular processes in which it has been linked to a number of disorders such as schizophrenia and autism. Despite extensive studies on the Ca(2+)-activated state of NCS proteins, little is known about the conformational dynamics of the Mg(2+)-bound and apo states, both of which are populated...... by populating one intermediate state consisting of a folded C-domain and an unfolded N-domain. The interconversion at equilibrium between the different molecular states populated by NCS-1 was monitored in real time through constant-force measurements and the energy landscapes underlying the observed transitions...

Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin.

Science.gov (United States)

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.

Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin

Science.gov (United States)

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

PolyUbiquitin chain linkage topology selects the functions from the underlying binding landscape.

Directory of Open Access Journals (Sweden)

Yong Wang

2014-07-01

Full Text Available Ubiquitin (Ub can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages.

PolyUbiquitin chain linkage topology selects the functions from the underlying binding landscape.

Science.gov (United States)

Wang, Yong; Tang, Chun; Wang, Erkang; Wang, Jin

2014-07-01

Ubiquitin (Ub) can generate versatile molecular signals and lead to different celluar fates. The functional poly-valence of Ub is believed to be resulted from its ability to form distinct polymerized chains with eight linkage types. To provide a full picture of ubiquitin code, we explore the binding landscape of two free Ub monomers and also the functional landscapes of of all eight linkage types by theoretical modeling. Remarkably, we found that most of the compact structures of covalently connected dimeric Ub chains (diUbs) pre-exist on the binding landscape. These compact functional states were subsequently validated by corresponding linkage models. This leads to the proposal that the folding architecture of Ub monomer has encoded all functional states into its binding landscape, which is further selected by different topologies of polymeric Ub chains. Moreover, our results revealed that covalent linkage leads to symmetry breaking of interfacial interactions. We further propose that topological constraint not only limits the conformational space for effective switching between functional states, but also selects the local interactions for realizing the corresponding biological function. Therefore, the topological constraint provides a way for breaking the binding symmetry and reaching the functional specificity. The simulation results also provide several predictions that qualitatively and quantitatively consistent with experiments. Importantly, the K48 linkage model successfully predicted intermediate states. The resulting multi-state energy landscape was further employed to reconcile the seemingly contradictory experimental data on the conformational equilibrium of K48-diUb. Our results further suggest that hydrophobic interactions are dominant in the functional landscapes of K6-, K11-, K33- and K48 diUbs, while electrostatic interactions play a more important role in the functional landscapes of K27, K29, K63 and linear linkages.

Co-designing energy landscapes: Application of participatory mapping and geographic information systems in the exploration of low carbon futures

NARCIS (Netherlands)

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,

Probing folding free energy landscape of small proteins through ...

Indian Academy of Sciences (India)

Unknown

36 ... of interaction parameters of the side residues obtained from the amino acid hydro- pathy scale. ... Elucidation of structures from the sequence of ... atom molecular dynamics18 and Monte Carlo simulations19 have also been carried out to.

Conjugate gradient filtering of instantaneous normal modes, saddles on the energy landscape, and diffusion in liquids.

Science.gov (United States)

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.

PREFACE Protein folding: lessons learned and new frontiers Protein folding: lessons learned and new frontiers

Science.gov (United States)

Pappu, Rohit V.; Nussinov, Ruth

2009-03-01

In appropriate physiological milieux proteins spontaneously fold into their functional three-dimensional structures. The amino acid sequences of functional proteins contain all the information necessary to specify the folds. This remarkable observation has spawned research aimed at answering two major questions. (1) Of all the conceivable structures that a protein can adopt, why is the ensemble of native-like structures the most favorable? (2) What are the paths by which proteins manage to robustly and reproducibly fold into their native structures? Anfinsen's thermodynamic hypothesis has guided the pursuit of answers to the first question whereas Levinthal's paradox has influenced the development of models for protein folding dynamics. Decades of work have led to significant advances in the folding problem. Mean-field models have been developed to capture our current, coarse grain understanding of the driving forces for protein folding. These models are being used to predict three-dimensional protein structures from sequence and stability profiles as a function of thermodynamic and chemical perturbations. Impressive strides have also been made in the field of protein design, also known as the inverse folding problem, thereby testing our understanding of the determinants of the fold specificities of different sequences. Early work on protein folding pathways focused on the specific sequence of events that could lead to a simplification of the search process. However, unifying principles proved to be elusive. Proteins that show reversible two-state folding-unfolding transitions turned out to be a gift of natural selection. Focusing on these simple systems helped researchers to uncover general principles regarding the origins of cooperativity in protein folding thermodynamics and kinetics. On the theoretical front, concepts borrowed from polymer physics and the physics of spin glasses led to the development of a framework based on energy landscape theories. These

The importance of on-site evaluation for placing renewable energy in the landscape: A case study of the Búrfell wind farm (Iceland

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.

Approximate scaling properties of RNA free energy landscapes

Science.gov (United States)

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.

Simple solvable energy-landscape model that shows a thermodynamic phase transition and a glass transition.

Science.gov (United States)

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.

Evidence and opportunities for integrating landscape ecology into natural resource planning across multiple-use landscapes

Science.gov (United States)

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.

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.

Frustration in the energy landscapes of multidomain protein misfolding.

Science.gov (United States)

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.

Multi-resonant wideband energy harvester based on a folded asymmetric M-shaped cantilever

Energy Technology Data Exchange (ETDEWEB)

Wu, Meng; Mao, Haiyang; Li, Zhigang; Liu, Ruiwen; Ming, Anjie [Key laboratory of Microelectronics Devices & Integrated Technology, Institute of Microelectronics, Chinese Academic of Sciences, Beijing 100029 (China); Ou, Yi; Ou, Wen [Key laboratory of Microelectronics Devices & Integrated Technology, Institute of Microelectronics, Chinese Academic of Sciences, Beijing 100029 (China); Smart Sensor Engineering Center, Jiangsu R& D Center for Internet of Things, Wuxi 214315 (China)

2015-07-15

This article reports a compact wideband piezoelectric vibration energy harvester consisting of three proof masses and an asymmetric M-shaped cantilever. The M-shaped beam comprises a main beam and two folded and dimension varied auxiliary beams interconnected through the proof mass at the end of the main cantilever. Such an arrangement constitutes a three degree-of-freedom vibrating body, which can tune the resonant frequencies of its first three orders close enough to obtain a utility wide bandwidth. The finite element simulation results and the experimental results are well matched. The operation bandwidth comprises three adjacent voltage peaks on account of the frequency interval shortening mechanism. The result shows that the proposed piezoelectric energy harvester could be efficient and adaptive in practical vibration circumstance based on multiple resonant modes.

Nucleus-Nucleus Scattering in the High-Energy Approximation and the Optical Folding Potential

CERN Document Server

Lukyanov, V K; Lukyanov, K V

2004-01-01

For the nucleus-nucleus scattering, the complex potential is obtained which corresponds to the eikonal phase of an optical limit of the Glauber-Sitenko high-energy approximation. The potential does not include free parameters, its real and imaginary parts depend on energy and are determined by the reported data on the nuclear density distributions and nucleon-nucleon scattering amplitude. Alternatively, for the real part, the folding potential can be utilized which includes the effective NN-forces and the exchange term, as well. As a result, the microscopic optical potential is constructed where contributions of the calculated real and imaginary parts are formed by fitting the two respective factors. An efficient of the approach is confirmed by agreements of calculations with the experimental data on elastic scattering cross-sections.

Multi-resonant wideband energy harvester based on a folded asymmetric M-shaped cantilever

International Nuclear Information System (INIS)

Wu, Meng; Mao, Haiyang; Li, Zhigang; Liu, Ruiwen; Ming, Anjie; Ou, Yi; Ou, Wen

2015-01-01

This article reports a compact wideband piezoelectric vibration energy harvester consisting of three proof masses and an asymmetric M-shaped cantilever. The M-shaped beam comprises a main beam and two folded and dimension varied auxiliary beams interconnected through the proof mass at the end of the main cantilever. Such an arrangement constitutes a three degree-of-freedom vibrating body, which can tune the resonant frequencies of its first three orders close enough to obtain a utility wide bandwidth. The finite element simulation results and the experimental results are well matched. The operation bandwidth comprises three adjacent voltage peaks on account of the frequency interval shortening mechanism. The result shows that the proposed piezoelectric energy harvester could be efficient and adaptive in practical vibration circumstance based on multiple resonant modes

Smart Landscape. The architecture of the "micro smart grid" as a resilience strategy for landscape

OpenAIRE

Garbarini, Giulia

2018-01-01

“Smart Landscape”, starting from energy devices for the management and distribution of electricity resources, tends to define a possible vision of landscape. The main structure and process are based on the architecture of a “micro smart grid”, which is generally associated with urban energy grids and districts, but may become a figurative reference for new forms of landscape, such as “Smart Landscape”. The output of the research would be to show how the main strategies of “Smart Landsc...

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.

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

Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding

Directory of Open Access Journals (Sweden)

Adami Christoph

2003-02-01

Full Text Available Background The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutations should tend to interact synergistically, such that the rate of mean fitness decline accelerates as the number of random mutations is increased. However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect has been observed. Results We studied in silico the net amount and form of epistatic interactions in RNA secondary structure folding by measuring the fraction of neutral mutants as a function of mutational distance d. We found a clear prevalence of antagonistic epistasis in RNA secondary structure folding. By relating the fraction of neutral mutants at distance d to the average neutrality at distance d, we showed that this prevalence derives from the existence of many compensatory mutations at larger mutational distances. Conclusions Our findings imply that the average direction of epistasis in simple fitness landscapes is directly related to the density with which fitness peaks are distributed in these landscapes.

Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding.

Science.gov (United States)

Wilke, Claus O; Lenski, Richard E; Adami, Christoph

2003-02-05

The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutations should tend to interact synergistically, such that the rate of mean fitness decline accelerates as the number of random mutations is increased. However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect) has been observed. We studied in silico the net amount and form of epistatic interactions in RNA secondary structure folding by measuring the fraction of neutral mutants as a function of mutational distance d. We found a clear prevalence of antagonistic epistasis in RNA secondary structure folding. By relating the fraction of neutral mutants at distance d to the average neutrality at distance d, we showed that this prevalence derives from the existence of many compensatory mutations at larger mutational distances. Our findings imply that the average direction of epistasis in simple fitness landscapes is directly related to the density with which fitness peaks are distributed in these landscapes.

Entropic and Electrostatic Effects on the Folding Free Energy of a Surface-Attached Biomolecule: An Experimental and Theoretical Study

Science.gov (United States)

Watkins, Herschel M.; Vallée-Bélisle, Alexis; Ricci, Francesco; Makarov, Dmitrii E.; Plaxco, Kevin W.

2012-01-01

Surface-tethered biomolecules play key roles in many biological processes and biotechnologies. However, while the physical consequences of such surface attachment have seen significant theoretical study, to date this issue has seen relatively little experimental investigation. In response we present here a quantitative experimental and theoretical study of the extent to which attachment to a charged –but otherwise apparently inert– surface alters the folding free energy of a simple biomolecule. Specifically, we have measured the folding free energy of a DNA stem loop both in solution and when site-specifically attached to a negatively charged, hydroxyl-alkane-coated gold surface. We find that, whereas surface attachment is destabilizing at low ionic strength it becomes stabilizing at ionic strengths above ~130 mM. This behavior presumably reflects two competing mechanisms: excluded volume effects, which stabilize the folded conformation by reducing the entropy of the unfolded state, and electrostatics, which, at lower ionic strengths, destabilizes the more compact folded state via repulsion from the negatively charged surface. To test this hypothesis we have employed existing theories of the electrostatics of surface-bound polyelectrolytes and the entropy of surface-bound polymers to model both effects. Despite lacking any fitted parameters, these theoretical models quantitatively fit our experimental results, suggesting that, for this system, current knowledge of both surface electrostatics and excluded volume effects is reasonably complete and accurate. PMID:22239220

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.

Time Series Analysis of Energy Production and Associated Landscape Fragmentation in the Eagle Ford Shale Play

Science.gov (United States)

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.

Nonequilibrium landscape theory of neural networks.

Science.gov (United States)

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.

Structure prediction of nanoclusters; a direct or a pre-screened search on the DFT energy landscape?

Science.gov (United States)

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

Coarsely resolved topography along protein folding pathways

Science.gov (United States)

Fernández, Ariel; Kostov, Konstantin S.; Berry, R. Stephen

2000-03-01

The kinetic data from the coarse representation of polypeptide torsional dynamics described in the preceding paper [Fernandez and Berry, J. Chem. Phys. 112, 5212 (2000), preceding paper] is inverted by using detailed balance to obtain a topographic description of the potential-energy surface (PES) along the dominant folding pathway of the bovine pancreatic trypsin inhibitor (BPTI). The topography is represented as a sequence of minima and effective saddle points. The dominant folding pathway displays an overall monotonic decrease in energy with a large number of staircaselike steps, a clear signature of a good structure-seeker. The diversity and availability of alternative folding pathways is analyzed in terms of the Shannon entropy σ(t) associated with the time-dependent probability distribution over the kinetic ensemble of contact patterns. Several stages in the folding process are evident. Initially misfolded states form and dismantle revealing no definite pattern in the topography and exhibiting high Shannon entropy. Passage down a sequence of staircase steps then leads to the formation of a nativelike intermediate, for which σ(t) is much lower and fairly constant. Finally, the structure of the intermediate is refined to produce the native state of BPTI. We also examine how different levels of tolerance to mismatches of side chain contacts influence the folding kinetics, the topography of the dominant folding pathway, and the Shannon entropy. This analysis yields upper and lower bounds of the frustration tolerance required for the expeditious and robust folding of BPTI.

Basin Hopping Graph

DEFF Research Database (Denmark)

Kucharik, Marcel; Hofacker, Ivo; Stadler, Peter

2014-01-01

of the folding free energy landscape, however, can provide the relevant information. Results We introduce the basin hopping graph (BHG) as a novel coarse-grained model of folding landscapes. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect...

Probabilistic analysis for identifying the driving force of protein folding

Science.gov (United States)

Tokunaga, Yoshihiko; Yamamori, Yu; Matubayasi, Nobuyuki

2018-03-01

Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.

Folding model analysis of Λ binding energies and three-body ΛNN force

International Nuclear Information System (INIS)

Mian, M.; Rahman Khan, M.Z.

1988-02-01

Working within the framework of the folding model, we analyze the Λ binding energy data of light hypernuclei with effective two-body ΛN plus three-body ΛNN interaction. The two-body density for the core nucleus required for evaluating the three-body force contribution is obtained in terms of the centre of mass pair correlation. It is found that except for Λ 5 He the data are fairly well explained. The three-body force seems to account for the density dependence of the effective two-body ΛN interaction proposed earlier. (author). 13 refs, 2 tabs

Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex.

Directory of Open Access Journals (Sweden)

Yunqiang Bian

2014-04-01

Full Text Available In this work we studied the folding process of the hybrid-1 type human telomeric DNA G-quadruplex with solvent and K(+ ions explicitly modeled. Enabled by the powerful bias-exchange metadynamics and large-scale conventional molecular dynamic simulations, the free energy landscape of this G-DNA was obtained for the first time and four folding intermediates were identified, including a triplex and a basically formed quadruplex. The simulations also provided atomistic pictures for the structures and cation binding patterns of the intermediates. The results showed that the structure formation and cation binding are cooperative and mutually supporting each other. The syn/anti reorientation dynamics of the intermediates was also investigated. It was found that the nucleotides usually take correct syn/anti configurations when they form native and stable hydrogen bonds with the others, while fluctuating between two configurations when they do not. Misfolded intermediates with wrong syn/anti configurations were observed in the early intermediates but not in the later ones. Based on the simulations, we also discussed the roles of the non-native interactions. Besides, the formation process of the parallel conformation in the first two G-repeats and the associated reversal loop were studied. Based on the above results, we proposed a folding pathway for the hybrid-1 type G-quadruplex with atomistic details, which is new and more complete compared with previous ones. The knowledge gained for this type of G-DNA may provide a general insight for the folding of the other G-quadruplexes.

The inherent dynamics of a molecular liquid: Geodesic pathways through the potential energy landscape of a liquid of linear molecules

Science.gov (United States)

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.

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.

Self-folding graphene-polymer bilayers

Energy Technology Data Exchange (ETDEWEB)

Deng, Tao [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China); Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Yoon, ChangKyu [Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Jin, Qianru [Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Li, Mingen [Department of Physics, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Liu, Zewen [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China); Gracias, David H., E-mail: dgracias@jhu.edu [Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States)

2015-05-18

In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression.

Science.gov (United States)

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.

Tuning Surface Energy Landscapes in Metallic Quantum Films using Alkali Adsorbates

Science.gov (United States)

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.

Free energy landscape and cooperatively rearranging region in a hard sphere glass

Science.gov (United States)

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.

Evaluating realized seed dispersal across fragmented tropical landscapes: a two-fold approach using parentage analysis and the neighbourhood model.

Science.gov (United States)

Ismail, Sascha A; Ghazoul, Jaboury; Ravikanth, Gudasalamani; Kushalappa, Cheppudira G; Uma Shaanker, Ramanan; Kettle, Chris J

2017-05-01

Despite the importance of seed dispersal for survival of plant species in fragmented landscapes, data on seed dispersal at landscape scales remain sparse. Effective seed dispersal among fragments determines recolonization and plant species persistence in such landscapes. We present the first large-scale (216-km 2 ) direct estimates of realized seed dispersal of a high-value timber tree (Dysoxylum malabaricum) across an agro-forest landscape in the Western Ghats, India. Based upon an exhaustive inventory of adult trees and a sample of 488 seedlings all genotyped at 10 microsatellite loci, we estimated realized seed dispersal using parentage analysis and the neighbourhood model. Our estimates found that most realized seed dispersal was within 200 m, which is insufficient to effectively bridge the distances between forest patches. We conclude that using mobility of putative animal dispersers can be misleading when estimating tropical tree species vulnerability to habitat fragmentation. This raises serious concerns about the potential of many tropical trees to recolonize isolated forest patches where high-value tree species have already been removed. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Physical mechanism of mind changes and tradeoffs among speed, accuracy, and energy cost in brain decision making: Landscape, flux, and path perspectives

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)

Experimental evidence of reorganizing landscape under changing climatic forcing

Science.gov (United States)

Singh, A.; Tejedor, A.; Zaliapin, I. V.; Reinhardt, L.; Foufoula-Georgiou, E.

2015-12-01

Quantification of the dynamics of landscape reorganization under changing climatic forcing is important to understand geomorphic transport laws under transient conditions, assess response of landscapes to external perturbations for future predictive modeling, and for interpreting past climate from stratigraphic record. For such an analysis, however, real landscape observations are limited. To this end, a series of controlled laboratory experiments on evolving landscape were conducted at the St. Anthony Falls laboratory at the University of Minnesota. High resolution elevation data at a temporal resolution of 5 mins and spatial resolution of 0.5 mm were collected as the landscape approached steady state (constant uplift and precipitation rate) and in the transient state (under the same uplift and 5 times precipitation rate). Our results reveal rapid topographic re-organization under a five-fold increase in precipitation with the fluvial regime encroaching into the previously debris dominated regime, widening and aggradation of channels and valleys, and accelerated erosion happening at hillslope scales. To better understand the initiation of the observed reorganization, we perform a connectivity and clustering analysis of the erosional and depositional events, showing strikingly different spatial patterns on landscape evolution under steady-state (SS) and transient-state (TS), even when the time under SS is renormalized to match the total volume of eroded and deposited sediment in TS. Our results suggest a regime shift in the behavior of transport processes on the landscape at the intermediate scales i.e., from supply-limited to transport-limited.

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

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

Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping

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.

Using enzyme folding to explore the mechanism of therapeutic touch: a feasibility study.

Science.gov (United States)

Strickland, Mallory L; Boylan, Helen M

2010-07-01

The goal of this research is to design a novel model using protein folding to study Therapeutic Touch, a noncontact form of energy manipulation healing. Presented is a feasibility study suggesting that the denaturation path of ribonuclease A may be a useful model to study the energy exchange underlying therapeutic touch. The folding of ribonuclease A serves as a controlled energy-requiring system in which energy manipulation can be measured by the degree of folding achieved. A kinetic assay and fluorescence spectroscopy are used to assess the enzyme-folding state. The data suggest that the kinetic assay is a useful means of assessing the degree of refolding, and specifically, the enzyme function. However, fluorescence spectroscopy was not shown to be an effective measurement of enzyme structure for the purposes of this work. More research is needed to assess the underlying mechanism of therapeutic touch to complement the existing studies. An enzyme-folding model may provide a useful means of studying the energy exchange in therapeutic touch.

Exploring the energy landscape of the charge transport levels in organic semiconductors at the molecular scale.

Science.gov (United States)

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.

Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.

Science.gov (United States)

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.

Thermodynamics of protein folding: a random matrix formulation.

Science.gov (United States)

Shukla, Pragya

2010-10-20

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters, e.g. the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows, however, that the evolution of the statistical measures, e.g. Gibbs free energy, heat capacity, and entropy, is single parametric. The information can explain the selection of specific folding pathways from an infinite number of possible ways as well as other folding characteristics observed in computer simulation studies. © 2010 IOP Publishing Ltd

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.

Nonequilibrium landscape theory of neural networks

Science.gov (United States)

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

Experimental Rugged Fitness Landscape in Protein Sequence Space

Science.gov (United States)

Hayashi, Yuuki; Aita, Takuyo; Toyota, Hitoshi; Husimi, Yuzuru; Urabe, Itaru; Yomo, Tetsuya

2006-01-01

The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12–130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7×104-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18–24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region. PMID:17183728

Experimental rugged fitness landscape in protein sequence space.

Science.gov (United States)

Hayashi, Yuuki; Aita, Takuyo; Toyota, Hitoshi; Husimi, Yuzuru; Urabe, Itaru; Yomo, Tetsuya

2006-12-20

The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7x10(4)-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1) the dependence of stationary fitness on library size, which increased gradually, and (2) the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18-24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.

Experimental rugged fitness landscape in protein sequence space.

Directory of Open Access Journals (Sweden)

Yuuki Hayashi

Full Text Available The fitness landscape in sequence space determines the process of biomolecular evolution. To plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein D2 domain, which is essential for phage infection. After 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phage showed a 1.7x10(4-fold increase in infectivity, defined as the number of infected cells per ml of phage suspension. Fitness was defined as the logarithm of infectivity, and we analyzed (1 the dependence of stationary fitness on library size, which increased gradually, and (2 the time course of changes in fitness in transitional phases, based on an original theory regarding the evolutionary dynamics in Kauffman's n-k fitness landscape model. In the landscape model, single mutations at single sites among n sites affect the contribution of k other sites to fitness. Based on the results of these analyses, k was estimated to be 18-24. According to the estimated parameters, the landscape was plotted as a smooth surface up to a relative fitness of 0.4 of the global peak, whereas the landscape had a highly rugged surface with many local peaks above this relative fitness value. Based on the landscapes of these two different surfaces, it appears possible for adaptive walks with only random substitutions to climb with relative ease up to the middle region of the fitness landscape from any primordial or random sequence, whereas an enormous range of sequence diversity is required to climb further up the rugged surface above the middle region.

Control over Structure and Function of Peptide Amphiphile Supramolecular Assemblies through Molecular Design and Energy Landscapes

Science.gov (United States)

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

Thermal Infrared Remote Sensing for Analysis of Landscape Ecological Processes: Methods and Applications

Science.gov (United States)

Quattrochi, Dale A.; Luvall, Jeffrey C.

1998-01-01

Thermal Infrared (TIR) remote sensing data can provide important measurements of surface energy fluxes and temperatures, which are integral to understanding landscape processes and responses. One example of this is the successful application of TIR remote sensing data to estimate evapotranspiration and soil moisture, where results from a number of studies suggest that satellite-based measurements from TIR remote sensing data can lead to more accurate regional-scale estimates of daily evapotranspiration. With further refinement in analytical techniques and models, the use of TIR data from airborne and satellite sensors could be very useful for parameterizing surface moisture conditions and developing better simulations of landscape energy exchange over a variety of conditions and space and time scales. Thus, TIR remote sensing data can significantly contribute to the observation, measurement, and analysis of energy balance characteristics (i.e., the fluxes and redistribution of thermal energy within and across the land surface) as an implicit and important aspect of landscape dynamics and landscape functioning. The application of TIR remote sensing data in landscape ecological studies has been limited, however, for several fundamental reasons that relate primarily to the perceived difficulty in use and availability of these data by the landscape ecology community, and from the fragmentation of references on TIR remote sensing throughout the scientific literature. It is our purpose here to provide evidence from work that has employed TIR remote sensing for analysis of landscape characteristics to illustrate how these data can provide important data for the improved measurement of landscape energy response and energy flux relationships. We examine the direct or indirect use of TIR remote sensing data to analyze landscape biophysical characteristics, thereby offering some insight on how these data can be used more robustly to further the understanding and modeling of

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction.

Science.gov (United States)

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.

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction

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.

Shapes of tree representations of spin-glass landscapes

International Nuclear Information System (INIS)

Hordijk, Wim; Fontanari, Jose F; Stadler, Peter F

2003-01-01

Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure - a barrier tree - the leaves and internal nodes of which represent, respectively, the local minima and the lowest energy saddles connecting those minima. Here we apply several statistics used in the study of phylogenetic trees to barrier trees that result from the energy landscapes of p-spin models. These statistics give information about the shape of these barrier trees, in particular about balance and symmetry. We then ask if they can be used to classify different types of landscapes, compare them with results obtained from random trees, and investigate the structure of subtrees of the barrier trees. We conclude that at least one of the used statistics is capable of distinguishing different types of landscapes, that the barrier trees from p-spin energy landscapes are quite different from random trees, and that subtrees of barrier trees do not reflect the overall tree structure, but their structure is correlated with their 'depth' in the tree

Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

Science.gov (United States)

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

Oil and Gas Development in Southwestern Wyoming - Energy Data and Services for the Wyoming Landscape Conservation Initiative (WLCI)

Science.gov (United States)

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.

Free energy landscape of a minimalist salt bridge model.

Science.gov (United States)

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.

A replica exchange Monte Carlo algorithm for protein folding in the HP model

Directory of Open Access Journals (Sweden)

Shmygelska Alena

2007-09-01

Full Text Available Abstract Background The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of the most important and challenging problems in biochemistry, molecular biology and biophysics. The ab initio protein folding problem is computationally challenging and has been shown to be NP MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaat0uy0HwzTfgDPnwy1egaryqtHrhAL1wy0L2yHvdaiqaacqWFneVtcqqGqbauaaa@3961@-hard even when conformations are restricted to a lattice. In this work, we implement and evaluate the replica exchange Monte Carlo (REMC method, which has already been applied very successfully to more complex protein models and other optimization problems with complex energy landscapes, in combination with the highly effective pull move neighbourhood in two widely studied Hydrophobic Polar (HP lattice models. Results We demonstrate that REMC is highly effective for solving instances of the square (2D and cubic (3D HP protein folding problem. When using the pull move neighbourhood, REMC outperforms current state-of-the-art algorithms for most benchmark instances. Additionally, we show that this new algorithm provides a larger ensemble of ground-state structures than the existing state-of-the-art methods. Furthermore, it scales well with sequence length, and it finds significantly better conformations on long biological sequences and sequences with a provably unique ground-state structure, which is believed to be a characteristic of real proteins. We also present evidence that our REMC algorithm can fold sequences which exhibit significant interaction between termini in the hydrophobic core relatively easily. Conclusion We demonstrate that REMC utilizing the pull move

Directing folding pathways for multi-component DNA origami nanostructures with complex topology

International Nuclear Information System (INIS)

Marras, A E; Zhou, L; Su, H-J; Castro, C E; Kolliopoulos, V

2016-01-01

Molecular self-assembly has become a well-established technique to design complex nanostructures and hierarchical mesoscale assemblies. The typical approach is to design binding complementarity into nucleotide or amino acid sequences to achieve the desired final geometry. However, with an increasing interest in dynamic nanodevices, the need to design structures with motion has necessitated the development of multi-component structures. While this has been achieved through hierarchical assembly of similar structural units, here we focus on the assembly of topologically complex structures, specifically with concentric components, where post-folding assembly is not feasible. We exploit the ability to direct folding pathways to program the sequence of assembly and present a novel approach of designing the strand topology of intermediate folding states to program the topology of the final structure, in this case a DNA origami slider structure that functions much like a piston-cylinder assembly in an engine. The ability to program the sequence and control orientation and topology of multi-component DNA origami nanostructures provides a foundation for a new class of structures with internal and external moving parts and complex scaffold topology. Furthermore, this work provides critical insight to guide the design of intermediate states along a DNA origami folding pathway and to further understand the details of DNA origami self-assembly to more broadly control folding states and landscapes. (paper)

Directing folding pathways for multi-component DNA origami nanostructures with complex topology

Science.gov (United States)

Marras, A. E.; Zhou, L.; Kolliopoulos, V.; Su, H.-J.; Castro, C. E.

2016-05-01

Molecular self-assembly has become a well-established technique to design complex nanostructures and hierarchical mesoscale assemblies. The typical approach is to design binding complementarity into nucleotide or amino acid sequences to achieve the desired final geometry. However, with an increasing interest in dynamic nanodevices, the need to design structures with motion has necessitated the development of multi-component structures. While this has been achieved through hierarchical assembly of similar structural units, here we focus on the assembly of topologically complex structures, specifically with concentric components, where post-folding assembly is not feasible. We exploit the ability to direct folding pathways to program the sequence of assembly and present a novel approach of designing the strand topology of intermediate folding states to program the topology of the final structure, in this case a DNA origami slider structure that functions much like a piston-cylinder assembly in an engine. The ability to program the sequence and control orientation and topology of multi-component DNA origami nanostructures provides a foundation for a new class of structures with internal and external moving parts and complex scaffold topology. Furthermore, this work provides critical insight to guide the design of intermediate states along a DNA origami folding pathway and to further understand the details of DNA origami self-assembly to more broadly control folding states and landscapes.

Nonlinear vs. linear biasing in Trp-cage folding simulations

Energy Technology Data Exchange (ETDEWEB)

Spiwok, Vojtěch, E-mail: spiwokv@vscht.cz; Oborský, Pavel; Králová, Blanka [Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, Prague 6 166 28 (Czech Republic); Pazúriková, Jana [Institute of Computer Science, Masaryk University, Botanická 554/68a, 602 00 Brno (Czech Republic); Křenek, Aleš [Institute of Computer Science, Masaryk University, Botanická 554/68a, 602 00 Brno (Czech Republic); Center CERIT-SC, Masaryk Univerzity, Šumavská 416/15, 602 00 Brno (Czech Republic)

2015-03-21

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.

Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.

Science.gov (United States)

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.

Ecological Functions of Landscapes

Science.gov (United States)

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

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...

Reheating-volume measure in the string theory landscape

International Nuclear Information System (INIS)

Winitzki, Sergei

2008-01-01

I recently proposed the ''reheating-volume'' (RV) prescription as a possible solution to the measure problem in ''multiverse'' cosmology. The goal of this work is to extend the RV measure to scenarios involving bubble nucleation, such as the string theory landscape. In the spirit of the RV prescription, I propose to calculate the distribution of observable quantities in a landscape that is conditioned in probability to nucleate a finite total number of bubbles to the future of an initial bubble. A general formula for the relative number of bubbles of different types can be derived. I show that the RV measure is well defined and independent of the choice of the initial bubble type, as long as that type supports further bubble nucleation. Applying the RV measure to a generic landscape, I find that the abundance of Boltzmann brains is always negligibly small compared with the abundance of ordinary observers in the bubbles of the same type. As an illustration, I present explicit results for a toy landscape containing four vacuum states, and for landscapes with a single high-energy vacuum and a large number of low-energy vacua.

Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.

Science.gov (United States)

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.

Pest control of aphids depends on landscape complexity and natural enemy interactions.

Science.gov (United States)

Martin, Emily A; Reineking, Björn; Seo, Bumsuk; Steffan-Dewenter, Ingolf

2015-01-01

Aphids are a major concern in agricultural crops worldwide, and control by natural enemies is an essential component of the ecological intensification of agriculture. Although the complexity of agricultural landscapes is known to influence natural enemies of pests, few studies have measured the degree of pest control by different enemy guilds across gradients in landscape complexity. Here, we use multiple natural-enemy exclosures replicated in 18 fields across a gradient in landscape complexity to investigate (1) the strength of natural pest control across landscapes, measured as the difference between pest pressure in the presence and in the absence of natural enemies; (2) the differential contributions of natural enemy guilds to pest control, and the nature of their interactions across landscapes. We show that natural pest control of aphids increased up to six-fold from simple to complex landscapes. In the absence of pest control, aphid population growth was higher in complex than simple landscapes, but was reduced by natural enemies to similar growth rates across all landscapes. The effects of enemy guilds were landscape-dependent. Particularly in complex landscapes, total pest control was supplied by the combined contribution of flying insects and ground-dwellers. Birds had little overall impact on aphid control. Despite evidence for intraguild predation of flying insects by ground-dwellers and birds, the overall effect of enemy guilds on aphid control was complementary. Understanding pest control services at large spatial scales is critical to increase the success of ecological intensification schemes. Our results suggest that, where aphids are the main pest of concern, interactions between natural enemies are largely complementary and lead to a strongly positive effect of landscape complexity on pest control. Increasing the availability of seminatural habitats in agricultural landscapes may thus benefit not only natural enemies, but also the effectiveness of

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...

Quantitative analysis of the publishing landscape in High-Energy Physics

CERN Document Server

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...

The nature of folded states of globular proteins.

Science.gov (United States)

Honeycutt, J D; Thirumalai, D

1992-06-01

We suggest, using dynamical simulations of a simple heteropolymer modelling the alpha-carbon sequence in a protein, that generically the folded states of globular proteins correspond to statistically well-defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several free energy minima separated by barriers of various heights such that the folded conformations of a polypeptide chain in each of the minima have similar structural characteristics but have different energies from one another. The calculated structural characteristics, such as bond angle and dihedral angle distribution functions, are assumed to arise from only those configurations belonging to a given minimum. The validity of this hypothesis is illustrated by simulations of a continuum model of a heteropolymer whose low temperature state is a well-defined beta-barrel structure. The simulations were done using a molecular dynamics algorithm (referred to as the "noisy" molecular dynamics method) containing both friction and noise terms. It is shown that for this model there are several distinct metastable minima in which the structural features are similar. Several new methods of analyzing fluctuations in structures belonging to two distinct minima are introduced. The most notable one is a dynamic measure of compactness that can in principle provide the time required for maximal compactness to be achieved. The analysis shows that for a given metastable state in which the protein has a well-defined folded structure the transition to a state of higher compactness occurs very slowly, lending credence to the notion that the system encounters a late barrier in the process of folding to the most compact structure. The examination of the fluctuations in the structures near the unfolding----folding transition temperature indicates that the transition state for the unfolding to folding process occurs closer to the folded state.

Flips for 3-folds and 4-folds

CERN Document Server

Corti, Alessio

2007-01-01

This edited collection of chapters, authored by leading experts, provides a complete and essentially self-contained construction of 3-fold and 4-fold klt flips. A large part of the text is a digest of Shokurov's work in the field and a concise, complete and pedagogical proof of the existence of 3-fold flips is presented. The text includes a ten page glossary and is accessible to students and researchers in algebraic geometry.

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...

PELE:  Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique.

Science.gov (United States)

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.

Early Events, Kinetic Intermediates and the Mechanism of Protein Folding in Cytochrome c

Directory of Open Access Journals (Sweden)

David S. Kliger

2009-04-01

Full Text Available Kinetic studies of the early events in cytochrome c folding are reviewed with a focus on the evidence for folding intermediates on the submillisecond timescale. Evidence from time-resolved absorption, circular dichroism, magnetic circular dichroism, fluorescence energy and electron transfer, small-angle X-ray scattering and amide hydrogen exchange studies on the t £ 1 ms timescale reveals a picture of cytochrome c folding that starts with the ~ 1-ms conformational diffusion dynamics of the unfolded chains. A fractional population of the unfolded chains collapses on the 1 – 100 ms timescale to a compact intermediate IC containing some native-like secondary structure. Although the existence and nature of IC as a discrete folding intermediate remains controversial, there is extensive high time-resolution kinetic evidence for the rapid formation of IC as a true intermediate, i.e., a metastable state separated from the unfolded state by a discrete free energy barrier. Final folding to the native state takes place on millisecond and longer timescales, depending on the presence of kinetic traps such as heme misligation and proline mis-isomerization. The high folding rates observed in equilibrium molten globule models suggest that IC may be a productive folding intermediate. Whether it is an obligatory step on the pathway to the high free energy barrier associated with millisecond timescale folding to the native state, however, remains to be determined.

Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

Science.gov (United States)

Maity, Hiranmay; Reddy, Govardhan

2018-04-01

Small single-domain globular proteins, which are believed to be dominantly two-state folders, played an important role in elucidating various aspects of the protein folding mechanism. However, recent single molecule fluorescence resonance energy transfer experiments [H. Y. Aviram et al. J. Chem. Phys. 148, 123303 (2018)] on a single-domain two-state folding protein L showed evidence for the population of an intermediate state and it was suggested that in this state, a β-hairpin present near the C-terminal of the native protein state is unfolded. We performed molecular dynamics simulations using a coarse-grained self-organized-polymer model with side chains to study the folding pathways of protein L. In agreement with the experiments, an intermediate is populated in the simulation folding pathways where the C-terminal β-hairpin detaches from the rest of the protein structure. The lifetime of this intermediate structure increased with the decrease in temperature. In low temperature conditions, we also observed a second intermediate state, which is globular with a significant fraction of the native-like tertiary contacts satisfying the features of a dry molten globule.

Flowscapes : Infrastructure as landscape, landscape as infrastructure. Graduation Lab Landscape Architecture 2012/2013

NARCIS (Netherlands)

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

Folding pathways explored with artificial potential functions

International Nuclear Information System (INIS)

Ulutaş, B; Bozma, I; Haliloglu, T

2009-01-01

This paper considers the generation of trajectories to a given protein conformation and presents a novel approach based on artificial potential functions—originally proposed for multi-robot navigation. The artificial potential function corresponds to a simplified energy model, but with the novelty that—motivated by work on robotic navigation—a nonlinear compositional scheme of constructing the energy model is adapted instead of an additive formulation. The artificial potential naturally gives rise to a dynamic system for the protein structure that ensures collision-free motion to an equilibrium point. In cases where the equilibrium point is the native conformation, the motion trajectory corresponds to the folding pathway. This framework is used to investigate folding in a variety of protein structures, and the results are compared with those of other approaches including experimental studies

RNA folding: structure prediction, folding kinetics and ion electrostatics.

Science.gov (United States)

Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

2015-01-01

Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

Do geographically isolated wetlands influence landscape functions?

OpenAIRE

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...

Many Activities, One Structure: Functional Plasticity of Ribozyme Folds

Directory of Open Access Journals (Sweden)

Matthew W.L. Lau

2016-11-01

Full Text Available Catalytic RNAs, or ribozymes, are involved in a number of essential biological processes, such as replication of RNA genomes and mobile genetic elements, RNA splicing, translation, and RNA degradation. The function of ribozymes requires the formation of active sites decorated with RNA functional groups within defined three-dimensional (3D structures. The genotype (sequence of RNAs ultimately determines what 3D structures they adopt (as a function of their environmental conditions. These 3D structures, in turn, give rise to biochemical activity, which can further elaborate them by catalytic rearrangements or association with other molecules. The fitness landscape of a non-periodic linear polymer, such as RNA, relates its primary structure to a phenotype. Two major challenges in the analysis of ribozymes is to map all possible genotypes to their corresponding catalytic activity (that is, to determine their fitness landscape experimentally, and to understand whether their genotypes and three-dimensional structures can support multiple different catalytic functions. Recently, the combined results of experiments that employ in vitro evolution methods, high-throughput sequencing and crystallographic structure determination have hinted at answers to these two questions: while the fitness landscape of ribozymes is rugged, meaning that their catalytic activity cannot be optimized by a smooth trajectory in sequence space, once an RNA achieves a stable three-dimensional fold, it can be endowed with distinctly different biochemical activities through small changes in genotype. This functional plasticity of highly structured RNAs may be particularly advantageous for the adaptation of organisms to drastic changes in selective pressure, or for the development of new biotechnological tools.

Landscape metrics application in ecological and visual landscape assessment

Directory of Open Access Journals (Sweden)

Gavrilović Suzana

2017-01-01

Full Text Available The development of landscape-ecological approach application in spatial planning provides exact theoretical and empirical evidence for monitoring ecological consequences of natural and/or anthropogenic factors, particularly changes in spatial structures caused by them. Landscape pattern which feature diverse landscape values is the holder of the unique landscape character at different spatial levels and represents a perceptual domain for its users. Using the landscape metrics, the parameters of landscape composition and configuration are mathematical algorithms that quantify the specific spatial characteristics used for interpretation of landscape features and processes (physical and ecological aspect, as well as forms (visual aspect and the meaning (cognitive aspect of the landscape. Landscape metrics has been applied mostly in the ecological and biodiversity assessments as well as in the determination of the level of structural change of landscape, but more and more applied in the assessment of the visual character of the landscape. Based on a review of relevant literature, the aim of this work is to show the main trends of landscape metrics within the aspect of ecological and visual assessments. The research methodology is based on the analysis, classification and systematization of the research studies published from 2000 to 2016, where the landscape metrics is applied: (1 the analysis of landscape pattern and its changes, (2 the analysis of biodiversity and habitat function and (3 a visual landscape assessment. By selecting representative metric parameters for the landscape composition and configuration, for each category is formed the basis for further landscape metrics research and application for the integrated ecological and visual assessment of the landscape values. Contemporary conceptualization of the landscape is seen holistically, and the future research should be directed towards the development of integrated landscape assessment

Stretched versus compressed exponential kinetics in α-helix folding

International Nuclear Information System (INIS)

Hamm, Peter; Helbing, Jan; Bredenbeck, Jens

2006-01-01

In a recent paper (J. Bredenbeck, J. Helbing, J.R. Kumita, G.A. Woolley, P. Hamm, α-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time resolved IR spectroscopy, Proc. Natl. Acad. Sci USA 102 (2005) 2379), we have investigated the folding of a photo-switchable α-helix with a kinetics that could be fit by a stretched exponential function exp(-(t/τ) β ). The stretching factor β became smaller as the temperature was lowered, a result which has been interpreted in terms of activated diffusion on a rugged energy surface. In the present paper, we discuss under which conditions diffusion problems occur with stretched exponential kinetics (β 1). We show that diffusion problems do have a strong tendency to yield stretched exponential kinetics, yet, that there are conditions (strong perturbation from equilibrium, performing the experiment in the folding direction) under which compressed exponential kinetics would be expected instead. We discuss the kinetics on free energy surfaces predicted by simple initiation-propagation models (zipper models) of α-helix folding, as well as by folding funnel models. We show that our recent experiment has been performed under condition for which models with strong downhill driving force, such as the zipper model, would predict compressed, rather than stretched exponential kinetics, in disagreement with the experimental observation. We therefore propose that the free energy surface along a reaction coordinate that governs the folding kinetics must be relatively flat and has a shape similar to a 1D golf course. We discuss how this conclusion can be unified with the thermodynamically well established zipper model by introducing an additional kinetic reaction coordinate

Analyzing high resolution topography for advancing the understanding of mass and energy transfer through landscapes: A review

Science.gov (United States)

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

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

Hierarchical Diagnosis of Vocal Fold Disorders

Science.gov (United States)

Nikkhah-Bahrami, Mansour; Ahmadi-Noubari, Hossein; Seyed Aghazadeh, Babak; Khadivi Heris, Hossein

This paper explores the use of hierarchical structure for diagnosis of vocal fold disorders. The hierarchical structure is initially used to train different second-level classifiers. At the first level normal and pathological signals have been distinguished. Next, pathological signals have been classified into neurogenic and organic vocal fold disorders. At the final level, vocal fold nodules have been distinguished from polyps in organic disorders category. For feature selection at each level of hierarchy, the reconstructed signal at each wavelet packet decomposition sub-band in 5 levels of decomposition with mother wavelet of (db10) is used to extract the nonlinear features of self-similarity and approximate entropy. Also, wavelet packet coefficients are used to measure energy and Shannon entropy features at different spectral sub-bands. Davies-Bouldin criterion has been employed to find the most discriminant features. Finally, support vector machines have been adopted as classifiers at each level of hierarchy resulting in the diagnosis accuracy of 92%.

Protein folding simulations by generalized-ensemble algorithms.

Science.gov (United States)

Yoda, Takao; Sugita, Yuji; Okamoto, Yuko

2014-01-01

In the protein folding problem, conventional simulations in physical statistical mechanical ensembles, such as the canonical ensemble with fixed temperature, face a great difficulty. This is because there exist a huge number of local-minimum-energy states in the system and the conventional simulations tend to get trapped in these states, giving wrong results. Generalized-ensemble algorithms are based on artificial unphysical ensembles and overcome the above difficulty by performing random walks in potential energy, volume, and other physical quantities or their corresponding conjugate parameters such as temperature, pressure, etc. The advantage of generalized-ensemble simulations lies in the fact that they not only avoid getting trapped in states of energy local minima but also allows the calculations of physical quantities as functions of temperature or other parameters from a single simulation run. In this article we review the generalized-ensemble algorithms. Four examples, multicanonical algorithm, replica-exchange method, replica-exchange multicanonical algorithm, and multicanonical replica-exchange method, are described in detail. Examples of their applications to the protein folding problem are presented.

Landscape Studio

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....

Landscape impact assessment of wind farm development in Dyfed

International Nuclear Information System (INIS)

Blandford, C.; White, S.; Garrad, A.D.; Morgan, C.A.

1992-01-01

Chris Blandford Associates, in association with Garrad Hassan and Partners, was commissioned to carry out a landscape impact assessment of wind turbine development in Dyfed. The study aims to identify those areas in Dyfed where, in terms of landscape impact, local authorities might seek either to exclude or encourage wind turbine development; provide guidelines to assist local authorities in judging the impact of wind turbine developments on the landscape; provide a basis and framework for the preparation of planning policy guidelines for acceptable wind turbine and wind farm developments in Dyfed. The study context reviews current Government energy and planning policies for the encouragement of wind turbine developments, as set out in the ''non-fossil fuel obligation'' and the draft planning policy guidance note for renewable energy published last December. (author)

Heterochiral Knottin Protein: Folding and Solution Structure.

Science.gov (United States)

Mong, Surin K; Cochran, Frank V; Yu, Hongtao; Graziano, Zachary; Lin, Yu-Shan; Cochran, Jennifer R; Pentelute, Bradley L

2017-10-31

Homochirality is a general feature of biological macromolecules, and Nature includes few examples of heterochiral proteins. Herein, we report on the design, chemical synthesis, and structural characterization of heterochiral proteins possessing loops of amino acids of chirality opposite to that of the rest of a protein scaffold. Using the protein Ecballium elaterium trypsin inhibitor II, we discover that selective β-alanine substitution favors the efficient folding of our heterochiral constructs. Solution nuclear magnetic resonance spectroscopy of one such heterochiral protein reveals a homogeneous global fold. Additionally, steered molecular dynamics simulation indicate β-alanine reduces the free energy required to fold the protein. We also find these heterochiral proteins to be more resistant to proteolysis than homochiral l-proteins. This work informs the design of heterochiral protein architectures containing stretches of both d- and l-amino acids.

Covering folded shapes

Directory of Open Access Journals (Sweden)

Oswin Aichholzer

2014-05-01

Full Text Available Can folding a piece of paper flat make it larger? We explore whether a shape S must be scaled to cover a flat-folded copy of itself. We consider both single folds and arbitrary folds (continuous piecewise isometries \\(S\\to\\mathbb{R}^2\\. The underlying problem is motivated by computational origami, and is related to other covering and fixturing problems, such as Lebesgue's universal cover problem and force closure grasps. In addition to considering special shapes (squares, equilateral triangles, polygons and disks, we give upper and lower bounds on scale factors for single folds of convex objects and arbitrary folds of simply connected objects.

Fluorescence of Alexa fluor dye tracks protein folding.

Directory of Open Access Journals (Sweden)

Simon Lindhoud

Full Text Available Fluorescence spectroscopy is an important tool for the characterization of protein folding. Often, a protein is labeled with appropriate fluorescent donor and acceptor probes and folding-induced changes in Förster Resonance Energy Transfer (FRET are monitored. However, conformational changes of the protein potentially affect fluorescence properties of both probes, thereby profoundly complicating interpretation of FRET data. In this study, we assess the effects protein folding has on fluorescence properties of Alexa Fluor 488 (A488, which is commonly used as FRET donor. Here, A488 is covalently attached to Cys69 of apoflavodoxin from Azotobacter vinelandii. Although coupling of A488 slightly destabilizes apoflavodoxin, the three-state folding of this protein, which involves a molten globule intermediate, is unaffected. Upon folding of apoflavodoxin, fluorescence emission intensity of A488 changes significantly. To illuminate the molecular sources of this alteration, we applied steady state and time-resolved fluorescence techniques. The results obtained show that tryptophans cause folding-induced changes in quenching of Alexa dye. Compared to unfolded protein, static quenching of A488 is increased in the molten globule. Upon populating the native state both static and dynamic quenching of A488 decrease considerably. We show that fluorescence quenching of Alexa Fluor dyes is a sensitive reporter of conformational changes during protein folding.

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.

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage mini protein

Science.gov (United States)

Day, Ryan; Paschek, Dietmar; Garcia, Angel E.

2012-01-01

We study the unbiased folding/unfolding thermodynamics of the Trp-cage miniprotein using detailed molecular dynamics simulations of an all-atom model of the protein in explicit solvent, using the Amberff99SB force field. Replica-exchange molecular dynamics (REMD) simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states, and at two densities. The obtained ensembles are shown to reach equilibrium in the 1 μs per replica timescale. The total simulation time employed in the calculations exceeds 100 μs. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, ΔG(P,T), over the whole region of temperature and pressures sampled in the simulations. The ΔG(P,T) diagram describes an ellipse over the range of temperatures and pressures sampled, predicting that the system can undergo pressure induced unfolding and cold denaturation at low temperatures and high pressures, and unfolding at low pressures and high temperatures. The calculated free energy function exhibits remarkably good agreement with the experimental folding transition temperature (Tf = 321 K), free energy and specific heat changes. However, changes in enthalpy and entropy are significantly different than the experimental values. We speculate that these differences may be due to the simplicity of the semi-empirical force field used in the simulations and that more elaborate force fields may be required to describe appropriately the thermodynamics of proteins. PMID:20408169

Recoverable and Programmable Collapse from Folding Pressurized Origami Cellular Solids.

Science.gov (United States)

Li, S; Fang, H; Wang, K W

2016-09-09

We report a unique collapse mechanism by exploiting the negative stiffness observed in the folding of an origami solid, which consists of pressurized cells made by stacking origami sheets. Such a collapse mechanism is recoverable, since it only involves rigid folding of the origami sheets and it is programmable by pressure control and the custom design of the crease pattern. The collapse mechanism features many attractive characteristics for applications such as energy absorption. The reported results also suggest a new branch of origami study focused on its nonlinear mechanics associated with folding.

Self-folding mechanics of graphene tearing and peeling from a substrate

Science.gov (United States)

He, Ze-Zhou; Zhu, Yin-Bo; Wu, Heng-An

2018-06-01

Understanding the underlying mechanism in the tearing and peeling processes of graphene is crucial for the further hierarchical design of origami-like folding and kirigami-like cutting of graphene. However, the complex effects among bending moduli, adhesion, interlayer interaction, and local crystal structure during origami-like folding and kirigami-like cutting remain unclear, resulting in challenges to the practical applications of existing theoretical and experimental findings as well as to potential manipulations of graphene in metamaterials and nanodevices. Toward this end, classical molecular dynamics (MD) simulations are performed with synergetic theoretical analysis to explore the tearing and peeling of self-folded graphene from a substrate driven by external force and by thermal activation. It is found that the elastic energy localized at the small folding ridge plays a significant role in the crack trajectory. Due to the extremely small bending modulus of monolayer graphene, its taper angle when pulled by an external force follows a scaling law distinct from that in case of bilayer graphene. With the increase in the initial width of the folding ridge, the self-folded graphene, motivated by thermal fluctuations, can be self-assembled by spontaneous self-tearing and peeling from a substrate. Simultaneously, the scaling law between the taper angle and adhesive energy is independent of the motivations for thermal activation-induced self-assembly and external force tearing, providing effective insights into the underlying physics for graphene-based origami-like folding and kirigami-like cutting.

Landscape moderation of biodiversity patterns and processes - eight hypotheses.

Science.gov (United States)

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

Jointly optimizing selection of fuel treatments and siting of forest biomass-based energy production facilities for landscape-scale fire hazard reduction.

Science.gov (United States)

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...

Sustainable City Regions: Re-localising Landscapes in a Globalising World

Directory of Open Access Journals (Sweden)

Robert Thayer Jnr

2004-06-01

Full Text Available This paper emphasises physical, technological and economic variables in a globalising world, and how they might influence local economies and local landscapes. With the expected 'big rollover' in demand versus supply of oil in the next decade, the scale of the landscape will change in response to a permanent rise in the price of transportation and shipping fuels. Air travel will become less accessible, as will shipping of high mass, low value-added materials and goods. This will necessitate the re-establishment of more local supplies and shorter transport distances for people and goods, and for the first time in human history the perceived size of the world will expand. In response, the 'grain' of the landscape will become finer. More people will populate the rural landscape, while cities and towns will become more compact. The landscape is influenced by the three major operative technological systems (matter, energy and information. While the depletion of oil will greatly affect matter and energy, it will have less influence on information, which is relatively immune from entropic thermodynamic effects. While source-to-end-use distances will shorten, world per-capita energy expenditures will fall, and more local goods will be created and consumed, it remains to be seen whether this contraction in the scale of the instrumental landscape will be matched by more localised ownership, or by continued globalisation of corporate systems of production and distribution. Assuming the former is preferable, the paper concludes by suggesting that the bioregion, or natural 'life place', is the appropriate location for the protection of biodiversity, sustained use of resources, and identity and life satisfaction of local inhabitants.

The greenGain project - Biomass from landscape conservation and maintenance work for renewable energy production in the EU

Science.gov (United States)

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.

Landscape Ecology

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...

Landscape evolution space and the relative importance of geomorphic processes and controls

Science.gov (United States)

Phillips, Jonathan D.

2009-08-01

The concept of landscape evolution space (LES) is introduced as a tool for assessing landscapes and geomorphic systems, intended to be a systematic means for assessing the various factors that contribute to the potential for change in geomorphic systems. The LES conceptual model is based on the energy and mass available to drive and accommodate landscape evolution. An n-dimensional landscape evolution space is defined not only by spatial coordinates, but also by the availability of mass and energy. The LES is thus a space or hypervolume representing the resources available for geomorphic evolution and landscape change. An expression for LES is derived based on elevation, material density, surface area, and inputs of solar, meteoric, and biological energy and mass. Though primarily an heuristic device, the LES model can be used to address concrete problems. Two examples are given. In one, increased surface area due to topographic roughening and dissection of an incised plateau is found to only slightly offset erosional removals of mass in terms of the magnitude of the LES. In the other, sensitivity of coastal plain rivers to several impacts of sea level and climate change is explored. The LES model also leads to the concept of a geomorphological niche, representing the resources available to drive or support a specific process or suite of processes. Considerations of landscape evolution have traditionally focused on the interplay of endogenic vs. exogenic processes, uplift vs. denudation, or soil formation vs. erosion. The LES model explicitly broadens the conceptual framework of landscape evolution beyond the traditional dialectics.

European landscape architecture and territorial strategies for water landscapes

DEFF Research Database (Denmark)

Diedrich, Lisa Babette

2010-01-01

This article sums up the author’s lecture at the 2009 Sydney Resilient Water Landscapes Symposium and presents a series of realized or planned European landscape architectural and urbanistic projects on water landscapes taken from the recently published book On Site/ Landscape Architecture Europe...... and accompanying reflections. The hypothesis is that further scientific research can help defining weaknesses and strengths of the existing water landscape designs in terms of resilience, extract principles and tools, improve the weak ones and communicate the strong ones and develop general quality criteria...... and tools for future resilient water landscapes....

Fold distributions at clover, crystal and segment levels for segmented clover detectors

International Nuclear Information System (INIS)

Kshetri, R; Bhattacharya, P

2014-01-01

Fold distributions at clover, crystal and segment levels have been extracted for an array of segmented clover detectors for various gamma energies. A simple analysis of the results based on a model independant approach has been presented. For the first time, the clover fold distribution of an array and associated array addback factor have been extracted. We have calculated the percentages of the number of crystals and segments that fire for a full energy peak event

Microclimate landscape design at southern integrated terminal Bandar Tasik Selatan, Kuala Lumpur

Science.gov (United States)

Phin, L. H.; Krisantia, I.

2018-01-01

Bandar Tasik Selatan is the integrated transport terminal has high energy consuming, high carbon emission and poor linkage. However, microclimate can be reduced through landscape design. This paper is a study to achieve energy efficiency and improve microclimate in the urban area. The research area is at Southern integrated terminal Bandar Tasik Selatan Kuala Lumpur Malaysia. It is carried out through a case study and microclimate analyzed using System Modeling method. System modelling using in this research is system energy budget of the microclimate at a site is a balance between the radiant energy supplied and the energy removed by all consumers. The finding indicated the microclimatic components that can be modified through landscape design are solar radiation, wind and precipitation can create thermal comfort, energy efficiency and others benefits.Through this research, provide more green space to achieve energy efficiency and improve microclimate of the site, introducing vertical landscape and proper planting selection to improve air quality, introducing green energy as part of the source of power supply and to promote integration of terminal building and rail systems by unify them using softscape

Partial wave analysis for folded differential cross sections

Science.gov (United States)

Machacek, J. R.; McEachran, R. P.

2018-03-01

The value of modified effective range theory (MERT) and the connection between differential cross sections and phase shifts in low-energy electron scattering has long been recognized. Recent experimental techniques involving magnetically confined beams have introduced the concept of folded differential cross sections (FDCS) where the forward (θ ≤ π/2) and backward scattered (θ ≥ π/2) projectiles are unresolved, that is the value measured at the angle θ is the sum of the signal for particles scattered into the angles θ and π - θ. We have developed an alternative approach to MERT in order to analyse low-energy folded differential cross sections for positrons and electrons. This results in a simplified expression for the FDCS when it is expressed in terms of partial waves and thereby enables one to extract the first few phase shifts from a fit to an experimental FDCS at low energies. Thus, this method predicts forward and backward angle scattering (0 to π) using only experimental FDCS data and can be used to determine the total elastic cross section solely from experimental results at low-energy, which are limited in angular range.

Vocal Fold Paralysis

Science.gov (United States)

... here Home » Health Info » Voice, Speech, and Language Vocal Fold Paralysis On this page: What is vocal fold ... Where can I get additional information? What is vocal fold paralysis? Structures involved in speech and voice production ...

Folding models for elastic and inelastic scattering

International Nuclear Information System (INIS)

Satchler, G.R.

1982-01-01

The most widely used models are the optical model potential (OMP) for elastic scattering, and its generalization to non-spherical shapes, the deformed optical model potential (DOMP) for inelastic scattering. These models are simple and phenomenological; their parameters are adjusted so as to reproduce empirical data. Nonetheless, there are certain, not always well-defined, constraints to be imposed. The potential shapes and their parameter values must be reasonable and should vary in a smooth and systematic way with the masses of the colliding nuclei and their energy. One way of satisfying these constraints, without going back to a much more fundamental theory, is through the use of folding models. The basic justification for using potentials of the Woods-Saxon shape for nucleon-nucleus scattering, for example, is our knowledge that a nuclear density distribution is more-or-less constant in the nuclear interior with a diffuse surface. When this is folded with a short-range nucleon-nucleon interaction, the result is a similar shape with a more diffuse surface. Folding procedures allow us to incorporate many aspects of nuclear structure (although the nuclear size is one of the most important), as well as theoretical ideas about the effective interaction of two nucleons within nuclear matter. It also provides us with a means of linking information obtained from nuclear (hadronic) interactions with that from other sources, as well as correlating that from the use of different hadronic probes. Folding model potentials, single-folded potentials, and the double-folding model including applications to heavy-ion scattering are discussed

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments

DEFF Research Database (Denmark)

Seemann, Ernst Stefan; Gorodkin, Jan; Backofen, Rolf

2008-01-01

Computational methods for determining the secondary structure of RNA sequences from given alignments are currently either based on thermodynamic folding, compensatory base pair substitutions or both. However, there is currently no approach that combines both sources of information in a single...... the corresponding probability of being single stranded. Furthermore, we found that structurally conserved RNA motifs are mostly supported by folding energies. Other problems (e.g. RNA-folding kinetics) may also benefit from employing the principles of the model we introduce. Our implementation, PETfold, was tested...

The significance of the amorphous potential energy landscape for dictating glassy dynamics and driving solid-state crystallisation

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...

There and back again: Two views on the protein folding puzzle.

Science.gov (United States)

Finkelstein, Alexei V; Badretdin, Azat J; Galzitskaya, Oxana V; Ivankov, Dmitry N; Bogatyreva, Natalya S; Garbuzynskiy, Sergiy O

2017-07-01

The ability of protein chains to spontaneously form their spatial structures is a long-standing puzzle in molecular biology. Experimentally measured folding times of single-domain globular proteins range from microseconds to hours: the difference (10-11 orders of magnitude) is the same as that between the life span of a mosquito and the age of the universe. This review describes physical theories of rates of overcoming the free-energy barrier separating the natively folded (N) and unfolded (U) states of protein chains in both directions: "U-to-N" and "N-to-U". In the theory of protein folding rates a special role is played by the point of thermodynamic (and kinetic) equilibrium between the native and unfolded state of the chain; here, the theory obtains the simplest form. Paradoxically, a theoretical estimate of the folding time is easier to get from consideration of protein unfolding (the "N-to-U" transition) rather than folding, because it is easier to outline a good unfolding pathway of any structure than a good folding pathway that leads to the stable fold, which is yet unknown to the folding protein chain. And since the rates of direct and reverse reactions are equal at the equilibrium point (as follows from the physical "detailed balance" principle), the estimated folding time can be derived from the estimated unfolding time. Theoretical analysis of the "N-to-U" transition outlines the range of protein folding rates in a good agreement with experiment. Theoretical analysis of folding (the "U-to-N" transition), performed at the level of formation and assembly of protein secondary structures, outlines the upper limit of protein folding times (i.e., of the time of search for the most stable fold). Both theories come to essentially the same results; this is not a surprise, because they describe overcoming one and the same free-energy barrier, although the way to the top of this barrier from the side of the unfolded state is very different from the way from the

Multiple coupled landscapes and non-adiabatic dynamics with applications to self-activating genes.

Science.gov (United States)

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.

Experimental evidence of dynamic re-organization of evolving landscapes under changing climatic forcing

Science.gov (United States)

Singh, Arvind; Tejedor, Alejandro; Zaliapin, Ilya; Reinhardt, Liam; Foufoula-Georgiou, Efi

2015-04-01

The aim of this study is to better understand the dynamic re-organization of an evolving landscape under a scenario of changing climatic forcing for improving our knowledge of geomorphic transport laws under transient conditions and developing predictive models of landscape response to external perturbations. Real landscape observations for long-term analysis are limited and to this end a high resolution controlled laboratory experiment was conducted at the St. Anthony Falls laboratory at the University of Minnesota. Elevation data were collected at temporal resolution of 5 mins and spatial resolution of 0.5 mm as the landscape approached steady state (constant uplift and precipitation rate) and in the transient state (under the same uplift and 5x precipitation). The results reveal rapid topographic re-organization under a five-fold precipitation increase with the fluvial regime expanding into the previously debris dominated regime, accelerated erosion happening at hillslope scales, and rivers shifting from an erosion-limited to a transport-limited regime. From a connectivity and clustering analysis of the erosional and depositional events, we demonstrate the strikingly different spatial patterns of landscape evolution under steady-state (SS) and transient-state (TS), even when the time under SS is "stretched" compared to that under TS such as to match the total volume and PDF of erosional and depositional amounts. We quantify the spatial coupling of hillslopes and channels and demonstrate that hillslopes lead and channels follow in re-organizing the whole landscape under such an amplified precipitation regime.

Emergent reorganization of an evolving experimental landscape under changing climatic forcing

Science.gov (United States)

Singh, A.; Tejedor, A.; Zaliapin, I. V.; Reinhardt, L.; Foufoula-Georgiou, E.

2014-12-01

Understanding landscape re-organization under changing climatic forcing is fundamental to advancing our understanding of geomorphic transport laws under transient conditions, developing predictive models of landscape response to external perturbations, and interpreting the stratigraphic record for past climates by incorporating possible regime shifts. Real landscape observations for long-term analysis are limited and to this end a high resolution controlled laboratory experiment was conducted at the St. Anthony Falls laboratory at the University of Minnesota. Elevation data were collected at temporal resolution of 5 mins and spatial resolution of 0.5 mm as the landscape approached steady state (for a constant uplift and precipitation rate) and in the transient state (under the same uplift and 5x precipitation). The results reveal rapid topographic re-organization under a five-fold precipitation increase with the fluvial regime expanding into previously debris dominated regime, accelerated erosion happening at hillslope scales, and rivers shifting from an erosion-limited to a transport-limited regime. By studying the space-time structure of the individual erosional and depositional events in terms of their size, location, clustering, and total volume we report complex space-time patterns of change which are scale-dependent and bounded by the river network topology. At the same time, the river network topology itself adjusts at smaller scales, with new channels added to accommodate increased hillslope erosional transport, further adjusting the landscape. Some new ideas related to landscape variability and entropy evolution at different scales during steady and transient states and the possibility of analyzing the self-organization with Optimal Mass Transport (OMT) metrics to infer possible underlying "optimality" principles governing the re-organization will also be presented.

Directed Magnetic Particle Transport above Artificial Magnetic Domains Due to Dynamic Magnetic Potential Energy Landscape Transformation.

Science.gov (United States)

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.

A multi-directional rapidly exploring random graph (mRRG) for protein folding

KAUST Repository

Nath, Shuvra Kanti; Thomas, Shawna; Ekenna, Chinwe; Amato, Nancy M.

2012-01-01

Modeling large-scale protein motions, such as those involved in folding and binding interactions, is crucial to better understanding not only how proteins move and interact with other molecules but also how proteins misfold, thus causing many devastating diseases. Robotic motion planning algorithms, such as Rapidly Exploring Random Trees (RRTs), have been successful in simulating protein folding pathways. Here, we propose a new multi-directional Rapidly Exploring Random Graph (mRRG) specifically tailored for proteins. Unlike traditional RRGs which only expand a parent conformation in a single direction, our strategy expands the parent conformation in multiple directions to generate new samples. Resulting samples are connected to the parent conformation and its nearest neighbors. By leveraging multiple directions, mRRG can model the protein motion landscape with reduced computational time compared to several other robotics-based methods for small to moderate-sized proteins. Our results on several proteins agree with experimental hydrogen out-exchange, pulse-labeling, and F-value analysis. We also show that mRRG covers the conformation space better as compared to the other computation methods. Copyright © 2012 ACM.

Landscape services as boundary concept in landscape governance: Building social capital in collaboration and adapting the landscape

NARCIS (Netherlands)

Westerink, Judith; Opdam, Paul; Rooij, Van Sabine; Steingröver, Eveliene

2017-01-01

The landscape services concept provides a lens to study relations within the social-ecological networks that landscapes are, and to identify stakeholders as either providers or beneficiaries. However, landscape services can also be used as a boundary concept in collaborative landscape governance. We

Critical Zone Services as a Measure for Evaluating the Trade-offs in Intensively Managed Landscapes

Science.gov (United States)

Richardson, M.; Kumar, P.

2015-12-01

The Critical Zone includes the range of biophysical processes occurring from the top of the vegetation canopy to the weathering zone below the groundwater table. These services (Field et al. 2015) provide a measure to value processes that support the goods and services from our landscapes. In intensively managed landscapes the provisioning and regulating services are being altered through anthropogenic energy inputs so as to derive more agricultural productivity from the landscapes. Land use change and other alterations to the environment result in positive and/or negative net Critical Zone services. Through studies in the Critical Zone Observatory for Intensively Managed Landscapes (IMLCZO), this research seeks to answer questions such as: Are perennial bioenergy crops or annual replaced crops better for the land and surrounding environment? How do we evaluate the products and services from the land for the energy and resources we put in? Before the economic valuation of Critical Zone services, these questions seemed abstract. However, with developments such as Critical Zone services and life cycle assessments, they are more concrete. To evaluate the trade-offs between positive and negative impacts, life cycle assessments are used to create an inventory of all the energy inputs and outputs in a landscape management system. Total energy is computed by summing the mechanical energy used to construct tile drains, fertilizer, and other processes involved in intensely managed landscapes and the chemical energy gained by the production of biofuels from bioenergy crops. A multi-layer canopy model (MLCan) computes soil, water, and nutrient outputs for each crop type, which can be translated into Critical Zone services. These values are then viewed alongside the energy inputs into the system to show the relationship between agricultural practices and their corresponding ecosystem and environmental impacts.

Impacts of the cultivation of energy crops for generation of biogas on the landscape structure and avifauna; Auswirkungen des Energiepflanzenanbaus zur Biogaserzeugung auf Landschaftsstruktur und Avifauna

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

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.

Landscape and Energy%景观和能源

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.

A landscape ecology approach to assessing development impacts in the tropics: A geothermal energy example in Hawaii

Science.gov (United States)

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.

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

KAUST Repository

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.

Hybrid organic–inorganic inks flatten the energy landscape in colloidal quantum dot solids

KAUST Repository

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.

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.

Geomorpho-Landscapes

Science.gov (United States)

Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

2014-05-01

Landscape is the object of human perceptions, being the image of spatial organization of elements and structures: mankind lives the first approach with the environment, viewing and feeling the landscape. Many definitions of landscape have been given over time: in this case we refer to the Landscape defined as the result of interaction among physical, biotic and anthropic phenomena acting in a different spatial-temporal scale (Foreman & Godron) Following an Aristotelic approach in studying nature, we can assert that " Shape is synthesis": so it is possible to read the land features as the expression of the endogenous and exogenous processes that mould earth surfaces; moreover, Landscape is the result of the interaction of natural and cultural components, and conditions the spatial-temporal development of a region. The study of the Landscape offers results useful in order to promote sustainable development, ecotourism, enhancement of natural and cultural heritage, popularization of the scientific knowledge. In Italy, a very important GIS-based tool to represent the territory is the "Carta della Natura" ("Map of Nature", presently coordinated by the ISPRA) that aims at assessing the state of the whole Italian territory, analyzing Landscape. The methodology follows a holistic approach, taking into consideration all the components of a landscape and then integrating the information. Each individual landscape, studied at different scales, shows distinctive elements: structural, which depend on physical form and specific spatial organization; functional, which depend on relationships created between biotic and abiotic elements, and dynamic, which depend on the successive evolution of the structure. The identification of the landscape units, recognized at different scales of analysis, allows an evaluation of the state of the land, referring to the dual risk/resource which characterizes the Italian country. An interesting opportunity is to discover those areas of unusual

Landscape impact assessment for wind turbine development in Dyfed

International Nuclear Information System (INIS)

Blandford, C.; White, S.; Thomas, B.; Osment, F.

1994-01-01

The study aims to identify those areas in Dyfed where, in terms of landscape impact, local authorities might seek to exclude or encourage wind turbine development, provide guidelines which will assist local authorities in judging the impact of wind turbine developments on the landscape and provide a basis and framework for the preparation of planning policy guidelines for acceptable wind turbine and wind farm developments in Dyfed. The study context reviews current Government energy and planning policies for the encouragement of wind turbine developments. Dyfed County Council's relevant Structure Plan policies are also considered, as are the new draft policies relating directly to wind energy released by other authorities. The sizes and status of planning applications are summarised and the landscape implications and precedent set by the test case at Mynydd-y-Cemais is discussed. Public perception of wind power is reviewed in the context of research in Europe and the USA. (author)

Protein folding: Over half a century lasting quest. Comment on "There and back again: Two views on the protein folding puzzle" by Alexei V. Finkelstein et al.

Science.gov (United States)

Krokhotin, Andrey; Dokholyan, Nikolay V.

2017-07-01

Most proteins fold into unique three-dimensional (3D) structures that determine their biological functions, such as catalytic activity or macromolecular binding. Misfolded proteins can pose a threat through aberrant interactions with other proteins leading to a number of diseases including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis [1,2]. What does determine 3D structure of proteins? The first clue to this question came more than fifty years ago when Anfinsen demonstrated that unfolded proteins can spontaneously fold to their native 3D structures [3,4]. Anfinsen's experiments lead to the conclusion that proteins fold to unique native structure corresponding to the stable and kinetically accessible free energy minimum, and protein native structure is solely determined by its amino acid sequence. The question of how exactly proteins find their free energy minimum proved to be a difficult problem. One of the puzzles, initially pointed out by Levinthal, was an inconsistency between observed protein folding times and theoretical estimates. A self-avoiding polymer model of a globular protein of 100-residues length on a cubic lattice can sample at least 1047 states. Based on the assumption that conformational sampling occurs at the highest vibrational mode of proteins (∼picoseconds), predicted folding time by searching among all the possible conformations leads to ∼1027 years (much larger than the age of the universe) [5]. In contrast, observed protein folding time range from microseconds to minutes. Due to tremendous theoretical progress in protein folding field that has been achieved in past decades, the source of this inconsistency is currently understood that is thoroughly described in the review by Finkelstein et al. [6].

Biomass yield from an urban landscape

Science.gov (United States)

Utilizing biomass from urban landscapes could significantly contribute to the nation’s renewable energy needs. In 2007, an experiment was begun to evaluate the biomass production from a bermudagrass, Cynodon dactylon var. dactylon (L.) Pers., lawn in Woodward, Oklahoma and to estimate the potential...

Free energy landscape of dissociative adsorption of methane on ideal and defected graphene from ab initio simulations

Science.gov (United States)

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.

Do geographically isolated wetlands influence landscape functions?

Science.gov (United States)

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.

Folding model study of the charge-exchange scattering to the isobaric analog state and implication for the nuclear symmetry energy

International Nuclear Information System (INIS)

Khoa, Dao T.; Thang, Dang Ngoc; Loc, Bui Minh

2014-01-01

The Fermi transition (ΔL = ΔS = 0 and ΔT = 1) between the nuclear isobaric analog states (IAS), induced by the charge-exchange (p, n) or ( 3 He, t) reaction, can be considered as ''elastic'' scattering of proton or 3 He by the isovector term of the optical potential (OP) that flips the projectile isospin. The accurately measured (p, n) or ( 3 He, t) scattering cross section to the IAS can be used, therefore, to probe the isospin dependence of the proton or 3 He optical potential. Within the folding model, the isovector part of the OP is determined exclusively by the neutron-proton difference in the nuclear densities and the isospin dependence of the effective nucleon-nucleon (NN) interaction. Because the isovector coupling explicitly links the isovector part of the proton or 3 He optical potential to the cross section of the charge-exchange (p, n) or ( 3 He, t) scattering to the IAS, the isospin dependence of the effective (in-medium) NN interaction can be well tested in the folding model analysis of these charge-exchange reactions. On the other hand, the same isospin- and density-dependent NN interaction can also be used in a Hartree-Fock calculation of asymmetric nuclear matter, to estimate the nuclear matter energy and its asymmetry part (the nuclear symmetry energy). As a result, the fine-tuning of the isospin dependence of the effective NN interaction against the measured (p, n) or ( 3 He, t) cross sections should allow us to make some realistic prediction of the nuclear symmetry energy and its density dependence. (orig.)

Vocal fold contact patterns based on normal modes of vibration.

Science.gov (United States)

Smith, Simeon L; Titze, Ingo R

2018-05-17

The fluid-structure interaction and energy transfer from respiratory airflow to self-sustained vocal fold oscillation continues to be a topic of interest in vocal fold research. Vocal fold vibration is driven by pressures on the vocal fold surface, which are determined by the shape of the glottis and the contact between vocal folds. Characterization of three-dimensional glottal shapes and contact patterns can lead to increased understanding of normal and abnormal physiology of the voice, as well as to development of improved vocal fold models, but a large inventory of shapes has not been directly studied previously. This study aimed to take an initial step toward characterizing vocal fold contact patterns systematically. Vocal fold motion and contact was modeled based on normal mode vibration, as it has been shown that vocal fold vibration can be almost entirely described by only the few lowest order vibrational modes. Symmetric and asymmetric combinations of the four lowest normal modes of vibration were superimposed on left and right vocal fold medial surfaces, for each of three prephonatory glottal configurations, according to a surface wave approach. Contact patterns were generated from the interaction of modal shapes at 16 normalized phases during the vibratory cycle. Eight major contact patterns were identified and characterized by the shape of the flow channel, with the following descriptors assigned: convergent, divergent, convergent-divergent, uniform, split, merged, island, and multichannel. Each of the contact patterns and its variation are described, and future work and applications are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Identifying Greater Sage-Grouse source and sink habitats for conservation planning in an energy development landscape.

Science.gov (United States)

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

The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study

Science.gov (United States)

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

Crosstalk properties of 36-fold segmented symmetric hexagonal HPGe detectors

International Nuclear Information System (INIS)

Bruyneel, Bart; Reiter, Peter; Wiens, Andreas; Eberth, Juergen; Hess, Herbert; Pascovici, Gheorghe; Warr, Nigel; Weisshaar, Dirk

2009-01-01

Crosstalk properties of three 36-fold segmented, symmetric, large volume, HPGe detectors from the AGATA Collaboration were deduced from coincidence measurements performed with digitized segment and core signals after interaction of γ rays with energies of 1.33 MeV. The mean energy values measured by the core signal fluctuate for γ-ray interactions with energy deposited in two segments. A regular pattern is observed depending on the hit segment combinations. The core energy shifts deviate 0.03-0.06% from the average energy calibration. The segment-sum energy is reduced with respect to the core energy as a function of the decoupling capacitance and the segment multiplicity. The deviation of the segment-sum energies from multiplicity two events fluctuates within an interval of less than 0.1% depending on the different segment combinations. The energy shifts caused by crosstalk for the core and segment signals are comparable for all three detectors. A linear electronic model of the detector and preamplifier assembly was developed to evaluate the results. The fold-dependent energy shifts of the segment-sum energies are reproduced. The model yields a constant shift in all segments, proportional to the core signal. The measured crosstalk pattern and its intensity variation in the segments agree well with the calculated values. The regular variation observed in the core energies cannot be directly related to crosstalk and may be caused by other effects like electron trapping.

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

Science.gov (United States)

Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

2016-04-20

RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Bayesian energy landscape tilting: towards concordant models of molecular ensembles.

Science.gov (United States)

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.

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.)

Numerical construction of the p(fold) (committor) reaction coordinate for a Markov process.

Science.gov (United States)

Krivov, Sergei V

2011-10-06

To simplify the description of a complex multidimensional dynamical process, one often projects it onto a single reaction coordinate. In protein folding studies, the folding probability p(fold) is an optimal reaction coordinate which preserves many important properties of the dynamics. The construction of the coordinate is difficult. Here, an efficient numerical approach to construct the p(fold) reaction coordinate for a Markov process (satisfying the detailed balance) is described. The coordinate is obtained by optimizing parameters of a chosen functional form to make a generalized cut-based free energy profile the highest. The approach is illustrated by constructing the p(fold) reaction coordinate for the equilibrium folding simulation of FIP35 protein reported by Shaw et al. (Science 2010, 330, 341-346). © 2011 American Chemical Society

Connecting Brabant's cover sand landscapes through landscape history

Science.gov (United States)

Heskes, Erik; van den Ancker, Hanneke; Jungerius, Pieter Dirk; Harthoorn, Jaap; Maes, Bert; Leenders, Karel; de Jongh, Piet; Kluiving, Sjoerd; van den Oetelaar, Ger

2015-04-01

Noord-Brabant has the largest variety of cover sand landscapes in The Netherlands, and probably in Western Europe. During the Last Ice Age the area was not covered by land ice and a polar desert developed in which sand dunes buried the existing river landscapes. Some of these polar dune landscapes experienced a geomorphological and soil development that remained virtually untouched up to the present day, such as the low parabolic dunes of the Strabrechtse Heide or the later and higher dunes of the Oisterwijkse Vennen. As Noord-Brabant lies on the fringe of a tectonic basin, the thickness of cover sand deposits in the Centrale Slenk, part of a rift through Europe, amounts up to 20 metres. Cover sand deposits along the fault lines cause the special phenomenon of 'wijst' to develop, in which the higher grounds are wetter than the boarding lower grounds. Since 4000 BC humans settled in these cover sand landscapes and made use of its small-scale variety. An example are the prehistoric finds on the flanks and the historic towns on top of the 'donken' in northwest Noord-Brabant, where the cover sand landscapes are buried by river and marine deposits and only the peaks of the dunes protrude as donken. Or the church of Handel that is built beside a 'wijst' source and a site of pilgrimage since living memory. Or the 'essen' and plaggen agriculture that developed along the stream valleys of Noord-Brabant from 1300 AD onwards, giving rise to geomorphological features as 'randwallen' and plaggen soils of more than a metre thickness. Each region of Brabant each has its own approach in attracting tourists and has not yet used this common landscape history to connect, manage and promote their territories. We propose a landscape-historical approach to develop a national or European Geopark Brabants' cover sand landscapes, in which each region focuses on a specific part of the landscape history of Brabant, that stretches from the Late Weichselian polar desert when the dune

Mountains and energy transition. Status of use of renewable energies and challenges for their development in mountain areas - Renewable energies Volume 1

International Nuclear Information System (INIS)

Peguin, Marion; Moncorps, Sebastien; Fourcade, Michel; Denis, Helene

2013-10-01

After an overview of challenges related to the development of renewable energies in mountain areas (conservation of biodiversity and landscapes, main legal measures regarding biodiversity and landscapes), this report proposes an overview of the status and potentials of the different renewable energies (solar, wind, hydroelectricity, bio-energies, geothermal) in mountain areas. It proposes an assessment (strengths and weaknesses) and recommendations for solar, wind, hydroelectricity and bio energies in mountain areas

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 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.

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

Towards an Integrated Energy Landscape

NARCIS (Netherlands)

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

Machine learning for the structure-energy-property landscapes of molecular crystals.

Science.gov (United States)

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.

Uncovering the underlying physical mechanisms of biological systems via quantification of landscape and flux

International Nuclear Information System (INIS)

Xu Li; Chu Xiakun; Yan Zhiqiang; Zheng Xiliang; Zhang Kun; Zhang Feng; Yan Han; Wu Wei; Wang Jin

2016-01-01

In this review, we explore the physical mechanisms of biological processes such as protein folding and recognition, ligand binding, and systems biology, including cell cycle, stem cell, cancer, evolution, ecology, and neural networks. Our approach is based on the landscape and flux theory for nonequilibrium dynamical systems. This theory provides a unifying principle and foundation for investigating the underlying mechanisms and physical quantification of biological systems. (topical review)

Solitons and protein folding: An In Silico experiment

Energy Technology Data Exchange (ETDEWEB)

Ilieva, N., E-mail: nevena.ilieva@parallel.bas.bg [Institute of Information and Communication Technologies, Bulgarian Aacademy of Sciences, Sofia (Bulgaria); Dai, J., E-mail: daijing491@gmail.com [School of Physics, Beijing Institute of Technology, Beijing (China); Sieradzan, A., E-mail: adams86@wp.pl [Faculty of Chemistry, University of Gdańsk, Gdańsk (Poland); Niemi, A., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden); LMPT–CNRS, Université de Tours, Tours (France)

2015-10-28

Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

Solitons and protein folding: An In Silico experiment

International Nuclear Information System (INIS)

Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.

2015-01-01

Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics

Assessment of landscape diversity and determination of landscape hotspots - a case of Slovenia

Science.gov (United States)

Perko, Drago; Ciglič, Rok; Hrvatin, Mauro

2017-04-01

Areas with high landscape diversity can be regarded as landscape hotspots, and vice versa areas with low landscape diversity can be marked as landscape coldspots. The main purpose of this paper is to use quantitative geoinformatical approach and identify parts of our test area (the country of Slovenia) that can be described as very diverse according to natural landscapes and natural elements. We used different digital raster data of natural elements and landscape classifications and defined landscape diversity and landscape hotspots. We defined diversity for each raster pixel by counting the number of different unique types of landscape elements and types of landscapes in its neighborhood. Namely, the method was used separately to define diversity according to natural elements (types of relief forms, rocks, and vegetation) and diversity according to existing geographical landscape classifications of Slovenia (types of landscapes). In both cases one-tenth of Slovenia's surface with the highest landscape diversity was defined as landscape hotspots. The same applies to the coldspots. Additionally we tested the same method of counting different types of landscapes in certain radius also for the area of Europe in order to find areas that are more diverse at continental level. By doing so we were able to find areas that have similar level of diversity as Slovenia according to different European landscape classifications. Areas with landscape diversity may have an advantage in economic development, especially in tourism. Such areas are also important for biodiversity, habitat, and species diversity. On the other hand, localities where various natural influences mix can also be areas where it is hard to transfer best practices from one place to another because of the varying responses of the landscapes to human intervention. Thus it is important to know where areas with high landscape diversity are.

Folding model study of the charge-exchange scattering to the isobaric analog state and implication for the nuclear symmetry energy

Energy Technology Data Exchange (ETDEWEB)

Khoa, Dao T.; Thang, Dang Ngoc [VINATOM, Institute for Nuclear Science and Technique, Hanoi (Viet Nam); Loc, Bui Minh [VINATOM, Institute for Nuclear Science and Technique, Hanoi (Viet Nam); University of Pedagogy, Ho Chi Minh City (Viet Nam)

2014-02-15

The Fermi transition (ΔL = ΔS = 0 and ΔT = 1) between the nuclear isobaric analog states (IAS), induced by the charge-exchange (p, n) or ({sup 3}He, t) reaction, can be considered as ''elastic'' scattering of proton or {sup 3}He by the isovector term of the optical potential (OP) that flips the projectile isospin. The accurately measured (p, n) or ({sup 3}He, t) scattering cross section to the IAS can be used, therefore, to probe the isospin dependence of the proton or {sup 3}He optical potential. Within the folding model, the isovector part of the OP is determined exclusively by the neutron-proton difference in the nuclear densities and the isospin dependence of the effective nucleon-nucleon (NN) interaction. Because the isovector coupling explicitly links the isovector part of the proton or {sup 3}He optical potential to the cross section of the charge-exchange (p, n) or ({sup 3}He, t) scattering to the IAS, the isospin dependence of the effective (in-medium) NN interaction can be well tested in the folding model analysis of these charge-exchange reactions. On the other hand, the same isospin- and density-dependent NN interaction can also be used in a Hartree-Fock calculation of asymmetric nuclear matter, to estimate the nuclear matter energy and its asymmetry part (the nuclear symmetry energy). As a result, the fine-tuning of the isospin dependence of the effective NN interaction against the measured (p, n) or ({sup 3}He, t) cross sections should allow us to make some realistic prediction of the nuclear symmetry energy and its density dependence. (orig.)

Quantum Nuclear Extension of Electron Nuclear Dynamics on Folded Effective-Potential Surfaces

DEFF Research Database (Denmark)

Hall, B.; Deumens, E.; Ohrn, Y.

2014-01-01

A perennial problem in quantum scattering calculations is accurate theoretical treatment of low energy collisions. We propose a method of extracting a folded, nonadiabatic, effective potential energy surface from electron nuclear dynamics (END) trajectories; we then perform nuclear wave packet...

Does reintroducing large wood influence the hydraulic landscape of a lowland river system?

Science.gov (United States)

Matheson, Adrian; Thoms, Martin; Reid, Michael

2017-09-01

Our understanding of the effectiveness of reintroduced large wood for restoration is largely based on studies from high energy river systems. By contrast, few studies of the effectiveness of reintroducing large wood have been undertaken on large, low energy, lowland river systems: river systems where large wood is a significant physical feature on the in-channel environment. This study investigated the effect of reintroduced large wood on the hydraulic landscape of the Barwon-Darling River, Australia, at low flows. To achieve this, the study compared three hydraulic landscapes of replicated reference (naturally wooded), control (unwooded,) and managed (wood reintroduced) treatments on three low flow periods. These time periods were prior to the reintroduction of large wood to managed reaches; several months after the reintroduction of large wood into the managed reaches; and then more than four years after wood reintroduction following several large flood events. Hydraulic landscapes of reaches were characterised using a range of spatial measures calculated from velocity measurements taken with a boat-mounted Acoustic Doppler Profiler. We hypothesised that reintroduced large wood would increase the diversity of the hydraulic landscape at low flows and that managed reaches would be more similar to the reference reaches. Our results suggest that the reintroduction of large wood did not significantly change the character of the hydraulic landscape at the reach scale after several months (p = 0.16) or several years (p = 0.29). Overall, the character of the hydraulic landscape in the managed reaches was more similar to the hydraulic landscape of the control reaches than the hydraulic landscape of the reference reaches, at low flows. Some variability in the hydraulic landscapes was detected over time, and this may reflect reworking of riverbed sediments and sensitivity to variation in discharge. The lack of a response in the low flow hydraulic landscape to the

Conference on wind power development in the face of landscape and local project acceptability challenges

International Nuclear Information System (INIS)

Victoire Lejzerzon; Sauron, Claire; Villot, Marie; Ratzbor, Guenter; Tausch, Christian; Cagneaux, Bertrand; Jouneau, Agathe; Stemmer, Boris; Huebner, Gundula; Orozco-Souel, Paola; Lhermitte, Charles; Ferus, Elisabeth; Benezech, Philippe; Gunzelmann, Thomas

2015-01-01

The French-German office for Renewable energies (OFAEnR) organised a conference on n wind power development in the face of landscape and local project acceptability challenges. In the framework of this French-German exchange of experience, participants addressed the following points: the conciliation between landscape protection and wind power development, the definition of landscape environmental quality criteria, the needs and usages of the departments in charge of the treatment of landscape studies in France, the socio-psychological approach of the local acceptability of wind farm projects, the re-powering tool for the improvement of the wind farm integration in the landscape, and the conciliation between the monuments maintenance and wind power development. This document brings together the available presentations (slides) made during this event: 1 - Conciliating landscape protection and wind power development goals in France (Marie Villot); 2 - Wind turbines: Conflicts between development goals, landscape and acceptance - Perception and criteria (Guenter Ratzbor); 3 - Bayern's wind power atlas: a planning tool which takes into account the landscape aspects (Christian Tausch); 4 - Landscape assessment in wind farms projects: what and how to do in French administrative procedures? (Bertrand Cagneaux); 5 - Methods for evaluation of landscape for wind farms projects - A French project developer's feedback (Agathe Jouneau); 6 - Landscape Assessment: Methods from German Landscape Practice (Boris Stemmer); 7 - Acceptance of Wind Turbines - Social Psychological Research (Gundula Huebner); 8 - Local consultation: who to involve, when and how? (Paola Orozco-Souel); 9 - Local acceptability: what dialogue concepts and strategies, and how to manage wind energy objection (Charles Lhermitte); 10 - Re-powering and landscape: chances and limits (Elisabeth Ferus); 11 - Wind power and cultural heritage: consultation and dialogue to succeed (Philippe Benezech); 12

Planetary Landscape Geography

Science.gov (United States)

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

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

Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts.

Science.gov (United States)

Zhu, Jianwei; Zhang, Haicang; Li, Shuai Cheng; Wang, Chao; Kong, Lupeng; Sun, Shiwei; Zheng, Wei-Mou; Bu, Dongbo

2017-12-01

Accurate recognition of protein fold types is a key step for template-based prediction of protein structures. The existing approaches to fold recognition mainly exploit the features derived from alignments of query protein against templates. These approaches have been shown to be successful for fold recognition at family level, but usually failed at superfamily/fold levels. To overcome this limitation, one of the key points is to explore more structurally informative features of proteins. Although residue-residue contacts carry abundant structural information, how to thoroughly exploit these information for fold recognition still remains a challenge. In this study, we present an approach (called DeepFR) to improve fold recognition at superfamily/fold levels. The basic idea of our approach is to extract fold-specific features from predicted residue-residue contacts of proteins using deep convolutional neural network (DCNN) technique. Based on these fold-specific features, we calculated similarity between query protein and templates, and then assigned query protein with fold type of the most similar template. DCNN has showed excellent performance in image feature extraction and image recognition; the rational underlying the application of DCNN for fold recognition is that contact likelihood maps are essentially analogy to images, as they both display compositional hierarchy. Experimental results on the LINDAHL dataset suggest that even using the extracted fold-specific features alone, our approach achieved success rate comparable to the state-of-the-art approaches. When further combining these features with traditional alignment-related features, the success rate of our approach increased to 92.3%, 82.5% and 78.8% at family, superfamily and fold levels, respectively, which is about 18% higher than the state-of-the-art approach at fold level, 6% higher at superfamily level and 1% higher at family level. An independent assessment on SCOP_TEST dataset showed consistent

A Classification of Landscape Services to Support Local Landscape Planning

Directory of Open Access Journals (Sweden)

María Vallés-Planells

2014-03-01

Full Text Available The ecosystem services approach has been proven successful to measure the contributions of nature and greenery to human well-being. Ecosystems have an effect on quality of life, but landscapes also, as a broader concept, may contribute to people's well-being. The concept of landscape services, compared to ecosystem services, involves the social dimension of landscape and the spatial pattern resulting from both natural and human processes in the provision of benefits for human-well being. Our aim is to develop a classification for landscape services. The proposed typology of services is built on the Common International Classification of Ecosystem Services (CICES and on a critical review of existing literature on human well-being dimensions, existing ecosystem service classifications, and landscape perception. Three themes of landscape services are defined, each divided into several groups: provisioning, regulation and maintenance, cultural and social life fulfillment, with the latter focusing on health, enjoyment, and personal and social fulfillment. A special emphasis is made on cultural services, which are especially important when applied to landscape and which have received less attention.

LANDSCAPE PLANNING IN UKRAINE: THE FIRST LANDSCAPE-PLANNING PROGRAM

Directory of Open Access Journals (Sweden)

Leonid Rudenko

2013-01-01

Full Text Available The paper presents the results of the first, in Ukraine; project on landscape planning widely accepted in European countries. Under the project implemented in 2010–2013, a landscape-planning program has been developed for the Cherkassy oblast. This is the first document of this kind in Ukraine. The program is mainly based on the experience of the German and Russian schools of landscape planning and on research and assessment conducted by the authors, which allowed identifying approaches to landscape planning, principles of the national policy, and characteristics and potential of environmentally friendly planning in Ukraine. The paper discusses the main phases of the work on the development of the landscape program for the oblast. It also identifies the main stages and key concepts and principles of landscape planning. The paper presents the results of integrated research on the identification and classification of conflicts in land use and the integral concept of the developmental goals for the oblast. The results can be the foundation for adopting management decisions and development of action plans for the lower hierarchal branches.

Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

Science.gov (United States)

Mondal, Abhisek; Datta, Saumen

2017-06-01

Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Coherent topological phenomena in protein folding

DEFF Research Database (Denmark)

Bohr, Henrik; Brunak, Søren; Bohr, Jakob

1997-01-01

A theory is presented for coherent topological phenomena in protein dynamics with implications for protein folding and stability. We discuss the relationship to the writhing number used in knot diagrams of DNA. The winding state defines a long-range order along the backbone of a protein with long......-range excitations, `wring' modes, that play an important role in protein denaturation and stability. Energy can be pumped into these excitations, either thermally or by an external force....

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...

A study of the deep structure of the energy landscape of glassy polystyrene: the exponential distribution of the energy barriers revealed by high-field electron spin resonance spectroscopy

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)

Examining the Role of Cultural Landscape in Regional Development: Defining Criteria and Looking at Ephesus

Directory of Open Access Journals (Sweden)

Gökçe Şimşek

2017-06-01

Full Text Available The link between regional development and cultural heritage has been at the center of theoretical discussions and practices in the field of preservation. Especially, varieties of practices and regional plans have been developed in different parts of the World such as Europe, Russia and South Africa in order to ensure regional development through cultural heritage. In this paper, it is accepted that a cultural landscape, as a sub-region of a particular region, is a relevant and meaningful unit that can contribute to the qualities of the region in terms of socio-cultural and economic aspects. In this context, the main goal of this paper is to develop a set of criteria that will act as a tool for identifying to which aspects of a cultural landscape has the potential to contribute regional development and to evaluate possible contributions of Ephesus and its cultural landscape to regional development. These criteria can be classified according to a framework implying a three-fold classification; improvements in the physical quality of the cultural landscape, economic dimension and socio-cultural dimension. As a result, this case indicates that cultural landscape has great potential to contribute to the social and economic development of a region. There is a great need to support community through tools such as awareness raising programmes, regional heritage planning, regional heritage institutions acting as regional agencies.

Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)

Science.gov (United States)

Bartl, Nikolaus; Bretis, Bernhard; Grasemann, Bernhard; Lockhart, Duncan

2010-05-01

The Zagros mountains extends over 1800 km from Kurdistan in N-Iraq to the Strait of Hormuz in Iran and is one of the world most promising regions for the future hydrocarbon exploration. The Zagros Mountains started to form as a result of the collision between the Eurasian and Arabian Plates, whose convergence began in the Late Cretaceous as part of the Alpine-Himalayan orogenic system. Geodetic and seismological data document that both plates are still converging and that the fold and thrust belt of the Zagros is actively growing. Extensive hydrocarbon exploration mainly focuses on the antiforms of this fold and thrust belt and therefore the growth history of the folds is of great importance. This work investigates by means of structural field work and quantitative geomorphological techniques the progressive fold growth of the Permam, Bana Bawi- and Safeen- Anticlines located in the NE of the city of Erbil in the Kurdistan region of Northern Iraq. This part of the Zagros fold and thrust belt belongs to the so-called Simply Folded Belt, which is dominated by gentle to open folding. Faults or fault related folds have only minor importance. The mechanical anisotropy of the formations consisting of a succession of relatively competent (massive dolomite and limestone) and incompetent (claystone and siltstone) sediments essentially controls the deformation pattern with open to gentle parallel folding of the competent layers and flexural flow folding of the incompetent layers. The characteristic wavelength of the fold trains is around 10 km. Due to faster erosion of the softer rock layers in the folded sequence, the more competent lithologies form sharp ridges with steeply sloping sides along the eroded flanks of the anticlines. Using an ASTER digital elevation model in combination with geological field data we quantified 250 drainage basins along the different limbs of the subcylindrical Permam, Bana Bawi- and Safeen- Anticlines. Geomorphological indices of the drainage

Multifunctional landscape practice and accessibility in manorial landscapes

DEFF Research Database (Denmark)

Brandt, Jesper; Svenningsen, Stig Roar; Christensen, Andreas Aagaard

. However classical manorial estates seems to represent an opposite trend. Allthough working at the same market conditions as other large specialized holdings developed through the process of structural rationalization, they have often maintained and elaborated a land use strategy based on a multifunctional...... use of the potential ecosystem services present within their domain. The targeted combination of agriculture, forestry, hunting rents, rental housing, and a variety of recreational activities influences makes a certain public accessibility to an integrated part of this strategy, diverging from...... the multifunctional landscape strategy supporting a certain public access. A study of this thesis is presented based on an analysis of multifunctionality, landscape development and accessibility in Danish Manorial landscapes and eventual linkages between their multifunctional landscape strategy, their history...

Beyond Landscape MacArchitecture: new languages, new landscapes

Directory of Open Access Journals (Sweden)

Simon Rackham

1996-03-01

Full Text Available The sine qua non of landscape architecture is respect for the genius loci, but even in the landscape, as in architecture and society more generally, a process of cultural homogenisation has been taking place. Against this process, a resurgence of interest in minority languages in Europe can be seen as an assertion of pride, and a desire to preserve difference. In Scotland, landscape architects are attempting to reinterpret Scottish and northern European urban design influences and materials: in effect to develop a new regional dialect for the new landscapes. Rooted in sound design principles and materials which respond to and reflect the climate, way of life and traditions of the place, design languages can communicate effectively about cultural values and differences.

PESP Landscaping Initiative

Science.gov (United States)

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.

Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol

DEFF Research Database (Denmark)

Christensen, Niels Johan; Kepp, Kasper Planeta

2012-01-01

) with up to 11 simultaneously mutated sites with good correlation against experimental stability trends. Molecular dynamics simulations of the two laccases show that FoldX is very structure-sensitive, since all mutants and the wild-type must share structural configuration to avoid artifacts of local...... sampling. However, using the average of 50 MD snapshots of the equilibrated trajectories restores correlation (r ~0.7-0.9, r2 ~0.49-0.81) and provides a root-mean-square accuracy of ~1.2 kcal/mol for ∆∆G or 3.5 ○C for T50, suggesting that the time-average of the crystal structure is recovered. MD......-averaged input also reduces the spread in ∆∆G, suggesting that local FoldX sampling overestimates free energy changes because of neglected protein relaxation. FoldX can be viewed as a simple “linear interaction energy” method using sampling of wild-type and mutant and a parameterized relative free energy...

Theory of the Protein Equilibrium Population Snapshot by H/D Exchange Electrospray Ionization Mass Spectrometry (PEPS-HDX-ESI-MS) Method used to obtain Protein Folding Energies/Rates and Selected Supporting Experimental Evidence.

Science.gov (United States)

Liyanage, Rohana; Devarapalli, Nagarjuna; Pyland, Derek B; Puckett, Latisha M; Phan, N H; Starch, Joel A; Okimoto, Mark R; Gidden, Jennifer; Stites, Wesley E; Lay, Jackson O

2012-12-15

Protein equilibrium snapshot by hydrogen/deuterium exchange electrospray ionization mass spectrometry (PEPS-HDX-ESI-MS or PEPS) is a method recently introduced for estimating protein folding energies and rates. Herein we describe the basis for this method using both theory and new experiments. Benchmark experiments were conducted using ubiquitin because of the availability of reference data for folding and unfolding rates from NMR studies. A second set of experiments was also conducted to illustrate the surprising resilience of the PEPS to changes in HDX time, using staphylococcal nuclease and time frames ranging from a few seconds to several minutes. Theory suggests that PEPS experiments should be conducted at relatively high denaturant concentrations, where the protein folding/unfolding rates are slow with respect to HDX and the life times of both the closed and open states are long enough to be sampled experimentally. Upon deliberate denaturation, changes in folding/unfolding are correlated with associated changes in the ESI-MS signal upon fast HDX. When experiments are done quickly, typically within a few seconds, ESI-MS signals, corresponding to the equilibrium population of the native (closed) and denatured (open) states can both be detected. The interior of folded proteins remains largely un-exchanged. Amongst MS methods, the simultaneous detection of both states in the spectrum is unique to PEPS and provides a "snapshot" of these populations. The associated ion intensities are used to estimate the protein folding equilibrium constant (or the free energy change, ΔG). Linear extrapolation method (LEM) plots of derived ΔG values for each denaturant concentration can then be used to calculate ΔG in the absence of denaturant, ΔG(H(2)O). In accordance with the requirement for detection of signals for both the folded and unfolded states, this theoretical framework predicts that PEPS experiments work best at the middle of the denaturation curve where natured

Coupling movement and landscape ecology for animal conservation in production landscapes.

Science.gov (United States)

Doherty, Tim S; Driscoll, Don A

2018-01-10

Habitat conversion in production landscapes is among the greatest threats to biodiversity, not least because it can disrupt animal movement. Using the movement ecology framework, we review animal movement in production landscapes, including areas managed for agriculture and forestry. We consider internal and external drivers of altered animal movement and how this affects navigation and motion capacities and population dynamics. Conventional management approaches in fragmented landscapes focus on promoting connectivity using structural changes in the landscape. However, a movement ecology perspective emphasizes that manipulating the internal motivations or navigation capacity of animals represents untapped opportunities to improve movement and the effectiveness of structural connectivity investments. Integrating movement and landscape ecology opens new opportunities for conservation management in production landscapes. © 2018 The Authors.

RNA folding kinetics using Monte Carlo and Gillespie algorithms.

Science.gov (United States)

Clote, Peter; Bayegan, Amir H

2018-04-01

RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny ([Formula: see text]20 nt) RNA sequences, the folding kinetics for larger sequences can only be approximated by binning structures into macrostates in a coarse-grained model, or by repeatedly simulating secondary structure folding with either the Monte Carlo algorithm or the Gillespie algorithm. Here we investigate the relation between the Monte Carlo algorithm and the Gillespie algorithm. We prove that asymptotically, the expected time for a K-step trajectory of the Monte Carlo algorithm is equal to [Formula: see text] times that of the Gillespie algorithm, where [Formula: see text] denotes the Boltzmann expected network degree. If the network is regular (i.e. every node has the same degree), then the mean first passage time (MFPT) computed by the Monte Carlo algorithm is equal to MFPT computed by the Gillespie algorithm multiplied by [Formula: see text]; however, this is not true for non-regular networks. In particular, RNA secondary structure folding kinetics, as computed by the Monte Carlo algorithm, is not equal to the folding kinetics, as computed by the Gillespie algorithm, although the mean first passage times are roughly correlated. Simulation software for RNA secondary structure folding according to the Monte Carlo and Gillespie algorithms is publicly available, as is our software to compute the expected degree of the network of secondary structures of a given RNA sequence-see http://bioinformatics.bc.edu/clote/RNAexpNumNbors .

Pedo-environmental evolution and agricultural landscape transformation

Directory of Open Access Journals (Sweden)

Gilmo Vianello

Full Text Available Landscapes represent the stage setting of the ecosystem, the great theatre where the evolution of the environment, the changing of things and plant and animal life are played out; the diversity of landscapes derives from the combination, over time, of different environmental factors having perceptibly different roles, as in the case of climate, vegetation and human activity. Less perceptible and scarcely known is the role of soil, which has the ability not only to diversify the ecosystem’s landscapes but also to differentiate its level of productivity and liveability. The role of soil as part of the landscape is not always so evident, especially when it is covered by vegetation that precludes observation. At times, however, soils show themselves conspicuously, at least on the surface, when the colours of the epipedons invade the landscape and – in the ploughing season – dominate it. While it may be reassuring to see neatly cultivated fields and crops growing luxuriantly and homogeneously, the increasingly marked and evident signs of soil degradation or erosion are a cause for concern. In the recent past, the relationship between man and soil resources was strongly influenced by natural factors inside and outside the soil itself, socio-economic conditions and above all the labour force, i.e. the people employed in the primary sector; consequently, it was based on such factors that crop-growing choices were adapted to the different ecosystems, resulting in a diversification of rural landscapes. Starting from the second half of the twentieth century, the introduction of chemicals, mechanisation and exploitation of various forms of energy drastically transformed land use in the space of just a few years, with a logic aimed at improving the production capacity of farmland and forest land in both qualitative and quantitative terms. As a consequence, farming choices that were formerly adapted to the natural and socio-economic conditions of

Pedo-environmental evolution and agricultural landscape transformation

Directory of Open Access Journals (Sweden)

Gilmo Vianello

2009-10-01

Full Text Available Landscapes represent the stage setting of the ecosystem, the great theatre where the evolution of the environment, the changing of things and plant and animal life are played out; the diversity of landscapes derives from the combination, over time, of different environmental factors having perceptibly different roles, as in the case of climate, vegetation and human activity. Less perceptible and scarcely known is the role of soil, which has the ability not only to diversify the ecosystem’s landscapes but also to differentiate its level of productivity and liveability. The role of soil as part of the landscape is not always so evident, especially when it is covered by vegetation that precludes observation. At times, however, soils show themselves conspicuously, at least on the surface, when the colours of the epipedons invade the landscape and – in the ploughing season – dominate it. While it may be reassuring to see neatly cultivated fields and crops growing luxuriantly and homogeneously, the increasingly marked and evident signs of soil degradation or erosion are a cause for concern. In the recent past, the relationship between man and soil resources was strongly influenced by natural factors inside and outside the soil itself, socio-economic conditions and above all the labour force, i.e. the people employed in the primary sector; consequently, it was based on such factors that crop-growing choices were adapted to the different ecosystems, resulting in a diversification of rural landscapes. Starting from the second half of the twentieth century, the introduction of chemicals, mechanisation and exploitation of various forms of energy drastically transformed land use in the space of just a few years, with a logic aimed at improving the production capacity of farmland and forest land in both qualitative and quantitative terms. As a consequence, farming choices that were formerly adapted to the natural and socio-economic conditions of

The importance of on-site evaluation for placing renewable energy in the landscape: A case study of the Búrfell wind farm (Iceland)

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

The Risk of Vocal Fold Atrophy after Serial Corticosteroid Injections of the Vocal Fold.

Science.gov (United States)

Shi, Lucy L; Giraldez-Rodriguez, Laureano A; Johns, Michael M

2016-11-01

The aim of this study was to illustrate the risk of vocal fold atrophy in patients who receive serial subepithelial steroid injections for vocal fold scar. This study is a retrospective case report of two patients who underwent a series of weekly subepithelial infusions of 10 mg/mL dexamethasone for benign vocal fold lesion. Shortly after the procedures, both patients developed a weak and breathy voice. The first patient was a 53-year-old man with radiation-induced vocal fold stiffness. Six injections were performed unilaterally, and 1 week later, he developed unilateral vocal fold atrophy with new glottal insufficiency. The second patient was a 67-year-old woman with severe vocal fold inflammation related to laryngitis and calcinosis, Raynaud's phenomenon, esophagean dysmotility, sclerodactyly, and telangiectasia (CREST) syndrome. Five injections were performed bilaterally, and 1 week later, she developed bilateral vocal fold atrophy with a large midline glottal gap during phonation. In both cases, the steroid-induced vocal atrophy resolved spontaneously after 4 months. Serial subepithelial steroid infusions of the vocal folds, although safe in the majority of patients, carry the risk of causing temporary vocal fold atrophy when given at short intervals. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

A collaborative visual analytics suite for protein folding research.

Science.gov (United States)

Harvey, William; Park, In-Hee; Rübel, Oliver; Pascucci, Valerio; Bremer, Peer-Timo; Li, Chenglong; Wang, Yusu

2014-09-01

Molecular dynamics (MD) simulation is a crucial tool for understanding principles behind important biochemical processes such as protein folding and molecular interaction. With the rapidly increasing power of modern computers, large-scale MD simulation experiments can be performed regularly, generating huge amounts of MD data. An important question is how to analyze and interpret such massive and complex data. One of the (many) challenges involved in analyzing MD simulation data computationally is the high-dimensionality of such data. Given a massive collection of molecular conformations, researchers typically need to rely on their expertise and prior domain knowledge in order to retrieve certain conformations of interest. It is not easy to make and test hypotheses as the data set as a whole is somewhat "invisible" due to its high dimensionality. In other words, it is hard to directly access and examine individual conformations from a sea of molecular structures, and to further explore the entire data set. There is also no easy and convenient way to obtain a global view of the data or its various modalities of biochemical information. To this end, we present an interactive, collaborative visual analytics tool for exploring massive, high-dimensional molecular dynamics simulation data sets. The most important utility of our tool is to provide a platform where researchers can easily and effectively navigate through the otherwise "invisible" simulation data sets, exploring and examining molecular conformations both as a whole and at individual levels. The visualization is based on the concept of a topological landscape, which is a 2D terrain metaphor preserving certain topological and geometric properties of the high dimensional protein energy landscape. In addition to facilitating easy exploration of conformations, this 2D terrain metaphor also provides a platform where researchers can visualize and analyze various properties (such as contact density) overlayed on the

Vfold: a web server for RNA structure and folding thermodynamics prediction.

Science.gov (United States)

Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

NoFold: RNA structure clustering without folding or alignment.

Science.gov (United States)

Middleton, Sarah A; Kim, Junhyong

2014-11-01

Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Colloids exposed to random potential energy landscapes: From particle number density to particle-potential and particle-particle interactions

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.

Craters of elevation / forced folds: more examples of shallow magma accumulation and its consequences

Science.gov (United States)

van Wyk de Vries, Benjamin; Marquez, Alvaro; Craig, Magee; Valdislav, Rapprich; Hetherington, Rachel; Bastow, Ian

2016-04-01

Craters of elevation are uplifts with apical depressions that are caused by shallow magma intrusion. Forced folds are dome-like folds caused by magma intrusion that also have apical extensional structures. They are the same feature described from the different viewpoints of the volcanologist and the structural geologist. While working on such features in the Chaîne des Puys (Central France), and Ethiopia we have been searching for other examples in the world. This is our most up to date review of such phenomena taken from a global search in the world of volcanology where some stunning examples are seen in the landscape, and in outcrop. We also show such features from tectonics data and literature, where such features are superbly displayed in seismic data. We take three examples, the Puy de Gouttes, in the Chaîne des Puys, the Montana Encantada in Lanzarote, which we have mapped in the field, and the Diamond Craters National Monument in Oregon to show the different structures and possible evolutionary trends that such features can follow. We use the observations to integrate the possible eruptive, deformational and structural events that can combine in a forced fold to create the surface features observed at such craters of elevation. The hazard implications of the growth and destruction of such features are assessed.

Landscapes for Energy and Wildlife: Conservation Prioritization for Golden Eagles across Large Spatial Scales.

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.

LANDSCAPE ECOLOGICAL METHOD TO STUDY AGRICULTURAL VEGETATION: SOME EXAMPLES FROM THE PO VALLEY

Directory of Open Access Journals (Sweden)

E. GIGLIO

2006-01-01

Full Text Available Vegetation is the most important landscape component, as regards to its ability to catch solar energy and to transform it, but also to shape the landscape, to structure the space, to create the fit environment for different animal species, to contribute to the maintenance of a correct metastability level for the landscape, etc. It is a biological system which acts under the constraints of the principles of the System Theory and owns the same properties of any other living system: so, it is a complex adaptive, hierarchical, dynamic, dissipative, self-organizing, self-transcendent, autocatalytic, self-maintaining system and follows the non-equilibrium thermodynamic. Its ecological state can be investigated through the comparison between “gathered data” (pathology and “normal data” (physiology for analogous types of vegetation. The Biological Integrated School of Landscape Ecology provides an integrated methodology to define ecological threshold limits of the different Agricultural Landscape types and applies to agricultural vegetation the specific part of the new methodology already tested to studying forests (the Landscape Biological Survey of Vegetation. Ecological quality, better and worst parameters, biological territorial capacity of vegetated corridors, agricultural field, poplar groves, orchards and woody remnant patches are investigated. Some examples from diverse agricultural landscapes of the Po Valley will be discussed. KEY WORDS: agricultural landscape, vegetation, landscape ecology, landscape health, Biological Integrated Landscape Ecology, Landscape Biological Survey of vegetation.

LANDSCAPE ECOLOGICAL METHOD TO STUDY AGRICULTURAL VEGETATION: SOME EXAMPLES FROM THE PO VALLEY

Directory of Open Access Journals (Sweden)

E. GIGLIO

2006-05-01

Full Text Available Vegetation is the most important landscape component, as regards to its ability to catch solar energy and to transform it, but also to shape the landscape, to structure the space, to create the fit environment for different animal species, to contribute to the maintenance of a correct metastability level for the landscape, etc. It is a biological system which acts under the constraints of the principles of the System Theory and owns the same properties of any other living system: so, it is a complex adaptive, hierarchical, dynamic, dissipative, self-organizing, self-transcendent, autocatalytic, self-maintaining system and follows the non-equilibrium thermodynamic. Its ecological state can be investigated through the comparison between “gathered data” (pathology and “normal data” (physiology for analogous types of vegetation. The Biological Integrated School of Landscape Ecology provides an integrated methodology to define ecological threshold limits of the different Agricultural Landscape types and applies to agricultural vegetation the specific part of the new methodology already tested to studying forests (the Landscape Biological Survey of Vegetation. Ecological quality, better and worst parameters, biological territorial capacity of vegetated corridors, agricultural field, poplar groves, orchards and woody remnant patches are investigated. Some examples from diverse agricultural landscapes of the Po Valley will be discussed. KEY WORDS: agricultural landscape, vegetation, landscape ecology, landscape health, Biological Integrated Landscape Ecology, Landscape Biological Survey of vegetation.

TBI server: a web server for predicting ion effects in RNA folding.

Science.gov (United States)

Zhu, Yuhong; He, Zhaojian; Chen, Shi-Jie

2015-01-01

Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²⁺, are essential for RNA tertiary structure formation. These ions can possibly become strongly correlated in the close vicinity of RNA surface. Most of the currently available software packages, which have widespread success in predicting ion effects in biomolecular systems, however, do not explicitly account for the ion correlation effect. Therefore, it is important to develop a software package/web server for the prediction of ion electrostatics in RNA folding by including ion correlation effects. The TBI web server http://rna.physics.missouri.edu/tbi_index.html provides predictions for the total electrostatic free energy, the different free energy components, and the mean number and the most probable distributions of the bound ions. A novel feature of the TBI server is its ability to account for ion correlation and ion distribution fluctuation effects. By accounting for the ion correlation and fluctuation effects, the TBI server is a unique online tool for computing ion-mediated electrostatic properties for given RNA structures. The results can provide important data for in-depth analysis for ion effects in RNA folding including the ion-dependence of folding stability, ion uptake in the folding process, and the interplay between the different energetic components.

TBI server: a web server for predicting ion effects in RNA folding.

Directory of Open Access Journals (Sweden)

Yuhong Zhu

Full Text Available Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²⁺, are essential for RNA tertiary structure formation. These ions can possibly become strongly correlated in the close vicinity of RNA surface. Most of the currently available software packages, which have widespread success in predicting ion effects in biomolecular systems, however, do not explicitly account for the ion correlation effect. Therefore, it is important to develop a software package/web server for the prediction of ion electrostatics in RNA folding by including ion correlation effects.The TBI web server http://rna.physics.missouri.edu/tbi_index.html provides predictions for the total electrostatic free energy, the different free energy components, and the mean number and the most probable distributions of the bound ions. A novel feature of the TBI server is its ability to account for ion correlation and ion distribution fluctuation effects.By accounting for the ion correlation and fluctuation effects, the TBI server is a unique online tool for computing ion-mediated electrostatic properties for given RNA structures. The results can provide important data for in-depth analysis for ion effects in RNA folding including the ion-dependence of folding stability, ion uptake in the folding process, and the interplay between the different energetic components.

Glycoprotein folding and quality-control mechanisms in protein-folding diseases

Directory of Open Access Journals (Sweden)

Sean P. Ferris

2014-03-01

Full Text Available Biosynthesis of proteins – from translation to folding to export – encompasses a complex set of events that are exquisitely regulated and scrutinized to ensure the functional quality of the end products. Cells have evolved to capitalize on multiple post-translational modifications in addition to primary structure to indicate the folding status of nascent polypeptides to the chaperones and other proteins that assist in their folding and export. These modifications can also, in the case of irreversibly misfolded candidates, signal the need for dislocation and degradation. The current Review focuses on the glycoprotein quality-control (GQC system that utilizes protein N-glycosylation and N-glycan trimming to direct nascent glycopolypeptides through the folding, export and dislocation pathways in the endoplasmic reticulum (ER. A diverse set of pathological conditions rooted in defective as well as over-vigilant ER quality-control systems have been identified, underlining its importance in human health and disease. We describe the GQC pathways and highlight disease and animal models that have been instrumental in clarifying our current understanding of these processes.

Understanding the whole city as landscape. A multivariate approach to urban landscape morphology

Directory of Open Access Journals (Sweden)

Richard Stiles

2014-05-01

Full Text Available The European Landscape Convention implies a requirement for signatory states to identify their urban landscapes which goes beyond the traditional focus on individual parks and green spaces and the links between them. Landscape ecological approaches can provide a useful model for identifying urban landscape types across a whole territory, but the variables relevant for urban landscapes are very different to those usually addressing rural areas. This paper presents an approach to classifying the urban landscape of Vienna that was developed in a research project funded by the Austrian Ministry for Transport, Innovation and Technology: ‘Urban Fabric and Microclimate Response’. Nine landscape types and a number of sub-types were defined, using a multivariate statistical approach which takes account of both morphological and urban climate related variables. Although the variables were selected to objectively reflect the factors that could best represent the urban climatic characteristics of the urban landscape, the results also provided a widely plausible representation of the structure of the city’s landscapes. Selected examples of the landscape types that were defined in this way were used both to simulate current microclimatic conditions and also to model the effects of possible climatic amelioration measures. Finally the paper looks forward to developing a more general-purpose urban landscape typology that allows investigating a much broader complex of urban landscape functions.

Energy from biomass. Ethics and practice; Energie aus Biomasse. Ethik und Praxis

Energy Technology Data Exchange (ETDEWEB)

Franke, Silke [ed.

2013-06-01

The implementation of the energy policy turnaround inevitably results in modifications of the land use and landscape. Besides the discussion about the environmental consequences, a debate about ethical issues increasingly arose. Under this aspect, the booklet under consideration contains the following contributions: (1) Renewable energy sources - the role of bioenergy (Bernard Widmann); (2) Energy from biomass - An ethic analysis (Stephan Schleissing); (3) Culture for our landscapes - combination of biomass and water protection (Frank Wagener); (4) Cultivation of energy crops - short rotation coppices (Frank Burger); (5) Bioenergy region Straubing-Bogen: Excellent in the matter of renewable energy sources (Josefine Eichwald); (6) Rural development - motor for the energy policy turnaround (Roland Spiller).

Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements

Science.gov (United States)

PENEDO, J. CARLOS; WILSON, TIMOTHY J.; JAYASENA, SUMEDHA D.; KHVOROVA, ANASTASIA; LILLEY, DAVID M.J.

2004-01-01

It has been shown that the activity of the hammerhead ribozyme at μM magnesium ion concentrations is markedly increased by the inclusion of loops in helices I and II. We have studied the effect of such loops on the magnesium ion-induced folding of the ribozyme, using fluorescence resonance energy transfer. We find that with the loops in place, folding into the active conformation occurs in a single step, in the μM range of magnesium ion concentration. Disruption of the loop–loop interaction leads to a reversion to two-step folding, with the second stage requiring mM concentrations of magnesium ion. Sodium ions also promote the folding of the natural form of the ribozyme at high concentrations, but the folding occurs as a two-stage process. The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions. PMID:15100442

Urban landscape infrastructures: Designing operative landscape structures for the built environment

OpenAIRE

Nijhuis, S.; Jauslin, D.T.

2015-01-01

This paper explores infrastructure as a type of landscape and landscape as a type of infrastructure. The hybridisation of the two concepts, landscape and infrastructure, seeks to redefine infrastructure beyond its strictly utilitarian definition, while allowing design disciplines to gain operative force in territorial transformation processes. This paper aims to put forward urban landscape infrastructures as a design concept, considering them as armatures for urban development and for facilit...

Contemporary danish landscape research

DEFF Research Database (Denmark)

Vejre, H.; Brandt, J.

2004-01-01

Danish landscape research blossomed during the 1990’ies 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...

Evidence from mixed hydrate nucleation for a funnel model of crystallization

Science.gov (United States)

Hall, Kyle Wm.; Carpendale, Sheelagh; Kusalik, Peter G.

2016-01-01

The molecular-level details of crystallization remain unclear for many systems. Previous work has speculated on the phenomenological similarities between molecular crystallization and protein folding. Here we demonstrate that molecular crystallization can involve funnel-shaped potential energy landscapes through a detailed analysis of mixed gas hydrate nucleation, a prototypical multicomponent crystallization process. Through this, we contribute both: (i) a powerful conceptual framework for exploring and rationalizing molecular crystallization, and (ii) an explanation of phenomenological similarities between protein folding and crystallization. Such funnel-shaped potential energy landscapes may be typical of broad classes of molecular ordering processes, and can provide a new perspective for both studying and understanding these processes. PMID:27790987

Shedding light on protein folding, structural and functional dynamics by single molecule studies

DEFF Research Database (Denmark)

Bavishi, Krutika; Hatzakis, Nikos

2014-01-01

property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out...

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

Responding to Landscape Change: Stakeholder Participation and Social Capital in Five European Landscapes

Directory of Open Access Journals (Sweden)

Thanasis Kizos

2018-01-01

Full Text Available The concept of landscape has been increasingly used, in the last decades, in policy and land use planning, both in regard to so-called “special” and to “ordinary” or “everyday” landscapes. This has raised the importance of local and public participation in all issues that refer to landscapes and the definition of the groups that “have a stake” in the landscape. In this paper, we provide insights into how stakeholders perceive the dynamics of local processes of landscape change (and continuity and which processes of landscape change they perceive as important, in positive and negative ways, from five communities within the European Union. These landscapes involve different landscape issues “at stake”, different national and local planning and decision-making traditions and practices, and varying degrees of engagement. The understanding of these complexities and the unraveling of the insights is done through the concept of social capital and its different forms. We report on three series of workshops that have been organized to discuss landscape issues and approaches or ideas for landscape management. We witnessed interactions between the different stakeholders and gained insights into how social capital affects landscape change. We found that despite differences, similarities emerged concerning the interplay between “expert” and “local” knowledge and between “insideness” and “outsideness”. Social capital plays an important part, as it provides the template for personal and collective evaluation of landscape changes, who should manage these changes and how they should be managed. These findings are important to develop in-depth insights on dynamics and values of cultural landscapes and visions for re-coupling social and ecological components in cultural landscapes and translate them into policy and management options.

Urban landscape infrastructures : Designing operative landscape structures for the built environment

NARCIS (Netherlands)

Nijhuis, S.; Jauslin, D.T.

2015-01-01

This paper explores infrastructure as a type of landscape and landscape as a type of infrastructure. The hybridisation of the two concepts, landscape and infrastructure, seeks to redefine infrastructure beyond its strictly utilitarian definition, while allowing design disciplines to gain operative

Folding of multidomain proteins: biophysical consequences of tethering even in apparently independent folding.

Science.gov (United States)

Arviv, Oshrit; Levy, Yaakov

2012-12-01

Most eukaryotic and a substantial fraction of prokaryotic proteins are composed of more than one domain. The tethering of these evolutionary, structural, and functional units raises, among others, questions regarding the folding process of conjugated domains. Studying the folding of multidomain proteins in silico enables one to identify and isolate the tethering-induced biophysical determinants that govern crosstalks generated between neighboring domains. For this purpose, we carried out coarse-grained and atomistic molecular dynamics simulations of two two-domain constructs from the immunoglobulin-like β-sandwich fold. Each of these was experimentally shown to behave as the "sum of its parts," that is, the thermodynamic and kinetic folding behavior of the constituent domains of these constructs seems to occur independently, with the folding of each domain uncoupled from the folding of its partner in the two-domain construct. We show that the properties of the individual domains can be significantly affected by conjugation to another domain. The tethering may be accompanied by stabilizing as well as destabilizing factors whose magnitude depends on the size of the interface, the length, and the flexibility of the linker, and the relative stability of the domains. Accordingly, the folding of a multidomain protein should not be viewed as the sum of the folding patterns of each of its parts, but rather, it involves abrogating several effects that lead to this outcome. An imbalance between these effects may result in either stabilization or destabilization owing to the tethering. Copyright © 2012 Wiley Periodicals, Inc.

6 MV Folded Tandem Ion Accelerator facility at BARC

International Nuclear Information System (INIS)

Gupta, S.K.

2010-01-01

The 6 MV Folded Tandem Ion Accelerator (FOTIA) facility is operational round the clock and accelerated beams of both light and heavy ions are being used extensively by various divisions of BARC, Universities, lIT Bombay and other R and D labs across the country. The FOTIA is an upgraded version of the old 5.5 MV single stage Van-de-Graaff accelerator (1962-1992). Since its commissioning in the year 2000, the poor beam transmission through the 180 deg folding magnet was a matter of concern. A systematic study for beam transmission through the accelerator was carried out and progressive modifications in folding magnet chamber, foil stripper holder and improvement in average vacuum level through the accelerator have resulted in large improvement of beam transmission leading to up to 2.0 micro-amp analyzed proton beams on target. Now the utilization of the beams from the accelerator has increased many folds for basic and applied research in the fields of atomic and nuclear physics, material science and radiation biology etc. Few new beam lines after the indigenously developed 5-port switching magnet are added and the experimental setup for PIXE, PIGE, External PIXE, 4 neutron detector, Proton Induced Positron Annihilation Spectroscopy (PIPAS) setup and the general purpose scattering chamber etc have been commissioned in the beam hall. The same team has developed a Low Energy Accelerator Facility (LEAF) which delivers negative ions of light and heavy ions for application in implantation, irradiation damage studies in semiconductor devices and testing of new beam line components being developed for Low Energy High Intensity Proton Accelerator (LEHIPA) programme at BARC. The LEAF has been developed as stand alone facility and can deliver beam quickly with minimum intervention of the operator. Few more features are being planned to deliver uniform scanned beams on large targets. (author)

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

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.

The Roles of Structural Order and Intermolecular Interactions in Determining Ionization Energies and Charge-Transfer State Energies in Organic Semiconductors

KAUST Repository

Graham, Kenneth; Ngongang Ndjawa, Guy Olivier; Conron, Sarah M.; Munir, Rahim; Vandewal, Koen; Chen, John J.; Sweetnam, Sean; Thompson, Mark E.; Salleo, Alberto; Mcgehee, Michael D.; Amassian, Aram

2016-01-01

The energy landscape in organic semiconducting materials greatly influences charge and exciton behavior, which are both critical to the operation of organic electronic devices. These energy landscapes can change dramatically depending on the phases

Energy Savers--Tips on Saving Energy and Money at Home (Fifth Printing)

International Nuclear Information System (INIS)

DOE Office of Building Technology, State and Community Programs

2001-01-01

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 and Money at Home (Fifth Printing)

Energy Technology Data Exchange (ETDEWEB)

DOE Office of Building Technology, State and Community Programs

2001-08-13

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.

The Swiss Energy Sector. Innovation landscape and chances for the Netherlands; De Zwitserse energiesector. Innovatielandschap en kansen voor Nederland

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.

U.S. Geological Survey Science for the Wyoming Landscape Conservation Initiative: 2012 annual report

Science.gov (United States)

Bowen, Zachary H.; Aldridge, Cameron L.; Anderson, Patrick J.; Assal, Timothy J.; Bern, Carleton R.; Biewick, Laura; Boughton, Gregory K.; Carr, Natasha B.; Chalfoun, Anna D.; Chong, Geneva W.; Clark, Melanie L.; Fedy, Bradford C.; Foster, Katharine; Garman, Steven L.; Germaine, Stephen S.; Hethcoat, Matthew G.; Homer, Collin G.; Kauffman, Matthew J.; Keinath, Douglas; Latysh, Natalie; Manier, Daniel J.; McDougal, Robert R.; Melcher, Cynthia P.; Miller, Kirk A.; Montag, Jessica; Potter, Christopher J.; Schell, Spencer; Shafer, Sarah L.; Smith, David B.; Sweat, Michael J.; Wilson, Anna B.

2014-01-01

Southwest Wyoming contains abundant energy resources, wildlife, habitat, open spaces, and outdoor recreational opportunities. Although energy exploration and development have been taking place in the region since the late 1800s, the pace of development for fossil fuels and renewable energy increased significantly in the early 2000s. This and the associated urban and exurban development are leading to landscape-level environmental and socioeconomic changes that have the potential to diminish wildlife habitat and other natural resources, and the quality of human lives, in Southwest Wyoming. The potential for negative effects of these changes prompted Federal, State, and local agencies to undertake the Wyoming Landscape Conservation Initiative for Southwest Wyoming.

GIS-based landscape design research: Stourhead landscape garden as a case study

Directory of Open Access Journals (Sweden)

Steffen Nijhuis

2017-11-01

Full Text Available Landscape design research is important for cultivating spatial intelligence in landscape architecture. This study explores GIS (geographic information systems as a tool for landscape design research - investigating landscape designs to understand them as architectonic compositions (architectonic plan analysis. The concept ‘composition’ refers to a conceivable arrangement, an architectural expression of a mental construct that is legible and open to interpretation. Landscape architectonic compositions and their representations embody a great wealth of design knowledge as objects of our material culture and reflect the possible treatment of the ground, space, image and program as a characteristic coherence. By exploring landscape architectonic compositions with GIS, design researchers can acquire design knowledge that can be used in the creation and refinement of a design.  The research aims to identify and illustrate the potential role of GIS as a tool in landscape design research, so as to provide insight into the possibilities and limitations of using GIS in this capacity. The critical, information-oriented case of Stourhead landscape garden (Wiltshire, UK, an example of a designed landscape that covers the scope and remit of landscape architecture design, forms the heart of the study. The exploration of Stourhead by means of GIS can be understood as a plausibility probe. Here the case study is considered a form of ‘quasi-experiment’, testing the hypothesis and generating a learning process that constitutes a prerequisite for advanced understanding, while using an adjusted version of the framework for landscape design analysis by Steenbergen and Reh (2003. This is a theoretically informed analytical method based on the formal interpretation of the landscape architectonic composition addressing four landscape architectonic categories: the basic, the spatial, the symbolic and the programmatic form. This study includes new aspects to be

Periodic and stochastic thermal modulation of protein folding kinetics.

Science.gov (United States)

Platkov, Max; Gruebele, Martin

2014-07-21

Chemical reactions are usually observed either by relaxation of a bulk sample after applying a sudden external perturbation, or by intrinsic fluctuations of a few molecules. Here we show that the two ideas can be combined to measure protein folding kinetics, either by periodic thermal modulation, or by creating artificial thermal noise that greatly exceeds natural thermal fluctuations. We study the folding reaction of the enzyme phosphoglycerate kinase driven by periodic temperature waveforms. As the temperature waveform unfolds and refolds the protein, its fluorescence color changes due to FRET (Förster resonant Energy Transfer) of two donor/acceptor fluorophores labeling the protein. We adapt a simple model of periodically driven kinetics that nicely fits the data at all temperatures and driving frequencies: The phase shifts of the periodic donor and acceptor fluorescence signals as a function of driving frequency reveal reaction rates. We also drive the reaction with stochastic temperature waveforms that produce thermal fluctuations much greater than natural fluctuations in the bulk. Such artificial thermal noise allows the recovery of weak underlying signals due to protein folding kinetics. This opens up the possibility for future detection of a stochastic resonance for protein folding subject to noise with controllable amplitude.

Landscape functioning assessment using Landsat multispectral remote sensing data

OpenAIRE

Hesslerová, Petra

2009-01-01

The main aim of the dissertation thesis was to develop method, based on the use of multispectral satellite data and the theory of dissipation, allowing the analysis of landscape functioning. The theoretical basis is Prigogine's theory of dissipation and self-organization of structures in which energy dissipation is seen as the transformation of solar energy to other forms of energy. In this process the essential role play water availability and vegetation, which is able to bind solar radiatio...

Industrious Landscaping

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...

Using Landscape metrics to analyze the landscape evolution under land abandonment