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Sample records for intrinsic energy landscapes

  1. Intrinsically Disordered Energy Landscapes

    NASA Astrophysics Data System (ADS)

    Chebaro, Yassmine; Ballard, Andrew J.; Chakraborty, Debayan; Wales, David J.

    2015-05-01

    Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such ‘intrinsically disordered’ landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an -helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium.

  2. Intrinsically Disordered Energy Landscapes

    PubMed Central

    Chebaro, Yassmine; Ballard, Andrew J.; Chakraborty, Debayan; Wales, David J.

    2015-01-01

    Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such ‘intrinsically disordered’ landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an -helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium. PMID:25999294

  3. Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

    PubMed Central

    Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin

    2013-01-01

    Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding–folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative “coupled binding–folding” and three-state noncooperative “folding prior to binding” scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding–folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding–folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found “U-shape” temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments. PMID:23754431

  4. Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition.

    PubMed

    Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin

    2013-06-25

    Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding-folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative "coupled binding-folding" and three-state noncooperative "folding prior to binding" scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding-folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding-folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found "U-shape" temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments.

  5. Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition

    PubMed Central

    Visnapuu, Mari-Liis; Greene, Eric C.

    2009-01-01

    Here we use single-molecule imaging to determine coarse-grained intrinsic energy landscapes for nucleosome deposition on model DNA substrates. Our results reveal distributions that are correlated with recent in silico predictions, reinforcing the hypothesis that DNA contains some intrinsic positioning information. We also show that cis-regulatory sequences in human DNA coincide with peaks in the intrinsic landscape, whereas valleys correspond to non-regulatory regions, and we present evidence arguing that nucleosome deposition in vertebrates is influenced by factors not accounted for by current theory. Finally, we demonstrate that intrinsic landscapes of nucleosomes containing the centromere-specific variant CenH3 are correlated with patterns observed for canonical nucleosomes, arguing that CenH3 does not alter sequence preferences of centromeric nucleosomes. However, the non-histone protein Scm3 alters the intrinsic landscape of CenH3-containing nucleosomes, enabling them to overcome the otherwise exclusionary effects of poly(dA–dT) tracts, which are enriched in centromeric DNA. PMID:19734899

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

    PubMed

    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.

  7. Constructing the Energy Landscape for Genetic Switching System Driven by Intrinsic Noise

    PubMed Central

    Li, Fangting; Li, Tiejun

    2014-01-01

    Genetic switching driven by noise is a fundamental cellular process in genetic regulatory networks. Quantitatively characterizing this switching and its fluctuation properties is a key problem in computational biology. With an autoregulatory dimer model as a specific example, we design a general methodology to quantitatively understand the metastability of gene regulatory system perturbed by intrinsic noise. Based on the large deviation theory, we develop new analytical techniques to describe and calculate the optimal transition paths between the on and off states. We also construct the global quasi-potential energy landscape for the dimer model. From the obtained quasi-potential, we can extract quantitative results such as the stationary distributions of mRNA, protein and dimer, the noise strength of the expression state, and the mean switching time starting from either stable state. In the final stage, we apply this procedure to a transcriptional cascades model. Our results suggest that the quasi-potential energy landscape and the proposed methodology are general to understand the metastability in other biological systems with intrinsic noise. PMID:24551081

  8. Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

    PubMed

    Higo, Junichi; Umezawa, Koji

    2014-01-01

    We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.

  9. Landscaping for energy efficiency

    SciTech Connect

    1995-04-01

    This publication by the National Renewable Energy Laboratory addresses the use of landscaping for energy efficiency. The topics of the publication include minimizing energy expenses; landscaping for a cleaner environment; climate, site, and design considerations; planning landscape; and selecting and planting trees and shrubs. A source list for more information on landscaping for energy efficiency and a reading list are included.

  10. Familial Alzheimer A2 V mutation reduces the intrinsic disorder and completely changes the free energy landscape of the Aβ1-28 monomer.

    PubMed

    Nguyen, Phuong H; Tarus, Bogdan; Derreumaux, Philippe

    2014-01-16

    The self-assembly of the amyloid-β (Aβ) peptide of 39-43 amino acids into senile plaques is one hallmark of Alzheimer's disease (AD) pathology. While A2 V carriers remain healthy in the heterozygous state, they suffer from early onset AD in the homozygous state. As a first toward understanding the impact of A2 V on Aβ at its earlier stage, we characterized the equilibrium ensemble of the Aβ1-28 wild type and Aβ1-28 A2 V monomers by means of extensive atomistic replica exchange molecular dynamics simulations. While global conformational properties such as the radius of gyration and the average secondary structure content of the whole peptides are very similar, the population of β-hairpins is increased by a factor of 4 in A2 V, and this may explain the enhanced Aβ1-40 A2 V aggregation kinetics with respect to Aβ1-40 wild type. Both peptides display a non-negligible population of extended metastable conformations differing however in their atomic details that represent ideal seeds for polymerization. Remarkably, upon A2 V mutation, the intrinsic disorder of Aβ1-28 monomer is reduced by a factor of 2, and the free energy landscape is completely different. This difference in the conformational ensembles of the two peptides may explain in part why the mixture of the Aβ40 WT and A2 V peptides protects against AD.

  11. Potential flux landscapes determine the global stability of a Lorenz chaotic attractor under intrinsic fluctuations

    NASA Astrophysics Data System (ADS)

    Li, Chunhe; Wang, Erkang; Wang, Jin

    2012-05-01

    We developed a potential flux landscape theory to investigate the dynamics and the global stability of a chemical Lorenz chaotic strange attractor under intrinsic fluctuations. Landscape was uncovered to have a butterfly shape. For chaotic systems, both landscape and probabilistic flux are crucial to the dynamics of chaotic oscillations. Landscape attracts the system down to the chaotic attractor, while flux drives the coherent motions along the chaotic attractors. Barrier heights from the landscape topography provide a quantitative measure for the robustness of chaotic attractor. We also found that the entropy production rate and phase coherence increase as the molecular numbers increase. Power spectrum analysis of autocorrelation function provides another way to quantify the global stability of chaotic attractor. We further found that limit cycle requires more flux and energy to sustain than the chaotic strange attractor. Finally, by detailed analysis we found that the curl probabilistic flux may provide the origin of the chaotic attractor.

  12. Energy landscape of social balance.

    PubMed

    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.

  13. Energy Landscape of Social Balance

    NASA Astrophysics Data System (ADS)

    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.

  14. Energy landscapes for machine learning.

    PubMed

    Ballard, Andrew J; Das, Ritankar; Martiniani, Stefano; Mehta, Dhagash; Sagun, Levent; Stevenson, Jacob D; Wales, David J

    2017-04-03

    Machine learning techniques are being increasingly used as flexible non-linear fitting and prediction tools in the physical sciences. Fitting functions that exhibit multiple solutions as local minima can be analysed in terms of the corresponding machine learning landscape. Methods to explore and visualise molecular potential energy landscapes can be applied to these machine learning landscapes to gain new insight into the solution space involved in training and the nature of the corresponding predictions. In particular, we can define quantities analogous to molecular structure, thermodynamics, and kinetics, and relate these emergent properties to the structure of the underlying landscape. This Perspective aims to describe these analogies with examples from recent applications, and suggest avenues for new interdisciplinary research.

  15. Renewable energy from urban landscapes

    USDA-ARS?s Scientific Manuscript database

    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 potential from a bermudagrass, Cynodon dactylon var. dactylon (L.) Pers., lawn in Woodward, OK and to estimate the potential biomas...

  16. Energy landscapes and persistent minima

    SciTech Connect

    Carr, Joanne M.; Wales, David J.; Mazauric, Dorian; Cazals, Frédéric

    2016-02-07

    We consider a coarse-graining of high-dimensional potential energy landscapes based upon persistences, which correspond to lowest barrier heights to lower-energy minima. Persistences can be calculated efficiently for local minima in kinetic transition networks that are based on stationary points of the prevailing energy landscape. The networks studied here represent peptides, proteins, nucleic acids, an atomic cluster, and a glassy system. Minima with high persistence values are likely to represent some form of alternative structural morphology, which, if appreciably populated at the prevailing temperature, could compete with the global minimum (defined as infinitely persistent). Threshold values on persistences (and in some cases equilibrium occupation probabilities) have therefore been used in this work to select subsets of minima, which were then analysed to see how well they can represent features of the full network. Simplified disconnectivity graphs showing only the selected minima can convey the funnelling (including any multiple-funnel) characteristics of the corresponding full graphs. The effect of the choice of persistence threshold on the reduced disconnectivity graphs was considered for a system with a hierarchical, glassy landscape. Sets of persistent minima were also found to be useful in comparing networks for the same system sampled under different conditions, using minimum oriented spanning forests.

  17. Topology of cyclo-octane energy landscape.

    PubMed

    Martin, Shawn; Thompson, Aidan; Coutsias, Evangelos A; Watson, Jean-Paul

    2010-06-21

    Understanding energy landscapes is a major challenge in chemistry and biology. Although a wide variety of methods have been invented and applied to this problem, very little is understood about the actual mathematical structures underlying such landscapes. Perhaps the most general assumption is the idea that energy landscapes are low-dimensional manifolds embedded in high-dimensional Euclidean space. While this is a very mild assumption, we have discovered an example of an energy landscape which is nonmanifold, demonstrating previously unknown mathematical complexity. The example occurs in the energy landscape of cyclo-octane, which was found to have the structure of a reducible algebraic variety, composed of the union of a sphere and a Klein bottle, intersecting in two rings.

  18. Topology of cyclo-octane energy landscape

    NASA Astrophysics Data System (ADS)

    Martin, Shawn; Thompson, Aidan; Coutsias, Evangelos A.; Watson, Jean-Paul

    2010-06-01

    Understanding energy landscapes is a major challenge in chemistry and biology. Although a wide variety of methods have been invented and applied to this problem, very little is understood about the actual mathematical structures underlying such landscapes. Perhaps the most general assumption is the idea that energy landscapes are low-dimensional manifolds embedded in high-dimensional Euclidean space. While this is a very mild assumption, we have discovered an example of an energy landscape which is nonmanifold, demonstrating previously unknown mathematical complexity. The example occurs in the energy landscape of cyclo-octane, which was found to have the structure of a reducible algebraic variety, composed of the union of a sphere and a Klein bottle, intersecting in two rings.

  19. Energy landscapes and functions of supramolecular systems

    NASA Astrophysics Data System (ADS)

    Tantakitti, Faifan; Boekhoven, Job; Wang, Xin; Kazantsev, Roman V.; Yu, Tao; Li, Jiahe; Zhuang, Ellen; Zandi, Roya; Ortony, Julia H.; Newcomb, Christina J.; Palmer, Liam C.; Shekhawat, Gajendra S.; de La Cruz, Monica Olvera; Schatz, George C.; Stupp, Samuel I.

    2016-04-01

    By means of two supramolecular systems--peptide amphiphiles engaged in hydrogen-bonded β-sheets, and chromophore amphiphiles driven to assemble by π-orbital overlaps--we show that the minima in the energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations. These competing interactions can be selectively switched on and off, with the order of doing so determining the position of the final product in the energy landscape. Within the same energy landscape, the peptide-amphiphile system forms a thermodynamically favoured product characterized by long bundled fibres that promote biological cell adhesion and survival, and a metastable product characterized by short monodisperse fibres that interfere with adhesion and can lead to cell death. Our findings suggest that, in supramolecular systems, functions and energy landscapes are linked, superseding the more traditional connection between molecular design and function.

  20. Energy landscapes and functions of supramolecular systems.

    PubMed

    Tantakitti, Faifan; Boekhoven, Job; Wang, Xin; Kazantsev, Roman V; Yu, Tao; Li, Jiahe; Zhuang, Ellen; Zandi, Roya; Ortony, Julia H; Newcomb, Christina J; Palmer, Liam C; Shekhawat, Gajendra S; de la Cruz, Monica Olvera; Schatz, George C; Stupp, Samuel I

    2016-04-01

    By means of two supramolecular systems--peptide amphiphiles engaged in hydrogen-bonded β-sheets, and chromophore amphiphiles driven to assemble by π-orbital overlaps--we show that the minima in the energy landscapes of supramolecular systems are defined by electrostatic repulsion and the ability of the dominant attractive forces to trap molecules in thermodynamically unfavourable configurations. These competing interactions can be selectively switched on and off, with the order of doing so determining the position of the final product in the energy landscape. Within the same energy landscape, the peptide-amphiphile system forms a thermodynamically favoured product characterized by long bundled fibres that promote biological cell adhesion and survival, and a metastable product characterized by short monodisperse fibres that interfere with adhesion and can lead to cell death. Our findings suggest that, in supramolecular systems, functions and energy landscapes are linked, superseding the more traditional connection between molecular design and function.

  1. Energy landscape and fluctuations in proteins

    NASA Astrophysics Data System (ADS)

    Frauenfelder, H.; McMahon, B. H.

    2000-10-01

    Complex systems such as biomolecules or glasses do not exist in a unique structure, but can assume a very large number of somewhat different conformations. The organization of the conformations can be described in the energy (or conformation) landscape, where individual valleys are called conformational substates. Proteins are systems where the energy landscape has been studied in some detail. Their landscape is organized in a hierarchy that contains three types of substates, taxonomic, statistical, and few-level. Conformational substates are found in a wide variety of proteins. Some of their characteristics are described and the open experimental and theoretical problems are listed.

  2. Graph representation of protein free energy landscape

    SciTech Connect

    Li, Minghai; Duan, Mojie; Fan, Jue; Huo, Shuanghong; Han, Li

    2013-11-14

    The thermodynamics and kinetics of protein folding and protein conformational changes are governed by the underlying free energy landscape. However, the multidimensional nature of the free energy landscape makes it difficult to describe. We propose to use a weighted-graph approach to depict the free energy landscape with the nodes on the graph representing the conformational states and the edge weights reflecting the free energy barriers between the states. Our graph is constructed from a molecular dynamics trajectory and does not involve projecting the multi-dimensional free energy landscape onto a low-dimensional space defined by a few order parameters. The calculation of free energy barriers was based on transition-path theory using the MSMBuilder2 package. We compare our graph with the widely used transition disconnectivity graph (TRDG) which is constructed from the same trajectory and show that our approach gives more accurate description of the free energy landscape than the TRDG approach even though the latter can be organized into a simple tree representation. The weighted-graph is a general approach and can be used on any complex system.

  3. Graph representation of protein free energy landscape.

    PubMed

    Li, Minghai; Duan, Mojie; Fan, Jue; Han, Li; Huo, Shuanghong

    2013-11-14

    The thermodynamics and kinetics of protein folding and protein conformational changes are governed by the underlying free energy landscape. However, the multidimensional nature of the free energy landscape makes it difficult to describe. We propose to use a weighted-graph approach to depict the free energy landscape with the nodes on the graph representing the conformational states and the edge weights reflecting the free energy barriers between the states. Our graph is constructed from a molecular dynamics trajectory and does not involve projecting the multi-dimensional free energy landscape onto a low-dimensional space defined by a few order parameters. The calculation of free energy barriers was based on transition-path theory using the MSMBuilder2 package. We compare our graph with the widely used transition disconnectivity graph (TRDG) which is constructed from the same trajectory and show that our approach gives more accurate description of the free energy landscape than the TRDG approach even though the latter can be organized into a simple tree representation. The weighted-graph is a general approach and can be used on any complex system.

  4. Constructing and exploring wells of energy landscapes

    NASA Astrophysics Data System (ADS)

    Aubin, Jean-Pierre; Lesne, Annick

    2005-04-01

    Landscape paradigm is ubiquitous in physics and other natural sciences, but it has to be supplemented with both quantitative and qualitatively meaningful tools for analyzing the topography of a given landscape. We here consider dynamic explorations of the relief and introduce as basic topographic features "wells of duration T and altitude y." We determine an intrinsic exploration mechanism governing the evolutions from an initial state in the well up to its rim in a prescribed time, whose finite-difference approximations on finite grids yield a constructive algorithm for determining the wells. Our main results are thus (i) a quantitative characterization of landscape topography rooted in a dynamic exploration of the landscape, (ii) an alternative to stochastic gradient dynamics for performing such an exploration, (iii) a constructive access to the wells, and (iv) the determination of some bare dynamic features inherent to the landscape. The mathematical tools used here are not familiar in physics: They come from set-valued analysis (differential calculus of set-valued maps and differential inclusions) and viability theory (capture basins of targets under evolutionary systems) that have been developed during the last two decades; we therefore propose a minimal Appendix exposing them at the end of this paper to bridge the possible gap.

  5. Evidence for an intrinsic factor promoting landscape genetic divergence in Madagascan leaf-litter frogs

    PubMed Central

    Wollenberg Valero, Katharina C.

    2015-01-01

    The endemic Malagasy frog radiations are an ideal model system to study patterns and processes of speciation in amphibians. Large-scale diversity patterns of these frogs, together with other endemic animal radiations, led to the postulation of new and the application of known hypotheses of species diversification causing diversity patterns in this biodiversity hotspot. Both extrinsic and intrinsic factors have been studied in a comparative framework, with extrinsic factors usually being related to the physical environment (landscape, climate, river catchments, mountain chains), and intrinsic factors being clade-specific traits or constraints (reproduction, ecology, morphology, physiology). Despite some general patterns emerging from such large-scale comparative analyses, it became clear that the mechanism of diversification in Madagascar may vary among clades, and may be a multifactorial process. In this contribution, I test for intrinsic factors promoting population-level divergence within a clade of terrestrial, diurnal leaf-litter frogs (genus Gephyromantis) that has previously been shown to diversify according to extrinsic factors. Landscape genetic analyses of the microendemic species Gephyromantis enki and its widely distributed, larger sister species Gephyromantis boulengeri over a rugged landscape in the Ranomafana area shows that genetic variance of the smaller species cannot be explained by landscape resistance alone. Both topographic and riverine barriers are found to be important in generating this divergence. This case study yields additional evidence for the probable importance of body size in lineage diversification. PMID:26136766

  6. Evidence for an intrinsic factor promoting landscape genetic divergence in Madagascan leaf-litter frogs.

    PubMed

    Wollenberg Valero, Katharina C

    2015-01-01

    The endemic Malagasy frog radiations are an ideal model system to study patterns and processes of speciation in amphibians. Large-scale diversity patterns of these frogs, together with other endemic animal radiations, led to the postulation of new and the application of known hypotheses of species diversification causing diversity patterns in this biodiversity hotspot. Both extrinsic and intrinsic factors have been studied in a comparative framework, with extrinsic factors usually being related to the physical environment (landscape, climate, river catchments, mountain chains), and intrinsic factors being clade-specific traits or constraints (reproduction, ecology, morphology, physiology). Despite some general patterns emerging from such large-scale comparative analyses, it became clear that the mechanism of diversification in Madagascar may vary among clades, and may be a multifactorial process. In this contribution, I test for intrinsic factors promoting population-level divergence within a clade of terrestrial, diurnal leaf-litter frogs (genus Gephyromantis) that has previously been shown to diversify according to extrinsic factors. Landscape genetic analyses of the microendemic species Gephyromantis enki and its widely distributed, larger sister species Gephyromantis boulengeri over a rugged landscape in the Ranomafana area shows that genetic variance of the smaller species cannot be explained by landscape resistance alone. Both topographic and riverine barriers are found to be important in generating this divergence. This case study yields additional evidence for the probable importance of body size in lineage diversification.

  7. Local energy landscape in a simple liquid

    DOE PAGES

    Iwashita, T.; Egami, Takeshi

    2014-11-26

    It is difficult to relate the properties of liquids and glasses directly to their structure because of complexity in the structure that defies precise definition. The potential energy landscape (PEL) approach is a very insightful way to conceptualize the structure-property relationship in liquids and glasses, particularly the effect of temperature and history. However, because of the highly multidimensional nature of the PEL it is hard to determine, or even visualize, the actual details of the energy landscape. In this article we introduce a modified concept of the local energy landscape (LEL), which is limited in phase space, and demonstrate itsmore » usefulness using molecular dynamics simulation on a simple liquid at high temperatures. The local energy landscape is given as a function of the local coordination number, the number of the nearest-neighbor atoms. The excitation in the LEL corresponds to the so-called β-relaxation process. The LEL offers a simple but useful starting point to discuss complex phenomena in liquids and glasses.« less

  8. Local energy landscape in a simple liquid

    SciTech Connect

    Iwashita, T.; Egami, Takeshi

    2014-11-26

    It is difficult to relate the properties of liquids and glasses directly to their structure because of complexity in the structure that defies precise definition. The potential energy landscape (PEL) approach is a very insightful way to conceptualize the structure-property relationship in liquids and glasses, particularly the effect of temperature and history. However, because of the highly multidimensional nature of the PEL it is hard to determine, or even visualize, the actual details of the energy landscape. In this article we introduce a modified concept of the local energy landscape (LEL), which is limited in phase space, and demonstrate its usefulness using molecular dynamics simulation on a simple liquid at high temperatures. The local energy landscape is given as a function of the local coordination number, the number of the nearest-neighbor atoms. The excitation in the LEL corresponds to the so-called β-relaxation process. The LEL offers a simple but useful starting point to discuss complex phenomena in liquids and glasses.

  9. Exploring the conformational energy landscape of proteins

    SciTech Connect

    Nienhaus, G.U. |; Mueller, J.D.; McMahon, B.H.

    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.

  10. Archetypal energy landscapes: dynamical diagnosis.

    PubMed

    Despa, Florin; Wales, David J; Berry, R Stephen

    2005-01-08

    Recent studies have identified several motifs for potential energy surfaces corresponding to distinct dynamic and thermodynamic properties. The corresponding disconnectivity graphs were identified as "palm tree," "willow tree," and "banyan tree" patterns. In the present contribution we present a quantitative analysis of the relation between the topography and dynamics for each of these motifs. For the palm tree and willow tree forms we find that the arrangement of the stationary points in the monotonic sequences with respect to the global minimum is the most important factor in establishing the kinetic properties. However, the results are somewhat different for motifs involving a rough surface with several deep basins (banyan tree motif), with large barriers relative to the energy differences between minima. Here it is the size of the barrier for escape from the region relative to the barriers at the bottom that is most important. The present results may be helpful in distinguishing between the dynamics of "structure seeking" and "glass forming" systems.

  11. How to quantify energy landscapes of solids.

    PubMed

    Oganov, Artem R; Valle, Mario

    2009-03-14

    We explore whether the topology of energy landscapes in chemical systems obeys any rules and what these rules are. To answer this and related questions we use several tools: (i) Reduced energy surface and its density of states, (ii) descriptor of structure called fingerprint function, which can be represented as a one-dimensional function or a vector in abstract multidimensional space, (iii) definition of a "distance" between two structures enabling quantification of energy landscapes, (iv) definition of a degree of order of a structure, and (v) definitions of the quasi-entropy quantifying structural diversity. Our approach can be used for rationalizing large databases of crystal structures and for tuning computational algorithms for structure prediction. It enables quantitative and intuitive representations of energy landscapes and reappraisal of some of the traditional chemical notions and rules. Our analysis confirms the expectations that low-energy minima are clustered in compact regions of configuration space ("funnels") and that chemical systems tend to have very few funnels, sometimes only one. This analysis can be applied to the physical properties of solids, opening new ways of discovering structure-property relations. We quantitatively demonstrate that crystals tend to adopt one of the few simplest structures consistent with their chemistry, providing a thermodynamic justification of Pauling's fifth rule.

  12. Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape Topography

    PubMed Central

    Chu, Xiakun; Wang, Jin

    2014-01-01

    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. PMID:25144525

  13. Potential energy landscapes of tetragonal pyramid molecules

    NASA Astrophysics Data System (ADS)

    Yoshida, Yuichiro; Sato, Hirofumi; Morgan, John W. R.; Wales, David J.

    2016-11-01

    Hiraoka et al. have developed a self-assembling system referred to as a nanocube (Hiraoka et al., 2008). In the present contribution a coarse-grained model for this system is analysed, focusing on how the potential energy landscape for self-assembly is related to the geometry of the building blocks. We find that six molecules assemble to form various clusters, with cubic and sheet structures the most stable. The relative stability is determined by the geometry of the building blocks.

  14. Energy landscape in protein folding and unfolding

    PubMed Central

    Mallamace, Francesco; Corsaro, Carmelo; Mallamace, Domenico; Vasi, Sebastiano; Vasi, Cirino; Baglioni, Piero; Buldyrev, Sergey V.; Chen, Sow-Hsin; Stanley, H. Eugene

    2016-01-01

    We use 1H NMR to probe the energy landscape in the protein folding and unfolding process. Using the scheme ⇄ reversible unfolded (intermediate) → irreversible unfolded (denatured) state, we study the thermal denaturation of hydrated lysozyme that occurs when the temperature is increased. Using thermal cycles in the range 295energy surface, we observe that the hydrophilic (the amide NH) and hydrophobic (methyl CH3 and methine CH) peptide groups evolve and exhibit different behaviors. We also discuss the role of water and hydrogen bonding in the protein configurational stability. PMID:26957601

  15. Energy landscape in protein folding and unfolding.

    PubMed

    Mallamace, Francesco; Corsaro, Carmelo; Mallamace, Domenico; Vasi, Sebastiano; Vasi, Cirino; Baglioni, Piero; Buldyrev, Sergey V; Chen, Sow-Hsin; Stanley, H Eugene

    2016-03-22

    We use (1)H NMR to probe the energy landscape in the protein folding and unfolding process. Using the scheme ⇄ reversible unfolded (intermediate) → irreversible unfolded (denatured) state, we study the thermal denaturation of hydrated lysozyme that occurs when the temperature is increased. Using thermal cycles in the range 295 < T < 365 K and following different trajectories along the protein energy surface, we observe that the hydrophilic (the amide NH) and hydrophobic (methyl CH3 and methine CH) peptide groups evolve and exhibit different behaviors. We also discuss the role of water and hydrogen bonding in the protein configurational stability.

  16. Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes

    PubMed Central

    Chu, Wen-Ting; Wang, Jin

    2016-01-01

    Enzyme activity (often quantified by kcat/Km) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the “hot-spot” within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat/Km. This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design. PMID:27298067

  17. Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes

    NASA Astrophysics Data System (ADS)

    Chu, Wen-Ting; Wang, Jin

    2016-06-01

    Enzyme activity (often quantified by kcat/Km) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the “hot-spot” within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat/Km. This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design.

  18. Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes.

    PubMed

    Chu, Wen-Ting; Wang, Jin

    2016-06-14

    Enzyme activity (often quantified by kcat/Km) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the "hot-spot" within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat/Km. This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design.

  19. Energy landscape of relaxed amorphous silicon

    NASA Astrophysics Data System (ADS)

    Valiquette, Francis; Mousseau, Normand

    2003-09-01

    We analyze the structure of the energy landscape of a well-relaxed 1000-atom model of amorphous silicon using the activation-relaxation technique (ART nouveau). Generating more than 40 000 events starting from a single minimum, we find that activated mechanisms are local in nature, that they are distributed uniformly throughout the model, and that the activation energy is limited by the cost of breaking one bond, independently of the complexity of the mechanism. The overall shape of the activation-energy-barrier distribution is also insensitive to the exact details of the configuration, indicating that well-relaxed configurations see essentially the same environment. These results underscore the localized nature of relaxation in this material.

  20. 'Energy landscapes': Meeting energy demands and human aspirations.

    PubMed

    Blaschke, Thomas; Biberacher, Markus; Gadocha, Sabine; Schardinger, Ingrid

    2013-08-01

    Renewable energy will play a crucial role in the future society of the 21st century. The various renewable energy sources need to be balanced and their use carefully planned since they are characterized by high temporal and spatial variability that will pose challenges to maintaining a well balanced supply and to the stability of the grid. This article examines the ways that future 'energy landscapes' can be modelled in time and space. Biomass needs a great deal of space per unit of energy produced but it is an energy carrier that may be strategically useful in circumstances where other renewable energy carriers are likely to deliver less. A critical question considered in this article is whether a massive expansion in the use of biomass will allow us to construct future scenarios while repositioning the 'energy landscape' as an object of study. A second important issue is the utilization of heat from biomass energy plants. Biomass energy also has a larger spatial footprint than other carriers such as, for example, solar energy. This article seeks to provide a bridge between energy modelling and spatial planning while integrating research and techniques in energy modelling with Geographic Information Science. This encompasses GIS, remote sensing, spatial disaggregation techniques and geovisualization. Several case studies in Austria and Germany demonstrate a top-down methodology and some results while stepwise calculating potentials from theoretical to technically feasible potentials and setting the scene for the definition of economic potentials based on scenarios and assumptions.

  1. Energy landscape diversity and supercooled liquid properties

    NASA Astrophysics Data System (ADS)

    Stillinger, Frank H.; Debenedetti, Pablo G.

    2002-02-01

    Families of model "rugged landscape" potential energy functions have been constructed and examined, in order to clarify the molecular-level basis for the relationship between thermodynamic and kinetic behaviors of glassforming substances. The general approach starts by forming elementary basin units, each of which contains a single local minimum (inherent structure). These units are then spliced together to create a continuous composite potential with the requisite number of basins, upper and lower limits, and boundary conditions. We demonstrate by example that this approach creates wide topographic diversity. Specifically, many pairs of model potential functions exist that share identical thermodynamic properties (depth distribution of minima), but drastically different kinetics (overall topography). Thus, within the confines of this purely mathematical exercise, the "strong" versus "fragile" classifications of thermodynamics and of kinetics are logically disconnected. We conclude that the empirically-observed correlation between thermodynamic and kinetic behaviors embodied, for example, in the Adam-Gibbs equation, must rest upon an additional physical principle involving details of interparticle interactions, transcending the purely mathematical aspects of potential energy landscape topography.

  2. MEPSA: minimum energy pathway analysis for energy landscapes.

    PubMed

    Marcos-Alcalde, Iñigo; Setoain, Javier; Mendieta-Moreno, Jesús I; Mendieta, Jesús; Gómez-Puertas, Paulino

    2015-12-01

    From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA's output such as the generation of molecular dynamics restraints from a calculated path. MEPSA is freely available (under GPLv3 license) at: http://bioweb.cbm.uam.es/software/MEPSA/ CONTACT: pagomez@cbm.csic.es. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process

    PubMed Central

    Lv, Cheng; Li, Xiaoguang; Li, Fangting; Li, Tiejun

    2015-01-01

    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. PMID:25794282

  4. Landscape framework and global stability for stochastic reaction diffusion and general spatially extended systems with intrinsic fluctuations.

    PubMed

    Wu, Wei; Wang, Jin

    2013-10-24

    Spatially extended systems are widely encountered in physics, chemistry, and biology for studying many important natural phenomena. In this work, we established a landscape framework for studying general stochastic spatially extended systems with intrinsic statistical fluctuations that can be applied to both equilibrium systems with detailed balance and nonequilibrium systems without detailed balance. We set up the master equation for general stochastic spatially extended systems (functional master equation) from two fundamental dynamical ingredients that characterize the elementary state transitions of spatially extended systems. We explored the entire spectrum of the various approximations of the functional master equation under certain conditions, from the functional Kramers-Moyal equation to the functional Fokker-Planck equation and its equivalent, the functional Langevin equation, to the macroscopic deterministic equation. We uncovered the Lyapunov functionals which are required to quantify the global stability and function of the system for both the deterministic and stochastic spatially extended systems. The global potential landscape functional for stochastic spatially extended systems can be quantified by the steady state probability distribution functional. In the small fluctuation limit, the potential landscape functional becomes the Lyapunov functional for the corresponding deterministic spatially extended system. The relative entropy functional (or free energy functional) proves to be the Lyapunov functional for the stochastic spatially extended systems. The potential landscape functional and the relative entropy functional quantify the global stability and function of the deterministic and stochastic spatially extended systems for both equilibrium and nonequilibrium conditions. The chemical reaction-diffusion systems as a typical and important class of spatially extended systems is explored on its own terms as well as used as a direct application of

  5. How animals distribute themselves in space: variable energy landscapes.

    PubMed

    Masello, Juan F; Kato, Akiko; Sommerfeld, Julia; Mattern, Thomas; Quillfeldt, Petra

    2017-01-01

    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 Island, Falkland/Malvinas Islands. In our study, the marine areas used by the penguins, parameters of dive depth and the proportion of pelagic and benthic dives varied both between years and colonies. As a consequence, the energy landscapes also varied between the years, and we discuss how this was related to differences in food availability, which were also reflected in differences in carbon and nitrogen stable isotope values and isotopic niche metrics. In the second year, the energy landscape was characterized by lower foraging costs per energy gain, and breeding success was also higher in this year. Additionally, an area around three South American Fur Seal Arctocephalus australis colonies was never used. These results confirm that energy landscapes vary in time and that the seabirds forage in areas of the energy landscapes that result in minimized energetic costs. Thus, our results support the view of energy landscapes and fear of predation as mechanisms underlying animal foraging behaviour. Furthermore, we show that energy landscapes are useful in linking energy gain and variable energy costs of foraging to breeding success.

  6. Intrinsic Changes: Energy Saving Behaviour among Resident University Students

    ERIC Educational Resources Information Center

    Black, Rosemary; Davidson, Penny; Retra, Karen

    2010-01-01

    This paper presents the results of a study that explored the effectiveness of three intervention strategies in facilitating energy saving behaviour among resident undergraduate university students. In contrast to a dominant practice of motivating with rewards or competition this study sought to appeal to students' intrinsic motivations. An…

  7. Intrinsic Changes: Energy Saving Behaviour among Resident University Students

    ERIC Educational Resources Information Center

    Black, Rosemary; Davidson, Penny; Retra, Karen

    2010-01-01

    This paper presents the results of a study that explored the effectiveness of three intervention strategies in facilitating energy saving behaviour among resident undergraduate university students. In contrast to a dominant practice of motivating with rewards or competition this study sought to appeal to students' intrinsic motivations. An…

  8. Evolution, Energy Landscapes and the Paradoxes of Protein Folding

    PubMed Central

    Wolynes, Peter G.

    2014-01-01

    Protein folding has been viewed as a difficult problem of molecular self-organization. The search problem involved in folding however has been simplified through the evolution of folding energy landscapes that are funneled. The funnel hypothesis can be quantified using energy landscape theory based on the minimal frustration principle. Strong quantitative predictions that follow from energy landscape theory have been widely confirmed both through laboratory folding experiments and from detailed simulations. Energy landscape ideas also have allowed successful protein structure prediction algorithms to be developed. The selection constraint of having funneled folding landscapes has left its imprint on the sequences of existing protein structural families. Quantitative analysis of co-evolution patterns allows us to infer the statistical characteristics of the folding landscape. These turn out to be consistent with what has been obtained from laboratory physicochemical folding experiments signalling a beautiful confluence of genomics and chemical physics. PMID:25530262

  9. Energy landscape analysis of neuroimaging data.

    PubMed

    Ezaki, Takahiro; Watanabe, Takamitsu; Ohzeki, Masayuki; Masuda, Naoki

    2017-06-28

    Computational neuroscience models have been used for understanding neural dynamics in the brain and how they may be altered when physiological or other conditions change. We review and develop a data-driven approach to neuroimaging data called the energy landscape analysis. The methods are rooted in statistical physics theory, in particular the Ising model, also known as the (pairwise) maximum entropy model and Boltzmann machine. The methods have been applied to fitting electrophysiological data in neuroscience for a decade, but their use in neuroimaging data is still in its infancy. We first review the methods and discuss some algorithms and technical aspects. Then, we apply the methods to functional magnetic resonance imaging data recorded from healthy individuals to inspect the relationship between the accuracy of fitting, the size of the brain system to be analysed and the data length.This article is part of the themed issue 'Mathematical methods in medicine: neuroscience, cardiology and pathology'. © 2017 The Authors.

  10. Energy landscape analysis of neuroimaging data

    NASA Astrophysics Data System (ADS)

    Ezaki, Takahiro; Watanabe, Takamitsu; Ohzeki, Masayuki; Masuda, Naoki

    2017-05-01

    Computational neuroscience models have been used for understanding neural dynamics in the brain and how they may be altered when physiological or other conditions change. We review and develop a data-driven approach to neuroimaging data called the energy landscape analysis. The methods are rooted in statistical physics theory, in particular the Ising model, also known as the (pairwise) maximum entropy model and Boltzmann machine. The methods have been applied to fitting electrophysiological data in neuroscience for a decade, but their use in neuroimaging data is still in its infancy. We first review the methods and discuss some algorithms and technical aspects. Then, we apply the methods to functional magnetic resonance imaging data recorded from healthy individuals to inspect the relationship between the accuracy of fitting, the size of the brain system to be analysed and the data length. This article is part of the themed issue `Mathematical methods in medicine: neuroscience, cardiology and pathology'.

  11. Landscape Design and Nursery Operation for Energy Conservation.

    ERIC Educational Resources Information Center

    Bell, Richard C.; Glazener, Dennis

    Landforms, vegetation, water bodies, climate and solar radiation can be analyzed and used to design an energy-conserving landscape and horticulture operation. Accordingly, this course instructor's manual covers the use of the elements of the environment to make landscaping and nursery design and operation more energy-efficient. Five sections…

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

    NASA Astrophysics Data System (ADS)

    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.

  13. Exploring Energy Landscapes with Monte Carlo Methods

    NASA Astrophysics Data System (ADS)

    Wales, David J.; Hernández-Rojas, Javier

    2003-11-01

    The potential energy surface of an atomic or molecular system can be transformed into a set of catchment basins for the local minima. Monte Carlo methods can be applied to explore the resulting landscape and search for the global potential minimum or calculate thermodynamic and dynamic properties. For example, the kinetic Monte Carlo (KMC) approach has been used to study the structure and dynamics of a supercooled binary Lennard-Jones liquid, which is a popular model glass former. The KMC technique allows us to explore the potential energy surface without suffering an exponential slowing down at low temperature. In agreement with previous studies we observe a distinct change in behaviour close to the dynamical transition temperature of mode-coupling theory. Below this temperature the number of different local minima visited by the system for the same number of KMC steps decreases by more than an order of magnitude. The mean number of atoms involved in each jump between local minima and the average distance they move also decreases significantly, and new features appear in the partial structure factor. At higher temperature the probability distribution for the magnitude of the atomic displacement per KMC step exhibits an exponential decay, which is only weakly temperature dependent.

  14. Enhanced stochastic fluctuations to measure steep adhesive energy landscapes.

    PubMed

    Haider, Ahmad; Potter, Daniel; Sulchek, Todd A

    2016-12-13

    Free-energy landscapes govern the behavior of all interactions in the presence of thermal fluctuations in the fields of physical chemistry, materials sciences, and the biological sciences. From the energy landscape, critical information about an interaction, such as the reaction kinetic rates, bond lifetimes, and the presence of intermediate states, can be determined. Despite the importance of energy landscapes to understanding reaction mechanisms, most experiments do not directly measure energy landscapes, particularly for interactions with steep force gradients that lead to premature jump to contact of the probe and insufficient sampling of transition regions. Here we present an atomic force microscopy (AFM) approach for measuring energy landscapes that increases sampling of strongly adhesive interactions by using white-noise excitation to enhance the cantilever's thermal fluctuations. The enhanced fluctuations enable the recording of subtle deviations from a harmonic potential to accurately reconstruct interfacial energy landscapes with steep gradients. Comparing the measured energy landscape with adhesive force measurements reveals the existence of an optimal excitation voltage that enables the cantilever fluctuations to fully sample the shape and depth of the energy surface.

  15. Enhanced stochastic fluctuations to measure steep adhesive energy landscapes

    PubMed Central

    Haider, Ahmad; Potter, Daniel; Sulchek, Todd A.

    2016-01-01

    Free-energy landscapes govern the behavior of all interactions in the presence of thermal fluctuations in the fields of physical chemistry, materials sciences, and the biological sciences. From the energy landscape, critical information about an interaction, such as the reaction kinetic rates, bond lifetimes, and the presence of intermediate states, can be determined. Despite the importance of energy landscapes to understanding reaction mechanisms, most experiments do not directly measure energy landscapes, particularly for interactions with steep force gradients that lead to premature jump to contact of the probe and insufficient sampling of transition regions. Here we present an atomic force microscopy (AFM) approach for measuring energy landscapes that increases sampling of strongly adhesive interactions by using white-noise excitation to enhance the cantilever’s thermal fluctuations. The enhanced fluctuations enable the recording of subtle deviations from a harmonic potential to accurately reconstruct interfacial energy landscapes with steep gradients. Comparing the measured energy landscape with adhesive force measurements reveals the existence of an optimal excitation voltage that enables the cantilever fluctuations to fully sample the shape and depth of the energy surface. PMID:27911778

  16. An energy landscape approach to protein aggregation

    NASA Astrophysics Data System (ADS)

    Buell, Alexander; Knowles, Tuomas

    2012-02-01

    Protein aggregation into ordered fibrillar structures is the hallmark of a class of diseases, the most prominent examples of which are Alzheimer's and Parkinson's disease. Recent results (e.g. Baldwin et al. J. Am. Chem. Soc. 2011) suggest that the aggregated state of a protein is in many cases thermodynamically more stable than the soluble state. Therefore the solubility of proteins in a cellular context appears to be to a large extent under kinetic control. Here, we first present a conceptual framework for the description of protein aggregation ( see AK Buell et al., Phys. Rev. Lett. 2010) that is an extension to the generally accepted energy landscape model for protein folding. Then we apply this model to analyse and interpret a large set of experimental data on the kinetics of protein aggregation, acquired mainly with a novel biosensing approach (see TPJK Knowles et al, Proc. Nat. Acad. Sc. 2007). We show how for example the effect of sequence modifications on the kinetics and thermodynamics of human lysozyme aggregation can be understood and quantified (see AK Buell et al., J. Am. Chem. Soc. 2011). These results have important implications for therapeutic strategies against protein aggregation disorders, in this case lysozyme systemic amyloidosis.

  17. Noise induced transitions in rugged energy landscapes

    NASA Astrophysics Data System (ADS)

    Pradas, Marc; Duncan, Andrew; Kalliadasis, Serafim; Pavliotis, Greg

    2016-11-01

    External or internal random fluctuations are ubiquitous in many physical and technological systems and can play a key role in their dynamics often inducing a wide variety of complex spatiotemporal phenomena, including noise-induced spatial patterns and noise-induced phase transitions. Many of these phenomena can be modelled by noisy multiscale systems characterized by the presence of a wide range of different time- and lengthscales interacting nontrivially with each other. Here we analyse the effects of additive noise on systems that are described in terms of a rugged energy landscape, modelled as a slowly-varying multiscale potential perturbed by periodic multiscale fluctuations. Some examples of this problem include the dynamics of sessile droplets on heterogeneous substrates, crystallization and the evolution of protein folding. We demonstrate that the interplay between noise and the small scale fluctuations in the potential can give rise to a dramatically different bifurcation structure and dynamical behaviour compared to that of the original, unperturbed model. For instance, we observe several nontrivial and largely unexpected dynamic-state transitions controlled by the noise intensity. We characterize these transitions in terms of critical exponents.

  18. Energy landscape exploration of the folding processes of biological molecules

    NASA Astrophysics Data System (ADS)

    Engel, Megan Clare

    For decades, scientists from every discipline have struggled to understand the mechanism of biological self-assembly, which allows proteins and nucleic acids to fold reliably into functional three-dimensional structures. Such an understanding may hold the key to eliminating diseases such as Alzheimer's and Parkinson's and to effective protein engineering. The current best framework for describing biological folding processes is that of statistical mechanical energy landscape theory, and one of the most promising experimental techniques for exploring molecular energy landscapes is single molecule force spectroscopy (SMFS), in which molecules are mechanically denatured. Theoretical advances have enabled the extraction of complete energy landscape profiles from SMFS data. Here, SMFS experiments performed using laser optical tweezers are analyzed to yield the first ever full landscape profile for an RNA pseudoknot. Further, a promising novel landscape reconstruction technique is validated for the first time using experimental data from a DNA hairpin.

  19. Energy landscapes in proteins and glasses

    NASA Astrophysics Data System (ADS)

    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

  20. Enzyme activation through the utilization of intrinsic dianion binding energy.

    PubMed

    Amyes, T L; Malabanan, M M; Zhai, X; Reyes, A C; Richard, J P

    2017-03-01

    We consider 'the proposition that the intrinsic binding energy that results from the noncovalent interaction of a specific substrate with the active site of the enzyme is considerably larger than is generally believed. An important part of this binding energy may be utilized to provide the driving force for catalysis, so that the observed binding energy represents only what is left over after this utilization' [Jencks,W.P. (1975) Adv. Enzymol. Relat. Areas. Mol. Biol. , , 219-410]. The large ~12 kcal/mol intrinsic substrate phosphodianion binding energy for reactions catalyzed by triosephosphate isomerase (TIM), orotidine 5'-monophosphate decarboxylase and glycerol-3-phosphate dehydrogenase is divided into 4-6 kcal/mol binding energy that is expressed on the formation of the Michaelis complex in anchoring substrates to the respective enzyme, and 6-8 kcal/mol binding energy that is specifically expressed at the transition state in activating the respective enzymes for catalysis. A structure-based mechanism is described where the dianion binding energy drives a conformational change that activates these enzymes for catalysis. Phosphite dianion plays the active role of holding TIM in a high-energy closed active form, but acts as passive spectator in showing no effect on transition-state structure. The result of studies on mutant enzymes is presented, which support the proposal that the dianion-driven enzyme conformational change plays a role in enhancing the basicity of side chain of E167, the catalytic base, by clamping the base between a pair of hydrophobic side chains. The insight these results provide into the architecture of enzyme active sites and the development of strategies for the de novo design of protein catalysts is discussed.

  1. Potential energy landscapes of elemental and heterogeneous chalcogen clusters

    SciTech Connect

    Mauro, John C.; Loucks, Roger J.; Balakrishnan, Jitendra; Varshneya, Arun K.

    2006-02-15

    We describe the potential energy landscapes of elemental S{sub 8}, Se{sub 8}, and Te{sub 8} clusters using disconnectivity graphs. Inherent structures include both ring and chain configurations, with rings especially dominant in Se{sub 8}. We also map the potential energy landscapes of heterogeneous Se{sub n}(S,Te){sub 8-n} clusters, which offer insights into the structure of heterogeneous chalcogen glasses.

  2. Effect of correlations between minima on a complex energy landscape

    NASA Astrophysics Data System (ADS)

    Pusuluri, Sai Teja; Lang, Alex H.; Mehta, Pankaj; Castillo, Horacio E.

    We recently modeled cellular interconvertion dynamics by using an epigenetic landscape model inspired by neural network models. Given an arbitrary set of patterns, the model can be used to construct an energy landscape in which those patterns are the global minima. We study the possible stable states and metastable states of the landscapes thus constructed. We consider three different cases: i) choosing the patterns to be random and independently distributed ii) choosing a set of patterns directly derived from the experimental cellular transcription factor expression data for a representative set of cell types in an organism and iii) choosing randomly generated trees of hierarchically correlated patterns, inspired by biology. For each of the three cases, we study the energy landscapes. In particular we study the basins of attraction of both the stable states and the metastable states, we compute the configurational entropy as a function of energy, and we demonstrate how those results depend on the correlations between the patterns.

  3. Aging, memory, and nonhierarchical energy landscape of spin jam.

    PubMed

    Samarakoon, Anjana; Sato, Taku J; Chen, Tianran; Chern, Gai-Wei; Yang, Junjie; Klich, Israel; Sinclair, Ryan; Zhou, Haidong; Lee, Seung-Hun

    2016-10-18

    The notion of complex energy landscape underpins the intriguing dynamical behaviors in many complex systems ranging from polymers, to brain activity, to social networks and glass transitions. The spin glass state found in dilute magnetic alloys has been an exceptionally convenient laboratory frame for studying complex dynamics resulting from a hierarchical energy landscape with rugged funnels. Here, we show, by a bulk susceptibility and Monte Carlo simulation study, that densely populated frustrated magnets in a spin jam state exhibit much weaker memory effects than spin glasses, and the characteristic properties can be reproduced by a nonhierarchical landscape with a wide and nearly flat but rough bottom. Our results illustrate that the memory effects can be used to probe different slow dynamics of glassy materials, hence opening a window to explore their distinct energy landscapes.

  4. Aging, memory, and nonhierarchical energy landscape of spin jam

    PubMed Central

    Samarakoon, Anjana; Sato, Taku J.; Chen, Tianran; Chern, Gai-Wei; Yang, Junjie; Klich, Israel; Sinclair, Ryan; Zhou, Haidong; Lee, Seung-Hun

    2016-01-01

    The notion of complex energy landscape underpins the intriguing dynamical behaviors in many complex systems ranging from polymers, to brain activity, to social networks and glass transitions. The spin glass state found in dilute magnetic alloys has been an exceptionally convenient laboratory frame for studying complex dynamics resulting from a hierarchical energy landscape with rugged funnels. Here, we show, by a bulk susceptibility and Monte Carlo simulation study, that densely populated frustrated magnets in a spin jam state exhibit much weaker memory effects than spin glasses, and the characteristic properties can be reproduced by a nonhierarchical landscape with a wide and nearly flat but rough bottom. Our results illustrate that the memory effects can be used to probe different slow dynamics of glassy materials, hence opening a window to explore their distinct energy landscapes. PMID:27698141

  5. Aging, memory, and nonhierarchical energy landscape of spin jam

    NASA Astrophysics Data System (ADS)

    Samarakoon, Anjana; Sato, Taku J.; Chen, Tianran; Chern, Gai-Wei; Yang, Junjie; Klich, Israel; Sinclair, Ryan; Zhou, Haidong; Lee, Seung-Hun

    2016-10-01

    The notion of complex energy landscape underpins the intriguing dynamical behaviors in many complex systems ranging from polymers, to brain activity, to social networks and glass transitions. The spin glass state found in dilute magnetic alloys has been an exceptionally convenient laboratory frame for studying complex dynamics resulting from a hierarchical energy landscape with rugged funnels. Here, we show, by a bulk susceptibility and Monte Carlo simulation study, that densely populated frustrated magnets in a spin jam state exhibit much weaker memory effects than spin glasses, and the characteristic properties can be reproduced by a nonhierarchical landscape with a wide and nearly flat but rough bottom. Our results illustrate that the memory effects can be used to probe different slow dynamics of glassy materials, hence opening a window to explore their distinct energy landscapes.

  6. Conformational ensembles and sampled energy landscapes: Analysis and comparison.

    PubMed

    Cazals, Frédéric; Dreyfus, Tom; Mazauric, Dorian; Roth, Christine-Andrea; Robert, Charles H

    2015-06-15

    We present novel algorithms and software addressing four core problems in computational structural biology, namely analyzing a conformational ensemble, comparing two conformational ensembles, analyzing a sampled energy landscape, and comparing two sampled energy landscapes. Using recent developments in computational topology, graph theory, and combinatorial optimization, we make two notable contributions. First, we present a generic algorithm analyzing height fields. We then use this algorithm to perform density-based clustering of conformations, and to analyze a sampled energy landscape in terms of basins and transitions between them. In both cases, topological persistence is used to manage (geometric) frustration. Second, we introduce two algorithms to compare transition graphs. The first is the classical earth mover distance metric which depends only on local minimum energy configurations along with their statistical weights, while the second incorporates topological constraints inherent to conformational transitions. Illustrations are provided on a simplified protein model (BLN69), whose frustrated potential energy landscape has been thoroughly studied. The software implementing our tools is also made available, and should prove valuable wherever conformational ensembles and energy landscapes are used. © 2015 Wiley Periodicals, Inc.

  7. Comparing the folding and misfolding energy landscapes of phosphoglycerate kinase.

    PubMed

    Agócs, Gergely; Szabó, Bence T; Köhler, Gottfried; Osváth, Szabolcs

    2012-06-20

    Partitioning of polypeptides between protein folding and amyloid formation is of outstanding pathophysiological importance. Using yeast phosphoglycerate kinase as model, here we identify the features of the energy landscape that decide the fate of the protein: folding or amyloidogenesis. Structure formation was initiated from the acid-unfolded state, and monitored by fluorescence from 10 ms to 20 days. Solvent conditions were gradually shifted between folding and amyloidogenesis, and the properties of the energy landscape governing structure formation were reconstructed. A gradual transition of the energy landscape between folding and amyloid formation was observed. In the early steps of both folding and misfolding, the protein searches through a hierarchically structured energy landscape to form a molten globule in a few seconds. Depending on the conditions, this intermediate either folds to the native state in a few minutes, or forms amyloid fibers in several days. As conditions are changed from folding to misfolding, the barrier separating the molten globule and native states increases, although the barrier to the amyloid does not change. In the meantime, the native state also becomes more unstable and the amyloid more stable. We conclude that the lower region of the energy landscape determines the final protein structure. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. Inflation, dark matter, and dark energy in the string landscape.

    PubMed

    Liddle, Andrew R; Ureña-López, L Arturo

    2006-10-20

    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.

  9. Intrinsic Energy Dissipation Limits in Nano and Micromechanical Resonators

    NASA Astrophysics Data System (ADS)

    Iyer, Srikanth Subramanian

    Resonant microelectromechanical Systems (MEMS) have enabled miniaturization of high-performance inertial sensors, radio-frequency filters, timing references and mass-based chemical sensors. Despite the increasing prevalence of MEMS resonators for these applications, the energy dissipation in these structures is not well-understood. Accurate prediction of the energy loss and the resulting quality factor (Q) has significant design implications because it is directly related to device performance metrics including sensitivity for resonant sensors, bandwidth for radio-frequency filters and phase-noise for timing references. In order to assess the future potential for MEMS resonators it is critically important to evaluate the energy dissipation limits, which will dictate the ultimate performance resonant MEMS devices can achieve. This work focuses on the derivation and evaluation of the intrinsic mechanical energy dissipation limit for single-crystal nano and micromechanical resonators due to anharmonic phonon-phonon scattering in the Akhiezer regime. The energy loss is derived using perturbation theory and the linearized Boltzmann transport equation for phonons, and includes the direction and polarization dependent mode-Gruneisen parameters in order to capture the strain-induced anharmonicity among phonon branches. Evaluation of the quality factor limit reveals that Akhiezer damping, previously thought to depend only on material properties, has a strong dependence on crystal orientation and resonant mode shape. The robust model provides a dissipation limit for all resonant modes including shear-mode vibrations, which have significantly reduced energy loss because dissipative phonon-phonon scattering is restricted to volume-preserving phonon branches, indicating that Lame or wine-glass mode resonators will have the highest upper limit on mechanical efficiency. Finally, the analytical dissipation model is integrated with commercial finite element software in order to

  10. Decoding heat capacity features from the energy landscape

    NASA Astrophysics Data System (ADS)

    Wales, David J.

    2017-03-01

    A general scheme is derived to connect transitions in configuration space with features in the heat capacity. A formulation in terms of occupation probabilities for local minima that define the potential energy landscape provides a quantitative description of how contributions arise from competition between different states. The theory does not rely on a structural interpretation for the local minima, so it is equally applicable to molecular energy landscapes and the landscapes defined by abstract functions. Applications are presented for low-temperature solid-solid transitions in atomic clusters, which involve just a few local minima with different morphologies, and for cluster melting, which is driven by the landscape entropy associated with the more numerous high-energy minima. Analyzing these features in terms of the balance between states with increasing and decreasing occupation probabilities provides a direct interpretation of the underlying transitions. This approach enables us to identify a qualitatively different transition that is caused by a single local minimum associated with an exceptionally large catchment volume in configuration space for a machine learning landscape.

  11. Saddles of the energy landscape and folding of model proteins

    NASA Astrophysics Data System (ADS)

    Angelani, L.; Ruocco, G.

    2009-07-01

    We numerically investigate the Potential Energy Landscape of an off-lattice β-sheet model protein, looking at saddles and minima probed by the system during the folding process. G {\\bar o} - like (with native-state-dependent force field and funnel-like landscape) and non-G {\\bar o} -like models are considered. In the G {\\bar o} -like case, on varying the temperature, we observe: i) a pronounced peak at the collapse/folding temperature T θsimeTf in the energy elevation of visited saddles from underlying minima, ii) a crossover at the same point of the saddle order. Saddles-based quantities seem then to be good candidates as indicators of the funneled shape of the landscape in protein models.

  12. Evaluating the landscape impact of renewable energy plants

    NASA Astrophysics Data System (ADS)

    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

  13. Understanding soft glassy materials using an energy landscape approach.

    PubMed

    Hwang, Hyun Joo; Riggleman, Robert A; Crocker, John C

    2016-09-01

    Many seemingly different soft materials-such as soap foams, mayonnaise, toothpaste and living cells-display strikingly similar viscoelastic behaviour. A fundamental physical understanding of such soft glassy rheology and how it can manifest in such diverse materials, however, remains unknown. Here, by using a model soap foam consisting of compressible spherical bubbles, whose sizes slowly evolve and whose collective motion is simply dictated by energy minimization, we study the foam's dynamics as it corresponds to downhill motion on an energy landscape function spanning a high-dimensional configuration space. We find that these downhill paths, when viewed in this configuration space, are, surprisingly, fractal. The complex behaviour of our model, including power-law rheology and non-diffusive bubble motion and avalanches, stems directly from the fractal dimension and energy function of these paths. Our results suggest that ubiquitous soft glassy rheology may be a consequence of emergent fractal geometry in the energy landscapes of many complex fluids.

  14. Understanding soft glassy materials using an energy landscape approach

    NASA Astrophysics Data System (ADS)

    Hwang, Hyun Joo; Riggleman, Robert A.; Crocker, John C.

    2016-09-01

    Many seemingly different soft materials--such as soap foams, mayonnaise, toothpaste and living cells--display strikingly similar viscoelastic behaviour. A fundamental physical understanding of such soft glassy rheology and how it can manifest in such diverse materials, however, remains unknown. Here, by using a model soap foam consisting of compressible spherical bubbles, whose sizes slowly evolve and whose collective motion is simply dictated by energy minimization, we study the foam's dynamics as it corresponds to downhill motion on an energy landscape function spanning a high-dimensional configuration space. We find that these downhill paths, when viewed in this configuration space, are, surprisingly, fractal. The complex behaviour of our model, including power-law rheology and non-diffusive bubble motion and avalanches, stems directly from the fractal dimension and energy function of these paths. Our results suggest that ubiquitous soft glassy rheology may be a consequence of emergent fractal geometry in the energy landscapes of many complex fluids.

  15. Landscaping for energy conservation: plan an energy-saving yard

    SciTech Connect

    Not Available

    1983-01-01

    This illustrated brochure covers the following aspects of landscaping: summer cooling, winter warming with emphasis on windbreaks, earth shettering, and materials for do-it-yourself planning. Lists of useful deciduous, and evergreen trees, vines, and shrubs are included with a chart of their characteristics. (MHR)

  16. Distributed energy tapestry for heating the landscape

    NASA Astrophysics Data System (ADS)

    Rocha, L. A. O.; Lorente, S.; Bejan, A.

    2010-12-01

    Here we show that the production and use of heating on an area must be distributed in clusters organized such that the losses associated with centers of production are balanced by the losses associated with distribution lines. The energy needs increase in time because the population density and the individual need increase. We consider only the increase in the individual need in time. We illustrate the "distributed energy systems" concept with the production and distribution of hot water on an area. Four classes of designs are analyzed and compared: (0) individual, i.e., one water heater for one user, (r) radial, i.e., N users supplied via radial pipes from a central heater, (2) dendritic network constructed by pairing N users around a central heating, and (4) dendritic network constructed by quadrupling the elemental areas occupied by the users. We show that there is an optimal cluster size (N) as a tradeoff between central losses and distributed losses. We also discover that several distinct (abrupt) design "transitions" must exist: the recommended design changes through designs 0, r, 2, and 4, as the amount of water used by each individual increases in time with the standard of living.

  17. Magnesium Dependence of the RNA Free Energy Landscape

    NASA Astrophysics Data System (ADS)

    Hayes, Ryan; Noel, Jeffrey; Mandic, Ana; Whitford, Paul; Sanbonmatsu, Karissa; Mohanty, Udayan; Onuchic, José

    2015-03-01

    The RNA free energy landscape is highly sensitive to ionic concentrations, and especially to Mg2+, as most RNA tertiary structure will not form in the absence of Mg2+. At physiological concentrations, the energy landscape must be smooth and funneled to fold on biological time scales, but changes in ionic concentration may affect the relative stability of alternative states. We perturb a structure-based model, which captures the funneled nature of the energy landscape, to include electrostatic effects. Our model includes explicit Mg2+ and screening by implicit KCl. A dynamic model for the local competition between Manning condensed Mg2+ and KCl is introduced, which makes the model more broadly applicable and transferable than a previous static model. We use the excess Mg2+ ions associated with the RNA (Γ2 +) to test the model. Γ2 + is an ideal metric because it is closely related to the Mg2+-RNA interaction free energy, and is easily measurable in both experiment and simulation. The model captures intermediate states of a small pseudoknot missed by models without electrostatics.

  18. Folding Free Energy Landscape of the Decapeptide Chignolin

    NASA Astrophysics Data System (ADS)

    Dou, Xianghua; Wang, Jihua

    Chignolin is an artificially designed ten-residue (GYDPETGTWG) folded peptide, which is the smallest protein and provides a good template for protein folding. In this work, we completed four explicit water molecular dynamics simulations of Chignolin folding using GROMOS and OPLS-AA force fields from extended initial states without any experiment informations. The four-folding free energy landscapes of the peptide has been drawn. The folded state of Chignolin has been successfully predicated based on the free energy landscapes. The four independent simulations gave similar results. (i) The four free energy landscapes have common characters. They are fairly smooth, barrierless, funnel-like and downhill without intermediate state, which consists with the experiment. (ii) The different extended initial structures converge at similar folded structures with the lowest free energy under GROMOS and OPLS-AA force fields. In the GROMOS force field, the backbone RMSD of the folded structures from the NMR native structure of Chignolin is only 0.114 nm, which is a stable structure in this force field. In the OPLS-AA force field, the similar results have been obtained. In addition, the smallest RMSD structure is in better agreement with the NMR native structure but unlikely stable in the force field.

  19. The energy landscape of adenylate kinase during catalysis

    PubMed Central

    Kerns, S. Jordan; Agafonov, Roman V.; Cho, Young-Jin; Pontiggia, Francesco; Otten, Renee; Pachov, Dimitar V.; Kutter, Steffen; Phung, Lien A.; Murphy, Padraig N.; Thai, Vu; Alber, Tom; Hagan, Michael F.; Kern, Dorothee

    2014-01-01

    Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, MD simulations, and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events, phosphoryl transfer (>105-fold) and lid-opening (103-fold). In contrast, mutation of an essential active-site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid-opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a pre-organized active site. PMID:25580578

  20. Deaging and asymmetric energy landscapes in electrically biased ferroelectrics.

    PubMed

    Tutuncu, Goknur; Damjanovic, Dragan; Chen, Jun; Jones, Jacob L

    2012-04-27

    In ferroic materials, the dielectric, piezoelectric, magnetic, and elastic coefficients are significantly affected by the motion of domain walls. This motion can be described as the propagation of a wall across various types and strengths of pinning centers that collectively constitute a force profile or energetic landscape. Biased domain structures and asymmetric energy landscapes can be created through application of high fields (such as during electrical poling), and the material behavior in such states is often highly asymmetric. In some cases, this behavior can be considered as the electric analogue to the Bauschinger effect. The present Letter uses time-resolved, high-energy x-ray Bragg scattering to probe this asymmetry and the associated deaging effect in the ferroelectric morphotropic phase boundary composition 0.36BiScO3 - 0.64PbTiO3.

  1. Deaging and Asymmetric Energy Landscapes in Electrically Biased Ferroelectrics

    SciTech Connect

    Tutuncu, Goknur; Damjanovic, Dragan; Chen, Jun; Jones, Jacob L.

    2015-09-01

    In ferroic materials, the dielectric, piezoelectric, magnetic, and elastic coefficients are significantly affected by the motion of domain walls. This motion can be described as the propagation of a wall across various types and strengths of pinning centers that collectively constitute a force profile or energetic landscape. Biased domain structures and asymmetric energy landscapes can be created through application of high fields (such as during electrical poling), and the material behavior in such states is often highly asymmetric. In some cases, this behavior can be considered as the electric analogue to the Bauschinger effect. The present Letter uses time-resolved, high-energy x-ray Bragg scattering to probe this asymmetry and the associated deaging effect in the ferroelectric morphotropic phase boundary composition 0.36BiScO{sub 3}-0.64PbTiO{sub 3}.

  2. Free Energy Landscape - Settlements of Key Residues.

    NASA Astrophysics Data System (ADS)

    Aroutiounian, Svetlana

    2007-03-01

    FEL perspective in studies of protein folding transitions reflects notion that since there are ˜10^N conformations to scan in search of lowest free energy state, random search is beyond biological timescale. Protein folding must follow certain fel pathways and folding kinetics of evolutionary selected proteins dominates kinetic traps. Good model for functional robustness of natural proteins - coarse-grained model protein is not very accurate but affords bringing simulations closer to biological realm; Go-like potential secures the fel funnel shape; biochemical contacts signify the funnel bottleneck. Boltzmann-weighted ensemble of protein conformations and histogram method are used to obtain from MC sampling of protein conformational space the approximate probability distribution. The fel is F(rmsd) = -1/βLn[Hist(rmsd)], β=kBT and rmsd is root-mean-square-deviation from native conformation. The sperm whale myoglobin has rich dynamic behavior, is small and large - on computational scale, has a symmetry in architecture and unusual sextet of residue pairs. Main idea: there is a mathematical relation between protein fel and a key residues set providing stability to folding transition. Is the set evolutionary conserved also for functional reasons? Hypothesis: primary sequence determines the key residues positions conserved as stabilizers and the fel is the battlefield for the folding stability. Preliminary results: primary sequence - not the architecture, is the rule settler, indeed.

  3. Energy landscapes for shells assembled from pentagonal and hexagonal pyramids.

    PubMed

    Fejer, Szilard N; James, Tim R; Hernández-Rojas, Javier; Wales, David J

    2009-03-28

    We present new rigid body potentials that should favour efficient self-assembly of pentagonal and hexagonal pyramids into icosahedral shells over a wide range of temperature. By adding an extra repulsive site opposite the existing apex sites of the pyramids considered in a previously published model, frustrated energy landscapes are transformed into systems identified with self-assembling properties. The extra interaction may be considered analogous to a hydrophobic-hydrophilic repulsion, as in micelle formation.

  4. BarMap: RNA folding on dynamic energy landscapes

    PubMed Central

    Hofacker, Ivo L.; Flamm, Christoph; Heine, Christian; Wolfinger, Michael T.; Scheuermann, Gerik; Stadler, Peter F.

    2010-01-01

    Dynamical changes of RNA secondary structures play an important role in the function of many regulatory RNAs. Such kinetic effects, especially in time-variable and externally triggered systems, are usually investigated by means of extensive and expensive simulations of large sets of individual folding trajectories. Here we describe the theoretical foundations of a generic approach that not only allows the direct computation of approximate population densities but also reduces the efforts required to analyze the folding energy landscapes to a one-time preprocessing step. The basic idea is to consider the kinetics on individual landscapes and to model external triggers and environmental changes as small but discrete changes in the landscapes. A “barmap” links macrostates of temporally adjacent landscapes and defines the transfer of population densities from one “snapshot” to the next. Implemented in the BarMap software, this approach makes it feasible to study folding processes at the level of basins, saddle points, and barriers for many nonstationary scenarios, including temperature changes, cotranscriptional folding, refolding in consequence to degradation, and mechanically constrained kinetics, as in the case of the translocation of a polymer through a pore. PMID:20504954

  5. Energy landscapes, folding mechanisms, and kinetics of RNA tetraloop hairpins.

    PubMed

    Chakraborty, Debayan; Collepardo-Guevara, Rosana; Wales, David J

    2014-12-31

    RNA hairpins play a pivotal role in a diverse range of cellular functions, and are integral components of ribozymes, mRNA, and riboswitches. However, the mechanistic and kinetic details of RNA hairpin folding, which are key determinants of most of its biological functions, are poorly understood. In this work, we use the discrete path sampling (DPS) approach to explore the energy landscapes of two RNA tetraloop hairpins, and provide insights into their folding mechanisms and kinetics in atomistic detail. Our results show that the potential energy landscapes have a distinct funnel-like bias toward the folded hairpin state, consistent with efficient structure-seeking properties. Mechanistic and kinetic information is analyzed in terms of kinetic transition networks. We find microsecond folding times, consistent with temperature jump experiments, for hairpin folding initiated from relatively compact unfolded states. This process is essentially driven by an initial collapse, followed by rapid zippering of the helix stem in the final phase. Much lower folding rates are predicted when the folding is initiated from extended chains, which undergo longer excursions on the energy landscape before nucleation events can occur. Our work therefore explains recent experiments and coarse-grained simulations, where the folding kinetics exhibit precisely this dependency on the initial conditions.

  6. Predictive energy landscapes for folding membrane protein assemblies

    NASA Astrophysics Data System (ADS)

    Truong, Ha H.; Kim, Bobby L.; Schafer, Nicholas P.; Wolynes, Peter G.

    2015-12-01

    We study the energy landscapes for membrane protein oligomerization using the Associative memory, Water mediated, Structure and Energy Model with an implicit membrane potential (AWSEM-membrane), a coarse-grained molecular dynamics model previously optimized under the assumption that the energy landscapes for folding α-helical membrane protein monomers are funneled once their native topology within the membrane is established. In this study we show that the AWSEM-membrane force field is able to sample near native binding interfaces of several oligomeric systems. By predicting candidate structures using simulated annealing, we further show that degeneracies in predicting structures of membrane protein monomers are generally resolved in the folding of the higher order assemblies as is the case in the assemblies of both nicotinic acetylcholine receptor and V-type Na+-ATPase dimers. The physics of the phenomenon resembles domain swapping, which is consistent with the landscape following the principle of minimal frustration. We revisit also the classic Khorana study of the reconstitution of bacteriorhodopsin from its fragments, which is the close analogue of the early Anfinsen experiment on globular proteins. Here, we show the retinal cofactor likely plays a major role in selecting the final functional assembly.

  7. Accelerated weight histogram method for exploring free energy landscapes

    NASA Astrophysics Data System (ADS)

    Lindahl, V.; Lidmar, J.; Hess, B.

    2014-07-01

    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.

  8. Graph theoretical analysis of the energy landscape of model polymers.

    PubMed

    Baiesi, Marco; Bongini, Lorenzo; Casetti, Lapo; Tattini, Lorenzo

    2009-07-01

    In systems characterized by a rough potential-energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and splitting of metastable states, have nontrivial effects on such networks and must be taken into account. We do this by means of a recently proposed renormalization procedure. This method is applied to analyze the topology of the network of metastable states for different polypeptidic sequences in a minimalistic polymer model. A smaller spectral dimension emerges as a hallmark of stability of the global energy minimum and highlights a nonobvious link between dynamic and thermodynamic properties.

  9. The dynamic energy landscape of dihydrofolate reductase catalysis.

    PubMed

    Boehr, David D; McElheny, Dan; Dyson, H Jane; Wright, Peter E

    2006-09-15

    We used nuclear magnetic resonance relaxation dispersion to characterize higher energy conformational substates of Escherichia coli dihydrofolate reductase. Each intermediate in the catalytic cycle samples low-lying excited states whose conformations resemble the ground-state structures of preceding and following intermediates. Substrate and cofactor exchange occurs through these excited substates. The maximum hydride transfer and steady-state turnover rates are governed by the dynamics of transitions between ground and excited states of the intermediates. Thus, the modulation of the energy landscape by the bound ligands funnels the enzyme through its reaction cycle along a preferred kinetic path.

  10. THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective

    NASA Astrophysics Data System (ADS)

    Onuchic, Jose Nelson; Luthey-Schulten, Zaida; Wolynes, Peter G.

    1997-10-01

    The energy landscape theory of protein folding is a statistical description of a protein's potential surface. It assumes that folding occurs through organizing an ensemble of structures rather than through only a few uniquely defined structural intermediates. It suggests that the most realistic model of a protein is a minimally frustrated heteropolymer with a rugged funnel-like landscape biased toward the native structure. This statistical description has been developed using tools from the statistical mechanics of disordered systems, polymers, and phase transitions of finite systems. We review here its analytical background and contrast the phenomena in homopolymers, random heteropolymers, and protein-like heteropolymers that are kinetically and thermodynamically capable of folding. The connection between these statistical concepts and the results of minimalist models used in computer simulations is discussed. The review concludes with a brief discussion of how the theory helps in the interpretation of results from fast folding experiments and in the practical task of protein structure prediction.

  11. New Methods for Exploring QM:MM Potential Energy Landscapes

    NASA Astrophysics Data System (ADS)

    Hratchian, Hrant P.

    2010-06-01

    In recent years, the applicability of quantum chemical methods for large system studies has been greatly enhanced by the development of hybrid QM:MM techniques. Despite these advancements, exploring the associated potential energy surfaces continues to present two key challenges. First, the QM energy and derivative evaluations may be too costly for simulations; and second, the system size for many QM:MM cases are too large to effectively store or use second-order information, an approach often used in QM studies to allow for larger integration steps and fewer QM evaluations of the potential energy surface. Our most recent work is focused on overcoming both computational bottlenecks. Using surface fitting models together with direct Hessian-vector and diagonalization algorithms, we are developing models that can accurately and efficiently explore QM:MM potential energy landscapes for very large systems. Our current development status and results from initial applications will be described.

  12. Characterizing structural transitions using localized free energy landscape analysis.

    PubMed

    Banavali, Nilesh K; Mackerell, Alexander D

    2009-01-01

    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.

  13. Energy landscape of an electron hole in hydrated DNA.

    PubMed

    Bongiorno, Angelo

    2008-11-06

    First-principles/molecular mechanics, force-field, and 1-D lattice model schemes are used to address the energy landscape of an electron hole in hydrated DNA. Force-field calculations are used to derive a statistical description of the electrostatic fluctuations in DNA yielded by the polar environment, and a periodic first-principles/molecular mechanics scheme is employed to calculate the hole energy at uniform DNA segments embedded in hydrated DNA double helices. The results are then mapped onto 1-D lattice models to address issues relevant to charge transfer in hydrated DNA. It is shown that the polar environment generates an intense dynamical energy disorder along the DNA strands, exhibiting exponential spatio-temporal correlations. The fluctuations of the polar environment lead to hole states localized over a few DNA bases and compete evenly with the DNA sequence to define the hole energy landscape. The spatial correlations of the environment-induced fluctuations are also shown to influence strongly the hole transfer dynamics in DNA.

  14. Topology, structures, and energy landscapes of human chromosomes

    PubMed Central

    Zhang, Bin; Wolynes, Peter G.

    2015-01-01

    Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conformations based on the resulting information theoretic landscape not only accurately reproduce experimental contact probabilities, but also provide a picture of chromosome dynamics and topology. The topology of the simulated chromosomes is probed by computing the distribution of their knot invariants. The simulated chromosome structures are largely free of knots. Topologically associating domains are shown to be crucial for establishing these knotless structures. The simulated chromosome conformations exhibit a tendency to form fibril-like structures like those observed via light microscopy. The topologically associating domains of the interphase chromosome exhibit multistability with varying liquid crystalline ordering that may allow discrete unfolding events and the landscape is locally funneled toward “ideal” chromosome structures that represent hierarchical fibrils of fibrils. PMID:25918364

  15. Topology, structures, and energy landscapes of human chromosomes.

    PubMed

    Zhang, Bin; Wolynes, Peter G

    2015-05-12

    Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conformations based on the resulting information theoretic landscape not only accurately reproduce experimental contact probabilities, but also provide a picture of chromosome dynamics and topology. The topology of the simulated chromosomes is probed by computing the distribution of their knot invariants. The simulated chromosome structures are largely free of knots. Topologically associating domains are shown to be crucial for establishing these knotless structures. The simulated chromosome conformations exhibit a tendency to form fibril-like structures like those observed via light microscopy. The topologically associating domains of the interphase chromosome exhibit multistability with varying liquid crystalline ordering that may allow discrete unfolding events and the landscape is locally funneled toward "ideal" chromosome structures that represent hierarchical fibrils of fibrils.

  16. RNA folding pathways and kinetics using 2D energy landscapes.

    PubMed

    Senter, Evan; Dotu, Ivan; Clote, Peter

    2015-01-01

    RNA folding pathways play an important role in various biological processes, such as (i) the hok/sok (host-killing/suppression of killing) system in E. coli to check for sufficient plasmid copy number, (ii) the conformational switch in spliced leader (SL) RNA from Leptomonas collosoma, which controls trans splicing of a portion of the '5 exon, and (iii) riboswitches--portions of the 5' untranslated region of messenger RNA that regulate genes by allostery. Since RNA folding pathways are determined by the energy landscape, we describe a novel algorithm, FFTbor2D, which computes the 2D projection of the energy landscape for a given RNA sequence. Given two metastable secondary structures A, B for a given RNA sequence, FFTbor2D computes the Boltzmann probability p(x, y) = Z(x,y)/Z that a secondary structure has base pair distance x from A and distance y from B. Using polynomial interpolationwith the fast Fourier transform,we compute p(x, y) in O(n(5)) time and O(n(2)) space, which is an improvement over an earlier method, which runs in O(n(7)) time and O(n(4)) space. FFTbor2D has potential applications in synthetic biology, where one might wish to design bistable switches having target metastable structures A, B with favorable pathway kinetics. By inverting the transition probability matrix determined from FFTbor2D output, we show that L. collosoma spliced leader RNA has larger mean first passage time from A to B on the 2D energy landscape, than 97.145% of 20,000 sequences, each having metastable structures A, B. Source code and binaries are freely available for download at http://bioinformatics.bc.edu/clotelab/FFTbor2D. The program FFTbor2D is implemented in C++, with optional OpenMP parallelization primitives.

  17. Jamming Proteins with Slipknots and Their Free Energy Landscape

    NASA Astrophysics Data System (ADS)

    Sułkowska, Joanna I.; Sułkowski, Piotr; Onuchic, José N.

    2009-12-01

    Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative unfolding routes that are dominant at different force ranges. The existence of an intermediate, metastable configuration where the slipknot is jammed is responsible for longer unfolding times at higher forces. Simulations are performed with a coarse-grained model with further quantification using a refined description of the geometry of the slipknots. The simulation data are used to determine the free energy landscape of the protein, which supports recent analytical predictions.

  18. Jamming proteins with slipknots and their free energy landscape.

    PubMed

    Sułkowska, Joanna I; Sułkowski, Piotr; Onuchic, José N

    2009-12-31

    Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative unfolding routes that are dominant at different force ranges. The existence of an intermediate, metastable configuration where the slipknot is jammed is responsible for longer unfolding times at higher forces. Simulations are performed with a coarse-grained model with further quantification using a refined description of the geometry of the slipknots. The simulation data are used to determine the free energy landscape of the protein, which supports recent analytical predictions.

  19. Kinetic reconstruction of the free-energy landscape.

    PubMed

    Wedekind, Jan; Reguera, David

    2008-09-04

    We present a new general method to trace back a lot of valuable information from direct simulations and experiments of activated processes. In particular, it allows the reconstruction of the free-energy landscape for an arbitrary reaction coordinate directly from the out-of-equilibrium dynamics of the process. We demonstrate the power of this concept by its application to a molecular dynamics simulation of nucleation of a Lennard-Jones vapor. The same method can be also applied to Brownian dynamics and stochastic simulations.

  20. Energy landscapes of quantum Lennard-Jones solids.

    PubMed

    Chakravarty, Charusita

    2011-06-30

    To generalize inherent structure analysis to understand structural changes in quantum liquids and solids, differences between classical (V(x)) and quantum-corrected (U(qeff)(x)) energy landscapes are estimated as a function of the de Boer parameter (Λ). Path integral simulations of quantum Lennard-Jones solids are performed at zero pressure and a dimensionless reduced temperature of 0.123, corresponding to an absolute temperature of 4.2K. At constant temperature and pressure, Λ is increased from the classical limit of zero to Λ = 0.28, corresponding to para-H(2). Increasing quantum delocalization effects result in a continuous decrease in density and local order but without a transition to a disordered, liquid state. The inherent structure landscape of bulk systems is strongly dependent on density with the energy and stability of crystalline minima decreasing relative to that of amorphous packing minima as the system is stretched. For Λ ≈ 0.23, the volume fluctuations in quantum solids are sufficient to result in sampling of disordered minima while for Λ = 0.28, the underlying classical inherent structures are completely disordered, indicating that the topography of U(qeff)(x) and V(x) are qualitatively different for such values of Λ. To assess the nature of the quantum-corrected energy landscape, effective pair potentials are defined by u(qeff)(r) = -kT ln g(r) using the pair correlation function (g(r)) of the quantum system in the neighborhood of the first peak. Our results show that as Λ increases, the pair potentials become increasingly softer, shallower, and of increasing range with a shifting of the potential minimum to larger distances. For example, the reduction of the entropy of fusion and melting temperatures of quantum solids with increasing Λ are analogous to the changes in thermodynamics of melting seen in classical solids with increasing range and softness of interactions. The energy landscapes associated with such coarse-grained potentials

  1. Biomolecular Dynamics: Order-Disorder Transitions and Energy Landscapes

    PubMed Central

    Whitford, Paul C.; Sanbonmatsu, Karissa Y.; Onuchic, José N.

    2013-01-01

    While the energy landscape theory of protein folding is now a widely accepted view for understanding how relatively-weak molecular interactions lead to rapid and cooperative protein folding, such a framework must be extended to describe the large-scale functional motions observed in molecular machines. In this review, we discuss 1) the development of the energy landscape theory of biomolecular folding, 2) recent advances towards establishing a consistent understanding of folding and function, and 3) emerging themes in the functional motions of enzymes, biomolecular motors, and other biomolecular machines. Recent theoretical, computational, and experimental lines of investigation are providing a very dynamic picture of biomolecular motion. In contrast to earlier ideas, where molecular machines were thought to function similarly to macroscopic machines, with rigid components that move along a few degrees of freedom in a deterministic fashion, biomolecular complexes are only marginally stable. Since the stabilizing contribution of each atomic interaction is on the order of the thermal fluctuations in solution, the rigid body description of molecular function must be revisited. An emerging theme is that functional motions encompass order-disorder transitions and structural flexibility provide significant contributions to the free-energy. In this review, we describe the biological importance of order-disorder transitions and discuss the statistical-mechanical foundation of theoretical approaches that can characterize such transitions. PMID:22790780

  2. Energy landscapes for diffusion: analysis of cage-breaking processes.

    PubMed

    de Souza, Vanessa K; Wales, David J

    2008-10-28

    A wide spectrum of potential energy barriers exists for binary Lennard-Jones systems. Here we examine the barriers and cage-breaking rearrangements that are pertinent to long-term diffusion. Single-step cage-breaking processes, which follow high-barrier routes, are identified, and different methods and criteria for defining a cage-breaking process are considered. We examine the extent to which a description of cage-breaking within the energy landscape is a description of long-term diffusion. This description includes the identification of cage-breaks that are reversed, and those that are productive towards long-term diffusion. At low temperatures, diffusion is adequately described by productive cage-breaks, or by considering all cage-breaks and accounting for the effect of reversals. To estimate the diffusion constant we require only the mean square displacement of a cage-break, the average waiting time for a cage-break, and a measure of the number of reversed cage-breaks. Cage-breaks can be visualized within the potential energy landscape using disconnectivity graphs, and we compare the use of productive cage-breaks with previous definitions of "megabasins" or "metabasins."

  3. New Energy Landscapes of Pennsylvania: Forests to Farms to Fracking

    NASA Astrophysics Data System (ADS)

    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

  4. Curvature of the energy landscape and folding of model proteins.

    PubMed

    Mazzoni, Lorenzo N; Casetti, Lapo

    2006-11-24

    We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical trajectories are the geodesics of the metric. Using numerical simulations, we show that the fluctuations of the curvature clearly mark the folding transition, and that this quantity allows to distinguish between polymers having a proteinlike behavior (i.e., that fold to a unique configuration) and polymers which undergo a hydrophobic collapse but do not have a folding transition. These geometrical properties are defined by the potential energy without requiring any prior knowledge of the native configuration.

  5. Temperature extrapolation of multicomponent grand canonical free energy landscapes

    NASA Astrophysics Data System (ADS)

    Mahynski, Nathan A.; Errington, Jeffrey R.; Shen, Vincent K.

    2017-08-01

    We derive a method for extrapolating the grand canonical free energy landscape of a multicomponent fluid system from one temperature to another. Previously, we introduced this statistical mechanical framework for the case where kinetic energy contributions to the classical partition function were neglected for simplicity [N. A. Mahynski et al., J. Chem. Phys. 146, 074101 (2017)]. Here, we generalize the derivation to admit these contributions in order to explicitly illustrate the differences that result. Specifically, we show how factoring out kinetic energy effects a priori, in order to consider only the configurational partition function, leads to simpler mathematical expressions that tend to produce more accurate extrapolations than when these effects are included. We demonstrate this by comparing and contrasting these two approaches for the simple cases of an ideal gas and a non-ideal, square-well fluid.

  6. Alternate states of proteins revealed by detailed energy landscape mapping.

    PubMed

    Tyka, Michael D; Keedy, Daniel A; André, Ingemar; Dimaio, Frank; Song, Yifan; Richardson, David C; Richardson, Jane S; Baker, David

    2011-01-14

    What conformations do protein molecules populate in solution? Crystallography provides a high-resolution description of protein structure in the crystal environment, while NMR describes structure in solution but using less data. NMR structures display more variability, but is this because crystal contacts are absent or because of fewer data constraints? Here we report unexpected insight into this issue obtained through analysis of detailed protein energy landscapes generated by large-scale, native-enhanced sampling of conformational space with Rosetta@home for 111 protein domains. In the absence of tightly associating binding partners or ligands, the lowest-energy Rosetta models were nearly all <2.5 Å C(α)RMSD from the experimental structure; this result demonstrates that structure prediction accuracy for globular proteins is limited mainly by the ability to sample close to the native structure. While the lowest-energy models are similar to deposited structures, they are not identical; the largest deviations are most often in regions involved in ligand, quaternary, or crystal contacts. For ligand binding proteins, the low energy models may resemble the apo structures, and for oligomeric proteins, the monomeric assembly intermediates. The deviations between the low energy models and crystal structures largely disappear when landscapes are computed in the context of the crystal lattice or multimer. The computed low-energy ensembles, with tight crystal-structure-like packing in the core, but more NMR-structure-like variability in loops, may in some cases resemble the native state ensembles of proteins better than individual crystal or NMR structures, and can suggest experimentally testable hypotheses relating alternative states and structural heterogeneity to function. Copyright © 2010 Elsevier Ltd. All rights reserved.

  7. The energy landscape of adenylate kinase during catalysis

    DOE PAGES

    Kerns, S. Jordan; Agafonov, Roman V.; Cho, Young-Jin; ...

    2015-01-12

    Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. In this paper, we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events: phosphoryl transfer (>105-fold) and lid opening (103-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 103-fold withoutmore » substantially affecting lid opening. Finally, our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.« less

  8. The energy landscape of adenylate kinase during catalysis

    SciTech Connect

    Kerns, S. Jordan; Agafonov, Roman V.; Cho, Young-Jin; Pontiggia, Francesco; Otten, Renee; Pachov, Dimitar V.; Kutter, Steffen; Phung, Lien A.; Murphy, Padraig N.; Thai, Vu; Alber, Tom; Hagan, Michael F.; Kern, Dorothee

    2015-01-12

    Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. In this paper, we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events: phosphoryl transfer (>105-fold) and lid opening (103-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid opening. Finally, our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.

  9. Protein energy landscapes determined by five-dimensional crystallography

    SciTech Connect

    Schmidt, Marius; Srajer, Vukica; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh

    2013-12-01

    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.

  10. Nonlinear response from the perspective of energy landscapes and beyond

    NASA Astrophysics Data System (ADS)

    Heuer, Andreas; Schroer, Carsten F. E.; Diddens, Diddo; Rehwald, Christian; Blank-Burian, Markus

    2017-08-01

    The paper discusses the nonlinear response of disordered systems. In particular we show how the nonlinear response can be interpreted in terms of properties of the potential energy landscape. It is shown why the use of relatively small systems is very helpful for this approach. For a standard model system we check which system sizes are particular suited. In case of the driving of a single particle via an external force the concept of an effective temperature helps to scale the force dependence for different temperature on a single master curve. In all cases the mobility increases with increasing external force. These results are compared with a stochastic process described by a 1d Langevin equation where a similar scaling is observed. Furthermore it is shown that for different classes of disordered systems the mobility can also decrease with increasing force. The results can be related to the properties of the chosen potential energy landscape. Finally, results for the crossover from the linear to the nonlinear conductivity of ionic liquids are presented, inspired by recent experimental results in the Roling group. Apart from a standard imidazolium-based ionic liquid we study a system which is characterized by a low conductivity as compared to other ionic liquids and very small nonlinear effects. We show via a real space structural analysis that for this system a particularly strong pair formation is observed and that the strength of the pair formation is insensitive to the application of strong electric fields. Consequences of this observation are discussed.

  11. Protein energy landscapes determined by five-dimensional crystallography

    PubMed Central

    Schmidt, Marius; Srajer, Vukica; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh

    2013-01-01

    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. PMID:24311594

  12. Landscape of Future Accelerators at the Energy and Intensity Frontier

    SciTech Connect

    Syphers, M. J.; Chattopadhyay, S.

    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.

  13. Combining pressure and temperature control in dynamics on energy landscapes

    NASA Astrophysics Data System (ADS)

    Hoffmann, Karl Heinz; Christian Schön, J.

    2017-05-01

    Complex systems from science, technology or mathematics usually appear to be very different in their specific dynamical evolution. However, the concept of an energy landscape with its basins corresponding to locally ergodic regions separated by energy barriers provides a unifying approach to the description of complex systems dynamics. In such systems one is often confronted with the task to control the dynamics such that a certain basin is reached with the highest possible probability. Typically one aims for the global minimum, e.g. when dealing with global optimization problems, but frequently other local minima such as the metastable compounds in materials science are of primary interest. Here we show how this task can be solved by applying control theory using magnesium fluoride as an example system, where different modifications of MgF2 are considered as targets. In particular, we generalize previous work restricted to temperature controls only and present controls which simultaneously adjust temperature and pressure in an optimal fashion.

  14. Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.

    PubMed

    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.

  15. Free energy landscape and molecular pathways of gas hydrate nucleation

    NASA Astrophysics Data System (ADS)

    Bi, Yuanfei; Porras, Anna; Li, Tianshu

    2016-12-01

    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), pB 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 pB 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.

  16. Energy Landscapes and Catalysis in Nitric-oxide Synthase*

    PubMed Central

    Sobolewska-Stawiarz, Anna; Leferink, Nicole G. H.; Fisher, Karl; Heyes, Derren J.; Hay, Sam; Rigby, Stephen E. J.; Scrutton, Nigel S.

    2014-01-01

    Nitric oxide (NO) plays diverse roles in mammalian physiology. It is involved in blood pressure regulation, neurotransmission, and immune response, and is generated through complex electron transfer reactions catalyzed by NO synthases (NOS). In neuronal NOS (nNOS), protein domain dynamics and calmodulin binding are implicated in regulating electron flow from NADPH, through the FAD and FMN cofactors, to the heme oxygenase domain, the site of NO generation. Simple models based on crystal structures of nNOS reductase have invoked a role for large scale motions of the FMN-binding domain in shuttling electrons from the FAD-binding domain to the heme oxygenase domain. However, molecular level insight of the dynamic structural transitions in NOS enzymes during enzyme catalysis is lacking. We use pulsed electron-electron double resonance spectroscopy to derive inter-domain distance relationships in multiple conformational states of nNOS. These distance relationships are correlated with enzymatic activity through variable pressure kinetic studies of electron transfer and turnover. The binding of NADPH and calmodulin are shown to influence interdomain distance relationships as well as reaction chemistry. An important effect of calmodulin binding is to suppress adventitious electron transfer from nNOS to molecular oxygen and thereby preventing accumulation of reactive oxygen species. A complex landscape of conformations is required for nNOS catalysis beyond the simple models derived from static crystal structures of nNOS reductase. Detailed understanding of this landscape advances our understanding of nNOS catalysis/electron transfer, and could provide new opportunities for the discovery of small molecule inhibitors that bind at dynamic protein interfaces of this multidimensional energy landscape. PMID:24610812

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

    PubMed

    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.

  18. Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer.

    PubMed

    Anthony, Peter C; Perez, Christian F; García-García, Cuauhtémoc; Block, Steven M

    2012-01-31

    Riboswitches are motifs in the untranslated regions (UTRs) of RNA transcripts that sense metabolite levels and modulate the expression of the corresponding genes for metabolite import, export, synthesis, or degradation. All riboswitches contain an aptamer: an RNA structure that, upon binding ligand, folds to expose or sequester regulatory elements in the adjacent sequence through alternative nucleotide pairing. The coupling between ligand binding and aptamer folding is central to the regulatory mechanisms of thiamine pyrophosphate (TPP) riboswitches and has not been fully characterized. Here, we show that TPP aptamer folding can be decomposed into ligand-independent and -dependent steps that correspond to the formation of secondary and tertiary structures, respectively. We reconstructed the full energy landscape for folding of the wild-type (WT) aptamer and measured perturbations of this landscape arising from mutations or ligand binding. We show that TPP binding proceeds in two steps, from a weakly to a strongly bound state. Our data imply a hierarchical folding sequence, and provide a framework for understanding molecular mechanism throughout the TPP riboswitch family.

  19. Nonequilibrium study of the intrinsic free-energy profile across a liquid-vapour interface

    SciTech Connect

    Braga, Carlos Muscatello, Jordan Lau, Gabriel Müller, Erich A. Jackson, George

    2016-01-28

    We calculate an atomistically detailed free-energy profile across a heterogeneous system using a nonequilibrium approach. The path-integral formulation of Crooks fluctuation theorem is used in conjunction with the intrinsic sampling method to calculate the free-energy profile for the liquid-vapour interface of the Lennard-Jones fluid. Free-energy barriers are found corresponding to the atomic layering in the liquid phase as well as a barrier associated with the presence of an adsorbed layer as revealed by the intrinsic density profile. Our findings are in agreement with profiles calculated using Widom’s potential distribution theorem applied to both the average and the intrinsic profiles as well as the literature values for the excess chemical potential.

  20. Nonequilibrium study of the intrinsic free-energy profile across a liquid-vapour interface

    NASA Astrophysics Data System (ADS)

    Braga, Carlos; Muscatello, Jordan; Lau, Gabriel; Müller, Erich A.; Jackson, George

    2016-01-01

    We calculate an atomistically detailed free-energy profile across a heterogeneous system using a nonequilibrium approach. The path-integral formulation of Crooks fluctuation theorem is used in conjunction with the intrinsic sampling method to calculate the free-energy profile for the liquid-vapour interface of the Lennard-Jones fluid. Free-energy barriers are found corresponding to the atomic layering in the liquid phase as well as a barrier associated with the presence of an adsorbed layer as revealed by the intrinsic density profile. Our findings are in agreement with profiles calculated using Widom's potential distribution theorem applied to both the average and the intrinsic profiles as well as the literature values for the excess chemical potential.

  1. Learning To Fold Proteins Using Energy Landscape Theory

    PubMed Central

    Schafer, N.P.; Kim, B.L.; Zheng, W.; Wolynes, P.G.

    2014-01-01

    This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy landscape theory of protein folding. We also present a review of the results of the AMH/AMC/AMW/AWSEM family of coarse-grained molecular dynamics protein folding models to illustrate the points covered in the first part of the article. Accurate coarse-grained structure prediction models can be used to investigate a wide range of conceptual and mechanistic issues outside of protein structure prediction; specifically, the paper concludes by reviewing how AWSEM has in recent years been able to elucidate questions related to the unusual kinetic behavior of artificially designed proteins, multidomain protein misfolding, and the initial stages of protein aggregation. PMID:25308991

  2. Measuring the energy landscape of complex bonds using AFM

    NASA Astrophysics Data System (ADS)

    Mayyas, Essa; Hoffmann, Peter; Runyan, Lindsay

    2009-03-01

    We measured rupture force of a complex bond of two interacting proteins with atomic force microscopy. Proteins of interest were active and latent Matrix metalloproteinases (MMPs), type 2 and 9, and their tissue inhibitors TIMP1 and TIMP2. Measurements show that the rupture force depends on the pulling speed; it ranges from 30 pN to 150 pN at pulling speeds 30nm/s to 48000nm/s. Analyzing data using an extended theory enabled us to understand the mechanism of MMP-TIMP interaction; we determined all physical parameters that form the landscape energy of the interaction, in addition to the life time of the bond and its length. Moreover, we used the pulling experiment to study the interaction of TIMP2 with the receptor MT1-MMP on the surface of living cells.

  3. Programmable energy landscapes for kinetic control of DNA strand displacement.

    PubMed

    Machinek, Robert R F; Ouldridge, Thomas E; Haley, Natalie E C; Bath, Jonathan; Turberfield, Andrew J

    2014-11-10

    DNA is used to construct synthetic systems that sense, actuate, move and compute. The operation of many dynamic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces another from a duplex. Kinetic control of strand displacement is particularly important in autonomous molecular machinery and molecular computation, in which non-equilibrium systems are controlled through rates of competing processes. Here, we introduce a new method based on the creation of mismatched base pairs as kinetic barriers to strand displacement. Reaction rate constants can be tuned across three orders of magnitude by altering the position of such a defect without significantly changing the stabilities of reactants or products. By modelling reaction free-energy landscapes, we explore the mechanistic basis of this control mechanism. We also demonstrate that oxDNA, a coarse-grained model of DNA, is capable of accurately predicting and explaining the impact of mismatches on displacement kinetics.

  4. Approximate scaling properties of RNA free energy landscapes

    NASA Technical Reports Server (NTRS)

    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.

  5. Monte Carlo simulations of systems with complex energy landscapes

    NASA Astrophysics Data System (ADS)

    Wüst, T.; Landau, D. P.; Gervais, C.; Xu, Y.

    2009-04-01

    Non-traditional Monte Carlo simulations are a powerful approach to the study of systems with complex energy landscapes. After reviewing several of these specialized algorithms we shall describe the behavior of typical systems including spin glasses, lattice proteins, and models for "real" proteins. In the Edwards-Anderson spin glass it is now possible to produce probability distributions in the canonical ensemble and thermodynamic results of high numerical quality. In the hydrophobic-polar (HP) lattice protein model Wang-Landau sampling with an improved move set (pull-moves) produces results of very high quality. These can be compared with the results of other methods of statistical physics. A more realistic membrane protein model for Glycophorin A is also examined. Wang-Landau sampling allows the study of the dimerization process including an elucidation of the nature of the process.

  6. Energy conversion modeling of the intrinsic persistent luminescence of solids via energy transfer paths between transition levels.

    PubMed

    Huang, Bolong; Sun, Mingzi

    2017-04-05

    An energy conversion model has been established for the intrinsic persistent luminescence in solids related to the native point defect levels, formations, and transitions. In this study, we showed how the recombination of charge carriers between different defect levels along the zero phonon line (ZPL) can lead to energy conversions supporting the intrinsic persistent phosphorescence in solids. This suggests that the key driving force for this optical phenomenon is the pair of electrons hopping between different charged defects with negative-Ueff. Such a negative correlation energy will provide a sustainable energy source for electron-holes to further recombine in a new cycle with a specific quantum yield. This will help us to understand the intrinsic persistent luminescence with respect to native point defect levels as well as the correlations of electronics and energetics.

  7. Energy landscape of LeuT from molecular simulations

    NASA Astrophysics Data System (ADS)

    Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

    2015-12-01

    The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ˜40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

  8. Energy landscape of LeuT from molecular simulations.

    PubMed

    Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

    2015-12-28

    The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na(+) ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates.

  9. Energy landscape of LeuT from molecular simulations

    PubMed Central

    Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet

    2015-01-01

    The bacterial sodium-coupled leucine transporter (LeuT) has been broadly used as a structural model for understanding the structure-dynamics-function of mammalian neurotransmitter transporters as well as other solute carriers that share the same fold (LeuT fold), as the first member of the family crystallographically resolved in multiple states: outward-facing open, outward-facing occluded, and inward-facing open. Yet, a complete picture of the energy landscape of (sub)states visited along the LeuT transport cycle has been elusive. In an attempt to visualize the conformational spectrum of LeuT, we performed extensive simulations of LeuT dimer dynamics in the presence of substrate (Ala or Leu) and co-transported Na+ ions, in explicit membrane and water. We used both conventional molecular dynamics (MD) simulations (with Anton supercomputing machine) and a recently introduced method, collective MD, that takes advantage of collective modes of motions predicted by the anisotropic network model. Free energy landscapes constructed based on ∼40 μs trajectories reveal multiple substates occluded to the extracellular (EC) and/or intracellular (IC) media, varying in the levels of exposure of LeuT to EC or IC vestibules. The IC-facing transmembrane (TM) helical segment TM1a shows an opening, albeit to a smaller extent and in a slightly different direction than that observed in the inward-facing open crystal structure. The study provides insights into the spectrum of conformational substates and paths accessible to LeuT and highlights the differences between Ala- and Leu-bound substates. PMID:26723619

  10. Temporal disconnectivity of the energy landscape in glassy systems

    NASA Astrophysics Data System (ADS)

    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

  11. Defining the free-energy landscape of curvature-inducing proteins on membrane bilayers

    PubMed Central

    Tourdot, Richard W.; Ramakrishnan, N.; Radhakrishnan, Ravi

    2015-01-01

    Curvature-sensing and curvature-remodeling proteins, such as Amphiphysin, Epsin, and Exo70, are known to reshape cell membranes, and this remodeling event is essential for key biophysical processes such as tubulation, exocytosis, and endocytosis. Curvature-inducing proteins can act as curvature sensors; they aggregate to membrane regions matching their intrinsic curvature; as well as induce curvature in cell membranes to stabilize emergent high curvature, nonspherical, structures such as tubules, discs, and caveolae. A definitive understanding of the interplay between protein recruitment and migration, the evolution of membrane curvature, and membrane morphological transitions is emerging but remains incomplete. Here, within a continuum framework and using the machinery of Monte Carlo simulations, we introduce and compare three free-energy methods to delineate the free-energy landscape of curvature-inducing proteins on bilayer membranes. We demonstrate the utility of the Widom test particle (or field) insertion methodology in computing the excess chemical potentials associated with curvature-inducing proteins on the membrane—in particular, we use this method to track the onset of morphological transitions in the membrane at elevated protein densities. We validate this approach by comparing the results from the Widom method with those of thermodynamic integration and Bennett acceptance ratio methods. Furthermore, the predictions from the Widom method have been tested against analytical calculations of the excess chemical potential at infinite dilution. Our results are useful in precisely quantifying the free-energy landscape, and also in determining the phase boundaries associated with curvature-induction, curvature-sensing, and morphological transitions. This approach can be extended to studies exploring the role of thermal fluctuations and other external (control) variables, such as membrane excess area, in shaping curvature-mediated interactions on bilayer

  12. Defining the free-energy landscape of curvature-inducing proteins on membrane bilayers

    NASA Astrophysics Data System (ADS)

    Tourdot, Richard W.; Ramakrishnan, N.; Radhakrishnan, Ravi

    2014-08-01

    Curvature-sensing and curvature-remodeling proteins, such as Amphiphysin, Epsin, and Exo70, are known to reshape cell membranes, and this remodeling event is essential for key biophysical processes such as tubulation, exocytosis, and endocytosis. Curvature-inducing proteins can act as curvature sensors; they aggregate to membrane regions matching their intrinsic curvature; as well as induce curvature in cell membranes to stabilize emergent high curvature, nonspherical, structures such as tubules, discs, and caveolae. A definitive understanding of the interplay between protein recruitment and migration, the evolution of membrane curvature, and membrane morphological transitions is emerging but remains incomplete. Here, within a continuum framework and using the machinery of Monte Carlo simulations, we introduce and compare three free-energy methods to delineate the free-energy landscape of curvature-inducing proteins on bilayer membranes. We demonstrate the utility of the Widom test particle (or field) insertion methodology in computing the excess chemical potentials associated with curvature-inducing proteins on the membrane—in particular, we use this method to track the onset of morphological transitions in the membrane at elevated protein densities. We validate this approach by comparing the results from the Widom method with those of thermodynamic integration and Bennett acceptance ratio methods. Furthermore, the predictions from the Widom method have been tested against analytical calculations of the excess chemical potential at infinite dilution. Our results are useful in precisely quantifying the free-energy landscape, and also in determining the phase boundaries associated with curvature-induction, curvature-sensing, and morphological transitions. This approach can be extended to studies exploring the role of thermal fluctuations and other external (control) variables, such as membrane excess area, in shaping curvature-mediated interactions on bilayer

  13. Characterization of the potential energy landscape of an antiplasticized polymer.

    PubMed

    Riggleman, Robert A; Douglas, Jack F; de Pablo, Juan J

    2007-07-01

    The nature of the individual transitions on the potential energy landscape (PEL) associated with particle motion are directly examined for model fragile glass-forming polymer melts, and the results are compared to those of an antiplasticized polymer system. In previous work, we established that the addition of antiplasticizer reduces the fragility of glass formation so that the antiplasticized material is a stronger glass former. In the present work, we find that the antiplasticizing molecules reduce the energy barriers for relaxation compared to the pure polymer, implying that the antiplasticized system has smaller barriers to overcome in order to explore its configuration space. We examine the cooperativity of segmental motion in these bulk fluids and find that more extensive stringlike collective motion enables the system to overcome larger potential energy barriers, in qualitative agreement with both the Stillinger-Weber and Adam-Gibbs views of glass formation. Notably, the stringlike collective motion identified by our PEL analysis corresponds to incremental displacements that occur within larger-scale stringlike particle displacement processes associated with PEL metabasin transitions that mediate structural relaxation. These "substrings" nonetheless seem to exhibit changes in relative size with antiplasticization similar to those observed in "superstrings" that arise at elevated temperatures. We also study the effects of confinement on the energy barriers in each system. Film confinement makes the energy barriers substantially smaller in the pure polymer, while it has little effect on the energy barriers in the antiplasticized system. This observation is qualitatively consistent with our previous studies of stringlike motion in these fluids at higher temperatures and with recent experimental measurements by Torkelson and co-workers.

  14. Role of Northern Lakes in Landscape Energy Balance

    NASA Astrophysics Data System (ADS)

    Rouse, W. R.; Oswald, C. J.; Spence, C.; Blanken, P. D.; Bussières, N.; Schertzer, W. M.; Duguay, C. R.; Binyamin, J.

    2004-05-01

    In the central Mackenzie River Valley of western Canada, from which most of the data used in this study are derived, there are about 32,370 lakes. For the specific study region used to determine the landscape energy balance, lakes comprise 37% of the landscape. They are classified as small (<1 km2), medium (1-100 km2) and large (>100 km2). The large lake is represented by the central portion of Great Slave Lake. The non-lake components of the landscape are divided into wetlands (8%) and uplands (55%). With such abundance, lakes are important features in regional climatic, meteorological and biogeochemical cycling. The purpose of this paper is to examine the regional role of lakes in the surface energy and water balance, to link this to the frequency-size distribution of lakes, and to cast some light on how the surface energy balance may influence regional climate and weather processes. Toward this end we employ recently-gathered data from northern lakes of various sizes, characterize their surface energy balances for both magnitude and temporal behavior of fluxes, and examine the impacts of combinations of various-size lakes and land-lake distributions on regional energy balances and evaporation cycles. The analysis is limited to the ice-free period. Net radiation was substantially greater over all water-dominated surfaces compared with uplands (U). Seasonal differences were 16% greater for wetlands (W), 25% greater for small (SL) and medium (ML) lakes and 73% greater for Great Slave Lake (LL). At maximum, the seasonal heat storage relative to net radiation was 6, 9, 26, 55 and 76 % for U, W, SL, ML and LL respectively. ML and LL are slow to warm in summer but their large cumulative heat storage near summer's end has a major impact on the regional energy balance, because this heat is available to feed convective heat fluxes in fall and early winter. The evaporation season for U, W, SL, ML and LL lasts for 19, 21, 22, 24 and 30 weeks respectively. The effects of

  15. Dynamic regulation on energy landscape evolution of single-molecule protein by conformational fluctuation.

    PubMed

    Lin, Chien Y; Huang, Jung Y; Lo, Leu-Wei

    2012-08-01

    We formalize a theory to help explore the effect of conformational fluctuation on the energy landscape evolution of single-molecule protein. Using this formalization, we investigate the photon emission from single photoactivated fluorescent protein. A bimodal regulation on the energy landscape evolution was discovered, and its origin was attributed to slow conformational fluctuations of the protein matrix.

  16. Effects of relaxation on the energy landscape of amorphous silicon

    NASA Astrophysics Data System (ADS)

    Kallel, Houssem; Mousseau, Normand; Schiettekatte, Francois

    2008-03-01

    Amorphous silicon is used in many devices around us, included as a thin-film transistor in most flat screens, it also serves as the reference for the study of disordered network systems. Recently, differential scanning calorimetry and nanocalorimetry measurements (DSC) ^1 have shown that the heat released as the temperature of the sample is raised following implantation, is temperature independent. To understand this behaviour, we characterize the energy landscape of model a-Si. Using the activation-relaxation technique (ART nouveau) with the modified Stillinger-Weber potential, we generate models at four levels of relaxation and identify the relaxation mechanisms by analysing 100 000 events for each model. We find that while the distribution of the activation barriers shifts to higher energy as the system is relaxed, the distribution of the relaxation energies is almost unchanged. The relation between these two phenomena is consistent with the DSC measurements. This work is supported, in part, by NSERC, FQRNT and the CRC Foundation. HK is grateful for a scholarship from the Tunisian Ministry of Higher Education, Scientific Research and Technology. ^1 R. Karmouch et al., Phys. Rev. B 75, 075304 (2007)

  17. Hybrid Topological Lie-Hamiltonian Learning in Evolving Energy Landscapes

    NASA Astrophysics Data System (ADS)

    Ivancevic, Vladimir G.; Reid, Darryn J.

    2015-11-01

    In this Chapter, a novel bidirectional algorithm for hybrid (discrete + continuous-time) Lie-Hamiltonian evolution in adaptive energy landscape-manifold is designed and its topological representation is proposed. The algorithm is developed within a geometrically and topologically extended framework of Hopfield's neural nets and Haken's synergetics (it is currently designed in Mathematica, although with small changes it could be implemented in Symbolic C++ or any other computer algebra system). The adaptive energy manifold is determined by the Hamiltonian multivariate cost function H, based on the user-defined vehicle-fleet configuration matrix W, which represents the pseudo-Riemannian metric tensor of the energy manifold. Search for the global minimum of H is performed using random signal differential Hebbian adaptation. This stochastic gradient evolution is driven (or, pulled-down) by `gravitational forces' defined by the 2nd Lie derivatives of H. Topological changes of the fleet matrix W are observed during the evolution and its topological invariant is established. The evolution stops when the W-topology breaks down into several connectivity-components, followed by topology-breaking instability sequence (i.e., a series of phase transitions).

  18. Statistical theory for protein ensembles with designed energy landscapes

    NASA Astrophysics Data System (ADS)

    Biswas, Parbati; Zou, Jinming; Saven, Jeffery G.

    2005-10-01

    Combinatorial protein libraries provide a promising route to investigate the determinants and features of protein folding and to identify novel folding amino acid sequences. A library of sequences based on a pool of different monomer types are screened for folding molecules, consistent with a particular foldability criterion. The number of sequences grows exponentially with the length of the polymer, making both experimental and computational tabulations of sequences infeasible. Herein a statistical theory is extended to specify the properties of sequences having particular values of global energetic quantities that specify their energy landscape. The theory yields the site-specific monomer probabilities. A foldability criterion is derived that characterizes the properties of sequences by quantifying the energetic separation of the target state from low-energy states in the unfolded ensemble and the fluctuations of the energies in the unfolded state ensemble. For a simple lattice model of proteins, excellent agreement is observed between the theory and the results of exact enumeration. The theory may be used to provide a quantitative framework for the design and interpretation of combinatorial experiments.

  19. Using Semantic Web Technologies to Develop Intrinsically Resilient Energy Control Systems

    SciTech Connect

    Sheldon, Frederick T; Huang, Jingshan; Fetzer, Daniel T; Morris, Thomas H; Jonathan, Kirsch; Goose, Stuart; Wei, Dong; Dang, Jiangbo; Manz, David

    2012-01-01

    To preserve critical energy control functions while under attack, it is necessary to perform comprehensive analysis on root causes and impacts of cyber intrusions without sacrificing the availability of energy delivery. We propose to design an intrinsically resilient energy control system where we extensively utilize Semantic Web technologies, which play critical roles in knowledge representation and acquisition. While our ultimate goal is to ensure availability/resiliency of energy delivery functions and the capability to assess root causes and impacts of cyber intrusions, the focus of this paper is to demonstrate a proof of concept of how Semantic Web technologies can significantly contribute to resilient energy control systems.

  20. Free energy landscape of a minimalist salt bridge model.

    PubMed

    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.

  1. The Energy Landscape of Hyperstable LacI-DNA Loops

    NASA Astrophysics Data System (ADS)

    Kahn, Jason

    2009-03-01

    The Escherichia coli LacI protein represses transcription of the lac operon by blocking access to the promoter through binding at a promoter-proximal DNA operator. The affinity of tetrameric LacI (and therefore the repression efficiency) is enhanced by simultaneous binding to an auxiliary operator, forming a DNA loop. Hyperstable LacI-DNA loops were previously shown to be formed on DNA constructs that include a sequence-directed bend flanked by operators. Biochemical experiments showed that two such constructs (9C14 and 11C12) with different helical phasing between the operators and the DNA bend form different DNA loop shapes. The geometry and topology of the loops and the relevance of alternative conformations suggested by probable flexible linkers in LacI remain unclear. Bulk and single molecule fluorescence resonance energy transfer (SM-FRET, with D. English) experiments on a dual fluorophore-labeled 9C14-LacI loop demonstrate that it adopts a single, stable, rigid closed-form loop conformation. Here, we characterize the LacI-9C14 loop by SM-FRET as a function of inducer isopropyl-β,D-thiogalactoside (IPTG) concentration. Energy transfer measurements reveal partial but incomplete destabilization of loop formation by IPTG. Surprisingly, there is no change in the energy transfer efficiency of the remaining looped population. Models for the regulation of the lac operon often assume complete disruption of LacI-operator complexes upon inducer binding to LacI. Our work shows that even at saturating IPTG there is still a significant population of LacI-DNA complexes in a looped state, in accord with previous in vivo experiments that show incomplete induction (with J. Maher). Finally, we will report progress on characterizing the ``energy landscape'' for DNA looping upon systematic variation of the DNA linkers between the operators and the bending locus. Rod mechanics simulations (with N. Perkins) provide testable predictions on loop stability, topology, and FRET.

  2. Free-Energy Landscape of the Amino-Terminal Fragment of Huntingtin in Aqueous Solution

    PubMed Central

    Binette, Vincent; Côté, Sébastien; Mousseau, Normand

    2016-01-01

    The first exon of Huntingtin—a protein with multiple biological functions whose misfolding is related to Huntington’s disease—modulates its localization, aggregation, and function within the cell. It is composed of a 17-amino-acid amphipathic segment (Htt17), an amyloidogenic segment of consecutive glutamines (QN), and a proline-rich segment. Htt17 is of fundamental importance: it serves as a membrane anchor to control the localization of huntingtin, it modulates huntingtin’s function through posttranslational modifications, and it controls the self-assembly of the amyloidogenic QN segment into oligomers and fibrils. Experimentally, the conformational ensemble of the Htt17 monomer, as well as the impact of the polyglutamine and proline-rich segments, remains, however, mostly uncharacterized at the atomic level due to its intrinsic flexibility. Here, we unveil the free-energy landscape of Htt17, Htt17Q17, and Htt17Q17P11 using Hamiltonian replica exchange combined with well-tempered metadynamics. We characterize the free-energy landscape of these three fragments in terms of a few selected collective variables. Extensive simulations reveal that the free energy of Htt17 is dominated by a broad ensemble of configurations that agree with solution NMR chemical shifts. Addition of Q17 at its carboxy-terminus reduces the extent of the main basin to more extended configurations of Htt17 with lower helix propensity. Also, the aliphatic carbons of Q17 partially sequester the nonpolar amino acids of Htt17. For its part, addition of Q17P11 shifts the overall landscape to a more extended and helical Htt17 stabilized by interactions with Q17 and P11, which almost exclusively form a PPII-helix, as well as by intramolecular H-bonds and salt bridges. Our characterization of Huntingtin’s amino-terminus provides insights into the structural origin of its ability to oligomerize and interact with phospholipid bilayers, processes closely linked to the biological functions of

  3. Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

    PubMed Central

    Beauchamp, Kyle A.; Pande, Vijay S.; Das, Rhiju

    2014-01-01

    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 3J 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. PMID:24655513

  4. Energy and the Transformation of a Metropolitan Landscape: Contrasting Contemporary and Future Settlement Geographies.

    ERIC Educational Resources Information Center

    Zeigler, Donald J.

    Because of the rising real cost of energy, geographic patterns that have dominated the contemporary metropolitan landscape are in a state of change. A conceptual model of the contemporary and future metropolitan landscape is presented to stimulate thought about the changes which may evolve in the spatial organization of urban regions as the real…

  5. A new heuristic method for approximating the number of local minima in partial RNA energy landscapes.

    PubMed

    Albrecht, Andreas A; Day, Luke; Abdelhadi Ep Souki, Ouala; Steinhöfel, Kathleen

    2016-02-01

    The analysis of energy landscapes plays an important role in mathematical modelling, simulation and optimisation. Among the main features of interest are the number and distribution of local minima within the energy landscape. Granier and Kallel proposed in 2002 a new sampling procedure for estimating the number of local minima. In the present paper, we focus on improved heuristic implementations of the general framework devised by Granier and Kallel with regard to run-time behaviour and accuracy of predictions. The new heuristic method is demonstrated for the case of partial energy landscapes induced by RNA secondary structures. While the computation of minimum free energy RNA secondary structures has been studied for a long time, the analysis of folding landscapes has gained momentum over the past years in the context of co-transcriptional folding and deeper insights into cell processes. The new approach has been applied to ten RNA instances of length between 99 nt and 504 nt and their respective partial energy landscapes defined by secondary structures within an energy offset ΔE above the minimum free energy conformation. The number of local minima within the partial energy landscapes ranges from 1440 to 3441. Our heuristic method produces for the best approximations on average a deviation below 3.0% from the true number of local minima.

  6. Hierarchic finite level energy landscape model: to describe the refolding kinetics of phosphoglycerate kinase.

    PubMed

    Osváth, Szabolcs; Herényi, Levente; Závodszky, Péter; Fidy, Judit; Köhler, Gottfried

    2006-08-25

    One of the most intriguing predictions of energy landscape models is the existence of non-exponential protein folding kinetics caused by hierarchical structures in the landscapes. Here we provide the strongest evidence so far of such hierarchy and determine the time constants and weights of the kinetic components of the suggested hierarchic energy landscape. To our knowledge, the idea of hierarchical folding energy barriers has never been tested over such a broad timescale. Refolding of yeast phosphoglycerate kinase was initiated from the guanidine-unfolded state by stopped-flow or manual mixing and monitored by tryptophan fluorescence from 1 ms to 15 min. The strategy to build a model that describes folding of yeast phosphoglycerate kinase was to start from the simplest paradigm and modify it stepwise to the necessary minimal extent after repeated comparisons with the experiments. We made no a priori assumptions about the folding landscape. The result was a hierarchic finite level landscape model that quantitatively describes the refolding of yeast phosphoglycerate kinase from 1 ms to 15 min. The early steps of the folding process happen in the upper region of the landscape, where the surface has a hierarchic structure. This leads to stretched kinetics in the early phase of the folding. The lower region of the energy landscape is dominated by a trap that reflects the accumulation of molten globule intermediate state. From this intermediate, the protein can reach the global energy minimum corresponding to the native state through a cross-barrier folding step.

  7. Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome

    NASA Astrophysics Data System (ADS)

    Zhang, Bin; Wolynes, Peter G.

    2016-06-01

    We derive an unbiased information theoretic energy landscape for chromosomes at metaphase using a maximum entropy approach that accurately reproduces the details of the experimentally measured pairwise contact probabilities between genomic loci. Dynamical simulations using this landscape lead to cylindrical, helically twisted structures reflecting liquid crystalline order. These structures are similar to those arising from a generic ideal homogenized chromosome energy landscape. The helical twist can be either right or left handed so chiral symmetry is broken spontaneously. The ideal chromosome landscape when augmented by interactions like those leading to topologically associating domain formation in the interphase chromosome reproduces these behaviors. The phase diagram of this landscape shows that the helical fiber order and the cylindrical shape persist at temperatures above the onset of chiral symmetry breaking, which is limited by the topologically associating domain interaction strength.

  8. The Free Energy Landscape of Small Molecule Unbinding

    PubMed Central

    Huang, Danzhi; Caflisch, Amedeo

    2011-01-01

    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. PMID:21390201

  9. The energy landscape of uranyl-peroxide species.

    PubMed

    Tiferet, Eitan; Gil, Adrià; Bo, Carles; Shvareva, Tatiana Y; Nyman, May; Navrotsky, Alexandra

    2014-03-24

    Nanoscale uranyl peroxide clusters containing UO2(2+) groups bonded through peroxide bridges to form polynuclear molecular species (polyoxometalates) exist both in solution and in the solid state. There is an extensive family of clusters containing 28 uranium atoms (U28 clusters), with an encapsulated anion in the center, for example, [UO2(O2)(3-x)(OH)(x)(4-)], [Nb(O2)4(3-)], or [Ta(O2)4(3-)]. The negative charge of these clusters is balanced by alkali ions, both encapsulated, and located exterior to the cluster. The present study reports measurement of enthalpy of formation for two such U28 compounds, one of which is uranyl centered and the other is peroxotantalate centered. The [(Ta(O2)4]-centered U28 capsule is energetically more stable than the [(UO2)(O2)3]-centered capsule. These data, along with our prior studies on other uranyl-peroxide solids, are used to explore the energy landscape and define thermochemical trends in alkali-uranyl-peroxide systems. It was suggested that the energetic role of charge-balancing alkali ions and their electrostatic interactions with the negatively charged uranyl-peroxide species is the dominant factor in defining energetic stability. These experimental data were supported by DFT calculations, which agree that the [(Ta(O2)4]-centered U28 capsule is more stable than the uranyl-centered capsule. Moreover, the relative stability is controlled by the interactions of the encapsulated alkalis with the encapsulated anion. Thus, the role of alkali-anion interactions was shown to be important at all length scales of uranyl-peroxide species: in both comparing clusters to clusters; and clusters to monomers or extended solids.

  10. Discovery of coumarin derivatives as fluorescence acceptors for intrinsic fluorescence resonance energy transfer of proteins.

    PubMed

    Kim, Ju Hwan; Sumranjit, Jitapa; Kang, Hyo Jin; Chung, Sang J

    2014-01-01

    Coumarin analogues were synthezised and evaluated as acceptors for the intrinsic fluorescence resonance energy transfer (iFRET) of tryptophan residues in target proteins. The fluorescence properties such as quantum yields, iFRET efficiencies, and Förster distances of the prepared coumarin analogs were determined in a model system, by their conjugation to biotin, utilizing streptavidin (SAV) as the iFRET donor. The coumarin derivatives reported here represent the most efficient iFRET acceptors for tryptophan, known to date.

  11. Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

    PubMed Central

    Quarta, Giulio; Sin, Ken; Schlick, Tamar

    2012-01-01

    Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design. PMID:22359488

  12. Intrinsic errors in several ab initio methods. The dissociation energy of N{sub 2}

    SciTech Connect

    Peterson, K.A. |; Dunning, T.H. Jr.

    1995-03-23

    Using sequences of correlation consistent basis sets, complete basis set (CBS) limits for the dissociation energy D{sub c} of N{sub 2} have been estimated for a variety of commonly used electron correlation methods. After extrapolation to the CBS limit, the difference between theory and experiment corresponds to the error intrinsic to the chosen theoretical method. Correlated wave functions (valence electrons correlated only) for which intrinsic errors have been estimated include internally contracted multireference configuration interaction (CMRCI), singles and doubles coupled cluster theory with and without perturbative triple excitations [CCSD, CCSD(T)], and second-, third-, and fourth-order Moller-Plesset perturbation theory (MP2, MP3, MP4). For CMRCI and CCSD(T), D{sub c} converges smoothly from below the experimental value and yields the smallest intrinsic errors, -0.8 and -1.6 kcal/mol, respectively. In contrast, for MP2 and MP4, D{sub c} exhibits fortuitously good agreement with experiment for small basis sets but leads to CBS limits that are 11.6 and 3.4 kcal/mol larger than experiment, respectively. Correlation of the 1s core electrons is predicted to yield intrinsic errors of less than 1 kcal/mol for CMRCI and CCSD(T), while those for MP2 and MP4 increase still further. 38 refs., 1 fig., 1 tab.

  13. Free-energy landscape of ion-channel voltage-sensor-domain activation.

    PubMed

    Delemotte, Lucie; Kasimova, Marina A; Klein, Michael L; Tarek, Mounir; Carnevale, Vincenzo

    2015-01-06

    Voltage sensor domains (VSDs) are membrane-bound protein modules that confer voltage sensitivity to membrane proteins. VSDs sense changes in the transmembrane voltage and convert the electrical signal into a conformational change called activation. Activation involves a reorganization of the membrane protein charges that is detected experimentally as transient currents. These so-called gating currents have been investigated extensively within the theoretical framework of so-called discrete-state Markov models (DMMs), whereby activation is conceptualized as a series of transitions across a discrete set of states. Historically, the interpretation of DMM transition rates in terms of transition state theory has been instrumental in shaping our view of the activation process, whose free-energy profile is currently envisioned as composed of a few local minima separated by steep barriers. Here we use atomistic level modeling and well-tempered metadynamics to calculate the configurational free energy along a single transition from first principles. We show that this transition is intrinsically multidimensional and described by a rough free-energy landscape. Remarkably, a coarse-grained description of the system, based on the use of the gating charge as reaction coordinate, reveals a smooth profile with a single barrier, consistent with phenomenological models. Our results bridge the gap between microscopic and macroscopic descriptions of activation dynamics and show that choosing the gating charge as reaction coordinate masks the topological complexity of the network of microstates participating in the transition. Importantly, full characterization of the latter is a prerequisite to rationalize modulation of this process by lipids, toxins, drugs, and genetic mutations.

  14. Free-energy landscape of ion-channel voltage-sensor–domain activation

    PubMed Central

    Delemotte, Lucie; Kasimova, Marina A.; Klein, Michael L.; Tarek, Mounir; Carnevale, Vincenzo

    2015-01-01

    Voltage sensor domains (VSDs) are membrane-bound protein modules that confer voltage sensitivity to membrane proteins. VSDs sense changes in the transmembrane voltage and convert the electrical signal into a conformational change called activation. Activation involves a reorganization of the membrane protein charges that is detected experimentally as transient currents. These so-called gating currents have been investigated extensively within the theoretical framework of so-called discrete-state Markov models (DMMs), whereby activation is conceptualized as a series of transitions across a discrete set of states. Historically, the interpretation of DMM transition rates in terms of transition state theory has been instrumental in shaping our view of the activation process, whose free-energy profile is currently envisioned as composed of a few local minima separated by steep barriers. Here we use atomistic level modeling and well-tempered metadynamics to calculate the configurational free energy along a single transition from first principles. We show that this transition is intrinsically multidimensional and described by a rough free-energy landscape. Remarkably, a coarse-grained description of the system, based on the use of the gating charge as reaction coordinate, reveals a smooth profile with a single barrier, consistent with phenomenological models. Our results bridge the gap between microscopic and macroscopic descriptions of activation dynamics and show that choosing the gating charge as reaction coordinate masks the topological complexity of the network of microstates participating in the transition. Importantly, full characterization of the latter is a prerequisite to rationalize modulation of this process by lipids, toxins, drugs, and genetic mutations. PMID:25535341

  15. Reconstructing Folding Energy Landscape Profiles from Nonequilibrium Pulling Curves with an Inverse Weierstrass Integral Transform

    NASA Astrophysics Data System (ADS)

    Engel, Megan C.; Ritchie, Dustin B.; Foster, Daniel A. N.; Beach, Kevin S. D.; Woodside, Michael T.

    2014-12-01

    The energy landscapes that drive structure formation in biopolymers are difficult to measure. Here we validate experimentally a novel method to reconstruct landscape profiles from single-molecule pulling curves using an inverse Weierstrass transform (IWT) of the Jarzysnki free-energy integral. The method was applied to unfolding measurements of a DNA hairpin, replicating the results found by the more-established weighted histogram (WHAM) and inverse Boltzmann methods. Applying both WHAM and IWT methods to reconstruct the folding landscape for a RNA pseudoknot having a stiff energy barrier, we found that landscape features with sharper curvature than the force probe stiffness could not be recovered with the IWT method. The IWT method is thus best for analyzing data from stiff force probes such as atomic force microscopes.

  16. The splitting of intrinsic energy and the origin of mass density in continuum mechanics

    NASA Astrophysics Data System (ADS)

    Fosdick, Roger; Serrin, James

    2013-05-01

    We show that the total intrinsic energy of a body must split into the sum of two terms—an internal energy which depends upon `state' and a kinetic energy which is quadratic in the square of the particle speed.We use the non-relativistic group invariance structure of a generalized form of the balance of energy in continuum thermomechanics, together with a fundamental axiomatic requirement. The fundamental concepts of motion, force, power, heating and intrinsic energy are introduced as primitive, and we derive the notion of mass and its balance. When James Serrin died on August 23, 2012, this work had just been completed. Jim was my close, personal and treasured friend for over 40 years. We collaborated on several works over those years, and we often talked together and socialized on various occasions. I had highest respect for him in all human and professional ways, and there was a definite mutual expression of affection and appreciation. A friendship could not contain more. This paper drew him back to a subject he had worked on years ago, and he was happy to be involved again with a fundamental issue in continuum mechanics. My efforts in this work are dedicated to the memory of James Serrin. He was such a scholar of great breadth and depth—He was wise and witty, and I benefited greatly from his presence. Roger Fosdick

  17. Modulation of folding energy landscape by charge-charge interactions: linking experiments with computational modeling.

    PubMed

    Tzul, Franco O; Schweiker, Katrina L; Makhatadze, George I

    2015-01-20

    The kinetics of folding-unfolding of a structurally diverse set of four proteins optimized for thermodynamic stability by rational redesign of surface charge-charge interactions is characterized experimentally. The folding rates are faster for designed variants compared with their wild-type proteins, whereas the unfolding rates are largely unaffected. A simple structure-based computational model, which incorporates the Debye-Hückel formalism for the electrostatics, was used and found to qualitatively recapitulate the experimental results. Analysis of the energy landscapes of the designed versus wild-type proteins indicates the differences in refolding rates may be correlated with the degree of frustration of their respective energy landscapes. Our simulations indicate that naturally occurring wild-type proteins have frustrated folding landscapes due to the surface electrostatics. Optimization of the surface electrostatics seems to remove some of that frustration, leading to enhanced formation of native-like contacts in the transition-state ensembles (TSE) and providing a less frustrated energy landscape between the unfolded and TS ensembles. Macroscopically, this results in faster folding rates. Furthermore, analyses of pairwise distances and radii of gyration suggest that the less frustrated energy landscapes for optimized variants are a result of more compact unfolded and TS ensembles. These findings from our modeling demonstrates that this simple model may be used to: (i) gain a detailed understanding of charge-charge interactions and their effects on modulating the energy landscape of protein folding and (ii) qualitatively predict the kinetic behavior of protein surface electrostatic interactions.

  18. Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding.

    PubMed

    Malhotra, Pooja; Jethva, Prashant N; Udgaonkar, Jayant B

    2017-08-08

    To characterize experimentally the ruggedness of the free energy landscape of protein folding is challenging, because the distributed small free energy barriers are usually dominated by one, or a few, large activation free energy barriers. This study delineates changes in the roughness of the free energy landscape by making use of the observation that a decrease in ruggedness is accompanied invariably by an increase in folding cooperativity. Hydrogen exchange (HX) coupled to mass spectrometry was used to detect transient sampling of local energy minima and the global unfolded state on the free energy landscape of the small protein single-chain monellin. Under native conditions, local noncooperative openings result in interconversions between Boltzmann-distributed intermediate states, populated on an extremely rugged "uphill" energy landscape. The cooperativity of these interconversions was increased by selectively destabilizing the native state via mutations, and further by the addition of a chemical denaturant. The perturbation of stability alone resulted in seven backbone amide sites exchanging cooperatively. The size of the cooperatively exchanging and/or unfolding unit did not depend on the extent of protein destabilization. Only upon the addition of a denaturant to a destabilized mutant variant did seven additional backbone amide sites exchange cooperatively. Segmentwise analysis of the HX kinetics of the mutant variants further confirmed that the observed increase in cooperativity was due to the smoothing of the ruggedness of the free energy landscape of folding of the protein by the chemical denaturant.

  19. Tropomyosin movement on F-actin during muscle activation explained by energy landscapes.

    PubMed

    Orzechowski, Marek; Moore, Jeffrey R; Fischer, Stefan; Lehman, William

    2014-03-01

    Muscle contraction is regulated by tropomyosin movement across the thin filament surface, which exposes or blocks myosin-binding sites on actin. Recent atomic structures of F-actin-tropomyosin have yielded the positions of tropomyosin on myosin-free and myosin-decorated actin. Here, the repositioning of α-tropomyosin between these locations on F-actin was systematically examined by optimizing the energy of the complex for a wide range of tropomyosin positions on F-actin. The resulting energy landscape provides a full-map of the F-actin surface preferred by tropomyosin, revealing a broad energy basin associated with the tropomyosin position that blocks myosin-binding. This is consistent with previously proposed low-energy oscillations of semi-rigid tropomyosin, necessary for shifting of tropomyosin following troponin-binding. In contrast, the landscape shows much less favorable energies when tropomyosin locates near its myosin-induced "open-state" position. This indicates that spontaneous movement of tropomyosin away from its energetic "ground-state" to the open-state is unlikely in absence of myosin. Instead, myosin-binding must drive tropomyosin toward the open-state to activate the thin filament. Additional energy landscapes were computed for disease-causing actin mutants that distort the topology of the actin-tropomyosin energy landscape, explaining their phenotypes. Thus, the computation of such energy landscapes offers a sensitive way to estimate the impact of mutations. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Energy Landscape of Fullerene Materials: A Comparison of Boron to Boron Nitride and Carbon

    NASA Astrophysics Data System (ADS)

    de, Sandip; Willand, Alexander; Amsler, Maximilian; Pochet, Pascal; Genovese, Luigi; Goedecker, Stefan

    2011-06-01

    Using the minima hopping global geometry optimization method on the density functional potential energy surface we show that the energy landscape of boron clusters is glasslike. Larger boron clusters have many structures which are lower in energy than the cages. This is in contrast to carbon and boron nitride systems which can be clearly identified as structure seekers. The differences in the potential energy landscape explain why carbon and boron nitride systems are found in nature whereas pure boron fullerenes have not been found. We thus present a methodology which can make predictions on the feasibility of the synthesis of new nanostructures.

  1. Geometry of the energy landscape of the self-gravitating ring.

    PubMed

    Monechi, Bernardo; Casetti, Lapo

    2012-10-01

    We study the global geometry of the energy landscape of a simple model of a self-gravitating system, the self-gravitating ring (SGR). This is done by endowing the configuration space with a metric such that the dynamical trajectories are identified with geodesics. The average curvature and curvature fluctuations of the energy landscape are computed by means of Monte Carlo simulations and, when possible, of a mean-field method, showing that these global geometric quantities provide a clear geometric characterization of the collapse phase transition occurring in the SGR as the transition from a flat landscape at high energies to a landscape with mainly positive but fluctuating curvature in the collapsed phase. Moreover, curvature fluctuations show a maximum in correspondence with the energy of a possible further transition, occurring at lower energies than the collapsed one, whose existence had been previously conjectured on the basis of a local analysis of the energy landscape and whose effect on the usual thermodynamic quantities, if any, is extremely weak. We also estimate the largest Lyapunov exponent λ of the SGR using the geometric observables. The geometric estimate always gives the correct order of magnitude of λ and is also quantitatively correct at small energy densities and, in the limit N→∞, in the whole homogeneous phase.

  2. Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions.

    PubMed

    Shao, Qiang

    2016-10-26

    Large-scale conformational changes in proteins are important for their functions. Tracking the conformational change in real time at the level of a single protein molecule, however, remains a great challenge. In this article, we present a novel in silico approach with the combination of normal mode analysis and integrated-tempering-sampling molecular simulation (NMA-ITS) to give quantitative data for exploring the conformational transition pathway in multi-dimensional energy landscapes starting only from the knowledge of the two endpoint structures of the protein. The open-to-closed transitions of three proteins, including nCaM, AdK, and HIV-1 PR, were investigated using NMA-ITS simulations. The three proteins have varied structural flexibilities and domain communications in their respective conformational changes. The transition state structure in the conformational change of nCaM and the associated free-energy barrier are in agreement with those measured in a standard explicit-solvent REMD simulation. The experimentally measured transition intermediate structures of the intrinsically flexible AdK are captured by the conformational transition pathway measured here. The dominant transition pathways between the closed and fully open states of HIV-1 PR are very similar to those observed in recent REMD simulations. Finally, the evaluated relaxation times of the conformational transitions of three proteins are roughly at the same level as reported experimental data. Therefore, the NMA-ITS method is applicable for a variety of cases, providing both qualitative and quantitative insights into the conformational changes associated with the real functions of proteins.

  3. The folding energy landscape and free energy excitations of cytochrome c.

    PubMed

    Weinkam, Patrick; Zimmermann, Jörg; Romesberg, Floyd E; Wolynes, Peter G

    2010-05-18

    The covalently bound heme cofactor plays a dominant role in the folding of cytochrome c. Because of the complicated inorganic chemistry of the heme, some might consider the folding of cytochrome c to be a special case, following principles different from those used to describe the folding of proteins without cofactors. Recent investigations, however, demonstrate that common models describing folding for many proteins work well for cytochrome c when heme is explicitly introduced, generally providing results that agree with experimental observations. In this Account, we first discuss results from simple native structure-based models. These models include attractive interactions between nonadjacent residues only if they are present in the crystal structure at pH 7. Because attractive nonnative contacts are not included in native structure-based models, their energy landscapes can be described as "perfectly funneled". In other words, native structure-based models are energetically guided towards the native state and contain no energetic traps that would hinder folding. Energetic traps are denoted sources of "frustration", which cause specific transient intermediates to be populated. Native structure-based models do, however, include repulsion between residues due to excluded volume. Nonenergetic traps can therefore exist if the chain, which cannot cross over itself, must partially unfold so that folding can proceed. The ability of native structure-based models to capture this kind of motion is partly responsible for their successful predictions of folding pathways for many types of proteins. Models without frustration describe the sequence of folding events for cytochrome c well (as inferred from hydrogen-exchange experiments), thereby justifying their use as a starting point. At low pH, the experimentally observed folding sequence of cytochrome c deviates from that at pH 7 and from models with perfectly funneled energy landscapes. Here, alternate folding pathways are

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

    PubMed

    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.

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

    PubMed Central

    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

  6. Transforming the Energy Landscape of a Coiled-Coil Peptide via Point Mutations.

    PubMed

    Röder, Konstantin; Wales, David J

    2017-03-14

    We analyze the effect of point mutations on the energy landscape of a coiled-coil peptide, GCN4-pLI, where the native state is a parallel tetrameric configuration formed from two identical dimers. Experimentally, a single mutation, E20S, supports both antiparallel and parallel structures. Here, we analyze the potential energy landscapes of the dimeric units for the parent sequence and four mutants, namely E20S, E20A, E20P, and E20G. Despite sharing characteristic funnels containing the parallel and antiparallel structures, the point mutations change some parts of the landscape quite dramatically, and we predict new intermediate structures and characterize the associated heat capacities. For the mutants we predict that kinked intermediate structures facilitate the transition between parallel and antiparallel morphologies, in contrast to the parent sequence. Furthermore, we predict a change from a multifunnel energy landscape in the E20S mutant to a landscape dominated by an underlying single funnel in the parent sequence, with accompanying heat capacity signatures. Our results imply that changes in the landscape due to mutations might provide useful tools for functional protein design.

  7. Geometry of the energy landscape and folding transition in a simple model of a protein.

    PubMed

    Mazzoni, Lorenzo N; Casetti, Lapo

    2008-05-01

    A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is completely determined by the potential energy. We consider different sequences, some with a definite proteinlike behavior, a unique native state and a folding transition, and others undergoing a hydrophobic collapse with no tendency to a unique native state. The global geometry of the energy landscape appears to contain relevant information on the behavior of the various sequences: in particular, the fluctuations of the curvature of the energy landscape, measured by means of numerical simulations, clearly mark the folding transition and allow the proteinlike sequences to be distinguished from the others.

  8. Exploring the complex free-energy landscape of the simplest glass by rheology

    NASA Astrophysics Data System (ADS)

    Jin, Yuliang; Yoshino, Hajime

    2017-04-01

    For amorphous solids, it has been intensely debated whether the traditional view on solids, in terms of the ground state and harmonic low energy excitations on top of it, such as phonons, is still valid. Recent theoretical developments of amorphous solids revealed the possibility of unexpectedly complex free-energy landscapes where the simple harmonic picture breaks down. Here we demonstrate that standard rheological techniques can be used as powerful tools to examine nontrivial consequences of such complex free-energy landscapes. By extensive numerical simulations on a hard sphere glass under quasistatic shear at finite temperatures, we show that above the so-called Gardner transition density, the elasticity breaks down, the stress relaxation exhibits slow, and ageing dynamics and the apparent shear modulus becomes protocol-dependent. Being designed to be reproducible in laboratories, our approach may trigger explorations of the complex free-energy landscapes of a large variety of amorphous materials.

  9. Energy landscape analysis of the subcortical brain network unravels system properties beneath resting state dynamics.

    PubMed

    Kang, Jiyoung; Pae, Chongwon; Park, Hae-Jeong

    2017-04-01

    The configuration of the human brain system at rest, which is in a transitory phase among multistable states, remains unknown. To investigate the dynamic systems properties of the human brain at rest, we constructed an energy landscape for the state dynamics of the subcortical brain network, a critical center that modulates whole brain states, using resting state fMRI. We evaluated alterations in energy landscapes following perturbation in network parameters, which revealed characteristics of the state dynamics in the subcortical brain system, such as maximal number of attractors, unequal temporal occupations, and readiness for reconfiguration of the system. Perturbation in the network parameters, even those as small as the ones in individual nodes or edges, caused a significant shift in the energy landscape of brain systems. The effect of the perturbation on the energy landscape depended on the network properties of the perturbed nodes and edges, with greater effects on hub nodes and hubs-connecting edges in the subcortical brain system. Two simultaneously perturbed nodes produced perturbation effects showing low sensitivity in the interhemispheric homologous nodes and strong dependency on the more primary node among the two. This study demonstrated that energy landscape analysis could be an important tool to investigate alterations in brain networks that may underlie certain brain diseases, or diverse brain functions that may emerge due to the reconfiguration of the default brain network at rest. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Comparing the energy landscapes for native folding and aggregation of PrP.

    PubMed

    Dee, Derek R; Woodside, Michael T

    2016-05-03

    Protein sequences are evolved to encode generally one folded structure, out of a nearly infinite array of possible folds. Underlying this code is a funneled free energy landscape that guides folding to the native conformation. Protein misfolding and aggregation are also a manifestation of free-energy landscapes. The detailed mechanisms of these processes are poorly understood, but often involve rare, transient species and a variety of different pathways. The inherent complexity of misfolding has hampered efforts to measure aggregation pathways and the underlying energy landscape, especially using traditional methods where ensemble averaging obscures important rare and transient events. We recently studied the misfolding and aggregation of prion protein by examining 2 monomers tethered in close proximity as a dimer, showing how the steps leading to the formation of a stable aggregated state can be resolved in the single-molecule limit and the underlying energy landscape thereby reconstructed. This approach allows a more quantitative comparison of native folding versus misfolding, including fundamental differences in the dynamics for misfolding. By identifying key steps and interactions leading to misfolding, it should help to identify potential drug targets. Here we describe the importance of characterizing free-energy landscapes for aggregation and the challenges involved in doing so, and we discuss how single-molecule studies can help test proposed structural models for PrP aggregates.

  11. Comparing the Folding and Misfolding Energy Landscapes of Phosphoglycerate Kinase

    PubMed Central

    Agócs, Gergely; Szabó, Bence T.; Köhler, Gottfried; Osváth, Szabolcs

    2012-01-01

    Partitioning of polypeptides between protein folding and amyloid formation is of outstanding pathophysiological importance. Using yeast phosphoglycerate kinase as model, here we identify the features of the energy landscape that decide the fate of the protein: folding or amyloidogenesis. Structure formation was initiated from the acid-unfolded state, and monitored by fluorescence from 10 ms to 20 days. Solvent conditions were gradually shifted between folding and amyloidogenesis, and the properties of the energy landscape governing structure formation were reconstructed. A gradual transition of the energy landscape between folding and amyloid formation was observed. In the early steps of both folding and misfolding, the protein searches through a hierarchically structured energy landscape to form a molten globule in a few seconds. Depending on the conditions, this intermediate either folds to the native state in a few minutes, or forms amyloid fibers in several days. As conditions are changed from folding to misfolding, the barrier separating the molten globule and native states increases, although the barrier to the amyloid does not change. In the meantime, the native state also becomes more unstable and the amyloid more stable. We conclude that the lower region of the energy landscape determines the final protein structure. PMID:22735533

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

    Treesearch

    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...

  13. High energy product permanent magnet having improved intrinsic coercivity and method of making same

    DOEpatents

    Ramesh, Ramamoorthy; Thomas, Gareth

    1990-01-01

    A high energy rare earth-ferromagnetic metal permanent magnet is disclosed which is characterized by improved intrinsic coercivity and is made by forming a particulate mixture of a permanent magnet alloy comprising one or more rare earth elements and one or more ferromagnetic metals and forming a second particulate mixture of a sintering alloy consisting essentially of 92-98 wt. % of one or more rare earth elements selected from the class consisting of Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, and mixtures of two or more of such rare earth elements, and 2-8 wt. % of one or more alloying metals selected from the class consisting of Al, Nb, Zr, V, Ta, Mo, and mixtures of two or more of such metals. The permanent magnet alloy particles and sintering aid alloy are mixed together and magnetically oriented by immersing the mixture in an axially aligned magnetic field while cold pressing the mixture. The compressed mixture is then sintered at a temperature above the melting point of the sintering aid and below the melting point of the permanent magnet alloy to thereby coat the particle surfaces of the permanent magnetic alloy particles with the sintering aid while inhibiting migration of the rare earth element in the sintering aid into the permanent magnet alloy particles to thereby raise the intrinsic coercivity of the permanent magnet alloy without substantially lowering the high energy of the permanent magnet alloy.

  14. Resonance saturation in the odd-intrinsic parity sector of low-energy QCD

    NASA Astrophysics Data System (ADS)

    Kampf, Karol; Novotný, Jiří

    2011-07-01

    Using the large NC approximation we have constructed the most general chiral resonance Lagrangian in the odd-intrinsic parity sector that can generate low-energy chiral constants up to O(p6). Integrating out the resonance fields these O(p6) constants are expressed in terms of resonance couplings and masses. The role of η' is discussed and its contribution is explicitly factorized. Using the resonance basis we have also calculated two QCD Green functions of currents, ⟨VVP⟩ and ⟨VAS⟩, and found, imposing high-energy constraints, additional relations for resonance couplings. We have studied several phenomenological implications based on these correlators which provided, for example, a prediction for the π0-pole contribution to the muon g-2 factor: aμπ0=65.8(1.2)×10-11.

  15. Intrinsic deep hole trap levels in Cu2O with self-consistent repulsive Coulomb energy

    NASA Astrophysics Data System (ADS)

    Huang, Bolong

    2016-03-01

    The large error of the DFT+U method on full-filled shell metal oxides is due to the residue of self-energy from the localized d orbitals of cations and p orbitals of the anions. U parameters are selfconsistently found to achieve the analytical self-energy cancellation. The improved band structures based on relaxed lattices of Cu2O are shown based on minimization of self-energy error. The experimentally reported intrinsic p-type trap levels are contributed by both Cu-vacancy and the O-interstitial defects in Cu2O. The latter defect has the lowest formation energy but contributes a deep hole trap level while the Cuvacancy has higher energy cost but acting as a shallow acceptor. Both present single-particle levels spread over nearby the valence band edge, consistent to the trend of defects transition levels. By this calculation approach, we also elucidated the entanglement of strong p-d orbital coupling to unravel the screened Coulomb potential of fully filled shells.

  16. Energy landscape and phase transitions in the self-gravitating ring model.

    PubMed

    Nardini, Cesare; Casetti, Lapo

    2009-12-01

    We apply a recently proposed criterion for the existence of phase transitions, which is based on the properties of the saddles of the energy landscape, to a simplified model of a system with gravitational interactions referred to as the self-gravitating ring model. We show analytically that the criterion correctly singles out the phase transition between a homogeneous and a clustered phase and also suggests the presence of another phase transition not previously known. On the basis of the properties of the energy landscape we conjecture on the nature of the latter transition.

  17. Exploring the energy landscape of proteins: A characterization of the activation-relaxation technique

    NASA Astrophysics Data System (ADS)

    Wei, Guanghong; Mousseau, Normand; Derreumaux, Philippe

    2002-12-01

    Finding the global energy minimum region of a polypeptide chain, independently of the starting conformation and in a reasonable computational time, is of fundamental interest. As the energy landscape of proteins is very rugged, sampling is hindered by the vast number of minima existing on this multidimensional landscape. In this study, we use activation-relaxation technique (ART) to explore the energy landscape of a series of peptide models with 14, 26, and 28 amino acids. Peptides are modeled by a reduced off-lattice representation and a simplified OPEP-like (optimized potential for efficient peptide-structure prediction) energy model. ART defines moves directly in the energy landscape and can generate with equal efficiency events with root-mean-square deviation as small as 0.1 or as large as 4 Å. Our results show that (i) ART trajectories are reversible and provide real activated paths; (ii) ART simulations converge to the same low-energy minimum region, for a wide range of starting configurations; (iii) ART method can sample the phase space effectively, going through many hyper-basins, and can generate significant moves in a single event. Possible applications of ART method to biomolecules are discussed.

  18. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.

    PubMed

    Whitford, Paul C; Blanchard, Scott C; Cate, Jamie H D; Sanbonmatsu, Karissa Y

    2013-01-01

    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.

  19. Surveying the free energy landscapes of continuum models: Application to soft matter systems.

    PubMed

    Kusumaatmaja, Halim

    2015-03-28

    A variety of methods are developed for characterising the free energy landscapes of continuum, Landau-type free energy models. Using morphologies of lipid vesicles and a multistable liquid crystal device as examples, I show that the methods allow systematic study of not only the most relevant minimum energy configurations, but also the transition pathways between any two minima, as well as their corresponding energy barriers and transition state configurations. A global view of the free energy landscapes can then be visualized using either a disconnectivity graph or a network representation. Different forms of free energy functionals and boundary conditions can be readily implemented, thus allowing these tools to be utilised for a broad range of problems.

  20. Modulation of folding energy landscape by charge–charge interactions: Linking experiments with computational modeling

    PubMed Central

    Tzul, Franco O.; Schweiker, Katrina L.; Makhatadze, George I.

    2015-01-01

    The kinetics of folding–unfolding of a structurally diverse set of four proteins optimized for thermodynamic stability by rational redesign of surface charge–charge interactions is characterized experimentally. The folding rates are faster for designed variants compared with their wild-type proteins, whereas the unfolding rates are largely unaffected. A simple structure-based computational model, which incorporates the Debye–Hückel formalism for the electrostatics, was used and found to qualitatively recapitulate the experimental results. Analysis of the energy landscapes of the designed versus wild-type proteins indicates the differences in refolding rates may be correlated with the degree of frustration of their respective energy landscapes. Our simulations indicate that naturally occurring wild-type proteins have frustrated folding landscapes due to the surface electrostatics. Optimization of the surface electrostatics seems to remove some of that frustration, leading to enhanced formation of native-like contacts in the transition-state ensembles (TSE) and providing a less frustrated energy landscape between the unfolded and TS ensembles. Macroscopically, this results in faster folding rates. Furthermore, analyses of pairwise distances and radii of gyration suggest that the less frustrated energy landscapes for optimized variants are a result of more compact unfolded and TS ensembles. These findings from our modeling demonstrates that this simple model may be used to: (i) gain a detailed understanding of charge–charge interactions and their effects on modulating the energy landscape of protein folding and (ii) qualitatively predict the kinetic behavior of protein surface electrostatic interactions. PMID:25564663

  1. Electricity, policy and landscape: An integrated geographic approach to renewable electric energy development

    NASA Astrophysics Data System (ADS)

    Serralles, Roberto Juan

    The development of a centralized electric energy infrastructure in industrialized areas of the world has significantly impacted the character and nature of local and regional landscapes. Since their development at the beginning of the 20th century, electric energy networks have become one of the most distinctive and visible landscape features found in industrialized regions today. At the same time, our perceptual relationship with the electric energy infrastructure, along with the meanings we ascribe to these electricity-related landscape features, has shifted dramatically over the last century. The early stages of the historical development of the electric energy infrastructure in the United States and Europe were marked by an optimistic popular perception that celebrated electricity's vast potential as an economic and social transformative agent. However, by the end of the 20th century, concerns in these industrialized regions over environmental degradation and resource scarcity significantly altered these popularized political and aesthetic judgments. Ironically, the recent growth of renewable energy projects, in particular large-scale wind energy facilities, while seeking to ameliorate the industrial causes of environmental degradation, has sparked an intense public debate over the visual impacts of these projects on local landscapes. To understand this shifting perceptual relationship between industrialized societies and the electricity landscapes found in these regions, in this dissertation I analyze the evolving social, economic and political milieu underlying the creation and reproduction of meanings ascribed to the visual landscape modifications spawned by the electricity network. In addition, I describe the political conditions and trends that are shaping and contextualizing the role of renewable electric energy facilities in the future electricity budgets of the United States and the EU. To address the concerns over negative visual impacts of renewable

  2. McFadden, Wyoming: A case study in narrating our changing energy landscapes

    NASA Astrophysics Data System (ADS)

    Anderson, Carly-Ann Marie

    This thesis uses McFadden, Wyoming, and the Rock Creek Valley to discuss Wyoming's changing energy landscapes and argues that a cultural landscape approach to documenting our historic and cultural resources can contribute to properly siting energy developments. Though Wyoming stands to gain from the construction of wind farms, they should be carefully sited in order to balance environmental and cultural resource preservation with energy needs. Wyoming has a long history as an energy hinterland and provides a significant portion of energy to the U.S. However, the nation's demand for energy should not take precedence over preserving the cultural resources and vast open landscapes that represent Wyoming's heritage. A history of the Rock Creek Valley as a home to Native Americans, a transportation corridor, oil field, and wind farm site is presented along with a discussion of energy consumption and Wyoming's role in the energy market. The thesis also considers the importance of education, public discourse, and narrative as tools for planning a sustainable future with regard to energy, the environment, and cultural resources.

  3. Resonant nature of intrinsic defect energy levels in PbTe revealed by infrared photoreflectance spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Bingpo; Cai, Chunfeng; Jin, Shuqiang; Ye, Zhenyu; Wu, Huizhen; Qi, Zhen

    2014-07-01

    Step-scan Fourier-transform infrared photoreflectance and modulated photoluminescence spectroscopy were used to characterize the optical transitions of the epitaxial PbTe thin film grown by molecular beam epitaxy on BaF2 (111) substrate in the vicinity of energy gap of lead telluride at 77 K. It is found that the intrinsic defect energy levels in the electronic structure are of resonant nature. The Te-vacancy energy level is located above the conduction band minimum by 29.1 meV. Another defect (VX) energy level situated below valance band maximum by 18.1 meV is also revealed. Whether it is associated with the Pb vacancy is still not clear. It might also be related to the misfit dislocations stemming from the lattice mismatch between PbTe and BaF2 substrate. The experimental results support the theory prediction (N. J. Parada and G. W. Pratt, Jr., Phys. Rev. Lett. 22, 180 (1969), N. J. Parada, Phys. Rev. B 3, 2042 (1971)) and are consistent with the reported Hall experimental results (G. Bauer, H. Burkhard, H. Heinrich, and A. Lopez-Otero, J. Appl. Phys. 47, 1721 (1976)).

  4. Crystal growth nucleation and equalization of Fermi energies of intrinsic nuclei and glass-forming melts

    NASA Astrophysics Data System (ADS)

    Tournier, Robert F.

    2009-01-01

    The energy saving produced by the equalization of Fermi energies of a crystal and its melt is determined by adding a negative fraction epsilonsl(T) of the fusion heat to the Gibbs free energy change ΔG2ls associated to a charged crystal formation in glass-forming melts. In bulk metallic glasses, epsilonls(Tm) is larger than 1 at the melting temperature Tm and only determined by the knowledge of the free volume disappearance temperature. When the unmelted intrinsic crystals have a radius Rnm much smaller than the critical radius R*2ls, epsilonsl(T) is strongly reduced by the quantification of electronic levels in the large electrostatic potential created by the electron transfer from the crystal to the melt. The reduced value epsilonnm0 of epsilonsl(Tm) for Rnm=3.2E-10m in Zr41.2Ti13.8Cu12.5Ni10Be22.5 is determined by comparing the experimental Time-Temperature-Transformation diagram measured by electrostatic levitation to the calculated one. It exactly corresponds to the first energy level of one s state electron moving in the same spherical attractive potential and in vacuum in spite of the fact that, in a metal, the charge screening is built by many-body effects.

  5. Influence of the membrane potential on the free energy of an intrinsic protein.

    PubMed Central

    Roux, B

    1997-01-01

    A modified Poisson-Boltzmann equation is developed from statistical mechanical considerations to describe the influence of the transmembrane potential on macromolecular systems. Using a Green's function formalism, the electrostatic free energy of a protein associated with the membrane is expressed as the sum of three terms: a contribution from the energy required to charge the system's capacitance, a contribution corresponding to the interaction of the protein charges with the membrane potential, and a contribution corresponding to a voltage-independent reaction field free energy. The membrane potential, which is due to the polarization interface, is calculated in the absence of the protein charges, whereas the reaction field is calculated in the absence of transmembrane potential. Variations in the capacitive energy associated with typical molecular processes are negligible under physiological conditions. The formulation of the theory is closely related to standard algorithms used to solve the Poisson-Boltzmann equation and only small modifications to current source codes are required for its implementation. The theory is illustrated by examining the voltage-dependent membrane insertion of a simple polyalanine alpha-helix and by computing the electrostatic potential across a 60-A-diameter sphere meant to represent a large intrinsic protein. Images FIGURE 2 PMID:9414213

  6. Crystal growth nucleation and Fermi energy equalization of intrinsic spherical nuclei in glass-forming melts

    NASA Astrophysics Data System (ADS)

    Tournier, Robert F.

    2009-01-01

    The energy saving resulting from the equalization of Fermi energies of a crystal and its melt is added to the Gibbs free-energy change ΔG2ls associated with a crystal formation in glass-forming melts. This negative contribution being a fraction ɛ ls(T) of the fusion heat is created by the electrostatic potential energy -U0 resulting from the electron transfer from the crystal to the melt and is maximum at the melting temperature Tm in agreement with a thermodynamics constraint. The homogeneous nucleation critical temperature T2, the nucleation critical barrier ΔG2ls*/kBT and the critical radius R*2ls are determined as functions of ɛls(T). In bulk metallic glass forming melts, ɛls(T) and T2 only depend on the free-volume disappearance temperature T0l, and ɛls(Tm) is larger than 1 (T0l>Tm/3) in conventional undercooled melts ɛls(Tm) is smaller than 1 (T0l>Tm/3). Unmelted intrinsic crystals act as growth nuclei reducing ΔG2ls*/kBT and the nucleation time. The temperature-time transformation diagrams of Mg65Y10 Cu25, Zr41.2Ti13.8 Cu12.5Ni10Be22.5, Pd43Cu27 Ni10P20, Fe83B17 and Ni melts are predicted using classic nucleation models including time lags in transient nucleation, by varying the intrinsic nucleus contribution to the reduction of ΔG2ls*/kBT. The energy-saving coefficient ɛ nm(T) of an unmelted crystal of radius Rnm is reduced when Rnm LtR*2ls; ɛnm is quantified and corresponds to the first energy level of one s-electron moving in vacuum in the same spherical attractive potential -U0 despite the fact that the charge screening is built by many-body effects.

  7. Crystal growth nucleation and Fermi energy equalization of intrinsic spherical nuclei in glass-forming melts.

    PubMed

    Tournier, Robert F

    2009-02-01

    The energy saving resulting from the equalization of Fermi energies of a crystal and its melt is added to the Gibbs free-energy change ΔG2ls associated with a crystal formation in glass-forming melts. This negative contribution being a fraction ε ls(T) of the fusion heat is created by the electrostatic potential energy -U0 resulting from the electron transfer from the crystal to the melt and is maximum at the melting temperature Tm in agreement with a thermodynamics constraint. The homogeneous nucleation critical temperature T2, the nucleation critical barrier ΔG2ls∗/kBT and the critical radius R∗2ls are determined as functions of εls(T). In bulk metallic glass forming melts, εls(T) and T2 only depend on the free-volume disappearance temperature T0l, and εls(Tm) is larger than 1 (T0l>Tm/3); in conventional undercooled melts εls(Tm) is smaller than 1 (T0l>Tm/3). Unmelted intrinsic crystals act as growth nuclei reducing ΔG2ls∗/kBT and the nucleation time. The temperature-time transformation diagrams of Mg65Y10Cu25, Zr41.2Ti13.8Cu12.5Ni10Be22.5, Pd43Cu27 Ni10P20, Fe83B17 and Ni melts are predicted using classic nucleation models including time lags in transient nucleation, by varying the intrinsic nucleus contribution to the reduction of ΔG2ls∗/kBT. The energy-saving coefficient ε nm(T) of an unmelted crystal of radius Rnm is reduced when Rnm ≪R∗2ls; εnm is quantified and corresponds to the first energy level of one s-electron moving in vacuum in the same spherical attractive potential -U0 despite the fact that the charge screening is built by many-body effects.

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

    PubMed

    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.

  9. Buffed energy landscapes: another solution to the kinetic paradoxes of protein folding.

    PubMed

    Plotkin, Steven S; Wolynes, Peter G

    2003-04-15

    The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological temperatures leads to energy landscapes having a single dominant basin and an overall funnel topography. We show here that, although such a landscape topography is indeed a sufficient condition for folding, another possibility also exists, giving a previously undescribed class of foldable sequences. These sequences have landscapes that are only weakly funneled in the conventional thermodynamic sense but have unusually low kinetic barriers for reconfigurational motion. Traps have been specifically removed by selection. Here we examine the possibility of folding on these "buffed" landscapes by mapping the determination of statistics of pathways for the heterogeneous nucleation processes involved in escaping from traps to the solution of an imaginary time Schroedinger equation. This equation is solved analytically in adiabatic and "soft-wall" approximations, and numerical results are shown for the general case. The fraction of funneled vs. buffed proteins in sequence space is estimated, suggesting the statistical dominance of the funneling mechanism for achieving foldability.

  10. Free-energy landscape of mono- and dinucleosomes: Enhanced rotational flexibility of interconnected nucleosomes

    NASA Astrophysics Data System (ADS)

    Nam, Gi-Moon; Arya, Gaurav

    2016-03-01

    The nucleosome represents the basic unit of eukaryotic genome organization, and its conformational fluctuations play a crucial role in various cellular processes. Here we provide insights into the flipping transition of a nucleosome by computing its free-energy landscape as a function of the linking number and nucleosome orientation using the density-of-states Monte Carlo approach. To investigate how the energy landscape is affected by the presence of neighboring nucleosomes in a chromatin fiber, we also compute the free-energy landscape for a dinucleosome array. We find that the mononucleosome is bistable between conformations with negatively and positively crossed linkers while the conformation with open linkers appears as a transition state. The dinucleosome exhibits a markedly different energy landscape in which the conformation with open linkers populates not only the transition state but also the global minimum. This enhanced stability of the open state is attributed to increased rotational flexibility of nucleosomes arising from their mechanical coupling with neighboring nucleosomes. Our results provide a possible mechanism by which chromatin may enhance the accessibility of its DNA and facilitate the propagation and mitigation of DNA torsional stresses.

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

    PubMed

    Long, Ryan A; Bowyer, R T; Porter, Warren P; Mathewson, Paul; Monteith, Kevin L; Findholt, Scott L; Dick, Brian L; Kie, John G

    2016-07-01

    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 American elk (Cervus elaphus) for areas that reduced costs of thermoregulation and activity, and increased access to high-quality forage, would influence four energetically mediated traits related to fitness: birth mass of young, nutritional condition of adult females at the onset of winter, change in nutritional condition of females between spring and winter, and neonatal survival. We used a biophysical model to map spatiotemporally explicit costs of thermoregulation and activity experienced by elk in a heterogeneous landscape. We then combined model predictions with data on forage characteristics, animal locations, nutritional condition, and mass and survival of young to evaluate behaviorally mediated effects of the energy landscape on fitness-related traits. During spring, when high-quality forage was abundant, female elk that consistently selected low-cost areas before parturition gave birth to larger young than less-selective individuals, and birth mass had a strong, positive influence on probability of survival. As forage quality declined during autumn, however, lactating females that consistently selected the highest quality forage available accrued more fat and entered winter in better condition than less-selective individuals. Results of our study highlight the importance of understanding the dynamic nature of energy landscapes experienced by free-ranging animals.

  12. Energy landscapes of a hairpin peptide including NMR chemical shift restraints.

    PubMed

    Carr, Joanne M; Whittleston, Chris S; Wade, David C; Wales, David J

    2015-08-21

    Methods recently introduced to improve the efficiency of protein structure prediction simulations by adding a restraint potential to a molecular mechanics force field introduce additional input parameters that can affect the performance. Here we investigate the changes in the energy landscape as the relative weight of the two contributions, force field and restraint potential, is systematically altered, for restraint functions constructed from calculated nuclear magnetic resonance chemical shifts. Benchmarking calculations were performed on a 12-residue peptide, tryptophan zipper 1, which features both secondary structure (a β-hairpin) and specific packing of tryptophan sidechains. Basin-hopping global optimization was performed to assess the efficiency with which lowest-energy structures are located, and the discrete path sampling approach was employed to survey the energy landscapes between unfolded and folded structures. We find that inclusion of the chemical shift restraints improves the efficiency of structure prediction because the energy landscape becomes more funnelled and the proportion of local minima classified as native increases. However, the funnelling nature of the landscape is reduced as the relative contribution of the chemical shift restraint potential is increased past an optimal value.

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

    PubMed

    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.

  14. Modulation of a protein free-energy landscape by circular permutation.

    PubMed

    Radou, Gaël; Enciso, Marta; Krivov, Sergei; Paci, Emanuele

    2013-11-07

    Circular permutations usually retain the native structure and function of a protein while inevitably perturbing its folding dynamics. By using simulations with a structure-based model and a rigorous methodology to determine free-energy surfaces from trajectories, we evaluate the effect of a circular permutation on the free-energy landscape of the protein T4 lysozyme. We observe changes which, although subtle, largely affect the cooperativity between the two subdomains. Such a change in cooperativity has been previously experimentally observed and recently also characterized using single molecule optical tweezers and the Crooks relation. The free-energy landscapes show that both the wild type and circular permutant have an on-pathway intermediate, previously experimentally characterized, in which one of the subdomains is completely formed. The landscapes, however, differ in the position of the rate-limiting step for folding, which occurs before the intermediate in the wild type and after in the circular permutant. This shift of transition state explains the observed change in the cooperativity. The underlying free-energy landscape thus provides a microscopic description of the folding dynamics and the connection between circular permutation and the loss of cooperativity experimentally observed.

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

    PubMed Central

    Iida, Shinji; Nakamura, Haruki; Higo, Junichi

    2016-01-01

    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. PMID:27288028

  16. NMR comparison of the native energy landscapes of DLC8 dimer and monomer.

    PubMed

    Krishna Mohan, P M; Barve, Maneesha; Chatterjee, Amarnath; Ghosh-Roy, Anindya; Hosur, Ramakrishna V

    2008-04-01

    Characterization of the low energy excited states on the energy landscape of a protein is one of the exciting and challenging problems in structural biology today. In this context, we present here residue level NMR description of the low energy excited states representing locally different alternative conformations in the dynein light chain protein, in its dimeric as well as monomeric forms. Important differences have been observed between the two cases and these are not necessarily restricted to the dimer interface. Simulations indicate that the low energy excited states are within a free energy of 2-3 kcal/mol above the native state. In both the monomer and the dimer the energy landscape is very sensitive to small pH perturbations. Nearly 25% of the residues (total of residues at pH 3.0 and 3.5 for the monomer, and at pH 7.0 and 6.0 for the dimer) access alternative conformations. The observations have been rationalized on the basis of protonation-deprotonation equilibria in the side chains; histidines in the case of the dimer and aspartates/glutamates in the case of the monomer. The possible relationship of the observed ruggedness of the native energy landscape with the protein structure, and its implications to protein adaptability and unfolding have been discussed.

  17. Model energy landscapes of low-temperature fluids: Dipolar hard spheres.

    PubMed

    Matyushov, Dmitry V

    2007-07-01

    An analytical model of non-Gaussian energy landscape of low-temperature fluids is developed based on the thermodynamics of the fluid of dipolar hard spheres. The entire excitation profile of the liquid, from the high-temperature liquid to the point of ideal-glass transition, has been obtained from Monte Carlo simulations. The fluid of dipolar hard spheres loses stability close to the point of ideal-glass transition transforming via a first-order transition into a columnar liquid phase of dipolar chains locally arranged in a body-centered-tetragonal order. Significant non-Gaussianity of the energy landscape is responsible for narrowing of the distribution of potential energies and energies of inherent structures with decreasing temperature. We suggest that the proposed functionality of the enumeration function is widely applicable to both polar and nonpolar low-temperature liquids.

  18. Optimizing the calculation of energy landscape parameters from single-molecule protein unfolding experiments.

    PubMed

    Tych, Katarzyna M; Hughes, Megan L; Bourke, James; Taniguchi, Yukinori; Kawakami, Masaru; Brockwell, David J; Dougan, Lorna

    2015-01-01

    Single-molecule force spectroscopy using an atomic force microscope (AFM) can be used to measure the average unfolding force of proteins in a constant velocity experiment. In combination with Monte Carlo simulations and through the application of the Zhurkov-Bell model, information about the parameters describing the underlying unfolding energy landscape of the protein can be obtained. Using this approach, we have completed protein unfolding experiments on the polyprotein (I27)(5) over a range of pulling velocities. In agreement with previous work, we find that the observed number of protein unfolding events observed in each approach-retract cycle varies between one and five, due to the nature of the interactions between the polyprotein, the AFM tip, and the substrate, and there is an unequal unfolding probability distribution. We have developed a Monte Carlo simulation that incorporates the impact of this unequal unfolding probability distribution on the median unfolding force and the calculation of the protein unfolding energy landscape parameters. These results show that while there is a significant, unequal unfolding probability distribution, the unfolding energy landscape parameters obtained from use of the Zhurkov-Bell model are not greatly affected. This result is important because it demonstrates that the minimum acceptance criteria typically used in force extension experiments are justified and do not skew the calculation of the unfolding energy landscape parameters. We further validate this approach by determining the error in the energy landscape parameters for two extreme cases, and we provide suggestions for methods that can be employed to increase the level of accuracy in single-molecule experiments using polyproteins.

  19. Europe's battery: The making of the Alpine energy landscape, 1870-1955

    NASA Astrophysics Data System (ADS)

    Landry, Marc D., II

    This study examines the environmental history of hydropower development in the Alps from the mid-nineteenth to the mid-twentieth centuries. Analyzing government archival files, associational journals, conference proceedings, and published contemporary material from several Alpine countries, it seeks to determine how and why Europeans modified the Alpine landscape to generate hydropower, and to explore the consequences of these decisions. I argue that during this time period, Europeans thoroughly transformed the Alpine environment, creating what I call "Europe's Battery": a gigantic system for storing hydropower and distributing it on a continental scale. This study shows how nineteenth-century innovations in energy technology contributed to a dramatic shift in the perception of the Alps as a landscape of "white coal." It demonstrates how at the outset of electrification, Europeans modified Alpine waterways on an unprecedented scale in order to tap into the power of flowing Alpine water. I show how after the turn of the twentieth century, Europeans took advantage of the unique mountain environment to store water, first by converting existing lakes into reservoirs. The practice countered what was perceived to be the greatest disadvantage of white coal: its climate-influenced inconstancy. This study shows the importance of war, and especially the First World War, in the forging of the new Alpine landscape. Finally, this study illustrates how from the interwar period to the aftermath of the Second World War, Europeans put the finishing touches on the new Alpine energy landscape by creating large reservoirs behind dams and feeding Alpine hydroelectricity into a burgeoning European electricity grid. By 1955 the Alps had become one of the most important energy landscapes in Europe. This history of the Alpine energy landscape contributes to a number of historiographical fields. It represents an important chapter in the environmental history of one of the world's most

  20. Ensemble-based characterization of unbound and bound states on protein energy landscape

    PubMed Central

    Ruvinsky, Anatoly M; Kirys, Tatsiana; Tuzikov, Alexander V; Vakser, Ilya A

    2013-01-01

    Physicochemical description of numerous cell processes is fundamentally based on the energy landscapes of protein molecules involved. Although the whole energy landscape is difficult to reconstruct, increased attention to particular targets has provided enough structures for mapping functionally important subspaces associated with the unbound and bound protein structures. The subspace mapping produces a discrete representation of the landscape, further called energy spectrum. We compiled and characterized ensembles of bound and unbound conformations of six small proteins and explored their spectra in implicit solvent. First, the analysis of the unbound-to-bound changes points to conformational selection as the binding mechanism for four proteins. Second, results show that bound and unbound spectra often significantly overlap. Moreover, the larger the overlap the smaller the root mean square deviation (RMSD) between the bound and unbound conformational ensembles. Third, the center of the unbound spectrum has a higher energy than the center of the corresponding bound spectrum of the dimeric and multimeric states for most of the proteins. This suggests that the unbound states often have larger entropy than the bound states. Fourth, the exhaustively long minimization, making small intrarotamer adjustments (all-atom RMSD ≤ 0.7 Å), dramatically reduces the distance between the centers of the bound and unbound spectra as well as the spectra extent. It condenses unbound and bound energy levels into a thin layer at the bottom of the energy landscape with the energy spacing that varies between 0.8–4.6 and 3.5–10.5 kcal/mol for the unbound and bound states correspondingly. Finally, the analysis of protein energy fluctuations showed that protein vibrations itself can excite the interstate transitions, including the unbound-to-bound ones. PMID:23526684

  1. Distributions of experimental protein structures on coarse-grained free energy landscapes

    NASA Astrophysics Data System (ADS)

    Sankar, Kannan; Liu, Jie; Wang, Yuan; Jernigan, Robert L.

    2015-12-01

    Predicting conformational changes of proteins is needed in order to fully comprehend functional mechanisms. With the large number of available structures in sets of related proteins, it is now possible to directly visualize the clusters of conformations and their conformational transitions through the use of principal component analysis. The most striking observation about the distributions of the structures along the principal components is their highly non-uniform distributions. In this work, we use principal component analysis of experimental structures of 50 diverse proteins to extract the most important directions of their motions, sample structures along these directions, and estimate their free energy landscapes by combining knowledge-based potentials and entropy computed from elastic network models. When these resulting motions are visualized upon their coarse-grained free energy landscapes, the basis for conformational pathways becomes readily apparent. Using three well-studied proteins, T4 lysozyme, serum albumin, and sarco-endoplasmic reticular Ca2+ adenosine triphosphatase (SERCA), as examples, we show that such free energy landscapes of conformational changes provide meaningful insights into the functional dynamics and suggest transition pathways between different conformational states. As a further example, we also show that Monte Carlo simulations on the coarse-grained landscape of HIV-1 protease can directly yield pathways for force-driven conformational changes.

  2. Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape

    PubMed Central

    Schuepbach, Thierry; Bovigny, Christophe; Chaskar, Prasad; Daina, Antoine; Röhrig, Ute F.

    2015-01-01

    Molecular docking is a computational approach for predicting the most probable position of ligands in the binding sites of macromolecules and constitutes the cornerstone of structure‐based computer‐aided drug design. Here, we present a new algorithm called Attracting Cavities that allows molecular docking to be performed by simple energy minimizations only. The approach consists in transiently replacing the rough potential energy hypersurface of the protein by a smooth attracting potential driving the ligands into protein cavities. The actual protein energy landscape is reintroduced in a second step to refine the ligand position. The scoring function of Attracting Cavities is based on the CHARMM force field and the FACTS solvation model. The approach was tested on the 85 experimental ligand–protein structures included in the Astex diverse set and achieved a success rate of 80% in reproducing the experimental binding mode starting from a completely randomized ligand conformer. The algorithm thus compares favorably with current state‐of‐the‐art docking programs. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26558715

  3. Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape.

    PubMed

    Zoete, Vincent; Schuepbach, Thierry; Bovigny, Christophe; Chaskar, Prasad; Daina, Antoine; Röhrig, Ute F; Michielin, Olivier

    2016-02-05

    Molecular docking is a computational approach for predicting the most probable position of ligands in the binding sites of macromolecules and constitutes the cornerstone of structure-based computer-aided drug design. Here, we present a new algorithm called Attracting Cavities that allows molecular docking to be performed by simple energy minimizations only. The approach consists in transiently replacing the rough potential energy hypersurface of the protein by a smooth attracting potential driving the ligands into protein cavities. The actual protein energy landscape is reintroduced in a second step to refine the ligand position. The scoring function of Attracting Cavities is based on the CHARMM force field and the FACTS solvation model. The approach was tested on the 85 experimental ligand-protein structures included in the Astex diverse set and achieved a success rate of 80% in reproducing the experimental binding mode starting from a completely randomized ligand conformer. The algorithm thus compares favorably with current state-of-the-art docking programs. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  4. Point Mutations in Membrane Proteins Reshape Energy Landscape and Populate Different Unfolding Pathways

    PubMed Central

    Sapra, K. Tanuj; Balasubramanian, G. Prakash; Labudde, Dirk; Bowie, James U.; Muller, Daniel J.

    2009-01-01

    Using single-molecule force spectroscopy, we investigated the effect of single point mutations on the energy landscape and unfolding pathways of the transmembrane protein bacteriorhodopsin. We show that the unfolding energy barriers in the energy landscape of the membrane protein followed a simple two-state behavior and represent a manifestation of many converging unfolding pathways. Although the unfolding pathways of wild-type and mutant bacteriorhodopsin did not change, indicating the presence of same ensemble of structural unfolding intermediates, the free energies of the rate-limiting transition states of the bacteriorhodopsin mutants decreased as the distance of those transition states to the folded intermediate states decreased. Thus, all mutants exhibited Hammond behavior and a change in the free energies of the intermediates along the unfolding reaction coordinate and, consequently, their relative occupancies. This is the first experimental proof showing that point mutations can reshape the free energy landscape of a membrane protein and force single proteins to populate certain unfolding pathways over others. PMID:18191146

  5. Point mutations in membrane proteins reshape energy landscape and populate different unfolding pathways.

    PubMed

    Sapra, K Tanuj; Balasubramanian, G Prakash; Labudde, Dirk; Bowie, James U; Muller, Daniel J

    2008-02-29

    Using single-molecule force spectroscopy, we investigated the effect of single point mutations on the energy landscape and unfolding pathways of the transmembrane protein bacteriorhodopsin. We show that the unfolding energy barriers in the energy landscape of the membrane protein followed a simple two-state behavior and represent a manifestation of many converging unfolding pathways. Although the unfolding pathways of wild-type and mutant bacteriorhodopsin did not change, indicating the presence of same ensemble of structural unfolding intermediates, the free energies of the rate-limiting transition states of the bacteriorhodopsin mutants decreased as the distance of those transition states to the folded intermediate states decreased. Thus, all mutants exhibited Hammond behavior and a change in the free energies of the intermediates along the unfolding reaction coordinate and, consequently, their relative occupancies. This is the first experimental proof showing that point mutations can reshape the free energy landscape of a membrane protein and force single proteins to populate certain unfolding pathways over others.

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

    PubMed

    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.

  7. The potential energy landscape for crystallisation of a Lennard-Jones fluid

    NASA Astrophysics Data System (ADS)

    de Souza, Vanessa K.; Wales, David J.

    2016-07-01

    Crystallisation pathways are explored by direct analysis of the potential energy landscape for a system of Lennard-Jones particles with periodic boundary conditions. A database of minima and transition states linking liquid and crystalline states is constructed using discrete path sampling and the entire potential energy landscape from liquid to crystal is visualised. We demonstrate that there is a strong negative correlation between the number of atoms in the largest crystalline cluster and the potential energy. In common with previous results we find a strong bias towards the growth of FCC rather than HCP clusters, despite a very small potential energy difference. We characterise three types of perfect crystals with very similar energies: pure FCC, pure HCP, and combinations of FCC and HCP layers. There are also many slightly defective crystalline structures. The effect of the simulation box is analysed for a supercell containing 864 atoms. There are low barriers between some of the different crystalline structures via pathways involving sliding layers, and many different defective structures with FCC layers stacked at an angle to the periodic box. Finally, we compare a binary Lennard-Jones system and visualise the potential energy landscape from supercooled liquid to crystal.

  8. Intrinsic potential for immediate biodegradation of toluene in a pristine, energy-limited aquifer.

    PubMed

    Herzyk, Agnieszka; Maloszewski, Piotr; Qiu, Shiran; Elsner, Martin; Griebler, Christian

    2014-06-01

    Pristine and energy-limited aquifers are considered to have a low resistance and resilience towards organic pollution. An experiment in an indoor aquifer system revealed an unexpected high intrinsic potential for the attenuation of a short-term toluene contamination. A 30 h pulse of 486 mg of toluene, used as a model contaminant, and deuterated water (D2O) through an initially pristine, oxic, and organic carbon poor sandy aquifer revealed an immediate aerobic toluene degradation potential. Based on contaminant and tracer break-through curves, as well as mass balance analyses and reactive transport modelling, a contaminant removal of 40 % over a transport distance of only 4.2 m in less than one week of travel time was obtained. The mean first-order degradation rate constant was λ = 0.178 day(-1), corresponding to a half-life time constant T1/2 of 3.87 days. Toluene-specific stable carbon isotope analysis independently proved that the contaminant mass removal can be attributed to microbial biodegradation. Since average doubling times of indigenous bacterial communities were in the range of months to years, the aerobic biodegradation potential observed is assumed to be present and active in the pristine, energy-limited groundwater ecosystems at any time. Follow-up experiments and field studies will help to quantify the immediate natural attenuation potential of aquifers for selected priority contaminants and will try to identify the key-degraders within the autochthonous microbial communities.

  9. Minimal cooling speed for glass transition in a simple solvable energy landscape model

    NASA Astrophysics Data System (ADS)

    Toledo-Marín, J. Quetzalcóatl; Castillo, Isaac Pérez; Naumis, Gerardo G.

    2016-06-01

    The minimal cooling speed required to form a glass is obtained for a simple solvable energy landscape model. The model, made from a two-level system modified to include the topology of the energy landscape, is able to capture either a glass transition or a crystallization depending on the cooling rate. In this setup, the minimal cooling speed to achieve glass formation is then found to be related with the crystallization relaxation time, energy barrier and with the thermal history. In particular, we obtain that the thermal history encodes small fluctuations around the equilibrium population which are exponentially amplified near the glass transition, which mathematically corresponds to the boundary layer of the master equation. The change in the glass transition temperature is also found as a function of the cooling rate. Finally, to verify our analytical results, a kinetic Monte Carlo simulation was implemented.

  10. Atomic bond fluctuations and crossover to potential-energy-landscape-influenced regime in supercooled liquid.

    PubMed

    Levashov, V A; Egami, T; Aga, R S; Morris, J R

    2008-10-01

    The ideas related to potential-energy landscape and cooperativity of atomic rearrangements are widely discussed in the research field of glass transition. The crossover transition from high-temperature regime to potential-energy-landscape-influenced regime was extensively studied using the concept of inherent structure. However, the interpretation of this crossover behavior in terms of microscopic changes in real structures is still lacking. In this paper we present several observations on the crossover behavior on real structures. We compare fluctuations in the global properties (total number of bonds, total potential energy, pressure) versus fluctuations in the local properties (coordination number, atomic potential energy, local atomic pressure) by means of molecular dynamics simulations. We then show that the total and local fluctuations in the number of atomic bonds in the system depend on temperature differently above and below the temperature of crossover to the landscape-influenced regime. Similarly, the ratio between the global and local fluctuations in the potential energy and pressure changes in the vicinity of the crossover temperature, whereas the change is less distinct than in the case of the bond fluctuations. Our results indicate that local fluctuations become more correlated below the crossover temperature, most likely via the interaction through the dynamic shear elastic field.

  11. Low energy supersymmetry from the heterotic string landscape.

    PubMed

    Lebedev, Oleg; Nilles, Hans-Peter; Raby, Stuart; Ramos-Sánchez, Saúl; Ratz, Michael; Vaudrevange, Patrick K S; Wingerter, Akin

    2007-05-04

    We study possible correlations between properties of the observable and hidden sectors in heterotic string theory. Specifically, we analyze the case of the Z6-II orbifold compactification which produces a significant number of models with the spectrum of the supersymmetric standard model. We find that requiring realistic features does affect the hidden sector such that hidden sector gauge group factors SU(4) and SO(8) are favored. In the context of gaugino condensation, this implies low energy supersymmetry breaking.

  12. The histone H3 N-terminal tail: a computational analysis of the free energy landscape and kinetics.

    PubMed

    Zheng, Yuqing; Cui, Qiang

    2015-05-28

    Histone tails are the short peptide protrusions outside of the nucleosome core particle and they play a critical role in regulating chromatin dynamics and gene activity. A histone H3 N-terminal tail, like other histone tails, can be covalently modified on different residues to activate or repress gene expression. Previous studies have indicated that, despite its intrinsically disordered nature, the histone H3 N-terminal tail has regions of notable secondary structural propensities. To further understand the structure-dynamics-function relationship in this system, we have carried out 75.6 μs long implicit solvent simulations and 29.3 μs long explicit solvent simulations. The extensive samplings allow us to better characterize not only the underlying free energy landscape but also kinetic properties through Markov state models (MSM). Dihedral principal component analysis (dPCA) and locally scaled diffusion map (LSDMap) analysis yield consistent results that indicate an overall flat free energy surface with several shallow basins that correspond to conformations with a high α-helical propensity in two regions of the peptide. Kinetic information extracted from Markov state models reveals rapid transitions between different metastable states with mean first passage times spanning from several hundreds of nanoseconds to hundreds of microseconds. These findings shed light on how the dynamical nature of the histone H3 N-terminal tail is related to its function. The complementary nature of dPCA, LSDMap and MSM for the analysis of biomolecules is also discussed.

  13. Denatured-state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding.

    PubMed

    Wang, Suwei; Gu, Jenny; Larson, Scott A; Whitten, Steven T; Hilser, Vincent J

    2008-09-19

    Position-specific denatured-state thermodynamics were determined for a database of human proteins by use of an ensemble-based model of protein structure. The results of modeling denatured protein in this manner reveal important sequence-dependent thermodynamic properties in the denatured ensembles as well as fundamental differences between the denatured and native ensembles in overall thermodynamic character. The generality and robustness of these results were validated by performing fold-recognition experiments, whereby sequences were matched with their respective folds based on amino acid propensities for the different energetic environments in the protein, as determined through cluster analysis. Correlation analysis between structure and energetic information revealed that sequence segments destined for beta-sheet in the final native fold are energetically more predisposed to a broader repertoire of states than are sequence segments destined for alpha-helix. These results suggest that within the subensemble of mostly unstructured states, the energy landscapes are dominated by states in which parts of helices adopt structure, whereas structure formation for sequences destined for beta-strand is far less probable. These results support a framework model of folding, which suggests that, in general, the denatured state has evolutionarily evolved to avoid low-energy conformations in sequences that ultimately adopt beta-strand. Instead, the denatured state evolved so that sequence segments that ultimately adopt alpha-helix and coil will have a high intrinsic structure formation capability, thus serving as potential nucleation sites.

  14. Modeling energy fluxes in heterogeneous landscapes employing a mosaic approach

    NASA Astrophysics Data System (ADS)

    Klein, Christian; Thieme, Christoph; Priesack, Eckart

    2015-04-01

    Recent studies show that uncertainties in regional and global climate and weather simulations are partly due to inadequate descriptions of the energy flux exchanges between the land surface and the atmosphere. One major shortcoming is the limitation of the grid-cell resolution, which is recommended to be about at least 3x3 km² in most models due to limitations in the model physics. To represent each individual grid cell most models select one dominant soil type and one dominant land use type. This resolution, however, is often too coarse in regions where the spatial diversity of soil and land use types are high, e.g. in Central Europe. An elegant method to avoid the shortcoming of grid cell resolution is the so called mosaic approach. This approach is part of the recently developed ecosystem model framework Expert-N 5.0. The aim of this study was to analyze the impact of the characteristics of two managed fields, planted with winter wheat and potato, on the near surface soil moistures and on the near surface energy flux exchanges of the soil-plant-atmosphere interface. The simulated energy fluxes were compared with eddy flux tower measurements between the respective fields at the research farm Scheyern, North-West of Munich, Germany. To perform these simulations, we coupled the ecosystem model Expert-N 5.0 to an analytical footprint model. The coupled model system has the ability to calculate the mixing ratio of the surface energy fluxes at a given point within one grid cell (in this case at the flux tower between the two fields). This approach accounts for the differences of the two soil types, of land use managements, and of canopy properties due to footprint size dynamics. Our preliminary simulation results show that a mosaic approach can improve modeling and analyzing energy fluxes when the land surface is heterogeneous. In this case our applied method is a promising approach to extend weather and climate models on the regional and on the global scale.

  15. Configurational Diffusion on a Locally Connected Correlated Energy Landscape; Application to Finite, Random Heteropolymers

    NASA Astrophysics Data System (ADS)

    Wang, Jin; Plotkin, Steven S.; Wolynes, Peter G.

    1997-03-01

    We study the time scale for diffusion on a correlated energy landscape using models based on the generalized random energy model (GREM) studied earlier in the context of spin glasses (Derrida B. and Gardner E., J. Phys. C 19 (1986) 2253) with kinetically local connections. The escape barrier and mean escape time are significantly reduced from the uncorrelated landscape (REM) values. Results for the mean escape time from a kinetic trap are obtained for two models approximating random heteropolymers in different regimes, with linear and bi-linear approximations to the configurational entropy versus similarity q with a given state. In both cases, a correlated landscape results in a shorter escape time from a meta-stable state than in the uncorrelated model (Bryngelson J.D. and Wolynes P.G., J. Phys. Chem 93 (1989) 6902). Results are compared to simulations of the diffusion constant for 27-mers. In general there is a second transition temperature above the thermodynamic glass temperature, at and above which kinetics becomes non-activated. In the special case of an entropy linear in q, there is no escape barrier for a model preserving ultrametricity. However, in real heteropolymers a barrier can result from the breaking of ultrametricity, as seen in our non-ultrametric model. The distribution of escape times for a model preserving microscopic ultrametricity is also obtained, and found to reduce to the uncorrelated landscape in well-defined limits.

  16. Protein folding trajectories can be described quantitatively by one-dimensional diffusion over measured energy landscapes

    NASA Astrophysics Data System (ADS)

    Neupane, Krishna; Manuel, Ajay P.; Woodside, Michael T.

    2016-07-01

    Protein folding features a diffusive search over a multidimensional energy landscape in conformational space for the minimum-energy structure. Experiments, however, are usually interpreted in terms of a one-dimensional (1D) projection of the full landscape onto a practical reaction coordinate. Although simulations have shown that folding kinetics can be described well by diffusion over a 1D projection, 1D approximations have not yet been fully validated experimentally. We used folding trajectories of single molecules held under tension in optical tweezers to compare the conditional probability of being on a transition path, calculated from the trajectory, with the prediction for ideal 1D diffusion over the measured 1D landscape, calculated from committor statistics. We found good agreement for the protein PrP (refs ,) and for one of the structural transitions in a leucine-zipper coiled-coil, but not for a second transition in the coiled-coil, owing to poor reaction-coordinate quality. These results show that 1D descriptions of folding can indeed be good, even for complex tertiary structures. More fundamentally, they also provide a fully experimental validation of the basic physical picture of folding as diffusion over a landscape.

  17. Potential energy landscapes identify the information-theoretic nature of the epigenome.

    PubMed

    Jenkinson, Garrett; Pujadas, Elisabet; Goutsias, John; Feinberg, Andrew P

    2017-03-27

    Epigenetics is the study of biochemical modifications carrying information independent of DNA sequence, which are heritable through cell division. In 1940, Waddington coined the term "epigenetic landscape" as a metaphor for pluripotency and differentiation, but methylation landscapes have not yet been rigorously computed. Using principles from statistical physics and information theory, we derive epigenetic energy landscapes from whole-genome bisulfite sequencing (WGBS) data that enable us to quantify methylation stochasticity genome-wide using Shannon's entropy, associating it with chromatin structure. Moreover, we consider the Jensen-Shannon distance between sample-specific energy landscapes as a measure of epigenetic dissimilarity and demonstrate its effectiveness for discerning epigenetic differences. By viewing methylation maintenance as a communications system, we introduce methylation channels and show that higher-order chromatin organization can be predicted from their informational properties. Our results provide a fundamental understanding of the information-theoretic nature of the epigenome that leads to a powerful approach for studying its role in disease and aging.

  18. Energy landscapes for water clusters in a uniform electric field

    NASA Astrophysics Data System (ADS)

    James, Tim; Wales, David J.; Hernández Rojas, Javier

    2007-02-01

    The behavior of small water clusters, (H2O)n, n =2-5 and n =8, in a uniform electric field is investigated for three related rigid-body models. Changes in the properties of the low-lying potential energy minima and the rearrangement pathways between them are examined. Results for certain structural transitions are compared with recent ab initio calculations. The models are found to give qualitatively similar trends, and there is some evidence that as the applied field strength is increased the quantitative differences between the models are also reduced.

  19. Graphene, a material for high temperature devices – intrinsic carrier density, carrier drift velocity, and lattice energy

    PubMed Central

    Yin, Yan; Cheng, Zengguang; Wang, Li; Jin, Kuijuan; Wang, Wenzhong

    2014-01-01

    Heat has always been a killing matter for traditional semiconductor machines. The underlining physical reason is that the intrinsic carrier density of a device made from a traditional semiconductor material increases very fast with a rising temperature. Once reaching a temperature, the density surpasses the chemical doping or gating effect, any p-n junction or transistor made from the semiconductor will fail to function. Here, we measure the intrinsic Fermi level (|EF| = 2.93 kBT) or intrinsic carrier density (nin = 3.87 × 106 cm−2K−2·T2), carrier drift velocity, and G mode phonon energy of graphene devices and their temperature dependencies up to 2400 K. Our results show intrinsic carrier density of graphene is an order of magnitude less sensitive to temperature than those of Si or Ge, and reveal the great potentials of graphene as a material for high temperature devices. We also observe a linear decline of saturation drift velocity with increasing temperature, and identify the temperature coefficients of the intrinsic G mode phonon energy. Above knowledge is vital in understanding the physical phenomena of graphene under high power or high temperature. PMID:25044003

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

    PubMed

    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.

  1. Exploring the aggregation free energy landscape of the amyloid-β protein (1-40).

    PubMed

    Zheng, Weihua; Tsai, Min-Yeh; Chen, Mingchen; Wolynes, Peter G

    2016-10-18

    A predictive coarse-grained protein force field [associative memory, water-mediated, structure, and energy model for molecular dynamics (AWSEM)-MD] is used to study the energy landscapes and relative stabilities of amyloid-β protein (1-40) in the monomer and all of its oligomeric forms up to an octamer. We find that an isolated monomer is mainly disordered with a short α-helix formed at the central hydrophobic core region (L17-D23). A less stable hairpin structure, however, becomes increasingly more stable in oligomers, where hydrogen bonds can form between neighboring monomers. We explore the structure and stability of both prefibrillar oligomers that consist of mainly antiparallel β-sheets and fibrillar oligomers with only parallel β-sheets. Prefibrillar oligomers are polymorphic but typically take on a cylindrin-like shape composed of mostly antiparallel β-strands. At the concentration of the simulation, the aggregation free energy landscape is nearly downhill. We use umbrella sampling along a structural progress coordinate for interconversion between prefibrillar and fibrillar forms to identify a conversion pathway between these forms. The fibrillar oligomer only becomes favored over its prefibrillar counterpart in the pentamer where an interconversion bottleneck appears. The structural characterization of the pathway along with statistical mechanical perturbation theory allow us to evaluate the effects of concentration on the free energy landscape of aggregation as well as the effects of the Dutch and Arctic mutations associated with early onset of Alzheimer's disease.

  2. Towards a microscopic description of the free-energy landscape of water

    NASA Astrophysics Data System (ADS)

    Prada-Gracia, Diego; Shevchuk, Roman; Hamm, Peter; Rao, Francesco

    2012-10-01

    Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005 model is applied to investigate the free-energy landscape of water. The latter is built on top of a large set of water microstates describing the kinetic stability of local hydrogen-bond arrangements up to the second solvation shell. In temperature space, the landscape displays three different regimes. At around ambient conditions, the free-energy surface is characterized by many short-lived basins of attraction which are structurally well-defined (inhomogeneous regime). At lower temperatures instead, the liquid rapidly becomes homogeneous. In this regime, the free energy is funneled-like, with fully coordinated water arrangements at the bottom of the funnel. Finally, a third regime develops below the temperature of maximal compressibility (Widom line) where the funnel becomes steeper with few interconversions between microstates other than the fully coordinated ones. Our results present a way to manage the complexity of water structure and dynamics, connecting microscopic properties to its ensemble behavior.

  3. Towards a microscopic description of the free-energy landscape of water.

    PubMed

    Prada-Gracia, Diego; Shevchuk, Roman; Hamm, Peter; Rao, Francesco

    2012-10-14

    Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005 model is applied to investigate the free-energy landscape of water. The latter is built on top of a large set of water microstates describing the kinetic stability of local hydrogen-bond arrangements up to the second solvation shell. In temperature space, the landscape displays three different regimes. At around ambient conditions, the free-energy surface is characterized by many short-lived basins of attraction which are structurally well-defined (inhomogeneous regime). At lower temperatures instead, the liquid rapidly becomes homogeneous. In this regime, the free energy is funneled-like, with fully coordinated water arrangements at the bottom of the funnel. Finally, a third regime develops below the temperature of maximal compressibility (Widom line) where the funnel becomes steeper with few interconversions between microstates other than the fully coordinated ones. Our results present a way to manage the complexity of water structure and dynamics, connecting microscopic properties to its ensemble behavior.

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

    PubMed

    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.

  5. Autonomous oscillation in supramolecular assemblies: Role of free energy landscape and fluctuations

    NASA Astrophysics Data System (ADS)

    Sereda, Yuriy V.; Ortoleva, Peter J.

    2015-11-01

    Molecular dynamics studies demonstrated that a supramolecular assembly can express autonomous structural oscillations about equilibrium. It is demonstrated here that for nanosystems such oscillations can result from the interplay of free energy landscape and structural fluctuations. Furthermore, these oscillations have intermittent character, reflecting the conflict between a tendency to oscillate due to features in the free energy landscape, and the Second Law's repression of perpetual oscillation in an isothermal, equilibrium system. The demonstration system is a T = 1 icosahedral structure constituted of 12 protein pentamers in contact with a bath at fixed temperature. The oscillations are explained in terms of a Langevin model accounting for interactions among neighboring pentamers. The model is based on a postulated free energy landscape in the 24-dimensional space of variables describing the centrifugal and rotational motion of each pentamer. The model includes features such as basins of attraction and low free energy corridors. When the system is driven slightly out of equilibrium, the oscillations are transformed into a limit cycle, as expressed in terms of power spectrum narrowing.

  6. Multifractality and freezing phenomena in random energy landscapes: An introduction

    NASA Astrophysics Data System (ADS)

    Fyodorov, Yan V.

    2010-10-01

    We start our lectures with introducing and discussing the general notion of multifractality spectrum for random measures on lattices, and how it can be probed using moments of that measure. Then we show that the Boltzmann-Gibbs probability distributions generated by logarithmically correlated random potentials provide a simple yet non-trivial example of disorder-induced multifractal measures. The typical values of the multifractality exponents can be extracted from calculating the free energy of the associated Statistical Mechanics problem. To succeed in such a calculation we introduce and discuss in some detail two analytically tractable models for logarithmically correlated potentials. The first model uses a special definition of distances between points in space and is based on the idea of multiplicative cascades which originated in theory of turbulent motion. It is essentially equivalent to statistical mechanics of directed polymers on disordered trees studied long ago by Derrida and Spohn (1988) in Ref. [12]. In this way we introduce the notion of the freezing transition which is identified with an abrupt change in the multifractality spectrum. Second model which allows for explicit analytical evaluation of the free energy is the infinite-dimensional version of the problem which can be solved by employing the replica trick. In particular, the latter version allows one to identify the freezing phenomenon with a mechanism of the replica symmetry breaking (RSB) and to elucidate its physical meaning. The corresponding one-step RSB solution turns out to be marginally stable everywhere in the low-temperature phase. We finish with a short discussion of recent developments and extensions of models with logarithmic correlations, in particular in the context of extreme value statistics. The first appendix summarizes the standard elementary information about Gaussian integrals and related subjects, and introduces the notion of the Gaussian free field characterized by

  7. Model energy landscapes and the force-induced dissociation of ligand-receptor bonds.

    PubMed

    Strunz, T; Oroszlan, K; Schumakovitch, I; Güntherodt, H; Hegner, M

    2000-09-01

    We discuss models for the force-induced dissociation of a ligand-receptor bond, occurring in the context of cell adhesion or single molecule unbinding force measurements. We consider a bond with a structured energy landscape which is modeled by a network of force dependent transition rates between intermediate states. The behavior of a model with only one intermediate state and a model describing a molecular zipper is studied. We calculate the bond lifetime as a function of an applied force and unbinding forces under an increasing applied load and determine the relationship between both quantities. The dissociation via an intermediate state can lead to distinct functional relations of the bond lifetime on force. One possibility is the occurrence of three force regimes where the lifetime of the bond is determined by different transitions within the energy landscape. This case can be related to recent experimental observations of the force-induced dissociation of single avidin-biotin bonds.

  8. Model energy landscapes and the force-induced dissociation of ligand-receptor bonds.

    PubMed Central

    Strunz, T; Oroszlan, K; Schumakovitch, I; Güntherodt, H; Hegner, M

    2000-01-01

    We discuss models for the force-induced dissociation of a ligand-receptor bond, occurring in the context of cell adhesion or single molecule unbinding force measurements. We consider a bond with a structured energy landscape which is modeled by a network of force dependent transition rates between intermediate states. The behavior of a model with only one intermediate state and a model describing a molecular zipper is studied. We calculate the bond lifetime as a function of an applied force and unbinding forces under an increasing applied load and determine the relationship between both quantities. The dissociation via an intermediate state can lead to distinct functional relations of the bond lifetime on force. One possibility is the occurrence of three force regimes where the lifetime of the bond is determined by different transitions within the energy landscape. This case can be related to recent experimental observations of the force-induced dissociation of single avidin-biotin bonds. PMID:10968985

  9. Real-time control of the energy landscape by force directs the folding of RNA molecules

    PubMed Central

    Li, Pan T. X.; Bustamante, Carlos; Tinoco, Ignacio

    2007-01-01

    The rugged folding-energy landscapes of RNAs often display many competing minima. How do RNAs discriminate among competing conformations in their search for the native state? By using optical tweezers, we show that the folding-energy landscape can be manipulated to control the fate of an RNA: individual RNA molecules can be induced into either native or misfolding pathways by modulating the relaxation rate of applied force and even be redirected during the folding process to switch from misfolding to native folding pathways. Controlling folding pathways at the single-molecule level provides a way to survey the manifold of folding trajectories and intermediates, a capability that previously was available only to theoretical studies. PMID:17438300

  10. Global exploration of the energy landscape of solids on the ab initio level.

    PubMed

    Doll, K; Schön, J C; Jansen, M

    2007-12-14

    Predicting which crystalline modifications can be present in a chemical system requires the global exploration of its energy landscape. Due to the large computational effort involved, in the past this search for sufficiently stable minima has been performed employing a variety of empirical potentials and cost functions followed by a local optimization on the ab initio level. However, this entails the risk of overlooking important modifications that are not modeled accurately using empirical potentials. In order to overcome this critical limitation, we develop an approach to employ ab initio energy functions during the global optimization phase of the structure prediction. As an example, we perform a global exploration of the landscape of LiF on the ab initio level and show that the relevant crystalline modifications are found during the search.

  11. Unsupervised machine learning on atomistic configurations: examples on amorphous defects and energy landscapes

    NASA Astrophysics Data System (ADS)

    Cubuk, Ekin; Schoenholz, Samuel; Liu, Andrea; Kaxiras, Efthimios

    2015-03-01

    Due to the recent availability of very large datasets, machine learning (ML) methods are gaining popularity as approximation and optimization tools in solid state physics. We have recently shown that supervised ML can also be used to identify and analyze soft particles, particles susceptible to rearrangement, in amorphous solids. Our method can be used to understand what makes certain configurations of particles more prone to rearrangement, and design stronger materials. We use unsupervised ML and nonlinear dimensionality reduction methods, where we do not need a ``training set'' to train the algorithm, to explore better representations of atomic configurations. These representations are shown to provide important physical insights into the structure of soft spots and stable regions in several computational and experimental glassy systems, as well as the energy landscapes of quantum mechanical systems based on Density Functional Theory calculations. By discovering an improved representation and visualization of relevant energy landscapes, discovery and optimization efforts can be simplified.

  12. The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family.

    PubMed

    Ferreiro, Diego U; Cho, Samuel S; Komives, Elizabeth A; Wolynes, Peter G

    2005-12-02

    Proteins consisting of repeating amino acid motifs are abundant in all kingdoms of life, especially in higher eukaryotes. Repeat-containing proteins self-organize into elongated non-globular structures. Do the same general underlying principles that dictate the folding of globular domains apply also to these extended topologies? Using a simplified structure-based model capturing a perfectly funneled energy landscape, we surveyed the predicted mechanism of folding for ankyrin repeat containing proteins. The ankyrin family is one of the most extensively studied classes of non-globular folds. The model based only on native contacts reproduces most of the experimental observations on the folding of these proteins, including a folding mechanism that is reminiscent of a nucleation propagation growth. The confluence of simulation and experimental results suggests that the folding of non-globular proteins is accurately described by a funneled energy landscape, in which topology plays a determinant role in the folding mechanism.

  13. The potential of computed crystal energy landscapes to aid solid-form development.

    PubMed

    Price, Sarah L; Reutzel-Edens, Susan M

    2016-06-01

    Solid-form screening to identify all solid forms of an active pharmaceutical ingredient (API) has become increasingly important in ensuring the quality by design of pharmaceutical products and their manufacturing processes. However, despite considerable enlargement of the range of techniques that have been shown capable of producing novel solid forms, it is possible that practically important forms might not be found in the short timescales currently allowed for solid-form screening. Here, we report on the state-of-the-art use of computed crystal energy landscapes to complement pharmaceutical solid-form screening. We illustrate how crystal energy landscapes can help establish molecular-level understanding of the crystallization behavior of APIs and enhance the ability of solid-form screening to facilitate pharmaceutical development.

  14. Evolving landscape of low-energy nuclear physics publications

    SciTech Connect

    Pritychenko, B.

    2016-10-01

    Evolution of low-energy nuclear physics publications over the last 120 years has been analyzed using nuclear physics databases. An extensive study of Nuclear Science References, Experimental Nuclear Reaction Data (EXFOR), and Evaluated Nuclear Structure Data File (ENSDF) contents provides a unique picture of refereed and non-refereed nuclear physics references. Significant fractional contributions of non-refereed reports, private communications and conference proceedings in EXFOR and ENSDF databases in the 1970’s reflect extensive experimental campaigns and an insufficient number of research journals. This trend has been reversed in recent years because the number of measurements is much lower, while number of journals is higher. In addition, nuclear physics results are mainly published in a limited number of journals, such as Physical Review C and Nuclear Physics A. In the present work, historic publication trends and averages have been extracted and analyzed using nuclear data mining techniques. Lastly, the results of this study and implications are discussed and conclusions presented.

  15. Evolving landscape of low-energy nuclear physics publications

    SciTech Connect

    Pritychenko, B.

    2016-10-01

    Evolution of low-energy nuclear physics publications over the last 120 years has been analyzed using nuclear physics databases. An extensive study of Nuclear Science References, Experimental Nuclear Reaction Data (EXFOR), and Evaluated Nuclear Structure Data File (ENSDF) contents provides a unique picture of refereed and non-refereed nuclear physics references. Significant fractional contributions of non-refereed reports, private communications and conference proceedings in EXFOR and ENSDF databases in the 1970’s reflect extensive experimental campaigns and an insufficient number of research journals. This trend has been reversed in recent years because the number of measurements is much lower, while number of journals is higher. In addition, nuclear physics results are mainly published in a limited number of journals, such as Physical Review C and Nuclear Physics A. In the present work, historic publication trends and averages have been extracted and analyzed using nuclear data mining techniques. Lastly, the results of this study and implications are discussed and conclusions presented.

  16. Evolving landscape of low-energy nuclear physics publications

    DOE PAGES

    Pritychenko, B.

    2016-10-01

    Evolution of low-energy nuclear physics publications over the last 120 years has been analyzed using nuclear physics databases. An extensive study of Nuclear Science References, Experimental Nuclear Reaction Data (EXFOR), and Evaluated Nuclear Structure Data File (ENSDF) contents provides a unique picture of refereed and non-refereed nuclear physics references. Significant fractional contributions of non-refereed reports, private communications and conference proceedings in EXFOR and ENSDF databases in the 1970’s reflect extensive experimental campaigns and an insufficient number of research journals. This trend has been reversed in recent years because the number of measurements is much lower, while number of journals ismore » higher. In addition, nuclear physics results are mainly published in a limited number of journals, such as Physical Review C and Nuclear Physics A. In the present work, historic publication trends and averages have been extracted and analyzed using nuclear data mining techniques. Lastly, the results of this study and implications are discussed and conclusions presented.« less

  17. Frustration in the energy landscapes of multidomain protein misfolding

    PubMed Central

    Zheng, Weihua; Schafer, Nicholas P.; Wolynes, Peter G.

    2013-01-01

    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. PMID:23319605

  18. Frustration in the energy landscapes of multidomain protein misfolding.

    PubMed

    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.

  19. Autonomously Folding Protein Fragments Reveal Differences in the Energy Landscapes of Homologous RNases H

    PubMed Central

    Rosen, Laura E.; Marqusee, Susan

    2015-01-01

    An important approach to understanding how a protein sequence encodes its energy landscape is to compare proteins with different sequences that fold to the same general native structure. In this work, we compare E. coli and T. thermophilus homologs of the protein RNase H. Using protein fragments, we create equilibrium mimics of two different potential partially-folded intermediates (Icore and Icore+1) hypothesized to be present on the energy landscapes of these two proteins. We observe that both T. thermophilus RNase H (ttRNH) fragments are folded and have distinct stabilities, indicating that both regions are capable of autonomous folding and that both intermediates are present as local minima on the ttRNH energy landscape. In contrast, the two E. coli RNase H (ecRNH) fragments have very similar stabilities, suggesting that the presence of additional residues in the Icore+1 fragment does not affect the folding or structure as compared to Icore. NMR experiments provide additional evidence that only the Icore intermediate is populated by ecRNH. This is one of the biggest differences that has been observed between the energy landscapes of these two proteins. Additionally, we used a FRET experiment in the background of full-length ttRNH to specifically monitor the formation of the Icore+1 intermediate. We determine that the ttRNH Icore+1 intermediate is likely the intermediate populated prior to the rate-limiting barrier to global folding, in contrast to E. coli RNase H for which Icore is the folding intermediate. This result provides new insight into the nature of the rate-limiting barrier for the folding of RNase H. PMID:25803034

  20. Atom-Scale Reaction Pathways and Free-Energy Landscapes in Oxygen Plasma Etching of Graphene.

    PubMed

    Koizumi, Kenichi; Boero, Mauro; Shigeta, Yasuteru; Oshiyama, Atsushi

    2013-05-16

    We report first-principles molecular dynamics calculations combined with rare events sampling techniques that clarify atom-scale mechanisms of oxygen plasma etching of graphene. The obtained reaction pathways and associated free-energy landscapes show that the etching proceeds near vacancies via a two-step mechanism, formation of precursor lactone structures and the subsequent exclusive CO2 desorption. We find that atomic oxygen among the plasma components is most efficient for etching, providing a guidline in tuning the plasma conditions.

  1. Shock compression of organic polymers and proteins: Ultrafast structural relaxation dynamics and energy landscapes

    SciTech Connect

    Kim, H.; Hambir, S.A.; Dlott, D.D.

    2000-05-04

    The response of organic polymers and proteins including poly(methyl methacrylate) and the protein bovine serum albumin (BSA) to a short duration 4.5 GPa shock pulse, termed a nanoshock, is studied using ultrafast coherent Raman spectroscopy (CARS) to monitor density-dependent vibrational frequency shifts of a dye molecule probe. In conventional shock compression experiments, a two-part response of PMMA to fast compression is usually explained with a phenomenological viscoelastic model. The molecular basis for this two-part response is discussed here using an energy landscape model to describe large-amplitude structural relaxation of shocked supercooled liquids. The polymers and the protein show an instantaneous response to the steeply rising shock front, viewed as a vertical transition to a new region of the energy landscape with radically different topography. A slower {approximately}300 ps response is also observed, attributed to large-amplitude structural relaxation along the rugged shocked energy landscape. A viscoelastic model is used to determine an effective shock viscosity {eta} {approx} 3 Pa{center_dot}s for the solid samples. This extremely small value (compared to {eta} > 10{sup 12} Pa{center_dot}s expected for supercooled liquids) is explained as a result of the very large strain rate and the extensive plastic deformation, which causes even seemingly rigid solids to flow. After the short duration ({approximately}2 ns) nanoshock unloads and the samples become frozen, for at least tens of nanoseconds, in a state where the dye vibrational shift indicates a negative pressure of about {minus}1 GPa. The negative pressure means the local density near the dye has decreased, the sample has become more permeable, and the sample is unstable to spontaneous expansion of the polymer chains. The energy landscape model provides a framework for understanding the fast cycle of compression and expansion and how to optimize the generation and detection of large

  2. Smoothing Protein Energy Landscapes by Integrating Folding Models with Structure Prediction

    PubMed Central

    Pritchard-Bell, Ari; Shell, M. Scott

    2011-01-01

    Decades of work has investigated the energy landscapes of simple protein models, but what do the landscapes of real, large, atomically detailed proteins look like? We explore an approach to this problem that systematically extracts simple funnel models of actual proteins using ensembles of structure predictions and physics-based atomic force fields and sampling. Central to our effort are calculations of a quantity called the relative entropy, which quantifies the extent to which a given set of structure decoys and a putative native structure can be projected onto a theoretical funnel description. We examine 86 structure prediction targets and one coupled folding-binding system, and find that in a majority of cases the relative entropy robustly signals which structures are nearest to native (i.e., which appear to lie closest to a funnel bottom). Importantly, the landscape model improves substantially upon purely energetic measures in scoring decoys. Our results suggest that physics-based models—including both folding theories and all-atom force fields—may be successfully integrated with structure prediction efforts. Conversely, detailed predictions of structures and the relative entropy approach enable one to extract coarse topographic features of protein landscapes that may enhance the development and application of simpler folding models. PMID:22067165

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

    PubMed

    Wilson, Rory P; Richards, Rebecca; Hartnell, Angharad; King, Andrew J; Piasecka, Justyna; Gaihre, Yogendra K; Butt, Tariq

    2014-01-01

    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.

  4. A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation

    NASA Astrophysics Data System (ADS)

    Limozin, Laurent; Bongrand, Pierre; Robert, Philippe

    2016-10-01

    Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2kBT, in the range of previously proposed rough parts of landscapes models during dissociation.

  5. A New Approach to Quantify Semiochemical Effects on Insects Based on Energy Landscapes

    PubMed Central

    Wilson, Rory P.; Richards, Rebecca; Hartnell, Angharad; King, Andrew J.; Piasecka, Justyna; Gaihre, Yogendra K.; Butt, Tariq

    2014-01-01

    Introduction 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. Results 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. Conclusions New sensitive, detailed indicators of insect motivation derived from this approach should prove important in pest control across the world. PMID:25171062

  6. Colloids in light fields: Particle dynamics in random and periodic energy landscapes

    NASA Astrophysics Data System (ADS)

    Evers, F.; Hanes, R. D. L.; Zunke, C.; Capellmann, R. F.; Bewerunge, J.; Dalle-Ferrier, C.; Jenkins, M. C.; Ladadwa, I.; Heuer, A.; Castañeda-Priego, R.; Egelhaaf, S. U.

    2013-11-01

    The dynamics of colloidal particles in potential energy landscapes have mainly been investigated theoretically. In contrast, here we discuss the experimental realization of potential energy landscapes with the help of laser light fields and the observation of the particle dynamics by video microscopy. The experimentally observed dynamics in periodic and random potentials are compared to simulation and theoretical results in terms of, e.g. the mean-squared displacement, the time-dependent diffusion coefficient or the non-Gaussian parameter. The dynamics are initially diffusive followed by intermediate subdiffusive behaviour which again becomes diffusive at long times. How pronounced and extended the different regimes are, depends on the specific conditions, in particular the shape of the potential as well as its roughness or amplitude but also the particle concentration. Here we focus on dilute systems, but the dynamics of interacting systems in external potentials, and thus the interplay between particle-particle and particle-potential interactions, are also mentioned briefly. Furthermore, the observed dynamics of dilute systems resemble the dynamics of concentrated systems close to their glass transition, with which it is compared. The effect of certain potential energy landscapes on the dynamics of individual particles appears similar to the effect of interparticle interactions in the absence of an external potential.

  7. A Rough Energy Landscape to Describe Surface-Linked Antibody and Antigen Bond Formation

    PubMed Central

    Limozin, Laurent; Bongrand, Pierre; Robert, Philippe

    2016-01-01

    Antibodies and B cell receptors often bind their antigen at cell-cell interface while both molecular species are surface-bound, which impacts bond kinetics and function. Despite the description of complex energy landscapes for dissociation kinetics which may also result in significantly different association kinetics, surface-bound molecule (2D) association kinetics usually remain described by an on-rate due to crossing of a single free energy barrier, and few experimental works have measured association kinetics under conditions implying force and two-dimensional relative ligand-receptor motion. We use a new laminar flow chamber to measure 2D bond formation with systematic variation of the distribution of encounter durations between antigen and antibody, in a range from 0.1 to 10 ms. Under physiologically relevant forces, 2D association is 100-fold slower than 3D association as studied by surface plasmon resonance assays. Supported by brownian dynamics simulations, our results show that a minimal encounter duration is required for 2D association; an energy landscape featuring a rough initial part might be a reasonable way of accounting for this. By systematically varying the temperature of our experiments, we evaluate roughness at 2kBT, in the range of previously proposed rough parts of landscapes models during dissociation. PMID:27731375

  8. Energy landscape analysis of native folding of the prion protein yields the diffusion constant, transition path time, and rates.

    PubMed

    Yu, Hao; Gupta, Amar Nath; Liu, Xia; Neupane, Krishna; Brigley, Angela M; Sosova, Iveta; Woodside, Michael T

    2012-09-04

    Protein folding is described conceptually in terms of diffusion over a configurational free-energy landscape, typically reduced to a one-dimensional profile along a reaction coordinate. In principle, kinetic properties can be predicted directly from the landscape profile using Kramers theory for diffusive barrier crossing, including the folding rates and the transition time for crossing the barrier. Landscape theory has been widely applied to interpret the time scales for protein conformational dynamics, but protein folding rates and transition times have not been calculated directly from experimentally measured free-energy profiles. We characterized the energy landscape for native folding of the prion protein using force spectroscopy, measuring the change in extension of a single protein molecule at high resolution as it unfolded/refolded under tension. Key parameters describing the landscape profile were first recovered from the distributions of unfolding and refolding forces, allowing the diffusion constant for barrier crossing and the transition path time across the barrier to be calculated. The full landscape profile was then reconstructed from force-extension curves, revealing a double-well potential with an extended, partially unfolded transition state. The barrier height and position were consistent with the previous results. Finally, Kramers theory was used to predict the folding rates from the landscape profile, recovering the values observed experimentally both under tension and at zero force in ensemble experiments. These results demonstrate how advances in single-molecule theory and experiment are harnessing the power of landscape formalisms to describe quantitatively the mechanics of folding.

  9. Landscape of finite-temperature equilibrium behaviour of curvature-inducing proteins on a bilayer membrane explored using a linearized elastic free energy model

    PubMed Central

    Agrawal, Neeraj J.; Weinstein, Joshua; Radhakrishnan, Ravi

    2011-01-01

    Using a recently developed multiscale simulation methodology, we describe the equilibrium behaviour of bilayer membranes under the influence of curvature-inducing proteins using a linearized elastic free energy model. In particular, we describe how the cooperativity associated with a multitude of protein–membrane interactions and protein diffusion on a membrane-mediated energy landscape elicits emergent behaviour in the membrane phase. Based on our model simulations, we predict that, depending on the density of membrane-bound proteins and the degree to which a single protein molecule can induce intrinsic mean curvature in the membrane, a range of membrane phase behaviour can be observed including two different modes of vesicle-bud nucleation and repressed membrane undulations. A state diagram as a function of experimentally tunable parameters to classify the underlying states is proposed. PMID:21243078

  10. Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling

    PubMed Central

    Iida, Shinji; Mashimo, Tadaaki; Kurosawa, Takashi; Hojo, Hironobu; Muta, Hiroya; Goto, Yuji; Fukunishi, Yoshifumi; Nakamura, Haruki

    2016-01-01

    The C‐terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non‐neutralized. Because of the flexibility of the unbound CTD, a free‐energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized. The fragments were expressed by an all‐atom model and were immersed in an explicit solvent. The acetylation and charge‐neutralization varied FEL greatly, which might be convenient to exert a hub property. The acetylation slightly enhanced alpha‐helix structures that are more compact than sheet/loop conformations. The charge‐neutralization produced hairpins. Additionally, circular dichroism experiments confirmed the computational results. We propose possible binding mechanisms of CTD to partners by investigating FEL. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27735058

  11. A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes.

    PubMed

    Clausen, Rudy; Shehu, Amarda

    2015-09-01

    Evidence is emerging that many proteins involved in proteinopathies are dynamic molecules switching between stable and semistable structures to modulate their function. A detailed understanding of the relationship between structure and function in such molecules demands a comprehensive characterization of their conformation space. Currently, only stochastic optimization methods are capable of exploring conformation spaces to obtain sample-based representations of associated energy surfaces. These methods have to address the fundamental but challenging issue of balancing computational resources between exploration (obtaining a broad view of the space) and exploitation (going deep in the energy surface). We propose a novel algorithm that strikes an effective balance by employing concepts from evolutionary computation. The algorithm leverages deposited crystal structures of wildtype and variant sequences of a protein to define a reduced, low-dimensional search space from where to rapidly draw samples. A multiscale technique maps samples to local minima of the all-atom energy surface of a protein under investigation. Several novel algorithmic strategies are employed to avoid premature convergence to particular minima and obtain a broad view of a possibly multibasin energy surface. Analysis of applications on different proteins demonstrates the broad utility of the algorithm to map multibasin energy landscapes and advance modeling of multibasin proteins. In particular, applications on wildtype and variant sequences of proteins involved in proteinopathies demonstrate that the algorithm makes an important first step toward understanding the impact of sequence mutations on misfunction by providing the energy landscape as the intermediate explanatory link between protein sequence and function.

  12. Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

    PubMed Central

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-01-01

    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. PMID:25340714

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

    PubMed

    Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

    2014-10-01

    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.

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

    PubMed

    Pierre, Jon Paul; Young, Michael H; Wolaver, Brad D; Andrews, John R; Breton, Caroline L

    2017-08-30

    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 km(2) in 2008 to 225.0 km(2) 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 km(2)) in 2008 at the onset of play development, and increased from 582.3 to 3913.9 km(2) 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 km(2) for all time periods, except in 2010 when alteration was recorded at 47 km(2). 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. Landscape alteration caused by hydrocarbon pipeline installation in Val Verde County, Texas.

  15. Intrinsic charge trapping in organic and polymeric semiconductors: a physical chemistry perspective

    SciTech Connect

    Kaake, Loren; Barbara, Paul F.; Zhu, Xiaoyang

    2010-01-12

    We aim to understand the origins of intrinsic charge carrier traps in organic and polymeric semiconductor materials from a physical chemistry perspective. In crystalline organic semiconductors, we point out some of the inadequacies in the description of intrinsic charge traps using language and concepts developed for inorganic semiconductors. In π-conjugated polymeric semiconductors, we suggest the presence of a two-tier electronic energy landscape, a bimodal majority landscape due to two dominant structural motifs and a minority electronic energy landscape from intrinsic charged defects. The bimodal majority electronic energy landscape results from a combination of amorphous domains and microcrystalline or liquid-crystalline domains. The minority tier of the electronic density of states is comprised of deep Coulomb traps embedded in the majority electronic energy landscape. This minority electronic energy landscape may dominate transport properties at low charge carrier densities, such as those expected for organic photovoltaic devices, while the bimodal majority electronic energy landscape becomes significant at high carrier densities, that is, in organic field effect transistors.

  16. Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.

    PubMed

    Price, Sarah Sally L

    2009-01-20

    The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible

  17. The free energy landscape for β hairpin folding in explicit water

    PubMed Central

    Zhou, Ruhong; Berne, Bruce J.; Germain, Robert

    2001-01-01

    The folding free energy landscape of the C-terminal β hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and oplsaa force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the β strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The β hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature. PMID:11752441

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

    PubMed

    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.

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

    PubMed Central

    Dahle, Håkon; Økland, Ingeborg; Thorseth, Ingunn H; Pederesen, Rolf B; Steen, Ida H

    2015-01-01

    Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent 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. PMID:25575309

  20. Molecular mechanism of polyacrylate helix sense switching across its free energy landscape.

    PubMed

    Pietropaolo, Adriana; Nakano, Tamaki

    2013-04-17

    Helical polymers with switchable screw sense are versatile frameworks for chiral functional materials. In this work, we reconstructed the free energy landscape of helical poly(2,7-bis(4-tert-butylphenyl)fluoren-9-yl acrylate) [poly(BBPFA)], as its racemization is selectively driven by light without any rearrangement of chemical bonds. The chirality inversion was enforced by atomistic free energy simulations using chirality indices as reaction coordinates. The free energy landscape reproduced the experimental electronic circular dichroism spectra. We propose that the chirality inversion of poly(BBPFA) proceeds from a left-handed 31 helix via multistate free energy pathways to reach the right-handed 31 helix. The inversion is triggered by the rotation of biphenyl units with an activation barrier of 38 kcal/mol. To the best of our knowledge, this is the first report on the chiral inversion mechanism of a helical polymer determined in a quantitative way in the framework of atomistic free energy simulations.

  1. Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation.

    SciTech Connect

    Meinhold, Lars; Smith, Jeremy C; Kitao, Akio; Zewail, Ahmed H.

    2007-10-01

    Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation.

  2. Picosecond fluctuating protein energy landscape mapped by pressure–temperature molecular dynamics simulation

    PubMed Central

    Meinhold, Lars; Smith, Jeremy C.; Kitao, Akio; Zewail, Ahmed H.

    2007-01-01

    Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation. PMID:17956984

  3. Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation.

    PubMed

    Meinhold, Lars; Smith, Jeremy C; Kitao, Akio; Zewail, Ahmed H

    2007-10-30

    Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation.

  4. Picosecond Fluctuating Protein Energy Landscape Mapped by Pressure-Temperature Molecular Dynamics Simulation

    SciTech Connect

    Meinhold, Lars; Smith, Jeremy C; Kitao, Akio; Zewail, Ahmed H.

    2007-08-01

    Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation.

  5. Role of extracellular glutamic acids in the stability and energy landscape of bacteriorhodopsin.

    PubMed

    Sapra, K Tanuj; Doehner, Jana; Renugopalakrishnan, V; Padrós, Esteve; Muller, Daniel J

    2008-10-01

    Bacteriorhodopsin (BR), a specialized nanomachine, converts light energy into a proton gradient to power Halobacterium salinarum. In this work, we analyze the mechanical stability of a BR triple mutant in which three key extracellular residues, Glu(9), Glu(194), and Glu(204), were mutated simultaneously to Gln. These three Glu residues are involved in a network of hydrogen bonds, in cation binding, and form part of the proton release pathway of BR. Changes in these features and the robust photocycle dynamics of wild-type (WT) BR are apparent when the three extracellular Glu residues are mutated to Gln. It is speculated that such functional changes of proteins go hand in hand with changes in their mechanical properties. Here, we apply single-molecule dynamic force spectroscopy to investigate how the Glu to Gln mutations change interactions, reaction pathways, and the energy barriers of the structural regions of WT BR. The altered heights and positions of individual energy barriers unravel the changes in the mechanical and the unfolding kinetic properties of the secondary structures of WT BR. These changes in the mechanical unfolding energy landscape cause the proton pump to choose unfolding pathways differently. We suggest that, in a similar manner, the changed mechanical properties of mutated BR alter the functional energy landscape favoring different reaction pathways in the light-induced proton pumping mechanism.

  6. Role of Extracellular Glutamic Acids in the Stability and Energy Landscape of Bacteriorhodopsin

    PubMed Central

    Sapra, K. Tanuj; Doehner, Jana; Renugopalakrishnan, V.; Padrós, Esteve; Muller, Daniel J.

    2008-01-01

    Bacteriorhodopsin (BR), a specialized nanomachine, converts light energy into a proton gradient to power Halobacterium salinarum. In this work, we analyze the mechanical stability of a BR triple mutant in which three key extracellular residues, Glu9, Glu194, and Glu204, were mutated simultaneously to Gln. These three Glu residues are involved in a network of hydrogen bonds, in cation binding, and form part of the proton release pathway of BR. Changes in these features and the robust photocycle dynamics of wild-type (WT) BR are apparent when the three extracellular Glu residues are mutated to Gln. It is speculated that such functional changes of proteins go hand in hand with changes in their mechanical properties. Here, we apply single-molecule dynamic force spectroscopy to investigate how the Glu to Gln mutations change interactions, reaction pathways, and the energy barriers of the structural regions of WT BR. The altered heights and positions of individual energy barriers unravel the changes in the mechanical and the unfolding kinetic properties of the secondary structures of WT BR. These changes in the mechanical unfolding energy landscape cause the proton pump to choose unfolding pathways differently. We suggest that, in a similar manner, the changed mechanical properties of mutated BR alter the functional energy landscape favoring different reaction pathways in the light-induced proton pumping mechanism. PMID:18621827

  7. Free energy landscape for the binding process of Huperzine A to acetylcholinesterase

    PubMed Central

    Bai, Fang; Xu, Yechun; Chen, Jing; Liu, Qiufeng; Gu, Junfeng; Wang, Xicheng; Ma, Jianpeng; Li, Honglin; Onuchic, José N.; Jiang, Hualiang

    2013-01-01

    Drug-target residence time (t = 1/koff, where koff is the dissociation rate constant) has become an important index in discovering better- or best-in-class drugs. However, little effort has been dedicated to developing computational methods that can accurately predict this kinetic parameter or related parameters, koff and activation free energy of dissociation (). In this paper, energy landscape theory that has been developed to understand protein folding and function is extended to develop a generally applicable computational framework that is able to construct a complete ligand-target binding free energy landscape. This enables both the binding affinity and the binding kinetics to be accurately estimated. We applied this method to simulate the binding event of the anti-Alzheimer’s disease drug (−)−Huperzine A to its target acetylcholinesterase (AChE). The computational results are in excellent agreement with our concurrent experimental measurements. All of the predicted values of binding free energy and activation free energies of association and dissociation deviate from the experimental data only by less than 1 kcal/mol. The method also provides atomic resolution information for the (−)−Huperzine A binding pathway, which may be useful in designing more potent AChE inhibitors. We expect this methodology to be widely applicable to drug discovery and development. PMID:23440190

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

    PubMed

    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.

  9. Energy landscapes for a machine-learning prediction of patient discharge

    NASA Astrophysics Data System (ADS)

    Das, Ritankar; Wales, David J.

    2016-06-01

    The energy landscapes framework is applied to a configuration space generated by training the parameters of a neural network. In this study the input data consists of time series for a collection of vital signs monitored for hospital patients, and the outcomes are patient discharge or continued hospitalisation. Using machine learning as a predictive diagnostic tool to identify patterns in large quantities of electronic health record data in real time is a very attractive approach for supporting clinical decisions, which have the potential to improve patient outcomes and reduce waiting times for discharge. Here we report some preliminary analysis to show how machine learning might be applied. In particular, we visualize the fitting landscape in terms of locally optimal neural networks and the connections between them in parameter space. We anticipate that these results, and analogues of thermodynamic properties for molecular systems, may help in the future design of improved predictive tools.

  10. Non-Gaussian energy landscape of a simple model for strong network-forming liquids: Accurate evaluation of the configurational entropy.

    PubMed

    Moreno, A J; Saika-Voivod, I; Zaccarelli, E; La Nave, E; Buldyrev, S V; Tartaglia, P; Sciortino, F

    2006-05-28

    We present a numerical study of the statistical properties of the potential energy landscape of a simple model for strong network-forming liquids. The model is a system of spherical particles interacting through a square-well potential, with an additional constraint that limits the maximum number of bonds Nmax per particle. Extensive simulations have been carried out as a function of temperature, packing fraction, and Nmax. The dynamics of this model are characterized by Arrhenius temperature dependence of the transport coefficients and by nearly exponential relaxation of dynamic correlators, i.e., features defining strong glass-forming liquids. This model has two important features: (i) Landscape basins can be associated with bonding patterns. (ii) The configurational volume of the basin can be evaluated in a formally exact way, and numerically with an arbitrary precision. These features allow us to evaluate the number of different topologies the bonding pattern can adopt. We find that the number of fully bonded configurations, i.e., configurations in which all particles are bonded to Nmax neighbors, is extensive, suggesting that the configurational entropy of the low temperature fluid is finite. We also evaluate the energy dependence of the configurational entropy close to the fully bonded state and show that it follows a logarithmic functional form, different from the quadratic dependence characterizing fragile liquids. We suggest that the presence of a discrete energy scale, provided by the particle bonds, and the intrinsic degeneracy of fully bonded disordered networks differentiates strong from fragile behavior.

  11. The environmental benefits of cellulosic energy crops at a landscape scale

    SciTech Connect

    Graham, R.L.; Liu, W.; English, B.C.

    1995-12-31

    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.

  12. The role of momentum transfer during incoherent neutron scattering is explained by the energy landscape model

    PubMed Central

    Frauenfelder, Hans; Young, Robert D.; Fenimore, Paul W.

    2017-01-01

    We recently introduced a model of incoherent quasielastic neutron scattering (QENS) that treats the neutrons as wave packets of finite length and the protein as a random walker in the free energy landscape. We call the model ELM for “energy landscape model.” In ELM, the interaction of the wave packet with a proton in a protein provides the dynamic information. During the scattering event, the momentum Q(t) is transferred by the wave packet to the struck proton and its moiety, exerting the force F(t)=dQ(t)/dt. The resultant energy E⋆ is stored elastically and returned to the neutron as it exits. The energy is given by E⋆=kB(T0+χQ), where T0 is the ambient temperature and χ (≈ 91 K Å) is a new elastobaric coefficient. Experiments yield the scattering intensity (dynamic structure factor) S(Q;T) as a function of Q and T. To test our model, we use published data on proteins where only thermal vibrations are active. ELM competes with the currently accepted theory, here called the spatial motion model (SMM), which explains S(Q,T) by motions in real space. ELM is superior to SMM: It can explain the experimental angular and temperature dependence, whereas SMM cannot do so. PMID:28461503

  13. Free energy landscapes of sodium ions bound to DMPC-cholesterol membrane surfaces at infinite dilution.

    PubMed

    Yang, Jing; Bonomi, Massimiliano; Calero, Carles; Martí, Jordi

    2016-04-07

    Exploring the free energy landscapes of metal cations on phospholipid membrane surfaces is important for the understanding of chemical and biological processes in cellular environments. Using metadynamics simulations we have performed systematic free energy calculations of sodium cations bound to DMPC phospholipid membranes with cholesterol concentration varying between 0% (cholesterol-free) and 50% (cholesterol-rich) at infinite dilution. The resulting free energy landscapes reveal the competition between binding of sodium to water and to lipid head groups. Moreover, the binding competitiveness of lipid head groups is diminished by cholesterol contents. As cholesterol concentration increases, the ionic affinity to membranes decreases. When cholesterol concentration is greater than 30%, the ionic binding is significantly reduced, which coincides with the phase transition point of DMPC-cholesterol membranes from a liquid-disordered phase to a liquid-ordered phase. We have also evaluated the contributions of different lipid head groups to the binding free energy separately. The DMPC's carbonyl group is the most favorable binding site for sodium, followed by DMPC's phosphate group and then the hydroxyl group of cholesterol.

  14. The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain.

    PubMed

    Lau, Albert Y; Roux, Benoît

    2007-10-01

    Ionotropic glutamate receptors are ligand-gated transmembrane ion channels activated by the binding of glutamate. The free energy landscapes governing the opening/closing of the GluR2 S1S2 ligand-binding domain in the apo, DNQX-, and glutamate-bound forms are computed by using all-atom molecular dynamics simulations with explicit solvent, in conjunction with an umbrella sampling strategy. The apo S1S2 easily accesses low-energy conformations that are more open than observed in X-ray crystal structures. A free energy of 9-12 kcal/mol becomes available upon glutamate binding for driving conformational changes in S1S2 associated with receptor activation. Small-angle X-ray scattering profiles calculated from computed ensemble averages agree better with experimental results than profiles calculated from static X-ray crystal structures. Water molecules in the cleft may contribute to stabilizing the apo S1S2 in open conformations. Free energy landscapes were also computed for the glutamate-bound T686A and T686S S1S2 mutants, and the results elaborate on findings from experimental functional studies.

  15. The Free Energy Landscapes Governing Conformational Changes in a Glutamate Receptor Ligand-Binding Domain

    PubMed Central

    Lau, Albert Y.; Roux, Benoît

    2008-01-01

    Summary Ionotropic glutamate receptors (iGluRs) are ligand-gated transmembrane ion channels activated by the binding of the agonist glutamate. All-atom molecular dynamics simulations with explicit solvent are used, in conjunction with an umbrella sampling strategy, to compute the free energy landscapes governing the opening or closing of the AMPA-sensitive GluR2 S1S2 ligand-binding domain in the apo, DNQX-, and glutamate-bound forms. The apo S1S2 is found to easily access low-energy conformations that are more open than observed in X-ray crystal structures. A free energy of 9 to 12 kcal/mol becomes available upon glutamate binding for driving the conformational changes in S1S2 associated with receptor activation. Small-angle X-ray scattering profiles calculated from computed ensemble averages were found to agree better with experimental results than profiles calculated from static X-ray crystal structures. Water molecules in the cleft may contribute to stabilizing the apo S1S2 in an open conformation. Free energy landscapes were also computed for the glutamate-bound T686A and T686S S1S2 mutants, and the results elaborate on findings from experimental functional studies. PMID:17937910

  16. Folding funnels and energy landscapes of larger proteins within the capillarity approximation

    PubMed Central

    Wolynes, Peter G.

    1997-01-01

    The characterization of protein-folding kinetics with increasing chain length under various thermodynamic conditions is addressed using the capillarity picture in which distinct spatial regions of the protein are imagined to be folded or trapped and separated by interfaces. The quantitative capillarity theory is based on the nucleation theory of first-order transitions and the droplet analysis of glasses and random magnets. The concepts of folding funnels and rugged energy landscapes are shown to be applicable in the large size limit just as for smaller proteins. An ideal asymptotic free-energy profile as a function of a reaction coordinate measuring progress down the funnel is shown to be quite broad. This renders traditional transition state theory generally inapplicable but allows a diffusive picture with a transition-state region to be used. The analysis unifies several scaling arguments proposed earlier. The importance of fluctuational fine structure both to the free-energy profile and to the glassy dynamics is highlighted. The fluctuation effects lead to a very broad trapping-time distribution. Considerations necessary for understanding the crossover between the mean field and capillarity pictures of the energy landscapes are discussed. A variety of mechanisms that may roughen the interfaces and may lead to a complex structure of the transition-state ensemble are proposed. PMID:9177189

  17. Dynamics of driven transitions between minima of a complex energy landscapes

    NASA Astrophysics Data System (ADS)

    Pusuluri, Sai Teja; Lang, Alex H.; Mehta, Pankaj; Castillo, Horacio E.

    We recently modeled cellular interconvertion dynamics by using an epigenetic landscape model inspired by neural network models. Given an arbitrary set of patterns, the model can be used to construct an energy landscape in which those patterns are the global minima. Here we study the transitions between stable states of the landscapes thus constructed, under the effect of an external driving force. We consider three different cases: i) choosing the patterns to be random and independendently distributed ii) choosing a set of patterns directly derived from the experimental cellular transcription factor expression data for a representative set of cell types in an organism and iii) choosing randomly generated trees of hierarchically correlated patterns, inspired by biology. For each of the three cases, we study the stability of the global minima against thermal fluctuations and external driving forces, and the dynamics of the driven transitions away from global minima. We compare the results obtained in the three cases defined above, and in particular we explore to what degree the correlations between patterns affect the transition dynamics.

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

    PubMed

    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.

  19. Measurement of two-state energy landscapes on amorphous hafnium diboride surface by direct observation of dynamics

    NASA Astrophysics Data System (ADS)

    Nguyen, Duc; Mallek, Justin; Cloud, Andrew; Abelson, John; Girolami, Gregory; Lyding, Joseph; Gruebele, Martin

    2014-03-01

    Direct visualization of free energy landscape for individual Cooperatively Rearranging Regions (CRRs) is important in glassy dynamics, both for the bulk and the surface. We used scanning tunneling microscopy to track individual CRRs on amorphous hafnium diboride surface, temporally from microseconds to hours with sub-nanometer spatial resolution. CRRs have a diameter of ~5 atoms and mostly relax in a two-state fashion. From single cluster tunneling current traces, we can reconstruct local free energy landscapes, complete with energy difference, barrier height, a numerically defined reaction corrdinate and shape of the free energy minima.

  20. Snow, Shrubs, Grasses, and Footprint Theory: Measuring Moisture and Energy Fluxes in Patchy Landscapes

    NASA Astrophysics Data System (ADS)

    Strack, J. E.; Liston, G. E.; Hiemstra, C. A.; Pielke, R. A.

    2004-12-01

    When measuring sensible and latent heat flux from a tower within a heterogeneous landscape, one must consider which part of the landscape influences the flux sampled by the instruments. This variable landscape fraction, known as a footprint, is dependent upon wind direction, wind speed and atmospheric stability (thermal and mechanical). From 1 December 2002 - 31 March 2003, the FLuxes Over Snow Surfaces II (FLOSS II) field campaign measured sensible and latent heat fluxes at various heights on a 34 m tower in North Park, Colorado. North Park is an intermountain basin covered with a mixture of shrubs and graminoids (grasses and sedges) that interact with winter snow and wind to produce heterogeneous snow covers and, depending on the depth, protruding vegetation. During this period, snow depth measurements were made along transects extending 400-600 m upwind of the tower roughly every ten days. These snow depth data, in combination with blowing-snow model (SnowTran-3D) simulations, provided daily snow-depth distributions on a 1-meter grid over the area surrounding the flux tower. In addition, shrub height and vertical biomass profiles were measured and combined with a vegetation map having a 1-meter sampling scale. Merging the snow-depth distributions with the vegetation-height map allowed us to quantify the amount of vegetation protruding above the snow. This, in turn, allowed us to analyze the influence of exposed vegetation on observed energy and moisture fluxes. In this poster we describe our model for identifying the landscape fraction gauged by the flux-tower instruments as a function of commonly observed atmospheric conditions.

  1. Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.

    PubMed

    Tsai, Min-Yeh; Zheng, Weihua; Balamurugan, D; Schafer, Nicholas P; Kim, Bobby L; Cheung, Margaret S; Wolynes, Peter G

    2016-01-01

    While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes. © 2015 The Protein Society.

  2. Correlations between the dynamics of parallel tempering and the free-energy landscape in spin glasses

    NASA Astrophysics Data System (ADS)

    Yucesoy, Burcu; Machta, Jonathan; Katzgraber, Helmut G.

    2013-01-01

    We present the results of a large-scale numerical study of the equilibrium three-dimensional Edwards-Anderson Ising spin glass with Gaussian disorder. Using parallel tempering (replica exchange) Monte Carlo we measure various static, as well as dynamical quantities, such as the autocorrelation times and round-trip times for the parallel tempering Monte Carlo method. The correlation between static and dynamic observables for 5000 disorder realizations and up to 1000 spins down to temperatures at 20% of the critical temperature is examined. Our results show that autocorrelation times are directly correlated with the roughness of the free-energy landscape.

  3. Geometry and symmetry presculpt the free-energy landscape of proteins

    PubMed Central

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

    2004-01-01

    We present a simple physical model that demonstrates that the native-state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and hydrophobicity are sufficient to yield a free-energy landscape with broad minima even for a homopolymer. These minima correspond to marginally compact structures comprising the menu of folds that proteins choose from to house their native states in. Our results provide a general framework for understanding the common characteristics of globular proteins. PMID:15148372

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

    PubMed

    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.

  5. A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks

    PubMed Central

    De Martino, Daniele; Figliuzzi, Matteo

    2012-01-01

    The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology. Constraint-based models in particular play a key role in the attempt to obtain a quantitative understanding of cellular metabolism at genome scale. In essence, their goal is to frame the metabolic capabilities of an organism based on minimal assumptions that describe the steady states of the underlying reaction network via suitable stoichiometric constraints, specifically mass balance and energy balance (i.e. thermodynamic feasibility). The implementation of these requirements to generate viable configurations of reaction fluxes and/or to test given flux profiles for thermodynamic feasibility can however prove to be computationally intensive. We propose here a fast and scalable stoichiometry-based method to explore the Gibbs energy landscape of a biochemical network at steady state. The method is applied to the problem of reconstructing the Gibbs energy landscape underlying metabolic activity in the human red blood cell, and to that of identifying and removing thermodynamically infeasible reaction cycles in the Escherichia coli metabolic network (iAF1260). In the former case, we produce consistent predictions for chemical potentials (or log-concentrations) of intracellular metabolites; in the latter, we identify a restricted set of loops (23 in total) in the periplasmic and cytoplasmic core as the origin of thermodynamic infeasibility in a large sample () of flux configurations generated randomly and compatibly with the prior information available on reaction reversibility. PMID:22737065

  6. Effect of TMAO and betaine on the energy landscape of photosystem I.

    PubMed

    Nieder, Jana B; Hussels, Martin; Bittl, Robert; Brecht, Marc

    2014-06-01

    The accumulation of organic co-solvents in cells is a basic strategy for organisms from various species to increase stress tolerance in extreme environments. Widespread representatives of this class of co-solvents are trimethylamine-N-oxide (TMAO) and betaine; these small molecules are able to stabilize the native conformation of proteins and prevent their aggregation. Despite their importance, detailed experimental studies on the impact of these co-solvents on the energy landscape of proteins have not yet been carried out. We use single-molecule spectroscopy at cryogenic temperatures to examine the influence of these physiological relevant co-solvents on photosystem I (PSI) from Thermosynechococcus elongatus. In contrast to PSI ensemble spectra, which are almost unaffected by the addition of TMAO and betaine, statistical analysis of the fluorescence emission from individual PSI trimers yields insight into the interaction of the co-solvents with PSI. The results show an increased homogeneity upon addition of TMAO or betaine. The number of detectable zero-phonon lines (ZPLs) is reduced, indicating spectral diffusion processes with faster rates. In the framework of energy landscape model these findings indicate that co-solvents lead to reduced barrier heights between energy valleys, and thus efficient screening of protein conformations can take place.

  7. How main-chains of proteins explore the free-energy landscape in native states

    PubMed Central

    Senet, Patrick; Maisuradze, Gia G.; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A.

    2008-01-01

    Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an α/β protein (crambin) and a β-sheet polypeptide (BS2) in their “native” states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive Cα atoms, increases as a power law of time, tα, with an exponent α between 0.08 and 0.39 (α = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles. PMID:19073932

  8. How main-chains of proteins explore the free-energy landscape in native states.

    PubMed

    Senet, Patrick; Maisuradze, Gia G; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A

    2008-12-16

    Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an alpha/beta protein (crambin) and a beta-sheet polypeptide (BS2) in their "native" states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive C(alpha) atoms, increases as a power law of time, t(alpha), with an exponent alpha between 0.08 and 0.39 (alpha = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles.

  9. Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot

    PubMed Central

    Li, Wenfei; Terakawa, Tsuyoshi; Wang, Wei; Takada, Shoji

    2012-01-01

    While fast folding of small proteins has been relatively well characterized by experiments and theories, much less is known for slow folding of larger proteins, for which recent experiments suggested quite complex and rich folding behaviors. Here, we address how the energy landscape theory can be applied to these slow folding reactions. Combining the perfect-funnel approximation with a multiscale method, we first extended our previous atomic-interaction based coarse grained (AICG) model to take into account local flexibility of protein molecules. Using this model, we then investigated the energy landscapes and folding routes of two proteins with complex topologies: a multidomain protein adenylate kinase (AKE) and a knotted protein 2ouf-knot. In the AKE folding, consistent with experimental results, the kinetic free energy surface showed several substates between the fully unfolded and native states. We characterized the structural features of these substates and transitions among them, finding temperature-dependent multiroute folding. For protein 2ouf-knot, we found that the improved atomic-interaction based coarse-grained model can spontaneously tie a knot and fold the protein with a probability up to 96%. The computed folding rate of the knotted protein was much slower than that of its unknotted counterpart, in agreement with experimental findings. Similar to the AKE case, the 2ouf-knot folding exhibited several substates and transitions among them. Interestingly, we found a dead-end substate that lacks the knot, thus suggesting backtracking mechanisms. PMID:22753508

  10. Nudged-elastic band method with two climbing images: Finding transition states in complex energy landscapes

    SciTech Connect

    Zarkevich, Nikolai A.; Johnson, Duane D.

    2015-01-09

    The nudged-elastic band (NEB) method is modified with concomitant two climbing images (C2-NEB) to find a transition state (TS) in complex energy landscapes, such as those with a serpentine minimal energy path (MEP). If a single climbing image (C1-NEB) successfully finds the TS, then C2-NEB finds it too. Improved stability of C2-NEB makes it suitable for more complex cases, where C1-NEB misses the TS because the MEP and NEB directions near the saddle point are different. Generally, C2-NEB not only finds the TS, but guarantees, by construction, that the climbing images approach it from the opposite sides along the MEP. In addition, C2-NEB provides an accuracy estimate from the three images: the highest-energy one and its climbing neighbors. C2-NEB is suitable for fixed-cell NEB and the generalized solid-state NEB.

  11. Nudged-elastic band method with two climbing images: Finding transition states in complex energy landscapes

    DOE PAGES

    Zarkevich, Nikolai A.; Johnson, Duane D.

    2015-01-09

    The nudged-elastic band (NEB) method is modified with concomitant two climbing images (C2-NEB) to find a transition state (TS) in complex energy landscapes, such as those with a serpentine minimal energy path (MEP). If a single climbing image (C1-NEB) successfully finds the TS, then C2-NEB finds it too. Improved stability of C2-NEB makes it suitable for more complex cases, where C1-NEB misses the TS because the MEP and NEB directions near the saddle point are different. Generally, C2-NEB not only finds the TS, but guarantees, by construction, that the climbing images approach it from the opposite sides along the MEP.more » In addition, C2-NEB provides an accuracy estimate from the three images: the highest-energy one and its climbing neighbors. C2-NEB is suitable for fixed-cell NEB and the generalized solid-state NEB.« less

  12. Generalized evolutionary metadynamics for sampling the energy landscapes and its applications

    NASA Astrophysics Data System (ADS)

    Zhu, Qiang; Oganov, Artem R.; Lyakhov, Andriy O.; Yu, Xiaoxiang

    2015-07-01

    We present an automated scheme to systematically sample energy landscapes of crystalline solids, based on the ideas of metadynamics and evolutionary algorithms. Phase transitions are driven by the evolution of the order parameter (in this case, 6-dimensional order parameters composed of cell vectors components) and aided by atomic displacements corresponding to both zero and nonzero wave vectors, enabling cell size to spontaneously change during simulation. Our technique can be used for efficient prediction of stable crystal structures, and is particularly powerful for mining numerous low-energy configurations and phase transition pathways. By applying this method to boron, we find numerous energetically competitive configurations, based on various packings of B12 icosahedra. We also observed a low-energy metastable structure of Si(T32) which is likely to be a product of decompression on Si-II. T32 is calculated to have a quasidirect band gap of 1.28 eV, making it promising for photovoltaic applications.

  13. Intrinsic Tryptophan Fluorescence in the Detection and Analysis of Proteins: A Focus on Förster Resonance Energy Transfer Techniques

    PubMed Central

    Ghisaidoobe, Amar B. T.; Chung, Sang J.

    2014-01-01

    Förster resonance energy transfer (FRET) occurs when the distance between a donor fluorophore and an acceptor is within 10 nm, and its application often necessitates fluorescent labeling of biological targets. However, covalent modification of biomolecules can inadvertently give rise to conformational and/or functional changes. This review describes the application of intrinsic protein fluorescence, predominantly derived from tryptophan (λEX ∼ 280 nm, λEM ∼ 350 nm), in protein-related research and mainly focuses on label-free FRET techniques. In terms of wavelength and intensity, tryptophan fluorescence is strongly influenced by its (or the protein’s) local environment, which, in addition to fluorescence quenching, has been applied to study protein conformational changes. Intrinsic Förster resonance energy transfer (iFRET), a recently developed technique, utilizes the intrinsic fluorescence of tryptophan in conjunction with target-specific fluorescent probes as FRET donors and acceptors, respectively, for real time detection of native proteins. PMID:25490136

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

    PubMed

    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.

  15. Power-law distributions for the areas of the basins of attraction on a potential energy landscape.

    PubMed

    Massen, Claire P; Doye, Jonathan P K

    2007-03-01

    Energy landscape approaches have become increasingly popular for analyzing a wide variety of chemical physics phenomena. Basic to many of these applications has been the inherent structure mapping, which divides up the potential energy landscape into basins of attraction surrounding the minima. Here, we probe the nature of this division by introducing a method to compute the basin area distribution and applying it to some archetypal supercooled liquids. We find that this probability distribution is a power law over a large number of decades with the lower-energy minima having larger basins of attraction. Interestingly, the exponent for this power law is approximately the same as that for a high-dimensional Apollonian packing, providing further support for the suggestion that there is a strong analogy between the way the energy landscape is divided into basins, and the way that space is packed in self-similar, space-filling hypersphere packings, such as the Apollonian packing. These results suggest that the basins of attraction provide a fractal-like tiling of the energy landscape, and that a scale-free pattern of connections between the minima is a general property of energy landscapes.

  16. Intrinsic ultraviolet (912-3200 A) energy distribution of OB stars

    NASA Technical Reports Server (NTRS)

    Longo, Renata; Stalio, Roberto; Polidan, Ronald S.; Rossi, Lucio

    1989-01-01

    Low-dispersion 500-3200-A spectra of 20 OB stars are used to derive three individual extinction curves in the wavelength range 912-1200 A. The dependence of the intrinsic UV fluxes of OB stars on both spectral type and luminosity is demonstrated. UV color indices are proposed. The results confirm the previous finding that O star spectra are not significantly bluer than the spectrum of the B0 main-sequence star Upsilon Ori.

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

    NASA Astrophysics Data System (ADS)

    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

  18. Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.

    PubMed

    Voelz, Vincent A; Dill, Ken A; Chorny, Ilya

    2011-01-01

    To test the accuracy of existing AMBER force field models in predicting peptoid conformation and dynamics, we simulated a set of model peptoid molecules recently examined by Butterfoss et al. (JACS 2009, 131, 16798-16807) using QM methods as well as three peptoid sequences with experimentally determined structures. We found that AMBER force fields, when used with a Generalized Born/Surface Area (GBSA) implicit solvation model, could accurately reproduce the peptoid torsional landscape as well as the major conformers of known peptoid structures. Enhanced sampling by replica exchange molecular dynamics (REMD) using temperatures from 300 to 800 K was used to sample over cis-trans isomerization barriers. Compared to (Nrch)5 and cyclo-octasarcosyl, the free energy of N-(2-nitro-3-hydroxyl phenyl)glycine-N-(phenyl)glycine has the most "foldable" free energy landscape, due to deep trans-amide minima dictated by N-aryl sidechains. For peptoids with (S)-N (1-phenylethyl) (Nspe) side chains, we observe a discrepancy in backbone dihedral propensities between molecular simulations and QM calculations, which may be due to force field effects or the inability to capture n --> n* interactions. For these residues, an empirical phi-angle biasing potential can "rescue" the backbone propensities seen in QM. This approach can serve as a general strategy for addressing force fields without resorting to a complete reparameterization. Overall, this study demonstrates the utility of implicit-solvent REMD simulations for efficient sampling to predict peptoid conformational landscapes, providing a potential tool for first-principles design of sequences with specific folding properties.

  19. The switching mechanism of the mitochondrial ADP/ATP carrier explored by free-energy landscapes.

    PubMed

    Pietropaolo, Adriana; Pierri, Ciro Leonardo; Palmieri, Ferdinando; Klingenberg, Martin

    2016-06-01

    The ADP/ATP carrier (AAC) of mitochondria has been an early example for elucidating the transport mechanism alternating between the external (c-) and internal (m-) states (M. Klingenberg, Biochim. Biophys. Acta 1778 (2008) 1978-2021). An atomic resolution crystal structure of AAC is available only for the c-state featuring a three repeat transmembrane domain structure. Modeling of transport mechanism remained hypothetical for want of an atomic structure of the m-state. Previous molecular dynamics studies simulated the binding of ADP or ATP to the AAC remaining in the c-state. Here, a full description of the AAC switching from the c- to the m-state is reported using well-tempered metadynamics simulations. Free-energy landscapes of the entire translocation from the c- to the m-state, based on the gyration radii of the c- and m-gates and of the center of mass, were generated. The simulations revealed three free-energy basins attributed to the c-, intermediate- and m-states separated by activation barriers. These simulations were performed with the empty and with the ADP- and ATP-loaded AAC as well as with the poorly transported AMP and guanine nucleotides, showing in the free energy landscapes that ADP and ATP lowered the activation free-energy barriers more than the other substrates. Upon binding AMP and guanine nucleotides a deeper free-energy level stabilized the intermediate-state of the AAC2 hampering the transition to the m-state. The structures of the substrate binding sites in the different states are described producing a full picture of the translocation events in the AAC.

  20. Evolution of the potential energy landscape with static pulling force for two model proteins.

    PubMed

    Wales, David J; Head-Gordon, Teresa

    2012-07-26

    The energy landscape is analyzed for off-lattice bead models of protein L and protein G as a function of a static pulling force. Two different pairs of attachment points (pulling directions) are compared in each case, namely, residues 1/56 and 10/32. For the terminal residue pulling direction 1/56, the distinct global minimum structures are all extended, aside from the compact geometry that correlates with zero force. The helical turns finally disappear at the highest pulling forces considered. For the 10/32 pulling direction, the changes are more complicated, with a variety of competing arrangements for beads outside the region where the force is directly applied. These alternatives produce frustrated energy landscapes, with low-lying minima separated by high barriers. The calculated folding pathways in the absence of force are in good agreement with previous work. The N-terminal hairpin folds first for protein L and the C-terminal hairpin for protein G, which exhibits an intermediate. However, for a relatively low static force, where the global minimum retains its structure, the folding mechanisms change, sometimes dramatically, depending on the protein and the attachment points. The scaling relations predicted by catastrophe theory are found to hold in the limit of short path lengths.

  1. Analysis of riboswitch structure and function by an energy landscape framework.

    PubMed

    Quarta, Giulio; Kim, Namhee; Izzo, Joseph A; Schlick, Tamar

    2009-11-06

    The thiamine pyrophosphate (TPP) riboswitch employs modular domains for binding TPP to form a platform for gene expression regulation. Specifically, TPP binding triggers a conformational switch in the RNA from a transcriptionally active "on" state to an inactive "off" state that concomitantly causes the formation of a terminator hairpin and halting of transcription. Here, clustering analysis of energy landscapes at different nucleotide lengths suggests a novel computational tool for analysis of the mechanics of transcription elongation in the presence or absence of the ligand. Namely, we suggest that the riboswitch's kinetics are tightly governed by a length-dependent switch, whereby the energy landscape has two clusters available during transcription elongation and where TPP's binding shifts the preference to one form. Significantly, the biologically active and inactive structures determined experimentally matched well the structures predominant in each computational set. These clustering/structural analyses combined with modular computational design suggest design principles that exploit the above features to analyze as well as create new functions and structures of RNA systems.

  2. Structure and energy landscape of a photoswitchable peptide: a replica exchange molecular dynamics study.

    PubMed

    Nguyen, Phuong H; Mu, Yuguang; Stock, Gerhard

    2005-08-15

    A replica exchange molecular dynamics (REMD) simulation of a bicyclic azobenzene peptide in explicit dimethyl sulfoxide solution is presented in order to characterize the conformational structures and energy landscape of a photoswitchable peptide. It is shown that an enhanced-sampling technique such as the REMD method is essential to obtain a converged conformational sampling of the peptide at room temperature. This is because conventional MD simulations of less than approximately 100-ns length are either trapped in local minima (at 295 K) or-if run at high temperature-do not resemble the room-temperature REMD results. Calculating various nuclear Overhauser effects (NOEs) and (3)J-couplings, a good overall agreement between the REMD simulations and the NMR experiments of Renner et al. (Biopolymers 2000;54:501-514) is found. In particular, the REMD study confirms the general picture drawn by Renner et al. that the trans-isomer of the azobenzene peptide exhibits a well-defined structure, while the cis-isomer is a conformational heterogeneous system; that is, the trans-isomer occurs in 2 well-defined conformers, while the cis-isomer represents an energetically frustrated system that leads to an ensemble of conformational structures. Employing a principal component analysis of the REMD data, the free energy landscape of the systems is studied at various temperatures. The implications for the folding and unfolding pathways of the system are discussed. (c) 2005 Wiley-Liss, Inc.

  3. Generation of droplet arrays with rational number spacing patterns driven by a periodic energy landscape

    NASA Astrophysics Data System (ADS)

    Rinberg, Anatoly; Katsikis, Georgios; Prakash, Manu

    2017-09-01

    The generation of droplets at low Reynolds numbers is driven by nonlinear dynamics that give rise to complex patterns concerning both the droplet-to-droplet spacing and the individual droplet sizes. Here we demonstrate an experimental system in which a time-varying energy landscape provides a periodic magnetic force that generates an array of droplets from an immiscible mixture of ferrofluid and silicone oil. The resulting droplet patterns are periodic, owing to the nature of the magnetic force, yet the droplet spacing and size can vary greatly by tuning a single bias pressure applied on the ferrofluid phase; for a given cycle period of the magnetic force, droplets can be generated either at integer multiples (1, 2, ...), or at rational fractions (3/2, 5/3, 5/2, ...) of this period with mono- or multidisperse droplet sizes. We develop a discrete-time dynamical systems model not only to reproduce the phenotypes of the observed patterns but also to provide a framework for understanding systems driven by such periodic energy landscapes.

  4. Predicting low-temperature free energy landscapes with flat-histogram Monte Carlo methods

    NASA Astrophysics Data System (ADS)

    Mahynski, Nathan A.; Blanco, Marco A.; Errington, Jeffrey R.; Shen, Vincent K.

    2017-02-01

    We present a method for predicting the free energy landscape of fluids at low temperatures from flat-histogram grand canonical Monte Carlo simulations performed at higher ones. We illustrate our approach for both pure and multicomponent systems using two different sampling methods as a demonstration. This allows us to predict the thermodynamic behavior of systems which undergo both first order and continuous phase transitions upon cooling using simulations performed only at higher temperatures. After surveying a variety of different systems, we identify a range of temperature differences over which the extrapolation of high temperature simulations tends to quantitatively predict the thermodynamic properties of fluids at lower ones. Beyond this range, extrapolation still provides a reasonably well-informed estimate of the free energy landscape; this prediction then requires less computational effort to refine with an additional simulation at the desired temperature than reconstruction of the surface without any initial estimate. In either case, this method significantly increases the computational efficiency of these flat-histogram methods when investigating thermodynamic properties of fluids over a wide range of temperatures. For example, we demonstrate how a binary fluid phase diagram may be quantitatively predicted for many temperatures using only information obtained from a single supercritical state.

  5. A cavitation transition in the energy landscape of simple cohesive liquids and glasses

    NASA Astrophysics Data System (ADS)

    Altabet, Y. Elia; Stillinger, Frank H.; Debenedetti, Pablo G.

    2016-12-01

    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 ρS. The tensile limit at ρS is due to cavitation that occurs upon energy minimization, and previous characterizations of this behavior suggested that ρS 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.

  6. Mapping the energy landscape for second-stage folding of a single membrane protein

    PubMed Central

    Min, Duyoung; Jefferson, Robert E; Bowie, James U; Yoon, Tae-Young

    2016-01-01

    Membrane proteins are designed to fold and function in a lipid membrane, yet folding experiments within a native membrane environment are challenging to design. Here we show that single-molecule forced unfolding experiments can be adapted to study helical membrane protein folding under native-like bicelle conditions. Applying force using magnetic tweezers, we find that a transmembrane helix protein, Escherichia coli rhomboid protease GlpG, unfolds in a highly cooperative manner, largely unraveling as one physical unit in response to mechanical tension above 25 pN. Considerable hysteresis is observed, with refolding occurring only at forces below 5 pN. Characterizing the energy landscape reveals only modest thermodynamic stability (ΔG = 6.5 kBT) but a large unfolding barrier (21.3 kBT) that can maintain the protein in a folded state for long periods of time (t1/2 ~3.5 h). The observed energy landscape may have evolved to limit the existence of troublesome partially unfolded states and impart rigidity to the structure. PMID:26479439

  7. Fragility of the free-energy landscape of a directed polymer in random media

    NASA Astrophysics Data System (ADS)

    Sales, Marta; Yoshino, Hajime

    2002-06-01

    We examine the sensitiveness of the free-energy landscape of a directed polymer in random media with respect to various kinds of infinitesimally weak perturbation including the intriguing case of temperature chaos. To this end, we combine the replica Bethe Ansatz approach outlined by Sales and Yoshino (e-print cond-mat/0112384), the mapping to a modified Sinai model, and numerically exact calculations by the transfer-matrix method. Our results imply that for all the perturbations under study there is a slow crossover from a weakly perturbed regime, where rare events take place, to a strongly perturbed regime at larger length scales beyond the so-called overlap length, where typical events take place leading to chaos, i.e., a complete reshuffling of the free-energy landscape. Within the replica space, the evidence for chaos is found in the factorization of the replicated partition function induced by infinitesimal perturbations. This is the reflex of explicit replica-symmetry breaking.

  8. Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning.

    PubMed

    Bello-Rivas, Juan M; Elber, Ron

    2016-03-05

    We investigated by computational means the kinetics and stationary behavior of stochastic dynamics on an ensemble of rough two-dimensional energy landscapes. There are no obvious separations of temporal scales in these systems, which constitute a simple model for the behavior of glasses and some biomaterials. Even though there are significant computational challenges present in these systems due to the large number of metastable states, the Milestoning method is able to compute their kinetic and thermodynamic properties exactly. We observe two clearly distinguished regimes in the overall kinetics: one in which diffusive behavior dominates and another that follows an Arrhenius law (despite the absence of a dominant barrier). We compare our results with those obtained with an exactly-solvable one-dimensional model, and with the results from the rough one-dimensional energy model introduced by Zwanzig. © 2015 Wiley Periodicals, Inc.

  9. Communication: Theoretical prediction of free-energy landscapes for complex self-assembly

    NASA Astrophysics Data System (ADS)

    Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan

    2015-01-01

    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.

  10. Simulations of thermodynamics and kinetics on rough energy landscapes with Milestoning

    PubMed Central

    Bello-Rivas, Juan M.; Elber, Ron

    2015-01-01

    We investigated by computational means the kinetics and stationary behavior of stochastic dynamics on an ensemble of rough two-dimensional energy landscapes. There are no obvious separations of temporal scales in these systems, which constitute a simple model for the behavior of glasses and some biomaterials. Even though there are significant computational challenges present in these systems due to the large number of metastable states, the Milestoning method is able to compute their kinetic and thermodynamic properties exactly. We observe two clearly distinguished regimes in the overall kinetics: one in which diffusive behavior dominates and another that follows an Arrhenius law (despite the absence of a dominant barrier). We compare our results with those obtained with an exactly-solvable one-dimensional model, and with the results from the rough one-dimensional energy model introduced by Zwanzig. PMID:26265358

  11. Following Gibbs states adiabatically: the energy landscape of mean field glassy systems

    SciTech Connect

    Zdeborova, Lenka; Krzakala, Florent

    2009-01-01

    We introduce a generalization of the cavity, or Bethe-Peierls, method that allows to follow Gibbs states when an external parameter, e.g. the temperature, is adiabatically changed. This allows to obtain new quantitative results on the static and dynamic behavior of mean field disordered systems such as models of glassy and amorphous materials or random constraint satisfaction problems. As a first application, we discuss the residual energy after a very slow annealing, the behavior of out-of-equilibrium states, and demonstrate the presence of temperature chaos in equilibrium. We also explore the energy landscape, and identify a new transition from an computationally easier canyons-dominated region to a harder valleys-dominated one.

  12. Extended law of corresponding states in short-range square wells: a potential energy landscape study.

    PubMed

    Foffi, Giuseppe; Sciortino, Francesco

    2006-11-01

    We study the statistical properties of the potential energy landscape of a system of particles interacting via a very short-range square-well potential (of depth -u0) as a function of the range of attraction Delta to provide thermodynamic insights of the Noro and Frenkel [M. G. Noro and D. Frenkel, J. Chem. Phys. 113, 2941 (2000)] scaling. We exactly evaluate the basin free energy and show that it can be separated into a vibrational (Delta dependent) and a floppy (Delta independent) component. We also show that the partition function is a function of Deltaebetauo, explaining the equivalence of the thermodynamics for systems characterized by the same second virial coefficient. An outcome of our approach is the possibility of counting the number of floppy modes (and their entropy).

  13. Metadynamics as a tool for exploring free energy landscapes of chemical reactions.

    PubMed

    Ensing, Bernd; De Vivo, Marco; Liu, Zhiwei; Moore, Preston; Klein, Michael L

    2006-02-01

    The metadynamics or hills method is a relatively new molecular dynamics technique aimed to enhance the sampling of separated regions in phase space and map out the underlying free energy landscape as a function of a small number of order parameters or collective variables. The high efficiency allows for the application of metadynamics in combination with first principles dynamics methods, in particular with Car-Parrinello molecular dynamics, to study processes in which changes in the electronic structure play a dominant role, such as chemical reactions. The option to choose several independent collective variables is important to tackle complex and concerted transformations that lack an obvious a priori choice for a single reaction coordinate. In this Account, we discuss the role of metadynamics in the search of transition states, local minima, reaction paths, free energy profiles, and reaction coordinates among a growing list of alternative methods.

  14. Chiral effects on helicity studied via the energy landscape of short (D, L)-alanine peptides.

    PubMed

    Neelamraju, Sridhar; Oakley, Mark T; Johnston, Roy L

    2015-10-28

    The homochirality of natural amino acids facilitates the formation of regular secondary structures such as α-helices and β-sheets. Here, we study the relationship between chirality and backbone structure for the example of hexa-alanine. The most stable stereoisomers are identified through global optimisation. Further, the energy landscape, a database of connected low-energy local minima and transition points, is constructed for various neutral and zwitterionic stereoisomers of hexa-alanine. Three order parameters for partial helicity are applied and metric disconnectivity graphs are presented with partial helicity as a metric. We also apply the Zimm-Bragg model to derive average partial helicities for Ace-(L-Ala)6-NHMe, Ace-(D-Ala-L-Ala)3-NHMe, and Ace-(L-Ala)3-(D-Ala)3-NHMe from the database of local minima and compare with previous studies.

  15. Role of pulling direction in understanding the energy landscape of proteins.

    PubMed

    Rajesh, R; Giri, D; Jensen, I; Kumar, S

    2008-08-01

    Single-molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in different directions relative to their secondary structure, one can gain a better understanding of the shape of the energy landscape. We consider simple lattice models which are anisotropic in nature to study the response of a force in unfolding of a polymer. Our analytical solution of the model, supported by extensive numerical calculations, reveal that the force temperature diagrams are very different depending on the direction of the applied force. We find that either unzipping or shearing kind transitions dominate the dynamics of the unfolding process depending solely on the direction of the applied force.

  16. Communication: Theoretical prediction of free-energy landscapes for complex self-assembly

    SciTech Connect

    Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan

    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.

  17. Alternating access mechanisms of LeuT-fold transporters: trailblazing towards the promised energy landscapes.

    PubMed

    Kazmier, Kelli; Claxton, Derek P; Mchaourab, Hassane S

    2016-12-29

    Secondary active transporters couple the uphill translocation of substrates to electrochemical ion gradients. Transporter conformational motion, generically referred to as alternating access, enables a central ligand binding site to change its orientation relative to the membrane. Here we review themes of alternating access and the transduction of ion gradient energy to power this process in the LeuT-fold class of transporters where crystallographic, computational and spectroscopic approaches have converged to yield detailed models of transport cycles. Specifically, we compare findings for the Na(+)-coupled amino acid transporter LeuT and the Na(+)-coupled hydantoin transporter Mhp1. Although these studies have illuminated multiple aspects of transporter structures and dynamics, a number of questions remain unresolved that so far hinder understanding transport mechanisms in an energy landscape perspective.

  18. Energy and Water Fluxes across a Heterogeneous Landscape in the Southern Great Plains

    NASA Astrophysics Data System (ADS)

    Bagley, J. E.; Williams, I. N.; Kueppers, L. M.; Lu, Y.; Torn, M. S.; Biraud, S.

    2015-12-01

    Fluxes of energy and water between the atmosphere and the land surface influence weather and climate. These fluxes depend on the state of the landscape, which contributes to differences in land-atmosphere coupling strength over space and time. One region with potentially strong land-atmosphere coupling is the Southern Great Plains (SGP) in North America. In this region, managed vegetation plays a key role in moderating the surface energy through effects on surface albedo, transpiration, precipitation interception, and other surface properties. However accurately modeling these effects is challenging because the vegetation in this region is very heterogeneous. Winter wheat is the dominant crop, but pasture, hayfields, corn, and recently introduced crops such as canola cover significant portions of the landscape as well. Winter wheat has a unique phenology with fall planting, maximum leaf area in late spring, and harvest in early summer. This phenology contrasts significantly with most other crops and with pastures and hayfields in the region, which have more typical spring-fall growing seasons. Therefore, to sufficiently model and assess land-atmosphere interactions in this region accurate characterization of differences in the seasonality of water and energy fluxes between vegetation types are necessary. We used observations including eddy covariance flux estimates, soil moisture data, state-of-the-art longwave and shortwave radiation measurements, and other observations available for several facilities within the SGP Atmospheric Radiation Measurement (ARM) site in north-central Oklahoma and southern Kansas. We compared the timing and variations in fluxes of water and energy between winter wheat and other land cover types, focusing on vegetation influences on rates of soil dry-down following precipitation events. We found distinct differences in fluxes between winter wheat and other land types. These flux differences had a nonlinear dependency on disparities in

  19. Free-Energy Landscape and Proton Transfer Pathways in Oxidative Deamination by Methylamine Dehydrogenase.

    PubMed

    Zelleke, Theodros; Marx, Dominik

    2017-01-18

    The rate-determining step in the reductive half-reaction of the bacterial enzyme methylamine dehydrogenase, which is proton abstraction from the native substrate methylamine, is investigated using accelerated QM/MM molecular dynamics simulations at room temperature. Generation of the multidimensional thermal free-energy landscape without restriction of the degrees of freedom beyond a multidimensional reaction subspace maps two rather similar pathways for the underlying proton transfer to one of two aspartate carboxyl oxygen atoms, termed OD1 and OD2, which hydrogen bond with Thr122 and Trp108, respectively. Despite significant large-amplitude motion perpendicular to the one-dimensional proton transfer coordinate, due to fluctuations of the donor-acceptor distance of about 3 Å, it is found that the one-dimensional proton transfer free-energy profiles are essentially identical to the minimum free-energy pathways on the multidimensional free-energy landscapes for both proton transfer channels. Proton transfer to one of the acceptor oxygen atoms-the OD2 site-is slightly favored in methylamine dehydrogenase by approximately 2 kcal mol(-1) , both kinetically and thermodynamically. Mechanistic analyses reveal that the hydrogen bond between Thr122β and OD1 is always present in the transition state independently of the proton transfer channel. Population analysis confirms that the electronic charge gained upon oxidation of the substrate is delocalized within the ring systems of the tryptophan tryptophylquinone cofactor. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Studying the energy dependence of intrinsic conversion efficiency of single crystal scintillators under X-ray excitation

    NASA Astrophysics Data System (ADS)

    Kalyvas, N.; Valais, I.; David, S.; Michail, Ch.; Fountos, G.; Liaparinos, P.; Kandarakis, I.

    2014-05-01

    Single crystal scintilators are used in various radiation detectors applications. The efficiency of the crystal can be determined by the Detector Optical Gain (DOG) defined as the ratio of the emitted optical photon flux over the incident radiation photons flux. A parameter affecting DOG is the intrinsic conversion efficiency ( n C ) giving the percentage of the X-ray photon power converted to optical photon power. n C is considered a constant value for X-ray energies in the order of keV although a non-proportional behavior has been reported. In this work an analytical model, has been utilized to single crystals scintillators GSO:Ce, LSO:Ce and LYSO:Ce to examine whether the intrinsic conversion efficiency shows non proportional behavior under X-ray excitation. DOG was theoretically calculated as a function of the incident X-ray spectrum, the X-ray absorption efficiency, the energy of the produced optical photons and the light transmission efficiency. The theoretical DOG values were compared with experimental data obtained by irradiating the crystals with X-rays at tube voltages from 50 to 140 kV and by measuring the light energy flux emitted from the irradiated screen. An initial value for n C (calculated from literature data) was assumed for the X-ray tube voltage of 50 kV. For higher X-ray tube voltages the optical photon propagation phenomena was assumed constant and any deviations between experimental and theoretical data were associated with changes in the intrinsic conversion efficiency. The experimental errors were below 7% for each experimental setup. The behavior of n C values for LSO:Ce and LYSO:Ce were found very similar, i.e., ranging with values from 0.089 at 50 kV to 0.015 at 140 kV, while for GSO:Ce, n C demonstrated a peak at 80 kV.

  1. Characterization of the dynamics of glass-forming liquids from the properties of the potential energy landscape.

    PubMed

    Banerjee, Sumilan; Dasgupta, Chandan

    2012-02-01

    We develop a framework for understanding the difference between strong and fragile behavior in the dynamics of glass-forming liquids from the properties of the potential energy landscape. Our approach is based on a master equation description of the activated jump dynamics among the local minima of the potential energy (the so-called inherent structures) that characterize the potential energy landscape of the system. We study the dynamics of a small atomic cluster using this description as well as molecular dynamics simulations and demonstrate the usefulness of our approach for this system. Many of the remarkable features of the complex dynamics of glassy systems emerge from the activated dynamics in the potential energy landscape of the atomic cluster. The dynamics of the system exhibits typical characteristics of a strong supercooled liquid when the system is allowed to explore the full configuration space. This behavior arises because the dynamics is dominated by a few lowest-lying minima of the potential energy and the potential energy barriers between these minima. When the system is constrained to explore only a limited region of the potential energy landscape that excludes the basins of attraction of a few lowest-lying minima, the dynamics is found to exhibit the characteristics of a fragile liquid. © 2012 American Physical Society

  2. Synthesis of chlorophyll-a derivatives methylated in the 3-vinyl group and their intrinsic site energy.

    PubMed

    Tamiaki, Hitoshi; Tsuji, Kazuki; Kuno, Masaki; Kimura, Yuki; Watanabe, Hiroaki; Miyatake, Tomohiro

    2016-07-01

    Wittig reaction of methyl pyropheophorbide-d possessing the 3-formyl group gave readily methyl pyropheophorbides-a bearing a variety of 3-alkenyl groups as semi-synthetic models of chlorophyll-a. The 3-substituents rotated around the C3-C3(1) bond from the coplanar conformation with the chlorin π-system, moving the redmost visible absorption maxima to a shorter wavelength. The model experiments showed that natural chlorophyll-a carrying the 3-vinyl group would take a similar rotamer to control its intrinsic site energy. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Landscape, kinetics, paths and statistics of curl flux, coherence, entanglement and energy transfer in non-equilibrium quantum systems

    NASA Astrophysics Data System (ADS)

    Zhang, Zhedong; Wang, Jin

    2015-04-01

    We develop a population and flux landscape theory for general non-equilibrium quantum systems. We illustrate our theory by modelling the quantum transport of donor-acceptor energy transfer. We find two driving forces for the non-equilibrium quantum dynamics. The symmetric part of the driving force corresponds to the population landscape contribution which mainly governs the equilibrium part of dynamics while the anti-symmetric part of the driving force generates the non-equilibrium curl quantum flux which leads to the detailed-balance-breaking and time-irreversibility. The multi-loop structure of the flux emerges forms the flux-landscape. We study the trend of changes in population and flux-landscape with respect to the voltage (temperature difference induced by environments) and electronic coupling. Improving the voltage and electronic coupling in general facilitates the quantum transport by reducing the population landscape barriers between major states and increasing the mean value of the flux. A limit-cycle mode emerges when the underlying flux-landscape becomes funnelled with a significant gap between the largest flux loop and the rest of them. On the kinetic level, we find that multiple kinetic paths between quantum states emerge and illustrate the interference effects. The degree of interference is determined by the landscape and flux. Furthermore, we quantify kinetic rate which strongly correlates with the population landscape and flux. For quantum transport, we demonstrate that as the coherence or the quantum entanglement is enhanced, the flux and energy transfer efficiency are increased. Finally it is surprising that the non-equilibriumness quantified by voltage has a non-trivial contribution on strengthening the entanglement, which is attributed to the non-local feature of the quantum curl flux.

  4. Free energy landscape of rim-pore expansion in membrane fusion.

    PubMed

    Risselada, Herre Jelger; Smirnova, Yuliya; Grubmüller, Helmut

    2014-11-18

    The productive fusion pore in membrane fusion is generally thought to be toroidally shaped. Theoretical studies and recent experiments suggest that its formation, in some scenarios, may be preceded by an initial pore formed near the rim of the extended hemifusion diaphragm (HD), a rim-pore. This rim-pore is characterized by a nontoroidal shape that changes with size. To determine this shape as well as the free energy along the pathway of rim-pore expansion, we derived a simple analytical free energy model. We argue that dilation of HD material via expansion of a rim-pore is favored over a regular, circular pore. Further, the expanding rim-pore faces a free energy barrier that linearly increases with HD size. In contrast, the tension required to expand the rim-pore decreases with HD size. Pore flickering, followed by sudden opening, occurs when the tension in the HD competes with the line energy of the rim-pore, and the rim-pore reaches its equilibrium size before reaching the critical pore size. The experimental observation of flickering and closing fusion pores (kiss-and-run) is very well explained by the observed behavior of rim-pores. Finally, the free energy landscape of rim-pore expansion/HD dilation may very well explain why some cellular fusion reactions, in their attempt to minimize energetic costs, progress via alternative formation and dilation of microscopic hemifusion intermediates.

  5. Free Energy Landscape of Rim-Pore Expansion in Membrane Fusion

    PubMed Central

    Risselada, Herre Jelger; Smirnova, Yuliya; Grubmüller, Helmut

    2014-01-01

    The productive fusion pore in membrane fusion is generally thought to be toroidally shaped. Theoretical studies and recent experiments suggest that its formation, in some scenarios, may be preceded by an initial pore formed near the rim of the extended hemifusion diaphragm (HD), a rim-pore. This rim-pore is characterized by a nontoroidal shape that changes with size. To determine this shape as well as the free energy along the pathway of rim-pore expansion, we derived a simple analytical free energy model. We argue that dilation of HD material via expansion of a rim-pore is favored over a regular, circular pore. Further, the expanding rim-pore faces a free energy barrier that linearly increases with HD size. In contrast, the tension required to expand the rim-pore decreases with HD size. Pore flickering, followed by sudden opening, occurs when the tension in the HD competes with the line energy of the rim-pore, and the rim-pore reaches its equilibrium size before reaching the critical pore size. The experimental observation of flickering and closing fusion pores (kiss-and-run) is very well explained by the observed behavior of rim-pores. Finally, the free energy landscape of rim-pore expansion/HD dilation may very well explain why some cellular fusion reactions, in their attempt to minimize energetic costs, progress via alternative formation and dilation of microscopic hemifusion intermediates. PMID:25418297

  6. Hybridizing rapidly exploring random trees and basin hopping yields an improved exploration of energy landscapes.

    PubMed

    Roth, Christine-Andrea; Dreyfus, Tom; Robert, Charles H; Cazals, Frédéric

    2016-03-30

    The number of local minima of the potential energy landscape (PEL) of molecular systems generally grows exponentially with the number of degrees of freedom, so that a crucial property of PEL exploration algorithms is their ability to identify local minima, which are low lying and diverse. In this work, we present a new exploration algorithm, retaining the ability of basin hopping (BH) to identify local minima, and that of transition based rapidly exploring random trees (T-RRT) to foster the exploration of yet unexplored regions. This ability is obtained by interleaving calls to the extension procedures of BH and T-RRT, and we show tuning the balance between these two types of calls allows the algorithm to focus on low lying regions. Computational efficiency is obtained using state-of-the art data structures, in particular for searching approximate nearest neighbors in metric spaces. We present results for the BLN69, a protein model whose conformational space has dimension 207 and whose PEL has been studied exhaustively. On this system, we show that the propensity of our algorithm to explore low lying regions of the landscape significantly outperforms those of BH and T-RRT.

  7. Energy landscape theory for Alzheimer's amyloid beta-peptide fibril elongation.

    PubMed

    Massi, F; Straub, J E

    2001-02-01

    Recent experiments on the kinetics of deposition and fibril elongation of the Alzheimer's beta-amyloid peptide on preexisting fibrils are analyzed. A mechanism is developed based on the dock-and-lock scheme recently proposed by Maggio and coworkers to organize their experimental observations of the kinetics of deposition of beta-peptide on preexisting amyloid fibrils and deposits. Our mechanism includes channels for (1) a one-step prion-like direct deposition on fibrils of activated monomeric peptide in solution, and (2) a two-step deposition of unactivated peptide on fibrils and subsequent reorganization of the peptide-fibril complex. In this way, the mechanism and implied "energy landscape" unify a number of schemes proposed to describe the process of fibril elongation. This beta-amyloid landscape mechanism (beta ALM) is found to be in good agreement with existing experimental data. A number of experimental tests of the mechanism are proposed. The mechanism leads to a clear definition of overall equilibrium or rate constants in terms of the energetics of the elementary underlying processes. Analysis of existing experimental data suggests that fibril elongation occurs through a two-step mechanism of nonspecific peptide absorption and reorganization. The mechanism predicts a turnover in the rate of fibril elongation as a function of temperature and denaturant concentration. Proteins 2001;42:217-229.

  8. Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape

    PubMed Central

    Yu, Hao; Dee, Derek R.; Liu, Xia; Brigley, Angela M.; Sosova, Iveta; Woodside, Michael T.

    2015-01-01

    The timescale for the microscopic dynamics of proteins during conformational transitions is set by the intrachain diffusion coefficient, D. Despite the central role of protein misfolding and aggregation in many diseases, it has proven challenging to measure D for these processes because of their heterogeneity. We used single-molecule force spectroscopy to overcome these challenges and determine D for misfolding of the prion protein PrP. Observing directly the misfolding of individual dimers into minimal aggregates, we reconstructed the energy landscape governing nonnative structure formation. Remarkably, rather than displaying multiple pathways, as typically expected for aggregation, PrP dimers were funneled into a thermodynamically stable misfolded state along a single pathway containing several intermediates, one of which blocked native folding. Using Kramers’ rate theory, D was found to be 1,000-fold slower for misfolding than for native folding, reflecting local roughening of the misfolding landscape, likely due to increased internal friction. The slow diffusion also led to much longer transit times for barrier crossing, allowing transition paths to be observed directly for the first time to our knowledge. These results open a new window onto the microscopic mechanisms governing protein misfolding. PMID:26109573

  9. The rough energy landscape of superfolder GFP is linked to the chromophore

    PubMed Central

    Andrews, Benjamin T.; Schoenfish, Andrea R.; Roy, Melinda; Waldo, Geoffrey; Jennings, Patricia A.

    2009-01-01

    Many GFP variants have been developed for use as fluorescent tags, and recently a superfolder GFP (sfGFP) has been developed as a robust folding reporter. This new variant shows increased stability and improved folding kinetics, as well as 100% recovery of native protein after denaturation. Here, we characterize sfGFP, and find that this variant exhibits hysteresis as unfolding and refolding equilibrium titration curves are non-coincident even after equilibration for more than eight half-lives as estimated from kinetic unfolding and refolding studies. This hysteresis is attributed to trapping in a native-like intermediate state. Mutational studies directed towards inhibiting chromophore formation indicate that the novel backbone cyclization is responsible for the hysteresis observed in equilibrium titrations of sfGFP. Slow equilibration and the presence of intermediates imply a rough landscape. However, de novo folding in the absence of the chromophore is dominated by a smoother energy landscape than that sampled during unfolding and refolding of the post-translationally modified polypeptide. PMID:17822714

  10. Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape

    SciTech Connect

    Wales, D. J.

    2015-04-07

    This perspective focuses on conceptual and computational aspects of the potential energy landscape framework. It has two objectives: first to summarise some key developments of the approach and second to illustrate how such techniques can be applied using a specific example that exploits knowledge of pathways. Recent developments in theory and simulation within the landscape framework are first outlined, including methods for structure prediction, analysis of global thermodynamic properties, and treatment of rare event dynamics. We then develop a connection between the kinetic transition network treatment of dynamics and a potential of mean force defined by a reaction coordinate. The effect of projection from the full configuration space to low dimensionality is illustrated for an atomic cluster. In this example, where a relatively successful structural order parameter is available, the principal change in cluster morphology is reproduced, but some details are not faithfully represented. In contrast, a profile based on configurations that correspond to the discrete path defined geometrically retains all the barriers and minima. This comparison provides insight into the physical origins of “friction” effects in low-dimensionality descriptions of dynamics based upon a reaction coordinate.

  11. Protein misfolding occurs by slow diffusion across multiple barriers in a rough energy landscape.

    PubMed

    Yu, Hao; Dee, Derek R; Liu, Xia; Brigley, Angela M; Sosova, Iveta; Woodside, Michael T

    2015-07-07

    The timescale for the microscopic dynamics of proteins during conformational transitions is set by the intrachain diffusion coefficient, D. Despite the central role of protein misfolding and aggregation in many diseases, it has proven challenging to measure D for these processes because of their heterogeneity. We used single-molecule force spectroscopy to overcome these challenges and determine D for misfolding of the prion protein PrP. Observing directly the misfolding of individual dimers into minimal aggregates, we reconstructed the energy landscape governing nonnative structure formation. Remarkably, rather than displaying multiple pathways, as typically expected for aggregation, PrP dimers were funneled into a thermodynamically stable misfolded state along a single pathway containing several intermediates, one of which blocked native folding. Using Kramers' rate theory, D was found to be 1,000-fold slower for misfolding than for native folding, reflecting local roughening of the misfolding landscape, likely due to increased internal friction. The slow diffusion also led to much longer transit times for barrier crossing, allowing transition paths to be observed directly for the first time to our knowledge. These results open a new window onto the microscopic mechanisms governing protein misfolding.

  12. Mapping transiently formed and sparsely populated conformations on a complex energy landscape

    PubMed Central

    Wang, Yong; Papaleo, Elena; Lindorff-Larsen, Kresten

    2016-01-01

    Determining the structures, kinetics, thermodynamics and mechanisms that underlie conformational exchange processes in proteins remains extremely difficult. Only in favourable cases is it possible to provide atomic-level descriptions of sparsely populated and transiently formed alternative conformations. Here we benchmark the ability of enhanced-sampling molecular dynamics simulations to determine the free energy landscape of the L99A cavity mutant of T4 lysozyme. We find that the simulations capture key properties previously measured by NMR relaxation dispersion methods including the structure of a minor conformation, the kinetics and thermodynamics of conformational exchange, and the effect of mutations. We discover a new tunnel that involves the transient exposure towards the solvent of an internal cavity, and show it to be relevant for ligand escape. Together, our results provide a comprehensive view of the structural landscape of a protein, and point forward to studies of conformational exchange in systems that are less characterized experimentally. DOI: http://dx.doi.org/10.7554/eLife.17505.001 PMID:27552057

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

    NASA Astrophysics Data System (ADS)

    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

  14. Energy landscape paving with local search for global optimization of the BLN off-lattice model

    NASA Astrophysics Data System (ADS)

    Liu, Jingfa; Huang, Weibo; Liu, Wenjie; Song, Beibei; Sun, Yuanyuan; Chen, Mao

    2014-02-01

    The optimization problem for finding the global minimum energy structure is one of the main problems of protein structure prediction and is known to be an NP-hard problem in computational molecular biology. The low-energy conformational search problem in the hydrophobic-hydrophilic-neutral (BLN) off-lattice model is studied. We convert the problem into an unconstrained optimization problem by introducing the penalty function. By putting forward a new updating mechanism of the histogram function in the energy landscape paving (ELP) method and incorporating heuristic conformation update strategies into the ELP method, we obtain an improved ELP (IELP) method. Subsequently, by combining the IELP method with the local search (LS) based on the gradient descent method, we propose a hybrid algorithm, denoted by IELP-LS, for the conformational search of the off-lattice BLN model. Simulation results indicate that IELP-LS can find lower-energy states than other methods in the literature, showing that the proposed method is an effective tool for global optimization in the BLN off-lattice protein model.

  15. Proton transfer pathways, energy landscape, and kinetics in creatine-water systems.

    PubMed

    Ivchenko, Olga; Whittleston, Chris S; Carr, Joanne M; Imhof, Petra; Goerke, Steffen; Bachert, Peter; Wales, David J

    2014-02-27

    We study the exchange processes of the metabolite creatine, which is present in both tumorous and normal tissues and has NH2 and NH groups that can transfer protons to water. Creatine produces chemical exchange saturation transfer (CEST) contrast in magnetic resonance imaging (MRI). The proton transfer pathway from zwitterionic creatine to water is examined using a kinetic transition network constructed from the discrete path sampling approach and an approximate quantum-chemical energy function, employing the self-consistent-charge density-functional tight-binding (SCC-DFTB) method. The resulting potential energy surface is visualized by constructing disconnectivity graphs. The energy landscape consists of two distinct regions corresponding to the zwitterionic creatine structures and deprotonated creatine. The activation energy that characterizes the proton transfer from the creatine NH2 group to water was determined from an Arrhenius fit of rate constants as a function of temperature, obtained from harmonic transition state theory. The result is in reasonable agreement with values obtained in water exchange spectroscopy (WEX) experiments.

  16. Golf-course and funnel energy landscapes: Protein folding concepts in martensites

    NASA Astrophysics Data System (ADS)

    Shankaraiah, N.

    2017-06-01

    We use protein folding energy landscape concepts such as golf course and funnel to study re-equilibration in athermal martensites under systematic temperature quench Monte Carlo simulations. On quenching below a transition temperature, the seeded high-symmetry parent-phase austenite that converts to the low-symmetry product-phase martensite, through autocatalytic twinning or elastic photocopying, has both rapid conversions and incubation delays in the temperature-time-transformation phase diagram. We find the rapid (incubation delays) conversions at low (high) temperatures arises from the presence of large (small) size of golf-course edge that has the funnel inside for negative energy states. In the incubating state, the strain structure factor enters into the Brillouin-zone golf course through searches for finite transitional pathways which close off at the transition temperature with Vogel-Fulcher divergences that are insensitive to Hamiltonian energy scales and log-normal distributions, as signatures of dominant entropy barriers. The crossing of the entropy barrier is identified through energy occupancy distributions, Monte Carlo acceptance fractions, heat emission, and internal work.

  17. Protein structure prediction and potential energy landscape analysis using continuous global minimization

    SciTech Connect

    Dill, K.A.; Phillips, A.T.; Rosen, J.B.

    1997-12-01

    Proteins require specific three-dimensional conformations to function properly. These {open_quotes}native{close_quotes} conformations result primarily from intramolecular interactions between the atoms in the macromolecule, and also intermolecular interactions between the macromolecule and the surrounding solvent. Although the folding process can be quite complex, the instructions guiding this process are specified by the one-dimensional primary sequence of the protein or nucleic acid: external factors, such as helper (chaperone) proteins, present at the time of folding have no effect on the final state of the protein. Many denatured proteins spontaneously refold into functional conformations once denaturing conditions are removed. Indeed, the existence of a unique native conformation, in which residues distant in sequence but close in proximity exhibit a densely packed hydrophobic core, suggests that this three-dimensional structure is largely encoded within the sequential arrangement of these specific amino acids. In any case, the native structure is often the conformation at the global minimum energy. In addition to the unique native (minimum energy) structure, other less stable structures exist as well, each with a corresponding potential energy. These structures, in conjunction with the native structure, make up an energy landscape that can be used to characterize various aspects of the protein structure. 22 refs., 10 figs., 2 tabs.

  18. Homogenous Nucleation and Crystal Growth in a Model Liquid from Direct Energy Landscape Sampling Simulation

    NASA Astrophysics Data System (ADS)

    Walter, Nathan; Zhang, Yang

    Nucleation and crystal growth are understood to be activated processes involving the crossing of free-energy barriers. Attempts to capture the entire crystallization process over long timescales with molecular dynamic simulations have met major obstacles because of molecular dynamics' temporal constraints. Herein, we circumvent this temporal limitation by using a brutal-force, metadynamics-like, adaptive basin-climbing algorithm and directly sample the free-energy landscape of a model liquid Argon. The algorithm biases the system to evolve from an amorphous liquid like structure towards an FCC crystal through inherent structure, and then traces back the energy barriers. Consequently, the sampled timescale is macroscopically long. We observe that the formation of a crystal involves two processes, each with a unique temperature-dependent energy barrier. One barrier corresponds to the crystal nucleus formation; the other barrier corresponds to the crystal growth. We find the two processes dominate in different temperature regimes. Compared to other computation techniques, our method requires no assumptions about the shape or chemical potential of the critical crystal nucleus. The success of this method is encouraging for studying the crystallization of more complex

  19. Molecular shape and the energetics of chemisorption: From simple to complex energy landscapes

    NASA Astrophysics Data System (ADS)

    Huang, David M.; Harrowell, Peter

    2012-07-01

    We enumerate all local minima of the energy landscape for model rigid adsorbates characterized by three or four equivalent binding sites (e.g., thiol groups) on a close-packed (111) surface of a face-centered-cubic crystal. We show that the number of energy minima increases linearly with molecular size with a rate of increase that depends on the degree of registry between the molecule shape and the surface structure. The sparseness of energy minima and the large variations in the center-of-mass positions of these minima vs molecular size for molecules that are incommensurate with the surface suggests a strong coupling in these molecules between surface mobility and shape or size fluctuations resulting from molecular vibrations. We also find that the variation in the binding energy with respect to molecular size decreases more rapidly with molecular size for molecules with a higher degree of registry with the surface. This indicates that surface adsorption should be better able to distinguish molecules by size if the molecules are incommensurate with the surface.

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

    NASA Astrophysics Data System (ADS)

    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

  1. Energy landscape-driven non-equilibrium evolution of inherent structure in disordered material

    NASA Astrophysics Data System (ADS)

    Fan, Yue; Iwashita, Takuya; Egami, Takeshi

    2017-05-01

    Complex states in glasses can be neatly expressed by the potential energy landscape (PEL). However, because PEL is highly multi-dimensional it is difficult to describe how the system moves around in PEL. Here we demonstrate that it is possible to predict the evolution of macroscopic state in a metallic glass, such as ageing and rejuvenation, through a set of simple equations describing excitations in the PEL. The key to this simplification is the realization that the step of activation from the initial state to the saddle point in PEL and the following step of relaxation to the final state are essentially decoupled. The model shows that the interplay between activation and relaxation in PEL is the key driving force that simultaneously explains both the equilibrium of supercooled liquid and the thermal hysteresis observed in experiments. It further predicts anomalous peaks in truncated thermal scanning, validated by independent molecular dynamics simulation.

  2. Free energy landscape of activation in a signalling protein at atomic resolution

    NASA Astrophysics Data System (ADS)

    Pontiggia, F.; Pachov, D. V.; Clarkson, M. W.; Villali, J.; Hagan, M. F.; Pande, V. S.; Kern, D.

    2015-06-01

    The interconversion between inactive and active protein states, traditionally described by two static structures, is at the heart of signalling. However, how folded states interconvert is largely unknown due to the inability to experimentally observe transition pathways. Here we explore the free energy landscape of the bacterial response regulator NtrC by combining computation and nuclear magnetic resonance, and discover unexpected features underlying efficient signalling. We find that functional states are defined purely in kinetic and not structural terms. The need of a well-defined conformer, crucial to the active state, is absent in the inactive state, which comprises a heterogeneous collection of conformers. The transition between active and inactive states occurs through multiple pathways, facilitated by a number of nonnative transient hydrogen bonds, thus lowering the transition barrier through both entropic and enthalpic contributions. These findings may represent general features for functional conformational transitions within the folded state.

  3. Navigating membrane protein structure, dynamics, and energy landscapes using spin labeling and EPR spectroscopy

    PubMed Central

    Claxton, Derek P; Kazmier, Kelli; Mishra, Smriti; Mchaourab, Hassane S

    2017-01-01

    A detailed understanding of the functional mechanism of a protein entails the characterization of its energy landscape. Achieving this ambitious goal requires the integration of multiple approaches including determination of high resolution crystal structures, uncovering conformational sampling under distinct biochemical conditions, characterizing the kinetics and thermodynamics of transitions between functional intermediates using spectroscopic techniques, and interpreting and harmonizing the data into novel computational models. With increasing sophistication in solution-based and ensemble-oriented biophysical approaches such as electron paramagnetic resonance (EPR) spectroscopy, atomic resolution structural information can be directly linked to conformational sampling in solution. Here, we detail how recent methodological and technological advances in EPR spectroscopy have contributed to the elucidation of membrane protein mechanisms. Furthermore, we aim to assist investigators interested in pursuing EPR studies by providing an introduction to the technique, a primer on experimental design, and a description of the practical considerations of the method towards generating high quality data. PMID:26477257

  4. Energy landscape-driven non-equilibrium evolution of inherent structure in disordered material

    DOE PAGES

    Fan, Yue; Iwashita, Takuya; Egami, Takeshi

    2017-05-19

    Complex states in glasses can be neatly expressed by the potential energy landscape (PEL). But, because PEL is highly multi-dimensional it is difficult to describe how the system moves around in PEL. We demonstrate that it is possible to predict the evolution of macroscopic state in a metallic glass, such as ageing and rejuvenation, through a set of simple equations describing excitations in the PEL. The key to this simplification is the realization that the step of activation from the initial state to the saddle point in PEL and the following step of relaxation to the final state are essentiallymore » decoupled. Furthermore, the model shows that the interplay between activation and relaxation in PEL is the key driving force that simultaneously explains both the equilibrium of supercooled liquid and the thermal hysteresis observed in experiments. It further predicts anomalous peaks in truncated thermal scanning, validated by independent molecular dynamics simulation.« less

  5. Free energy landscape of activation in a signaling protein at atomic resolution

    PubMed Central

    Pontiggia, F.; Pachov, D.V.; Clarkson, M.W.; Villali, J.; Hagan, M.F.; Pande, V.S.; Kern, D.

    2015-01-01

    The interconversion between inactive and active protein states, traditionally described by two static structures, is at the heart of signaling. However, how folded states interconvert is largely unknown due to the inability to experimentally observe transition pathways. Here we explore the free energy landscape of the bacterial response regulator NtrC by combining computation and NMR, and discover unexpected features underlying efficient signaling. We find that functional states are defined purely in kinetic and not structural terms. The need of a well-defined conformer, crucial to the active state, is absent in the inactive state, which comprises a heterogeneous collection of conformers. The transition between active and inactive states occurs through multiple pathways, facilitated by a number of nonnative transient hydrogen bonds, thus lowering the transition barrier through both entropic and enthalpic contributions. These findings may represent general features for functional conformational transitions within the folded state. PMID:26073309

  6. Up and away in the potential landscape of diatomic molecule potential energy curves

    NASA Astrophysics Data System (ADS)

    Stwalley, William C.

    2016-12-01

    The understanding of the potential curves of a given molecule has expanded in many ways during my last 52 years as an experimental and theoretical molecular chemist/physicist in graduate school in Chemistry at Harvard and in both the Chemistry and Physics Departments at University of Iowa and University of Connecticut. This expansion has been up in energy and vibrational and rotational quantum numbers and away from Re to long range as well. It is clear that Prof. Robert Le Roy, who I have known since the late 1960s, has made many important and greatly appreciated contributions to the landscape I describe below from my personal perspective, especially with regard to long range molecules and solution of the radial Schrödinger equations and related calculations.

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

    NASA Astrophysics Data System (ADS)

    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 (<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. HfB2 has a very high bulk glass transition temperature Tg, and we observe no three-state hopping or sequential two-state hopping previously seen on lower Tg 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.

  8. Rugged Energy Landscapes in Multiphase Porous Media Flow: A Discrete-Domain Description

    NASA Astrophysics Data System (ADS)

    Cueto-Felgueroso, L.; Juanes, R.

    2015-12-01

    Immiscible displacements in porous media involve a complex sequence of pore-scale events, from the smooth, reversible displacement of interfaces to abrupt interfacial reconfigurations and rapid pore invasion cascades. Discontinuous changes in pressure or saturation have been referred to as Haines jumps, and they emerge as a key mechanism to understand the origin of hysteresis in porous media flow. Hysteresis persists at the many-pore scale: when multiple cycles of drainage and imbibition of a porous sample are conducted, a dense hysteresis diagram emerges. The interpretation of hysteresis as a consequence of irreversible transitions and multistability is at the heart of early hysteresis models, and in recent experiments, and points to an inherently non-equilibrium behavior. For a given volume fraction of fluids occupying the pore space, many stable configurations are possible, due to the tortuous network of nonuniform pores and throats that compose the porous medium, and to complex wetting and capillary transitions. Multistability indicates that porous media systems exhibit rugged energy landscapes, where the system may remain pinned at local energy minima for long times. We address the question of developing a zero-dimensional model that inherits the path-dependence and `'bursty'' behavior of immiscible displacements, and propose a discrete-domain model that captures the role of metastability and local equilibria in the origin of hysteresis. We describe the porous medium and fluid system as a discrete set of weakly connected, multistable compartments, charaterized by a unique free energy function. This description does not depend explicitly on past saturations, turning points, or drainage/imbibition labels. The system behaves hysteretically, and we rationalize its behavior as sweeping a complex metastability diagram, with dissipation arising from discrete switches among metastable branches. The hysteretic behavior of the pressure-saturation curve is controlled by

  9. ENERGY-DEPENDENT GAMMA-RAY BURST PULSE WIDTH DUE TO THE CURVATURE EFFECT AND INTRINSIC BAND SPECTRUM

    SciTech Connect

    Peng, Z. Y.; Ma, L.; Zhao, X. H.; Yin, Y.; Bao, Y. Y.

    2012-06-20

    Previous studies have found that the width of the gamma-ray burst (GRB) pulse is energy dependent and that it decreases as a power-law function with increasing photon energy. In this work we have investigated the relation between the energy dependence of the pulse and the so-called Band spectrum by using a sample including 51 well-separated fast rise and exponential decay long-duration GRB pulses observed by BATSE (Burst and Transient Source Experiment on the Compton Gamma Ray Observatory). We first decompose these pulses into rise and decay phases and find that the rise widths and the decay widths also behave as a power-law function with photon energy. Then we investigate statistically the relations between the three power-law indices of the rise, decay, and total width of the pulse (denoted as {delta}{sub r}, {delta}{sub d}, and {delta}{sub w}, respectively) and the three Band spectral parameters, high-energy index ({alpha}), low-energy index ({beta}), and peak energy (E{sub p} ). It is found that (1) {alpha} is strongly correlated with {delta}{sub w} and {delta}{sub d} but seems uncorrelated with {delta}{sub r}; (2) {beta} is weakly correlated with the three power-law indices, and (3) E{sub p} does not show evident correlations with the three power-law indices. We further investigate the origin of {delta}{sub d}-{alpha} and {delta}{sub w}-{alpha}. We show that the curvature effect and the intrinsic Band spectrum could naturally lead to the energy dependence of the GRB pulse width and also the {delta}{sub d}-{alpha} and {delta}{sub w}-{alpha} correlations. Our results hold so long as the shell emitting gamma rays has a curved surface and the intrinsic spectrum is a Band spectrum or broken power law. The strong {delta}{sub d}-{alpha} correlation and inapparent correlations between {delta}{sub r} and the three Band spectral parameters also suggest that the rise and decay phases of the GRB pulses have different origins.

  10. Landscapes for energy and wildlife: conservation prioritization for golden eagles across large spatial scales

    USGS Publications Warehouse

    Tack, Jason D.; Fedy, Bradley C.

    2015-01-01

    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.

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

    PubMed Central

    Tack, Jason D.; Fedy, Bradley C.

    2015-01-01

    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. PMID:26262876

  12. Exploring the Energy Landscapes of Protein Folding Simulations with Bayesian Computation

    PubMed Central

    Burkoff, Nikolas S.; Várnai, Csilla; Wells, Stephen A.; Wild, David L.

    2012-01-01

    Nested sampling is a Bayesian sampling technique developed to explore probability distributions localized in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence (marginal likelihood) of the model. The nested sampling algorithm also provides an efficient way to calculate free energies and the expectation value of thermodynamic observables at any temperature, through a simple post processing of the output. Previous applications of the algorithm have yielded large efficiency gains over other sampling techniques, including parallel tempering. In this article, we describe a parallel implementation of the nested sampling algorithm and its application to the problem of protein folding in a Gō-like force field of empirical potentials that were designed to stabilize secondary structure elements in room-temperature simulations. We demonstrate the method by conducting folding simulations on a number of small proteins that are commonly used for testing protein-folding procedures. A topological analysis of the posterior samples is performed to produce energy landscape charts, which give a high-level description of the potential energy surface for the protein folding simulations. These charts provide qualitative insights into both the folding process and the nature of the model and force field used. PMID:22385859

  13. The energy landscape, folding pathways and the kinetics of a knotted protein.

    PubMed

    Prentiss, Michael C; Wales, David J; Wolynes, Peter G

    2010-07-01

    The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N or C terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N terminus portion of the knot and a rate-determining step where the C terminus is incorporated. The low-lying minima with the N terminus knotted and the C terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N and C termini into the knot occurs late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.

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

    PubMed

    Tack, Jason D; Fedy, Bradley C

    2015-01-01

    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.

  15. Resting and Energy Reserves of Aedes albopictus Collected in Common Landscaping Vegetation in St. Augustine, Florida

    PubMed Central

    Samson, Dayana M.; Qualls, Whitney A.; Roque, Deborah; Naranjo, Diana P.; Alimi, Temitope; Arheart, Kristopher L.; Müller, Günter C.; Beier, John C.

    2014-01-01

    The resting behavior of Aedes albopictus was evaluated by aspirating diurnal resting mosquitoes from common landscape vegetation in residential communities in St. Augustine, FL. Energy reserves of the resting mosquitoes were analyzed to determine if there was a correlation between mosquito resting habitat and energy accumulation. Six species of plants were selected and 9 collections of resting mosquitoes were aspirated from each plant using a modified John W. Hock backpack aspirator during June and July 2012. Eight mosquito species were collected, with Ae. albopictus representing 74% of the overall collection. The number of Ae. albopictus collected varied significantly with the species of vegetation. When comparing the vegetation and abundance of resting mosquitoes, the highest percentages of Ae. albopictus were collected resting on Ruellia brittoniana (Mexican petunia), Asplenium platyneuron (fern), Gibasis geniculate (Tahitian bridal veil), followed by Plumba goauriculata (plumbago), Setcreasea pallida (purple heart), and Hibiscus tiliaceus (hibiscus). There were significant differences in lipid and glycogen accumulation based on type of vegetation Ae. albopictus was found resting in. Resting mosquitoes' sugar reserves were not influenced by species of vegetation. However, there was an overall correlation between vegetation that serves as a resting habitat and energy reserve accumulation. The results of our study demonstrate the potential to target specific vegetation for control of diurnal resting mosquitoes. PMID:24199497

  16. NMR characterization of the energy landscape of SUMO-1 in the native-state ensemble.

    PubMed

    Kumar, Ashutosh; Srivastava, Sudha; Hosur, Ramakrishna V

    2007-04-13

    Characterizing the low energy excited states in the energy landscape of a protein is one of the exciting and demanding problems in structural biology at the present time. These describe the adaptability of the protein structure to external perturbations. In this context, we used here non-linear dependence of amide proton chemical shifts on temperature to identify residues accessing alternative conformations in SUMO-1 in the native state as well as in the near-native states created by sub-denaturing concentrations of urea. The number of residues accessing alternative conformations increases and the profiles of curved temperature dependence also change with increasing urea concentration. In every case these alternative conformations lie within 2 kcal/mol from the ground state, and are separated from it by low energy barriers. The residues that access alternative conformations span the length of the protein chain but are located at particular regions on the protein structure. These include many of the loops, beta2 and beta5 strands, and some edges of the helices. We observed that some of the regions of the protein structure that exhibit such fluctuations coincide with the protein's binding surfaces with different substrate like GTPase effector domain (GED) of dynamin, SUMO binding motifs (SBM), E1 (activating enzyme, SAE1/SAE2) and E2 (conjugating enzyme, UBC9) enzymes of sumoylation machinery, reported earlier. We speculate that this would have significant implications for the binding of diversity of targets by SUMO-1 for the variety of functions it is involved in.

  17. The potential and flux landscape theory of evolution

    NASA Astrophysics Data System (ADS)

    Zhang, Feng; Xu, Li; Zhang, Kun; Wang, Erkang; Wang, Jin

    2012-08-01

    We established the potential and flux landscape theory for evolution. We found explicitly the conventional Wright's gradient adaptive landscape based on the mean fitness is inadequate to describe the general evolutionary dynamics. We show the intrinsic potential as being Lyapunov function(monotonically decreasing in time) does exist and can define the adaptive landscape for general evolution dynamics for studying global stability. The driving force determining the dynamics can be decomposed into gradient of potential landscape and curl probability flux. Non-zero flux causes detailed balance breaking and measures how far the evolution from equilibrium state. The gradient of intrinsic potential and curl flux are perpendicular to each other in zero fluctuation limit resembling electric and magnetic forces on electrons. We quantified intrinsic energy, entropy and free energy of evolution and constructed non-equilibrium thermodynamics. The intrinsic non-equilibrium free energy is a Lyapunov function. Both intrinsic potential and free energy can be used to quantify the global stability and robustness of evolution. We investigated an example of three allele evolutionary dynamics with frequency dependent selection (detailed balance broken). We uncovered the underlying single, triple, and limit cycle attractor landscapes. We found quantitative criterions for stability through landscape topography. We also quantified evolution pathways and found paths do not follow potential gradient and are irreversible due to non-zero flux. We generalized the original Fisher's fundamental theorem to the general (i.e., frequency dependent selection) regime of evolution by linking the adaptive rate with not only genetic variance related to the potential but also the flux. We show there is an optimum potential where curl flux resulting from biotic interactions of individuals within a species or between species can sustain an endless evolution even if the physical environment is unchanged. We

  18. The potential and flux landscape theory of evolution.

    PubMed

    Zhang, Feng; Xu, Li; Zhang, Kun; Wang, Erkang; Wang, Jin

    2012-08-14

    We established the potential and flux landscape theory for evolution. We found explicitly the conventional Wright's gradient adaptive landscape based on the mean fitness is inadequate to describe the general evolutionary dynamics. We show the intrinsic potential as being Lyapunov function(monotonically decreasing in time) does exist and can define the adaptive landscape for general evolution dynamics for studying global stability. The driving force determining the dynamics can be decomposed into gradient of potential landscape and curl probability flux. Non-zero flux causes detailed balance breaking and measures how far the evolution from equilibrium state. The gradient of intrinsic potential and curl flux are perpendicular to each other in zero fluctuation limit resembling electric and magnetic forces on electrons. We quantified intrinsic energy, entropy and free energy of evolution and constructed non-equilibrium thermodynamics. The intrinsic non-equilibrium free energy is a Lyapunov function. Both intrinsic potential and free energy can be used to quantify the global stability and robustness of evolution. We investigated an example of three allele evolutionary dynamics with frequency dependent selection (detailed balance broken). We uncovered the underlying single, triple, and limit cycle attractor landscapes. We found quantitative criterions for stability through landscape topography. We also quantified evolution pathways and found paths do not follow potential gradient and are irreversible due to non-zero flux. We generalized the original Fisher's fundamental theorem to the general (i.e., frequency dependent selection) regime of evolution by linking the adaptive rate with not only genetic variance related to the potential but also the flux. We show there is an optimum potential where curl flux resulting from biotic interactions of individuals within a species or between species can sustain an endless evolution even if the physical environment is unchanged. We

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

    PubMed

    Seki, Kazuhiko; Bagchi, Kaushik; Bagchi, Biman

    2016-05-21

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  1. Characterizing Protein Energy Landscape by Self-Learning Multiscale Simulations: Application to a Designed β-Hairpin

    PubMed Central

    Li, Wenfei; Takada, Shoji

    2010-01-01

    Characterizing the energy landscape of proteins at atomic resolution is still a very challenging problem, since it simultaneously requires high accuracy in estimating specific interactions and high efficiency in conformational sampling. Here, for these two requirements to meet, we extended the self-learning multiscale simulation (SLMS) method developed recently and applied it to the designed β-hairpin CLN025. The SLMS integrates all-atom and coarse-grained (CG) models in an iterative way such that the conformational sampling is performed by the CG model, the AA energy is used to calibrate the energy landscape, and the CG model is improved by the calibrated energy landscape. We extended the SLMS in two aspects, use of the energy decomposition for self-learning of the CG potential and a two-bead/residue CG model. The results show that the self-learning greatly improved the CG potential, and with the derived CG potential, the β-hairpin CLN025 robustly folded to the native structure. The self-learning iteration progressively enhanced the context dependence in the CG potential and increased the energy gap between the native and the denatured states of the CG model, leading to a funnel-like energy landscape. By using the SLMS method, without prior knowledge of the native structure but with the help of the AA energy, we can obtain a tailor-made CG potential specific to the target protein. The method can be useful for de novo structure prediction as well. PMID:21044601

  2. Free energy landscapes for S-H bonds in Cp*2Mo2S4 complexes.

    PubMed

    Appel, Aaron M; Lee, Suh-Jane; Franz, James A; DuBois, Daniel L; DuBois, M Rakowski

    2009-04-15

    An extensive family of thermochemical data is presented for a series of complexes derived from Cp*Mo(mu-S)(2)(mu-SMe)(mu-SH)MoCp* and Cp*Mo(mu-S)(2)(mu-SH)(2)MoCp*. These data include electrochemical potentials, pK(a) values, homolytic solution bond dissociation free energies (SBDFEs), and hydride donor abilities in acetonitrile. Thermochemical data ranged from +0.6 to -2.0 V vs FeCp(2)(+/o) for electrochemical potentials, 5 to 31 for pK(a) values, 43 to 68 kcal/mol for homolytic SBDFEs, and 44 to 84 kcal/mol for hydride donor abilities. The observed values for these thermodynamic parameters are comparable to those of many transition metal hydrides, which is consistent with the many parallels in the chemistry of these two classes of compounds. The extensive set of thermochemical data is presented in free energy landscapes as a useful approach to visualizing and understanding the relative stabilities of all of the species under varying conditions of pH and H(2) overpressure. In addition to the previously studied homogeneous reactivity and catalysis, Mo(2)S(4) complexes are also models for heterogeneous molybdenum sulfide catalysts, and therefore, the present results demonstrate the dramatic range of S-H bond strengths available in both homogeneous and heterogeneous reaction pathways.

  3. Hybrid organic-inorganic inks flatten the energy landscape in colloidal quantum dot solids

    NASA Astrophysics Data System (ADS)

    Liu, Mengxia; Voznyy, Oleksandr; Sabatini, Randy; García de Arquer, F. Pelayo; Munir, Rahim; Balawi, Ahmed Hesham; Lan, Xinzheng; Fan, Fengjia; Walters, Grant; Kirmani, Ahmad R.; Hoogland, Sjoerd; Laquai, Frédéric; Amassian, Aram; Sargent, Edward H.

    2017-02-01

    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.

  4. Charting molecular free-energy landscapes with an atlas of collective variables

    NASA Astrophysics Data System (ADS)

    Hashemian, Behrooz; Millán, Daniel; Arroyo, Marino

    2016-11-01

    Collective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. However, identifying suitable CVs is challenging, and is increasingly addressed with systematic data-driven manifold learning techniques. Here, we provide a flexible framework to model molecular systems in terms of a collection of locally valid and partially overlapping CVs: an atlas of CVs. The specific motivation for such a framework is to enhance the applicability and robustness of CVs based on manifold learning methods, which fail in the presence of periodicities in the underlying conformational manifold. More generally, using an atlas of CVs rather than a single chart may help us better describe different regions of conformational space. We develop the statistical mechanics foundation for our multi-chart description and propose an algorithmic implementation. The resulting atlas of data-based CVs are then used to enhance sampling and compute free energy surfaces in two model systems, alanine dipeptide and β-D-glucopyranose, whose conformational manifolds have toroidal and spherical topologies.

  5. Hybrid organic-inorganic inks flatten the energy landscape in colloidal quantum dot solids

    NASA Astrophysics Data System (ADS)

    Liu, Mengxia; Voznyy, Oleksandr; Sabatini, Randy; García de Arquer, F. Pelayo; Munir, Rahim; Balawi, Ahmed Hesham; Lan, Xinzheng; Fan, Fengjia; Walters, Grant; Kirmani, Ahmad R.; Hoogland, Sjoerd; Laquai, Frédéric; Amassian, Aram; Sargent, Edward H.

    2016-11-01

    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.

  6. Hybrid organic-inorganic inks flatten the energy landscape in colloidal quantum dot solids.

    PubMed

    Liu, Mengxia; Voznyy, Oleksandr; Sabatini, Randy; García de Arquer, F Pelayo; Munir, Rahim; Balawi, Ahmed Hesham; Lan, Xinzheng; Fan, Fengjia; Walters, Grant; Kirmani, Ahmad R; Hoogland, Sjoerd; Laquai, Frédéric; Amassian, Aram; Sargent, Edward H

    2017-02-01

    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.

  7. Impact of Ion Binding on Poly-L-Lysine (Un)folding Energy Landscape and Kinetics

    PubMed Central

    Xiong, Kan; Asher, Sanford A.

    2012-01-01

    We utilize T-jump UV resonance Raman spectroscopy to study the impact of ion binding on the equilibrium energy landscape and on (un)folding kinetics of poly-L-lysine (PLL). We observe that the relaxation rates of the folded conformations (including π-helix (bulge), pure α-helix and turns) of PLL are slower than those of short alanine based peptides. The PLL pure α-helix folding time is similar to that of short alanine based peptides. We, for the first time have directly observed that turn conformations are α-helix and π-helix (bulge) unfolding intermediates. ClO4− binding to the lys side chain –NH3+ groups and the peptide backbone slows the α-helix unfolding rate compared to that in pure water, but little impacts the folding rate, resulting in an increased α-helix stability. ClO4− binding significantly increases the PLL unfolding activation barrier but little impacts the folding barrier. Thus, the PLL folding coordinate differs from the unfolding coordinate. The π-helix (bulge) unfolding and folding coordinates do not directly go through the α-helix energy well. Our results clearly demonstrate that PLL (un)folding is not a two-state process. PMID:22612556

  8. Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters.

    PubMed

    Tapia-Rojo, Rafael; Mazo, Juan José; Hernández, José Ángel; Peleato, María Luisa; Fillat, María F; Falo, Fernando

    2014-10-01

    The identification of protein binding sites in promoter sequences is a key problem to understand and control regulation in biochemistry and biotechnological processes. We use a computational method to analyze promoters from a given genome. Our approach is based on a physical model at the mesoscopic level of protein-DNA interaction based on the influence of DNA local conformation on the dynamics of a general particle along the chain. Following the proposed model, the joined dynamics of the protein particle and the DNA portion of interest, only characterized by its base pair sequence, is simulated. The simulation output is analyzed by generating and analyzing the Free Energy Landscape of the system. In order to prove the capacity of prediction of our computational method we have analyzed nine promoters of Anabaena PCC 7120. We are able to identify the transcription starting site of each of the promoters as the most populated macrostate in the dynamics. The developed procedure allows also to characterize promoter macrostates in terms of thermo-statistical magnitudes (free energy and entropy), with valuable biological implications. Our results agree with independent previous experimental results. Thus, our methods appear as a powerful complementary tool for identifying protein binding sites in promoter sequences.

  9. Evolution of intrinsic growth and energy acquisition rates. I. Trade-offs with swimming performance in Menidia menidia.

    PubMed

    Billerbeck, J M; Lankford, T E; Conover, D O

    2001-09-01

    Latitudinal populations of the Atlantic silverside, Menidia menidia, show substantial genetic variation in rates of energy acquistion and allocation. Reared in common environments, silversides from northern latitudes consume more food, grow faster and more efficiently, store more energy, and produce greater quantities of eggs than their southern conspecifics. The persistence of seemingly inferior southern genotypes in the face of ostensibly superior northern genotypes suggest that there are hidden evolutionary trade-offs associated with these elevated acquisition and allocation rates. We tested the hypothesis that rapid growth and high levels of food consumption trade-off against locomotory performance in M. menidia. We compared both aerobic (prolonged and endurance) and anaerobic (burst) swimming capacities between intrinsically fast-growing fish from the north (Nova Scotia, NS) and intrinsically slow-growing fish from the south (South Carolina, SC) and between growth-manipulated phenotypes within each population. We also compared swimming speeds and endurance between fasted and recently fed fish within populations. Maximum prolonged and burst swimming speeds of NS fish were significantly lower than those of SC fish, and swimming speeds of fast-growing phenotypes were lower than those of slow-growing phenotypes within populations. Fed fish had lower burst speeds and less endurance than fasted fish from the same population. Thus, high rates of growth and the consumption of large meals clearly diminish swimming performance, which likely increases vulnerability to predation and decreases survival and relative fitness. The submaximal growth rate of southern M. menidia appears to be adaptive, resulting from balancing selection on rates of somatic growth.

  10. A self-powered thin-film radiation detector using intrinsic high-energy current

    SciTech Connect

    Zygmanski, Piotr E-mail: Erno-Sajo@uml.edu; Sajo, Erno E-mail: Erno-Sajo@uml.edu

    2016-01-15

    Purpose: The authors introduce a radiation detection method that relies on high-energy current (HEC) formed by secondary charged particles in the detector material, which induces conduction current in an external readout circuit. Direct energy conversion of the incident radiation powers the signal formation without the need for external bias voltage or amplification. The detector the authors consider is a thin-film multilayer device, composed of alternating disparate electrically conductive and insulating layers. The optimal design of HEC detectors consists of microscopic or nanoscopic structures. Methods: Theoretical and computational developments are presented to illustrate the salient properties of the HEC detector and to demonstrate its feasibility. In this work, the authors examine single-sandwiched and periodic layers of Cu and Al, and Au and Al, ranging in thickness from 100 nm to 300 μm and separated by similarly sized dielectric gaps, exposed to 120 kVp x-ray beam (half-value thickness of 4.1 mm of Al). The energy deposition characteristics and the high-energy current were determined using radiation transport computations. Results: The authors found that in a dual-layer configuration, the signal is in the measurable range. For a defined total detector thickness in a multilayer structure, the signal sharply increases with decreasing thickness of the high-Z conductive layers. This paper focuses on the computational results while a companion paper reports the experimental findings. Conclusions: Significant advantages of the device are that it does not require external power supply and amplification to create a measurable signal; it can be made in any size and geometry, including very thin (sub-millimeter to submicron) flexible curvilinear forms, and it is inexpensive. Potential applications include medical dosimetry (both in vivo and external), radiation protection, and other settings where one or more of the above qualities are desired.

  11. Prototypes of Self-Powered Radiation Detectors Employing Intrinsic High-Energy Current (HEC) (POSTPRINT)

    DTIC Science & Technology

    2016-01-01

    most efficient when the incident x - rays interact with high- Z materials by photoelectric absorption , resulting in photo- electrons, Auger electrons...effect of direct energy conversion of x - rays via selfpowered Auger- and photocurrent, potentially suitable to practical radiation detection and...plane-parallel 60-120 kVp x - ray beams. For the experimental design and verification, the authors performed coupled electron-photon radiation transport

  12. A New Polymer Nanoprobe Based on Chemiluminescence Resonance Energy Transfer for Ultrasensitive Imaging of Intrinsic Superoxide Anion in Mice.

    PubMed

    Li, Ping; Liu, Lu; Xiao, Haibin; Zhang, Wei; Wang, Lulin; Tang, Bo

    2016-03-09

    Despite significant developments in optical imaging of superoxide anion (O2(•-)) as the preliminary reactive oxygen species, novel visualizing strategies that offer ultrahigh sensitivity are still imperative. This is mainly because intrinsic concentrations of O2(•-) are extremely low in living systems. Herein, we present the rational design and construction of a new polymer nanoprobe PCLA-O2(•-) for detecting O2(•-) based on chemiluminescence (CL) resonance energy transfer without an external excitation source. Structurally, PCLA-O2(•-) contains two moieties linked covalently, namely imidazopyrazinone that is capable of CL triggered by O2(•-) as the energy donor and conjugated polymers with light-amplifying property as the energy acceptor. Experiment results demonstrate that PCLA-O2(•-) exhibits ultrahigh sensitivity at the picomole level, dramatically prolonged luminescence time, specificity, and excellent biocompatibility. Without exogenous stimulation, this probe for the first time in situ visualizes O2(•-) level differences between normal and tumor tissues of mice. These exceptional features ensure that PCLA-O2(•-) as a self-luminescing probe is an alternative in vivo imaging approach for ultralow level O2(•-).

  13. Prototypes of self-powered radiation detectors employing intrinsic high-energy current

    SciTech Connect

    Zygmanski, Piotr Briovio, Davide; Shrestha, Suman; Karellas, Andrew; Sajo, Erno

    2016-01-15

    Purpose: The authors experimentally investigate the effect of direct energy conversion of x-rays via selfpowered Auger- and photocurrent, potentially suitable to practical radiation detection and dosimetry in medical applications. Experimental results are compared to computational predictions. The detector the authors consider is a thin-film multilayer device, composed of alternating disparate electrically conductive and insulating layers. This paper focuses on the experiments while a companion paper introduces the fundamental concepts of high-energy current (HEC) detectors. Methods: The energy of ionizing radiation is directly converted to detector signal via electric current induced by high-energy secondary electrons generated in the detector material by the incident primary radiation. The HEC electrons also ionize the dielectric and the resultant charge carriers are selfcollected due to the contact potential of the disparate electrodes. Thus, an electric current is induced in the conductors in two different ways without the need for externally applied bias voltage or amplification. Thus, generated signal in turn is digitized by a data acquisition system. To determine the fundamental properties of the HEC detector and to demonstrate its feasibility for medical applications, the authors used a planar geometry composed of multilayer microstructures. Various detectors with up to seven conducting layers with different combinations of materials (250 μm Al, 35 μm Cu, 100 μm Pb) and air gaps (100 μm) were exposed to nearly plane-parallel 60–120 kVp x-ray beams. For the experimental design and verification, the authors performed coupled electron–photon radiation transport computations. The detector signal was measured using a commercial data acquisition system with 24 bits dynamic range, 0.4 fC sensitivity, and 0.9 ms sampling time. Results: Measured signals for the prototype detector varied depending on the number of layers, material type, and incident photon

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

    SciTech Connect

    Nguyen, Duc; Girolami, Gregory S.; Mallek, Justin; Cloud, Andrew N.; Abelson, John R.; Lyding, Joseph; Gruebele, Martin

    2014-11-28

    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{sub 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{sub 2} has a very high bulk glass transition temperature T{sub g}, and we observe no three-state hopping or sequential two-state hopping previously seen on lower T{sub 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.

  15. Intrinsic Energy Localization Through Discrete Gap Breathers in One-Dimensional Diatomic Granular Crystals

    DTIC Science & Technology

    2010-05-01

    as fragmentation, anomalous reflec- tions, and energy trapping 21–24,28–34. It is well known from solid- state physics that localized vibrations in...of the prob- lem, we linearize Eqs. 3 and 8 about the equilibrium state in the presence of precompression. This yields müi = C1ui−1 − 2ui + ui+1...of the unstable eigen- values from the unit circle are bounded by 0.02, and numeri- cal integration of the nonlinear impurity modes up to times of

  16. Error-based extraction of states and energy landscapes from experimental single-molecule time-series.

    PubMed

    Taylor, J Nicholas; Li, Chun-Biu; Cooper, David R; Landes, Christy F; Komatsuzaki, Tamiki

    2015-03-17

    Characterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system.

  17. Characterization of the relation between energy landscape and the time evolution of complex materials using kinetic ART

    NASA Astrophysics Data System (ADS)

    N'tsouaglo, Kokou; Joly, Jean-Francois; Beland, Laurent; Brommer, Peter; Mousseau, Normand

    2013-03-01

    In the last two decades, there has been a considerable interest in the development of accelerated numerical methods for sampling the energy landscape of complex materials. Many of these methods are based on the kinetic Monte Carlo (KMC) algorithm introduced 40 years ago. This is the case of kinetic ART, for example, which uses a very efficient transition-state searching method, ART nouveau, coupled with a topological tool, NAUTY, to offer an off-lattice KMC method with on-the-fly catalog building to study complex systems, such as ion-bombarded and amorphous materials, on timescales of a second or more. Looking at two systems, vacancy aggregation in Fe and energy relaxation in ion-bombarded c-Si, we characterize the changes in the energy landscape and the relation to its time evolution with kinetic ART and its correspondence with the well-known Bell-Evans-Polanyi principle used in chemistry.

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

    NASA Astrophysics Data System (ADS)

    Chatterjee, A.; Bhattacharya, S.

    2016-10-01

    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 kBT 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.

  19. Error-based Extraction of States and Energy Landscapes from Experimental Single-Molecule Time-Series

    NASA Astrophysics Data System (ADS)

    Taylor, J. Nicholas; Li, Chun-Biu; Cooper, David R.; Landes, Christy F.; Komatsuzaki, Tamiki

    2015-03-01

    Characterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system.

  20. Error-based Extraction of States and Energy Landscapes from Experimental Single-Molecule Time-Series

    PubMed Central

    Taylor, J. Nicholas; Li, Chun-Biu; Cooper, David R.; Landes, Christy F.; Komatsuzaki, Tamiki

    2015-01-01

    Characterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system. PMID:25779909

  1. Energy-landscape paving for prediction of face-centered-cubic hydrophobic-hydrophilic lattice model proteins.

    PubMed

    Liu, Jingfa; Song, Beibei; Liu, Zhaoxia; Huang, Weibo; Sun, Yuanyuan; Liu, Wenjie

    2013-11-01

    Protein structure prediction (PSP) is a classical NP-hard problem in computational biology. The energy-landscape paving (ELP) method is a class of heuristic global optimization algorithm, and has been successfully applied to solving many optimization problems with complex energy landscapes in the continuous space. By putting forward a new update mechanism of the histogram function in ELP and incorporating the generation of initial conformation based on the greedy strategy and the neighborhood search strategy based on pull moves into ELP, an improved energy-landscape paving (ELP+) method is put forward. Twelve general benchmark instances are first tested on both two-dimensional and three-dimensional (3D) face-centered-cubic (fcc) hydrophobic-hydrophilic (HP) lattice models. The lowest energies by ELP+ are as good as or better than those of other methods in the literature for all instances. Then, five sets of larger-scale instances, denoted by S, R, F90, F180, and CASP target instances on the 3D FCC HP lattice model are tested. The proposed algorithm finds lower energies than those by the five other methods in literature. Not unexpectedly, this is particularly pronounced for the longer sequences considered. Computational results show that ELP+ is an effective method for PSP on the fcc HP lattice model.

  2. Free-energy landscape and nucleation pathway of polymorphic minerals from solution in a Potts lattice-gas model.

    PubMed

    Okamoto, Atsushi; Kuwatani, Tatsu; Omori, Toshiaki; Hukushima, Koji

    2015-10-01

    Metastable minerals commonly form during reactions between water and rock. The nucleation mechanism of polymorphic phases from solution are explored here using a two-dimensional Potts model. The model system is composed of a solvent and three polymorphic solid phases. The local state and position of the solid phase are updated by Metropolis dynamics. Below the critical temperature, a large cluster of the least stable solid phase initially forms in the solution before transitioning into more-stable phases following the Ostwald step rule. The free-energy landscape as a function of the modal abundance of each solid phase clearly reveals that before cluster formation, the least stable phase has an energetic advantage because of its low interfacial energy with the solution, and after cluster formation, phase transformation occurs along the valley of the free-energy landscape, which contains several minima for the regions of three phases. Our results indicate that the solid-solid and solid-liquid interfacial energy contribute to the formation of the complex free-energy landscape and nucleation pathways following the Ostwald step rule.

  3. Energy-landscape paving for prediction of face-centered-cubic hydrophobic-hydrophilic lattice model proteins

    NASA Astrophysics Data System (ADS)

    Liu, Jingfa; Song, Beibei; Liu, Zhaoxia; Huang, Weibo; Sun, Yuanyuan; Liu, Wenjie

    2013-11-01

    Protein structure prediction (PSP) is a classical NP-hard problem in computational biology. The energy-landscape paving (ELP) method is a class of heuristic global optimization algorithm, and has been successfully applied to solving many optimization problems with complex energy landscapes in the continuous space. By putting forward a new update mechanism of the histogram function in ELP and incorporating the generation of initial conformation based on the greedy strategy and the neighborhood search strategy based on pull moves into ELP, an improved energy-landscape paving (ELP+) method is put forward. Twelve general benchmark instances are first tested on both two-dimensional and three-dimensional (3D) face-centered-cubic (fcc) hydrophobic-hydrophilic (HP) lattice models. The lowest energies by ELP+ are as good as or better than those of other methods in the literature for all instances. Then, five sets of larger-scale instances, denoted by S, R, F90, F180, and CASP target instances on the 3D FCC HP lattice model are tested. The proposed algorithm finds lower energies than those by the five other methods in literature. Not unexpectedly, this is particularly pronounced for the longer sequences considered. Computational results show that ELP+ is an effective method for PSP on the fcc HP lattice model.

  4. Biodelignification of lignocellulose substrates: An intrinsic and sustainable pretreatment strategy for clean energy production.

    PubMed

    Chandel, Anuj K; Gonçalves, Bruna C M; Strap, Janice L; da Silva, Silvio S

    2015-01-01

    Lignocellulosic biomass (LB) is a promising sugar feedstock for biofuels and other high-value chemical commodities. The recalcitrance of LB, however, impedes carbohydrate accessibility and its conversion into commercially significant products. Two important factors for the overall economization of biofuel production is LB pretreatment to liberate fermentable sugars followed by conversion into ethanol. Sustainable biofuel production must overcome issues such as minimizing water and energy usage, reducing chemical usage and process intensification. Amongst available pretreatment methods, microorganism-mediated pretreatments are the safest, green, and sustainable. Native biodelignifying agents such as Phanerochaete chrysosporium, Pycnoporous cinnabarinus, Ceriporiopsis subvermispora and Cyathus stercoreus can remove lignin, making the remaining substrates amenable for saccharification. The development of a robust, integrated bioprocessing (IBP) approach for economic ethanol production would incorporate all essential steps including pretreatment, cellulase production, enzyme hydrolysis and fermentation of the released sugars into ethanol. IBP represents an inexpensive, environmentally friendly, low energy and low capital approach for second-generation ethanol production. This paper reviews the advancements in microbial-assisted pretreatment for the delignification of lignocellulosic substrates, system metabolic engineering for biorefineries and highlights the possibilities of process integration for sustainable and economic ethanol production.

  5. Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor.

    PubMed

    Miao, Yinglong; McCammon, J Andrew

    2016-10-25

    G-protein-coupled receptors (GPCRs) recognize ligands of widely different efficacies, from inverse to partial and full agonists, which transduce cellular signals at differentiated levels. However, the mechanism of such graded activation remains unclear. Using the Gaussian accelerated molecular dynamics (GaMD) method that enables both unconstrained enhanced sampling and free energy calculation, we have performed extensive GaMD simulations (∼19 μs in total) to investigate structural dynamics of the M2 muscarinic GPCR that is bound by the full agonist iperoxo (IXO), the partial agonist arecoline (ARC), and the inverse agonist 3-quinuclidinyl-benzilate (QNB), in the presence or absence of the G-protein mimetic nanobody. In the receptor-nanobody complex, IXO binding leads to higher fluctuations in the protein-coupling interface than ARC, especially in the receptor transmembrane helix 5 (TM5), TM6, and TM7 intracellular domains that are essential elements for GPCR activation, but less flexibility in the receptor extracellular region due to stronger binding compared with ARC. Two different binding poses are revealed for ARC in the orthosteric pocket. Removal of the nanobody leads to GPCR deactivation that is characterized by inward movement of the TM6 intracellular end. Distinct low-energy intermediate conformational states are identified for the IXO- and ARC-bound M2 receptor. Both dissociation and binding of an orthosteric ligand are observed in a single all-atom GPCR simulation in the case of partial agonist ARC binding to the M2 receptor. This study demonstrates the applicability of GaMD for exploring free energy landscapes of large biomolecules and the simulations provide important insights into the GPCR functional mechanism.

  6. Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor

    PubMed Central

    Miao, Yinglong; McCammon, J. Andrew

    2016-01-01

    G-protein–coupled receptors (GPCRs) recognize ligands of widely different efficacies, from inverse to partial and full agonists, which transduce cellular signals at differentiated levels. However, the mechanism of such graded activation remains unclear. Using the Gaussian accelerated molecular dynamics (GaMD) method that enables both unconstrained enhanced sampling and free energy calculation, we have performed extensive GaMD simulations (∼19 μs in total) to investigate structural dynamics of the M2 muscarinic GPCR that is bound by the full agonist iperoxo (IXO), the partial agonist arecoline (ARC), and the inverse agonist 3-quinuclidinyl-benzilate (QNB), in the presence or absence of the G-protein mimetic nanobody. In the receptor–nanobody complex, IXO binding leads to higher fluctuations in the protein-coupling interface than ARC, especially in the receptor transmembrane helix 5 (TM5), TM6, and TM7 intracellular domains that are essential elements for GPCR activation, but less flexibility in the receptor extracellular region due to stronger binding compared with ARC. Two different binding poses are revealed for ARC in the orthosteric pocket. Removal of the nanobody leads to GPCR deactivation that is characterized by inward movement of the TM6 intracellular end. Distinct low-energy intermediate conformational states are identified for the IXO- and ARC-bound M2 receptor. Both dissociation and binding of an orthosteric ligand are observed in a single all-atom GPCR simulation in the case of partial agonist ARC binding to the M2 receptor. This study demonstrates the applicability of GaMD for exploring free energy landscapes of large biomolecules and the simulations provide important insights into the GPCR functional mechanism. PMID:27791003

  7. Water complexes of important air pollutants: geometries, complexation energies, concentrations, infrared spectra, and intrinsic reactivity.

    PubMed

    Galano, Annia; Narciso-Lopez, Marcela; Francisco-Marquez, Misaela

    2010-05-13

    Water complexes involving methanol, ethanol, formaldehyde, formic acid, acetone, ammonia, acetylene, ethylene, chloroethene, trichloroethene, 1,1,1-trichloroethane, hydroxyl radical, and hydroperoxyl radical have been studied. Enthalpies, entropies, and Gibbs free energies of association have been estimated, as well as the concentrations of the complexes under lower-troposphere conditions. The influence of the relative air humidity on the complexation processes has been analyzed. The association processes yielding water complexes of methanol, ethanol, formic acid, ammonia, acetone, hydroxyl radical, and hydroperoxyl radical were found to be more exothermic than that of the water dimer. General trends for the reactivity of the studied water complexes, compared to those of the corresponding free species, are proposed based on global reactivity indexes. The previously reported increased reactivity of the (*)OOH self-reaction, when there is water present, has been explained. The IR spectra of the complexes have been analyzed and compared with those of the free species.

  8. Nucleation and Control of Magnetic Quasi-particles via Extrinsic and Intrinsic Energies

    NASA Astrophysics Data System (ADS)

    Pulecio, Javier; Warnicke, Peter; Arena, Dario; Im, Mi-Young; Pollard, Shawn; Fischer, Peter; Zhu, Yimei

    2015-03-01

    Magnetic quasi-particles present an excellent opportunity to study fundamental magnetic properties and dynamics. The fine balance of energies including demagnetization, direct exchange, external perturbations, crystalline anisotropy, indirect exchange, and DMI, allows for the nucleation of a diverse ensemble of spin textures such as vortices, merons, and skyrmions, all of which demonstrate unique behavior. We present our investigations of single vortex symmetry breaking under external perturbations and demonstrate a method to determine the core polarity using Lorentz Transmission Electron Microscopy. We also discuss how to tailor the high-frequency dynamics of coupled coaxial vortices using indirect exchange interactions. We conclude by discussing the nucleation of unconventional chiral spin textures in nano-disc heterostructures using a complementary multi-technique approach, i.e. micromagnetic modeling, FMR, MFM, MTXM, and LTEM. DOE BES #DE-AC02-98CH10886, DOE BES #DE-AC02-05-CH11231, NRF Korea MEST #2012K1A4A3053565.

  9. Can the energy gap in the protein-ligand binding energy landscape be used as a descriptor in virtual ligand screening?

    PubMed

    Grigoryan, Arsen V; Wang, Hong; Cardozo, Timothy J

    2012-01-01

    The ranking of scores of individual chemicals within a large screening library is a crucial step in virtual screening (VS) for drug discovery. Previous studies showed that the quality of protein-ligand recognition can be improved using spectrum properties and the shape of the binding energy landscape. Here, we investigate whether the energy gap, defined as the difference between the lowest energy pose generated by a docking experiment and the average energy of all other generated poses and inferred to be a measure of the binding energy landscape sharpness, can improve the separation power between true binders and decoys with respect to the use of the best docking score. We performed retrospective single- and multiple-receptor conformation VS experiments in a diverse benchmark of 40 domains from 38 therapeutically relevant protein targets. Also, we tested the performance of the energy gap on 36 protein targets from the Directory of Useful Decoys (DUD). The results indicate that the energy gap outperforms the best docking score in its ability to discriminate between true binders and decoys, and true binders tend to have larger energy gaps than decoys. Furthermore, we used the energy gap as a descriptor to measure the height of the native binding phase and obtained a significant increase in the success rate of near native binding pose identification when the ligand binding conformations within the boundaries of the native binding phase were considered. The performance of the energy gap was also evaluated on an independent test case of VS-identified PKR-like ER-localized eIF2α kinase (PERK) inhibitors. We found that the energy gap was superior to the best docking score in its ability to more highly rank active compounds from inactive ones. These results suggest that the energy gap of the protein-ligand binding energy landscape is a valuable descriptor for use in VS.

  10. Protein-like folding and free energy landscape of a homopolymer chain

    NASA Astrophysics Data System (ADS)

    Taylor, Mark; Paul, Wolfgang; Binder, Kurt

    2011-03-01

    Many small proteins fold via a first-order ``all-or-none'' transition directly from an expanded coil to a compact native state. We have recently reported an analogous direct coil-to-crystallite transition for a flexible homopolymer. Wang-Landau sampling was used to construct the 1D density of states for square-well chains up to length 256 and a microcanonical analysis shows that for short-range interactions the usual polymer collapse transition is preempted by a direct freezing transition. A 2D configurational probability landscape, built via multi-canonical sampling, reveals a dominant folding pathway and an inherent configurational barrier to folding. Despite the non-unique homopolymer ground state, the thermodynamics of this direct freezing transition are identical to those of two-state protein folding. Homopolymer folding proceeds over a free energy barrier via a transition state folding nucleus, displays a protein-like Chevron plot, and satisfies the van't Hoff two-state criterion. Funding: NSF DMR-0804370, DFG SFB-625/A3.

  11. Protein-like folding and free energy landscape of a homopolymer chain

    NASA Astrophysics Data System (ADS)

    Taylor, Mark; Paul, Wolfgang; Binder, Kurt

    2011-04-01

    Many small proteins fold via a first-order "all-or-none" transition directly from an expanded coil to a compact native state. We have recently reported an analogous direct coil-to-crystallite transition for a flexible homopolymer [1]. Wang-Landau sampling was used to construct the 1D density of states for square-well chains up to length 256 and a microcanonical analysis shows that for short-range interactions the usual polymer collapse transition is preempted by a direct freezing transition. A 2D configurational probability landscape, built via multi-canonical sampling, reveals a dominant folding pathway and an inherent configurational barrier to folding. Despite the non-unique homopolymer ground state, the thermodynamics of this direct freezing transition are identical to those of two-state protein folding. Homopolymer folding proceeds over a free energy barrier via a transition state folding nucleus, displays a protein-like Chevron plot, and satisfies the van't Hoff two-state criterion.[4pt] [1] Phys. Rev. E 79, 050801(R) (2009); J. Chem. Phys. 131, 114907 (2009).

  12. Study on the Dynamics of Influenza Hemagglutinin Based on Energy Landscape Theory

    NASA Astrophysics Data System (ADS)

    Lin, Xingcheng; Eddy, Nathanial; Noel, Jeffrey; Whitford, Paul; Ma, Jianpeng; Onuchic, Jose

    2014-03-01

    Hemagglutinin (HA2), a homotrimeric influenza surface protein crucial for membrane fusion, undergoes an drastic structural rearrangement during viral invasion of the host. X-ray crystallography shows that the pre- and post-fusion configurations have largely disparate secondary, tertiary and quaternary structures. Simulations allow us to explore the time-dependent high resolution structural information and function of HA2 dynamics. Here we use an approach based on energy landscape theory that combines the native information from both the starting and end points. Our simulation shows two key events in the conformational transition of HA2: The extension of its fusion peptides away from the viral membrane and the melting of its globular C-terminal portion. The similar timescale and a kinetic competition between these two events lead to two main pathways and generic kinetic intermediates during this transition. Through considering the biological context of HA, we test perturbations of the baseline model that are useful in understanding the robustness of our predictions and how they translate into the function of HA. The all-atom explicit solvent simulation is performed and convince the cracking phenomenon at the start of this protein dynamics. Center for Theoretical Biological Physics.

  13. Laser probes of the potential energy landscapes and conformational isomerization dynamics of flexible biomolecules

    NASA Astrophysics Data System (ADS)

    Dian, Brian; Clarkson, Jasper; Zwier, Timothy

    2003-03-01

    Using a combination of 2-color resonant two-photon ionization (R2PI), laser-induced fluorescence excitation (LIF), resonant ion-dip infrared spectroscopy (RIDIRS), fluorescence-dip infrared spectroscopy (FDIRS), and UV-UV hole-burning spectroscopy, the conformational preferences of a series of flexible biomolecules, including melatonin, N-acetyl-tryptophan methyl amide (NATMA), and their close analogs, have been determined in a molecular beam. These molecules are sufficiently complex to have hundreds of conformational minima, yet small enough that their potential energy landscapes can be explored in some detail. Once the conformational preferences of the molecules are established, these molecules are then studied using infrared-ultraviolet hole-filling and IR-induced population transfer spectroscopy. These methods utilize selective infrared excitation of single conformations of the molecule in the early portions of a gas-phase expansion, followed by collisional re-cooling of the excited population into its conformational minima for subsequent conformation-specific detection. Efficient isomerization is induced by the infrared excitation that redistributes population between the same conformations that have population in the absence of infrared excitation. Examples will be given in which the quantum yields for transfer of the population into the various conformational minima depend both on which conformation is excited and on which hydride stretch vibration is excited within a given conformation; that is, they are both conformation-selective and mode-selective.

  14. Exploration of the Energy Landscape of Acetylcholinesterase by Molecular Dynamics Simulation.

    NASA Astrophysics Data System (ADS)

    McCammon, J. Andrew

    2002-03-01

    Proteins have rough energy landscapes. Often more states than just the ground state are occupied and have biological functions. It is essential to study these conformational substates and the dynamical transitions among them. Acetylcholinesterase (AChE) is an important enzyme that has biological functions including the termination of synaptic transmission signals. X-ray structures show that it has an active site that is accessible only via a long and narrow channel from its surface. Therefore the fact that acetylcholine and larger ligands can reach the active site is believed to reflect the protein's structural fluctuation. We carried out long molecular dynamics simulations to investigate the dynamics of AChE and its relation to biological function, and compared our results with experiments. The results reveal several "doors" that open intermittantly between the active site and the surface. Instead of having simple exponential decay correlation functions, the time series of these channels reveal complex, fractal gating between conformations. We also compared the AChE dynamics data with those from an AchE-fasciculin complex. (Fasciculin is a small protein that is a natural inhibitor of AChE.) The results show remarkable effects of the protein-protein interaction, including allosteric and dynamical inhibition by fasciculin besides direct steric blocking. More information and images can be found at http://mccammon.ucsd.edu

  15. Heuristic-based energy landscape paving for the circular packing problem with performance constraints of equilibrium

    NASA Astrophysics Data System (ADS)

    Liu, Jingfa; Jiang, Yucong; Li, Gang; Xue, Yu; Liu, Zhaoxia; Zhang, Zhen

    2015-08-01

    The optimal layout problem of circle group in a circular container with performance constraints of equilibrium belongs to a class of NP-hard problem. The key obstacle of solving this problem is the lack of an effective global optimization method. We convert the circular packing problem with performance constraints of equilibrium into the unconstrained optimization problem by using quasi-physical strategy and penalty function method. By putting forward a new updating mechanism of the histogram function in energy landscape paving (ELP) method and incorporating heuristic conformation update strategies into the ELP method, we obtain an improved ELP (IELP) method. Subsequently, by combining the IELP method and the local search (LS) procedure, we put forward a hybrid algorithm, denoted by IELP-LS, for the circular packing problem with performance constraints of equilibrium. We test three sets of benchmarks consisting of 21 representative instances from the current literature. The proposed algorithm breaks the records of all 10 instances in the first set, and achieves the same or even better results than other methods in literature for 10 out of 11 instances in the second and third sets. The computational results show that the proposed algorithm is an effective method for solving the circular packing problem with performance constraints of equilibrium.

  16. Direct Observation of Folding Energy Landscape of RNA Hairpin at Mechanical Loading Rates.

    PubMed

    Xu, Huizhong; Plaut, Benjamin; Zhu, Xiran; Chen, Maverick; Mavinkurve, Udit; Maiti, Anindita; Song, Guangtao; Murari, Krishna; Mandal, Maumita

    2017-03-16

    By applying a controlled mechanical load using optical tweezers, we measured the diffusive barrier crossing in a 49 nt long P5ab RNA hairpin. We find that in the free-energy landscape the barrier height (G(‡)) and transition distance (x(‡)) are dependent on the loading rate (r) along the pulling direction, x, as predicted by Bell. The barrier shifted toward the initial state, whereas ΔG(‡) reduced significantly from 50 to 5 kT, as r increased from 0 to 32 pN/s. However, the equilibrium work (ΔG) during strand separation, as estimated by Crook's fluctuation theorem, remained unchanged at different rates. Previously, helix formation and denaturation have been described as two-state (F ↔ U) transitions for P5ab. Herein, we report three intermediate states I1, I, and I2 located at 4, 11, and 16 nm respectively, from the folded conformation. The intermediates were observed only when the hairpin was subjected to an optimal r, 7.6 pN/s. The results indicate that the complementary strands in P5ab can zip and unzip through complex routes, whereby mismatches act as checkpoints and often impose barriers. The study highlights the significance of loading rates in force-spectroscopy experiments that are increasingly being used to measure the folding properties of biomolecules.

  17. Efficient dielectrophoretic patterning of embryonic stem cells in energy landscapes defined by hydrogel geometries.

    PubMed

    Tsutsui, Hideaki; Yu, Edmond; Marquina, Sabrina; Valamehr, Bahram; Wong, Ieong; Wu, Hong; Ho, Chih-Ming

    2010-12-01

    In this study, we have developed an integrated microfluidic platform for actively patterning mammalian cells, where poly(ethylene glycol) (PEG) hydrogels play two important roles as a non-fouling layer and a dielectric structure. The developed system has an embedded array of PEG microwells fabricated on a planar indium tin oxide (ITO) electrode. Due to its dielectric properties, the PEG microwells define electrical energy landscapes, effectively forming positive dielectrophoresis (DEP) traps in a low-conductivity environment. Distribution of DEP forces on a model cell was first estimated by computationally solving quasi-electrostatic Maxwell's equations, followed by an experimental demonstration of cell and particle patterning without an external flow. Furthermore, efficient patterning of mouse embryonic stem (mES) cells was successfully achieved in combination with an external flow. With a seeding density of 10⁷ cells/mL and a flow rate of 3 μL/min, trapping of cells in the microwells was completed in tens of seconds after initiation of the DEP operation. Captured cells subsequently formed viable and homogeneous monolayer patterns. This simple approach could provide an efficient strategy for fabricating various cell microarrays for applications such as cell-based biosensors, drug discovery, and cell microenvironment studies.

  18. Free energy landscape of the Michaelis complex of lactate dehydrogenase: A network analysis of atomistic simulations

    NASA Astrophysics Data System (ADS)

    Pan, Xiaoliang; Schwartz, Steven

    2015-03-01

    It has long been recognized that the structure of a protein is a hierarchy of conformations interconverting on multiple time scales. However, the conformational heterogeneity is rarely considered in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD+). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they are catalytic competent at different reaction rates. In this study, millisecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network the Michaelis complex and the structures of the substates at atomistic scale. It also shed some light on understanding the complete picture of the catalytic mechanism of LDH.

  19. A complete thermodynamic analysis of enzyme turnover links the free energy landscape to enzyme catalysis.

    PubMed

    Jones, Hannah B L; Wells, Stephen A; Prentice, Erica J; Kwok, Anthony; Liang, Liyin L; Arcus, Vickery L; Pudney, Christopher R

    2017-09-01

    Our understanding of how enzymes work is coloured by static structure depictions where the enzyme scaffold is presented as either immobile, or in equilibrium between well-defined static conformations. Proteins, however, exhibit a large degree of motion over a broad range of timescales and magnitudes and this is defined thermodynamically by the enzyme free energy landscape (FEL). The role and importance of enzyme motion is extremely contentious. Much of the challenge is in the experimental detection of so called 'conformational sampling' involved in enzyme turnover. Herein we apply combined pressure and temperature kinetics studies to elucidate the full suite of thermodynamic parameters defining an enzyme FEL as it relates to enzyme turnover. We find that the key thermodynamic parameters governing vibrational modes related to enzyme turnover are the isobaric expansivity term and the change in heat capacity for enzyme catalysis. Variation in the enzyme FEL affects these terms. Our analysis is supported by a range of biophysical and computational approaches that specifically capture information on protein vibrational modes and the FEL (all atom flexibility calculations, red edge excitation shift spectroscopy and viscosity studies) that provide independent evidence for our findings. Our data suggest that restricting the enzyme FEL may be a powerful strategy when attempting to rationally engineer enzymes, particularly to alter thermal activity. Moreover, we demonstrate how rational predictions can be made with a rapid computational approach. © 2017 Federation of European Biochemical Societies.

  20. Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.

    PubMed

    Ikebe, Jinzen; Umezawa, Koji; Higo, Junichi

    2016-03-01

    Molecular dynamics (MD) simulations using all-atom and explicit solvent models provide valuable information on the detailed behavior of protein-partner substrate binding at the atomic level. As the power of computational resources increase, MD simulations are being used more widely and easily. However, it is still difficult to investigate the thermodynamic properties of protein-partner substrate binding and protein folding with conventional MD simulations. Enhanced sampling methods have been developed to sample conformations that reflect equilibrium conditions in a more efficient manner than conventional MD simulations, thereby allowing the construction of accurate free-energy landscapes. In this review, we discuss these enhanced sampling methods using a series of case-by-case examples. In particular, we review enhanced sampling methods conforming to trivial trajectory parallelization, virtual-system coupled multicanonical MD, and adaptive lambda square dynamics. These methods have been recently developed based on the existing method of multicanonical MD simulation. Their applications are reviewed with an emphasis on describing their practical implementation. In our concluding remarks we explore extensions of the enhanced sampling methods that may allow for even more efficient sampling.

  1. Energy landscape of ZnO clusters and low-density polymorphs

    NASA Astrophysics Data System (ADS)

    Rasoulkhani, Robabe; Tahmasbi, Hossein; Ghasemi, S. Alireza; Faraji, Somayeh; Rostami, Samare; Amsler, Maximilian

    2017-08-01

    We report on an extensive study of ZnO materials with cagelike motifs in clusters and bulk phases through structural searches using the minima hopping method. A novel putative ground state was discovered for the (ZnO) 32 cluster with a tubelike structure, closely related to the previously reported (ZnO) 24 ground-state cage geometry. Furthermore, the effect of ionization on the geometries and energetic ordering of (ZnO) n clusters with n =3 -10 ,12 was studied by directly sampling the energy landscape of the ionized system. Our results indicate that the transition from ring and planar structures to three-dimensional cages occurs at larger cluster sizes than in the neutral system. Inspired by the bottom-up design philosophy and the predominance of cagelike structures in medium-sized clusters, a search for crystalline ZnO was conducted aimed specifically at low-density polymorphs, resulting in the discovery of 57 novel metastable phases. The voids in these low-density materials closely resemble the hollow cage structures of small (ZnO) n/(ZnO)n + clusters with n <16 . Analogous to clathrate materials, these voids could serve to accommodate guest atoms to tailor the materials properties for various applications.

  2. Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations.

    PubMed

    Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

    2012-04-10

    To describe the structure and dynamics of oligomers during peptide aggregation, a method is proposed that considers both the intramolecular and intermolecular structures of the multimolecule system and correctly accounts for its degeneracy. The approach is based on the "by-parts" strategy, which partitions a complex molecular system into parts, determines the metastable conformational states of each part, and describes the overall conformational state of the system in terms of a product basis of the states of the parts. Starting from a molecular dynamics simulation of n molecules, the method consists of three steps: (i) characterization of the intramolecular structure, that is, of the conformational states of a single molecule in the presence of the other molecules (e.g., β-strand or random coil); (ii) characterization of the intermolecular structure through the identification of all occurring aggregate states of the peptides (dimers, trimers, etc.); and (iii) construction of the overall conformational states of the system in terms of a product basis of the n "single-molecule" states and the aggregate states. Considering the Alzheimer β-amyloid peptide fragment Aβ16-22 as a first application, about 700 overall conformational states of the trimer (Aβ16-22)3 were constructed from all-atom molecular dynamics simulation in explicit water. Based on these states, a transition network reflecting the free energy landscape of the aggregation process can be constructed that facilitates the identification of the aggregation pathways.

  3. Energy landscape of self-assembled superlattices of PbSe nanocrystals

    PubMed Central

    Quan, Zewei; Wu, Di; Zhu, Jinlong; Evers, Wiel H.; Boncella, James M.; Siebbeles, Laurens D. A.; Wang, Zhongwu; Navrotsky, Alexandra; Xu, Hongwu

    2014-01-01

    Self-assembly of nanocrystals (NCs) into superlattices is an intriguing multiscale phenomenon that may lead to materials with novel collective properties, in addition to the unique properties of individual NCs compared with their bulk counterparts. By using different dispersion solvents, we synthesized three types of PbSe NC superlattices—body-centered cubic (bcc), body-centered tetragonal (bct), and face-centered cubic (fcc)—as confirmed by synchrotron small-angle X-ray scattering. Solution calorimetric measurements in hexane show that the enthalpy of formation of the superlattice from dispersed NCs is on the order of −2 kJ/mol. The calorimetric measurements reveal that the bcc superlattice is the energetically most stable polymorph, with the bct being 0.32 and the fcc 0.55 kJ/mol higher in enthalpy. This stability sequence is consistent with the decreased packing efficiency of PbSe NCs from bcc (17.2%) to bct (16.0%) and to fcc (15.2%). The small enthalpy differences among the three polymorphs confirm a closely spaced energy landscape and explain the ease of formation of different NC superlattices at slightly different synthesis conditions. PMID:24927573

  4. Hiking down the energy landscape: progress toward the Kauzmann temperature via vapor deposition.

    PubMed

    Kearns, Kenneth L; Swallen, Stephen F; Ediger, M D; Wu, Tian; Sun, Ye; Yu, Lian

    2008-04-24

    Physical vapor deposition was employed to prepare amorphous samples of indomethacin and 1,3,5-(tris)naphthylbenzene. By depositing onto substrates held somewhat below the glass transition temperature and varying the deposition rate from 15 to 0.2 nm/s, glasses with low enthalpies and exceptional kinetic stability were prepared. Glasses with fictive temperatures that are as much as 40 K lower than those prepared by cooling the liquid can be made by vapor deposition. As compared to an ordinary glass, the most stable vapor-deposited samples moved about 40% toward the bottom of the potential energy landscape for amorphous materials. These results support the hypothesis that enhanced surface mobility allows stable glass formation by vapor deposition. A comparison of the enthalpy content of vapor-deposited glasses with aged glasses was used to evaluate the difference between bulk and surface dynamics for indomethacin; the dynamics in the top few nanometers of the glass are about 7 orders of magnitude faster than those in the bulk at Tg - 20 K.

  5. Energy landscape of self-assembled superlattices of PbSe nanocrystals.

    PubMed

    Quan, Zewei; Wu, Di; Zhu, Jinlong; Evers, Wiel H; Boncella, James M; Siebbeles, Laurens D A; Wang, Zhongwu; Navrotsky, Alexandra; Xu, Hongwu

    2014-06-24

    Self-assembly of nanocrystals (NCs) into superlattices is an intriguing multiscale phenomenon that may lead to materials with novel collective properties, in addition to the unique properties of individual NCs compared with their bulk counterparts. By using different dispersion solvents, we synthesized three types of PbSe NC superlattices--body-centered cubic (bcc), body-centered tetragonal (bct), and face-centered cubic (fcc)--as confirmed by synchrotron small-angle X-ray scattering. Solution calorimetric measurements in hexane show that the enthalpy of formation of the superlattice from dispersed NCs is on the order of -2 kJ/mol. The calorimetric measurements reveal that the bcc superlattice is the energetically most stable polymorph, with the bct being 0.32 and the fcc 0.55 kJ/mol higher in enthalpy. This stability sequence is consistent with the decreased packing efficiency of PbSe NCs from bcc (17.2%) to bct (16.0%) and to fcc (15.2%). The small enthalpy differences among the three polymorphs confirm a closely spaced energy landscape and explain the ease of formation of different NC superlattices at slightly different synthesis conditions.

  6. The nature of the sunspot phenomenon. III - Energy consumption and energy transport. IV - The intrinsic instability of the magnetic configuration

    NASA Technical Reports Server (NTRS)

    Parker, E. N.

    1975-01-01

    The basic relation is described between conversion of thermal energy into convective fluid motion and convective transport of thermal energy, and the equilibrium configuration of a sunspot's magnetic field is shown to be unstable to the hydromagnetic exchange instability. It is determined that heat transport necessarily accompanies convective driving of fluid motion and that the formation of cool sunspots requires convection extending coherently over several scale heights, a distance of at least 500 km. Several theoretical possibilities for sunspot stabilization are reviewed, and it is suggested that a suitable redistribution of cooling in the umbra may be the stabilization mechanism. It is believed that if cooling extends to a great depth in an elongated portion of a sunspot, the magnetic pressure on the boundary will be reduced, tending to reduce the elongation.

  7. The nature of the sunspot phenomenon. III - Energy consumption and energy transport. IV - The intrinsic instability of the magnetic configuration

    NASA Technical Reports Server (NTRS)

    Parker, E. N.

    1975-01-01

    The basic relation is described between conversion of thermal energy into convective fluid motion and convective transport of thermal energy, and the equilibrium configuration of a sunspot's magnetic field is shown to be unstable to the hydromagnetic exchange instability. It is determined that heat transport necessarily accompanies convective driving of fluid motion and that the formation of cool sunspots requires convection extending coherently over several scale heights, a distance of at least 500 km. Several theoretical possibilities for sunspot stabilization are reviewed, and it is suggested that a suitable redistribution of cooling in the umbra may be the stabilization mechanism. It is believed that if cooling extends to a great depth in an elongated portion of a sunspot, the magnetic pressure on the boundary will be reduced, tending to reduce the elongation.

  8. Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions.

    PubMed

    West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

    2017-02-09

    A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the juxtaposed nonbonded quasi-atoms and a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions, and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. The theoretical formulation of the resolution is quantitatively validated by an application to the C2 molecule.

  9. Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions

    DOE PAGES

    West, Aaron C.; Schmidt, Michael W.; Gordon, Mark S.; ...

    2017-01-30

    A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the non-bonded juxtaposed quasi-atoms andmore » a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. Lastly, the theoretical formulation of the resolution is quantitatively validated by an application to the C2 molecule.« less

  10. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

    PubMed Central

    Sripathi, Kamali N.; Tay, Wendy W.; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G.

    2014-01-01

    The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2′-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. PMID:24854621

  11. The energy landscape underpinning module dynamics in the human brain connectome.

    PubMed

    Ashourvan, Arian; Gu, Shi; Mattar, Marcelo G; Vettel, Jean M; Bassett, Danielle S

    2017-06-07

    Human brain dynamics can be viewed through the lens of statistical mechanics, where neurophysiological activity evolves around and between local attractors representing mental states. Many physically-inspired models of these dynamics define brain states based on instantaneous measurements of regional activity. Yet, recent work in network neuroscience has provided evidence that the brain might also be well-characterized by time-varying states composed of locally coherent activity or functional modules. We study this network-based notion of brain state to understand how functional modules dynamically interact with one another to perform cognitive functions. We estimate the functional relationships between regions of interest (ROIs) by fitting a pair-wise maximum entropy model to each ROI's pattern of allegiance to functional modules. This process uses an information theoretic notion of energy (as opposed to a metabolic one) to produce an energy landscape in which local minima represent attractor states characterized by specific patterns of modular structure. The clustering of local minima highlights three classes of ROIs with similar patterns of allegiance to community states. Visual, attention, sensorimotor, and subcortical ROIs are well-characterized by a single functional community. The remaining ROIs affiliate with a putative executive control community or a putative default mode and salience community. We simulate the brain's dynamic transitions between these community states using a random walk process. We observe that simulated transition probabilities between basins are statistically consistent with empirically observed transitions in resting state fMRI data. These results offer a view of the brain as a dynamical system that transitions between basins of attraction characterized by coherent activity in groups of brain regions, and that the strength of these attractors depends on the ongoing cognitive computations. Copyright © 2017 The Authors. Published by

  12. Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics.

    PubMed

    Preto, Jordane; Clementi, Cecilia

    2014-09-28

    The reaction pathways characterizing macromolecular systems of biological interest are associated with high free energy barriers. Resorting to the standard all-atom molecular dynamics (MD) to explore such critical regions may be inappropriate as the time needed to observe the relevant transitions can be remarkably long. In this paper, we present a new method called Extended Diffusion-Map-directed Molecular Dynamics (extended DM-d-MD) used to enhance the sampling of MD trajectories in such a way as to rapidly cover all important regions of the free energy landscape including deep metastable states and critical transition paths. Moreover, extended DM-d-MD was combined with a reweighting scheme enabling to save on-the-fly information about the Boltzmann distribution. Our algorithm was successfully applied to two systems, alanine dipeptide and alanine-12. Due to the enhanced sampling, the Boltzmann distribution is recovered much faster than in plain MD simulations. For alanine dipeptide, we report a speedup of one order of magnitude with respect to plain MD simulations. For alanine-12, our algorithm allows us to highlight all important unfolded basins in several days of computation when one single misfolded event is barely observable within the same amount of computational time by plain MD simulations. Our method is reaction coordinate free, shows little dependence on the a priori knowledge of the system, and can be implemented in such a way that the biased steps are not computationally expensive with respect to MD simulations thus making our approach well adapted for larger complex systems from which little information is known.

  13. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.

    PubMed

    Sripathi, Kamali N; Tay, Wendy W; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G

    2014-07-01

    The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2'-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape.

  14. Kinetic control over pathway complexity in supramolecular polymerization through modulating the energy landscape by rational molecular design.

    PubMed

    Ogi, Soichiro; Fukui, Tomoya; Jue, Melinda L; Takeuchi, Masayuki; Sugiyasu, Kazunori

    2014-12-22

    Far-from-equilibrium thermodynamic systems that are established as a consequence of coupled equilibria are the origin of the complex behavior of biological systems. Therefore, research in supramolecular chemistry has recently been shifting emphasis from a thermodynamic standpoint to a kinetic one; however, control over the complex kinetic processes is still in its infancy. Herein, we report our attempt to control the time evolution of supramolecular assembly in a process in which the supramolecular assembly transforms from a J-aggregate to an H-aggregate over time. The transformation proceeds through a delicate interplay of these two aggregation pathways. We have succeeded in modulating the energy landscape of the respective aggregates by a rational molecular design. On the basis of this understanding of the energy landscape, programming of the time evolution was achieved through adjusting the balance between the coupled equilibria. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed

    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.

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

    PubMed

    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.

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

    PubMed Central

    2015-01-01

    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. PMID:26574437

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

    PubMed Central

    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

  19. Energy landscape, structure and rate effects on strength properties of alpha-helical proteins.

    PubMed

    Bertaud, Jérémie; Hester, Joshua; Jimenez, Daniel D; Buehler, Markus J

    2010-01-27

    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

  20. Energy landscape, structure and rate effects on strength properties of alpha-helical proteins

    NASA Astrophysics Data System (ADS)

    Bertaud, Jérémie; 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

  1. Climatic effects of 30 years of landscape change over the Greater Phoenix, Arizona, region: 1. Surface energy budget changes

    USGS Publications Warehouse

    Georgescu, M.; Miguez-Macho, G.; Steyaert, L.T.; Weaver, C.P.

    2009-01-01

    This paper is part 1 of a two-part study that evaluates the climatic effects of recent landscape change for one of the nation's most rapidly expanding metropolitan complexes, the Greater Phoenix, Arizona, region. The region's landscape evolution over an approximate 30-year period since the early 1970s is documented on the basis of analyses of Landsat images and land use/land cover (LULC) data sets derived from aerial photography (1973) and Landsat (1992 and 2001). High-resolution, Regional Atmospheric Modeling System (RAMS), simulations (2-km grid spacing) are used in conjunction with consistently defined land cover data sets and associated biophysical parameters for the circa 1973, circa 1992, and circa 2001 time periods to quantify the impacts of intensive land use changes on the July surface temperatures and the surface radiation and energy budgets for the Greater Phoenix region. The main findings are as follows: since the early 1970s the region's landscape has been altered by a significant increase in urban/suburban land area, primarily at the expense of decreasing plots of irrigated agriculture and secondarily by the conversion of seminatural shrubland. Mean regional temperatures for the circa 2001 landscape were 0.12??C warmer than the circa 1973 landscape, with maximum temperature differences, located over regions of greatest urbanization, in excess of 1??C. The significant reduction in irrigated agriculture, for the circa 2001 relative to the circa 1973 landscape, resulted in dew point temperature decreases in excess of 1??C. The effect of distinct land use conversion themes (e.g., conversion from irrigated agriculture to urban land) was also examined to evaluate how the most important conversion themes have each contributed to the region's changing climate. The two urbanization themes studied (from an initial landscape of irrigated agriculture and seminatural shrubland) have the greatest positive effect on near-surface temperature, increasing maximum daily

  2. Nitrogen rate and landscape impacts on life cycle energy use and emissions from switchgrass-derived ethanol

    DOE PAGES

    Mbonimpa, Eric G.; Kumar, Sandeep; Owens, Vance N.; ...

    2015-08-24

    Switchgrass-derived ethanol has been proposed as an alternative to fossil fuels to improve sustainability of the US energy sector. In this study, life cycle analysis (LCA) was used to estimate the environmental benefits of this fuel. To better define the LCA environmental impacts associated with fertilization rates and farm-landscape topography, results from a controlled experiment were analyzed. Data from switchgrass plots planted in 2008, consistently managed with three nitrogen rates (0, 56, and 112 kg N ha–1), two landscape positions (shoulder and footslope), and harvested annually (starting in 2009, the year after planting) through 2014 were used as input intomore » the Greenhouse gases, Regulated Emissions and Energy use in transportation (GREET) model. Simulations determined nitrogen (N) rate and landscape impacts on the life cycle energy and emissions from switchgrass ethanol used in a passenger car as ethanol–gasoline blends (10% ethanol:E10, 85% ethanol:E85s). Results indicated that E85s may lead to lower fossil fuels use (58 to 77%), greenhouse gas (GHG) emissions (33 to 82%), and particulate matter (PM2.5) emissions (15 to 54%) in comparison with gasoline. However, volatile organic compounds (VOCs) and other criteria pollutants such as nitrogen oxides (NOx), particulate matter (PM10), and sulfur dioxides (SOx) were higher for E85s than those from gasoline. Nitrogen rate above 56 kg N ha–1 yielded no increased biomass production benefits; but did increase (up to twofold) GHG, VOCs, and criteria pollutants. Lower blend (E10) results were closely similar to those from gasoline. The landscape topography also influenced life cycle impacts. Biomass grown at the footslope of fertilized plots led to higher switchgrass biomass yield, lower GHG, VOCs, and criteria pollutants in comparison with those at the shoulder position. Lastly, results also showed that replacing switchgrass before maximum stand life (10–20 years.) can further reduce the energy and

  3. Free energy landscape and folding mechanism of a beta-hairpin in explicit water: a replica exchange molecular dynamics study.

    PubMed

    Nguyen, Phuong H; Stock, Gerhard; Mittag, Emil; Hu, Chin-Kun; Li, Mai Suan

    2005-12-01

    The free energy landscape and the folding mechanism of the C-terminal beta-hairpin of protein G is studied by extensive replica exchange molecular dynamics simulations (40 replicas and 340 ns total simulation time), using the GROMOS96 force field and the SPC explicit water solvent. The study reveals that the system preferentially adopts a beta-hairpin structure at biologically important temperatures, and that the helix content is low at all temperatures studied. Representing the free energy landscape as a function of several types of reaction coordinates, four local minima corresponding to the folded, partially folded, molten globule, and unfolded states are identified. The findings suggest that the folding of the beta-hairpin occurs as the sequence: collapse of hydrophobic core --> formation of H-bond --> formation of the turn. Identifying the folded and molten globule states as the main conformations, the free energy landscape of the beta-hairpin is consistent with a two-state behavior with a broad transition state. The temperature dependence of the folding-unfolding transition is investigated in some detail. The enthalpy and entropy jumps at the folding transition temperature are found to be about three times lower than the experimental estimates, indicating that the folding-unfolding transition in silico is less cooperative than its in vitro counterpart. Proteins 2005. 2005 Wiley-Liss, Inc.

  4. Displacement Threshold Energy and Recovery in an Al-Ti Nanolayered System with Intrinsic Point Defect Partitioning

    SciTech Connect

    Gerboth, Matthew D.; Setyawan, Wahyu; Henager, Charles H.

    2014-01-07

    A method is established and validated using molecular dynamics (MD) to determine the displacement threshold energies as Ed in nanolayered, multilayered systems of dissimilar metals. The method is applied to specifically oriented nanolayered films of Al-Ti where the crystal structure and interface orientations are varied in atomic models and Ed is calculated. Methods for defect detection are developed and discussed based on prior research in the literature and based on specific crystallographic directions available in the nanolayered systems. These are compared and contrasted to similar calculations in corresponding bulk materials, including fcc Al, fcc Ti, hcp Al, and hcp Ti. In all cases, the calculated Ed in the multilayers are intermediate to the corresponding bulk values but exhibit some important directionality. In the nanolayer, defect detection demonstrated systematic differences in the behavior of Ed in each layer. Importantly, collision cascade damage exhibits significant defect partitioning within the Al and Ti layers that is hypothesized to be an intrinsic property of dissimilar nanolayered systems. This type of partitioning could be partly responsible for observed asymmetric radiation damage responses in many multilayered systems. In addition, a pseudo-random direction was introduced to approximate the average Ed without performing numerous simulations with random directions.

  5. The extinction law in the open cluster NGC 457 and the intrinsic energy distribution of Phi Cassiopeiae (F0 Ia)

    NASA Technical Reports Server (NTRS)

    Rosenzweig, P.; Morrison, N. D.

    1986-01-01

    Five early B-type stars near the main-sequence turnoff in NGC 457 have been observed at low dispersion with the short-wavelength prime and the long-wavelength redundant cameras of the IUE satellite. The equivalent widths of spectral features that are particularly strong and sensitive to temperature and luminosity were computed in the cluster stars and in 20 lightly reddened stars of types O9-B3 and luminosity classes III-V. The comparison of the equivalent widths provides a reliable method for finding matching pairs. Having identified the best comparison star for each program star, binned fluxes were used to determine the mean extinction curve. In order to cover the visible region, monochromatic fluxes of Phi Cas were derived from observations with the intensified Reticon scanner mounted on the No. 2 0.9 m telescope of KPNO, and they were dereddened with the mean extinction curve of Savage and Mathis. Thus, the intrinsic energy distribution of Phi Cas were determined from 1500 to 5800 A for use in a detailed model-atmosphere analysis.

  6. The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape.

    PubMed

    Fajer, Mikolai; Meng, Yilin; Roux, Benoît

    2016-10-28

    Tyrosine kinases are important cellular signaling allosteric enzymes that regulate cell growth, proliferation, metabolism, differentiation, and migration. Their activity must be tightly controlled, and malfunction can lead to a variety of diseases, particularly cancer. The nonreceptor tyrosine kinase c-Src, a prototypical model system and a representative member of the Src-family, functions as complex multidomain allosteric molecular switches comprising SH2 and SH3 domains modulating the activity of the catalytic domain. The broad picture of self-inhibition of c-Src via the SH2 and SH3 regulatory domains is well characterized from a structural point of view, but a detailed molecular mechanism understanding is nonetheless still lacking. Here, we use advanced computational methods based on all-atom molecular dynamics simulations with explicit solvent to advance our understanding of kinase activation. To elucidate the mechanism of regulation and self-inhibition, we have computed the pathway and the free energy landscapes for the "inactive-to-active" conformational transition of c-Src for different configurations of the SH2 and SH3 domains. Using the isolated c-Src catalytic domain as a baseline for comparison, it is observed that the SH2 and SH3 domains, depending upon their bound orientation, promote either the inactive or active state of the catalytic domain. The regulatory structural information from the SH2-SH3 tandem is allosterically transmitted via the N-terminal linker of the catalytic domain. Analysis of the conformational transition pathways also illustrates the importance of the conserved tryptophan 260 in activating c-Src, and reveals a series of concerted events during the activation process.

  7. The Effect of Tensile Stress on the Conformational Free Energy Landscape of Disulfide Bonds

    PubMed Central

    Anjukandi, Padmesh; Dopieralski, Przemyslaw; Ribas–Arino, Jordi; Marx, Dominik

    2014-01-01

    Disulfide bridges are no longer considered to merely stabilize protein structure, but are increasingly recognized to play a functional role in many regulatory biomolecular processes. Recent studies have uncovered that the redox activity of native disulfides depends on their C–C–S–S dihedrals, and . Moreover, the interplay of chemical reactivity and mechanical stress of disulfide switches has been recently elucidated using force–clamp spectroscopy and computer simulation. The and angles have been found to change from conformations that are open to nucleophilic attack to sterically hindered, so–called closed states upon exerting tensile stress. In view of the growing evidence of the importance of C–C–S–S dihedrals in tuning the reactivity of disulfides, here we present a systematic study of the conformational diversity of disulfides as a function of tensile stress. With the help of force-clamp metadynamics simulations, we show that tensile stress brings about a large stabilization of the closed conformers, thereby giving rise to drastic changes in the conformational free energy landscape of disulfides. Statistical analysis shows that native TDi, DO and interchain Ig protein disulfides prefer open conformations, whereas the intrachain disulfide bridges in Ig proteins favor closed conformations. Correlating mechanical stress with the distance between the two –carbons of the disulfide moiety reveals that the strain of intrachain Ig protein disulfides corresponds to a mechanical activation of about 100 pN. Such mechanical activation leads to a severalfold increase of the rate of the elementary redox reaction step. All these findings constitute a step forward towards achieving a full understanding of functional disulfides. PMID:25286308

  8. The effect of tensile stress on the conformational free energy landscape of disulfide bonds.

    PubMed

    Anjukandi, Padmesh; Dopieralski, Przemyslaw; Ribas-Arino, Jordi; Marx, Dominik

    2014-01-01

    Disulfide bridges are no longer considered to merely stabilize protein structure, but are increasingly recognized to play a functional role in many regulatory biomolecular processes. Recent studies have uncovered that the redox activity of native disulfides depends on their C-C-S-S dihedrals, χ2 and χ'2. Moreover, the interplay of chemical reactivity and mechanical stress of disulfide switches has been recently elucidated using force-clamp spectroscopy and computer simulation. The χ2 and χ'2 angles have been found to change from conformations that are open to nucleophilic attack to sterically hindered, so-called closed states upon exerting tensile stress. In view of the growing evidence of the importance of C-C-S-S dihedrals in tuning the reactivity of disulfides, here we present a systematic study of the conformational diversity of disulfides as a function of tensile stress. With the help of force-clamp metadynamics simulations, we show that tensile stress brings about a large stabilization of the closed conformers, thereby giving rise to drastic changes in the conformational free energy landscape of disulfides. Statistical analysis shows that native TDi, DO and interchain Ig protein disulfides prefer open conformations, whereas the intrachain disulfide bridges in Ig proteins favor closed conformations. Correlating mechanical stress with the distance between the two a-carbons of the disulfide moiety reveals that the strain of intrachain Ig protein disulfides corresponds to a mechanical activation of about 100 pN. Such mechanical activation leads to a severalfold increase of the rate of the elementary redox S(N)2 reaction step. All these findings constitute a step forward towards achieving a full understanding of functional disulfides.

  9. DNA Free Energy Landscapes and RNA Nano-Self-Assembly Using Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

    Frey, Eric William

    There is an important conceptual lesson which has long been appreciated by those who work in biophysics and related interdisciplinary fields. While the extraordinary behavior of biological matter is governed by its detailed atomic structure and random fluctuations, and is therefore difficult to predict, it can nevertheless be understood within simplified frameworks. Such frameworks model the system as consisting of only one or a few components, and model the behavior of the system as the occupation of a single state out of a small number of states available. The emerging widespread application of nanotechnology, such as atomic force microscopy (AFM), has expanded this understanding in eye-opening new levels of detail by enabling nano-scale control, measurement, and visualization of biological molecules. This thesis describes two independent projects, both of which illuminate this understanding using AFM, but which do so from very different perspectives. The organization of this thesis is as follows. Chapter 1 begins with an experimental background and introduction to AFM, and then describes our setup in both single-molecule manipulation and imaging modes. In Chapter 2, we describe the first project, the motivation for which is to extend methods for the experimental determination of the free energy landscape of a molecule. This chapter relies on the analysis of single-molecule manipulation data. Chapter 3 describes the second project, the motivation for which is to create RNA-based nano-structures suitable for future applications in living mammalian cells. This chapter relies mainly on imaging. Chapters 2 and 3 can thus be read and understood separately.

  10. Energy landscapes: Coal canals, oil pipelines, and electricity transmission wires in the mid-Atlantic, 1820--1930

    NASA Astrophysics Data System (ADS)

    Jones, Christopher F.

    2009-12-01

    Coal canals, oil pipelines, and electricity transmission wires transformed the built environment of the American mid-Atlantic region between 1820 and 1930. By transporting coal, oil, and electrons cheaply, reliably, and in great quantities, these technologies reshaped the energy choices available to mid-Atlantic residents. In particular, canals, pipelines, and wires created new energy landscapes: systems of transport infrastructure that enabled the ever-increasing consumption of fossil fuels. Energy Landscapes integrates history of technology, environmental history, and business history to provide new perspectives on how Americans began to use fossil fuels and the social implications of these practices. First, I argue that the development of transport infrastructure played critical, and underappreciated, roles in shaping social energy choices. Rather than simply responding passively to the needs of producers and consumers, canals, pipelines, and wires structured how, when, where, and in what quantities energy was used. Second, I analyze the ways fossil fuel consumption transformed the society, economy, and environment of the mid-Atlantic. I link the consumption of coal, oil, and electricity to the development of an urban and industrialized region, the transition from an organic to a mineral economy, and the creation of a society dependent on fossil fuel energy.

  11. Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection.

    PubMed

    Scalley-Kim, Michelle; Baker, David

    2004-04-30

    To determine the extent to which protein folding rates and free energy landscapes have been shaped by natural selection, we have examined the folding kinetics of five proteins generated using computational design methods and, hence, never exposed to natural selection. Four of these proteins are complete computer-generated redesigns of naturally occurring structures and the fifth protein, called Top7, has a computer-generated fold not yet observed in nature. We find that three of the four redesigned proteins fold much faster than their naturally occurring counterparts. While natural selection thus does not appear to operate on protein folding rates, the majority of the designed proteins unfold considerably faster than their naturally occurring counterparts, suggesting possible selection for a high free energy barrier to unfolding. In contrast to almost all naturally occurring proteins of less than 100 residues but consistent with simple computational models, the folding energy landscape for Top7 appears to be quite complex, suggesting the smooth energy landscapes and highly cooperative folding transitions observed for small naturally occurring proteins may also reflect the workings of natural selection.

  12. Chlorobaculum tepidum Modulates Amino Acid Composition in Response to Energy Availability, as Revealed by a Systematic Exploration of the Energy Landscape of Phototrophic Sulfur Oxidation.

    PubMed

    Levy, Amalie T; Lee, Kelvin H; Hanson, Thomas E

    2016-11-01

    Microbial sulfur metabolism, particularly the formation and consumption of insoluble elemental sulfur (S(0)), is an important biogeochemical engine that has been harnessed for applications ranging from bioleaching and biomining to remediation of waste streams. Chlorobaculum tepidum, a low-light-adapted photoautolithotrophic sulfur-oxidizing bacterium, oxidizes multiple sulfur species and displays a preference for more reduced electron donors: sulfide > S(0) > thiosulfate. To understand this preference in the context of light energy availability, an "energy landscape" of phototrophic sulfur oxidation was constructed by varying electron donor identity, light flux, and culture duration. Biomass and cellular parameters of C. tepidum cultures grown across this landscape were analyzed. From these data, a correction factor for colorimetric protein assays was developed, enabling more accurate biomass measurements for C. tepidum, as well as other organisms. C. tepidum's bulk amino acid composition correlated with energy landscape parameters, including a tendency toward less energetically expensive amino acids under reduced light flux. This correlation, paired with an observation of increased cell size and storage carbon production under electron-rich growth conditions, suggests that C. tepidum has evolved to cope with changing energy availability by tuning its proteome for energetic efficiency and storing compounds for leaner times.

  13. Frustration-induced protein intrinsic disorder

    NASA Astrophysics Data System (ADS)

    Matsushita, Katsuyoshi; Kikuchi, Macoto

    2013-03-01

    Spontaneous folding into a specific native structure is the most important property of protein to perform their biological functions within organisms. Spontaneous folding is understood on the basis of an energy landscape picture based on the minimum frustration principle. Therefore, frustration seemingly only leads to protein functional disorder. However, frustration has recently been suggested to have a function in allosteric regulation. Functional frustration has the possibility to be a key to our deeper understanding of protein function. To explore another functional frustration, we theoretically examined structural frustration, which is designed to induce intrinsic disorder of a protein and its function through the coupled folding and binding. We extended the Wako-Saitô-Muñoz-Eaton model to take into account a frustration effect. With the model, we analyzed the binding part of neuron-restrictive silencer factor and showed that designed structural frustration in it induces intrinsic disorder. Furthermore, we showed that the folding and the binding are cooperative in interacting with a target protein. The cooperativity enables an intrinsically disordered protein to exhibit a sharp switch-like folding response to binding chemical potential change. Through this switch-like response, the structural frustration may contribute to the regulation function of interprotein interaction of the intrinsically disordered protein.

  14. Free Energy Landscape of Protein-Protein Encounter Resulting from Brownian Dynamics Simulations of Barnase:Barstar.

    PubMed

    Spaar, Alexander; Helms, Volkhard

    2005-07-01

    Over the past years Brownian dynamics (BD) simulations have been proven to be a suitable tool for the analysis of protein-protein association. The computed rates and relative trends for protein mutants and different ionic strength are generally in good agreement with experimental results, e.g. see ref 1. By design, BD simulations correspond to an intensive sampling over energetically favorable states, rather than to a systematic sampling over all possible states which is feasible only at rather low resolution. On the example of barnase and barstar, a well characterized model system of electrostatically steered diffusional encounter, we report here the computation of the 6-dimensional free energy landscape for the encounter process of two proteins by a novel, careful analysis of the trajectories from BD simulations. The aim of these studies was the clarification of the encounter state. Along the trajectories, the individual positions and orientations of one protein (relative to the other) are recorded and stored in so-called occupancy maps. Since the number of simulated trajectories is sufficiently high, these occupancy maps can be interpreted as a probability distribution which allows the calculation of the entropy landscape by the use of a locally defined entropy function. Additionally, the configuration dependent electrostatic and desolvation energies are recorded in separate maps. The free energy landscape of protein-protein encounter is finally obtained by summing the energy and entropy contributions. In the free energy profile along the reaction path, which is defined as the path along the minima in the free energy landscape, a minimum shows up suggesting this to be used as the definition of the encounter state. This minimum describes a state of reduced diffusion velocity where the electrostatic attraction is compensated by the repulsion due to the unfavorable desolvation of the charged residues and the entropy loss due to the increasing restriction of the

  15. Ab initio modeling of the two-dimensional energy landscape of screw dislocations in bcc transition metals

    NASA Astrophysics Data System (ADS)

    Dezerald, L.; Ventelon, Lisa; Clouet, E.; Denoual, C.; Rodney, D.; Willaime, F.

    2014-01-01

    A density functional theory (DFT) study of the 1/2<111> screw dislocation was performed in the following body-centered cubic transition metals: V, Nb, Ta, Cr, Mo, W, and Fe. The energies of the easy, hard, and split core configurations, as well as the pathways between them, were investigated and used to generate the two-dimensional (2D) Peierls potential, i.e. the energy landscape seen by the dislocation as a function of its position in the (111) plane. In all investigated elements, the nondegenerate easy core is the minimum energy configuration, while the split core configuration, centered in the immediate vicinity of a <111> atomic column, has a high energy near or above that of the hard core. This unexpected result yields 2D Peierls potentials very different from the usually assumed landscapes. The 2D Peierls potential in Fe differs from the other transition metals, with a monkey saddle instead of a local maximum located at the hard core. An estimation of the Peierls stress from the shape of the Peierls barrier is presented in all investigated metals. A strong group dependence of the core energy is also evidenced, related to the position of the Fermi level with respect to the minimum of the pseudogap of the electronic density of states.

  16. Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method.

    PubMed

    Yonezawa, Yasushige; Fukuda, Ikuo; Kamiya, Narutoshi; Shimoyama, Hiromitsu; Nakamura, Haruki

    2011-05-10

    Precise and rapid calculation of long-range interactions is of crucial importance for molecular dynamics (MD) and Monte Carlo simulations. Instead of the Ewald method or its high speed variant, PME, we applied our novel method, called the force-switching Wolf method, to computation of the free energy landscapes of a short peptide in explicit water. Wolf and co-workers showed that long-range electrostatic energy under a periodic boundary condition can be well reproduced even by truncating the contribution from the distant charges, when the charge neutrality is taken into account. We recently applied the procedure proposed by Wolf and co-workers to a mathematically consistent MD theory by means of a force-switching scheme, and we show that the total electrostatic energy for sodium chloride liquid was well conserved and stable during the MD simulation with the force-switching Wolf method. Our current results for an aqueous peptide solution with a series of canonical and multicanonical molecular dynamics simulations show that the force-switching Wolf method is not only in good accordance with the energies and forces calculated by the conventional PME method but also properly reproduces the solvation and the free energy landscapes of the peptide at 300 K.

  17. Modeling long-term changes in forested landscapes and their relation to the Earth's energy balance

    NASA Technical Reports Server (NTRS)

    Shugart, H. H.; Emanuel, W. R.; Solomon, A. M.

    1984-01-01

    The dynamics of the forested parts of the Earth's surface on time scales from decades to centuries are discussed. A set of computer models developed at Oak Ridge National Laboratory and elsewhere are applied as tools. These models simulate a landscape by duplicating the dynamics of growth, death and birth of each tree living on a 0.10 ha element of the landscape. This spatial unit is generally referred to as a gap in the case of the forest models. The models were tested against and applied to a diverse array of forests and appear to provide a reasonable representation for investigating forest-cover dynamics. Because of the climate linkage, one important test is the reconstruction of paleo-landscapes. Detailed reconstructions of changes in vegetation in response to changes in climate are crucial to understanding the association of the Earth's vegetation and climate and the response of the vegetation to climate change.

  18. Calculation of the Intrinsic Solvation Free Energy Profile of an Ionic Penetrant Across a Liquid–Liquid Interface with Computer Simulations

    PubMed Central

    2013-01-01

    We introduce the novel concept of an intrinsic free energy profile, allowing one to remove the artificial smearing caused by thermal capillary waves, which renders difficulties for the calculation of free energy profiles across fluid interfaces in computer simulations. We apply this concept to the problem of a chloride ion crossing the interface between water and 1,2-dichloroethane and show that the present approach is able to reveal several important features of the free energy profile which are not detected with the usual, nonintrinsic calculations. Thus, in contrast to the nonintrinsic profile, a free energy barrier is found at the aqueous side of the (intrinsic) interface, which is attributed to the formation of a water “finger” the ion pulls with itself upon approaching the organic phase. Further, by the presence of a nonsampled region, the intrinsic free energy profile clearly indicates the coextraction of the first hydration shell water molecules of the ion when entering the organic phase. PMID:24175995

  19. Uniform and Janus-like nanoparticles in contact with vesicles: energy landscapes and curvature-induced forces.

    PubMed

    Agudo-Canalejo, Jaime; Lipowsky, Reinhard

    2017-03-15

    Biological membranes and lipid vesicles often display complex shapes with non-uniform membrane curvature. When adhesive nanoparticles with chemically uniform surfaces come into contact with such membranes, they exhibit four different engulfment regimes as recently shown by a systematic stability analysis. Depending on the local curvature of the membrane, the particles either remain free, become partially or completely engulfed by the membrane, or display bistability between free and completely engulfed states. Here, we go beyond stability analysis and develop an analytical theory to leading order in the ratio of particle-to-vesicle size. This theory allows us to determine the local and global energy landscapes of uniform nanoparticles that are attracted towards membranes and vesicles. While the local energy landscape depends only on the local curvature of the vesicle membrane and not on the overall membrane shape, the global energy landscape describes the variation of the equilibrium state of the particle as it probes different points along the membrane surface. In particular, we find that the binding energy of a partially engulfed particle depends on the 'unperturbed' local curvature of the membrane in the absence of the particle. This curvature dependence leads to local forces that pull the partially engulfed particles towards membrane segments with lower and higher mean curvature if the particles originate from the exterior and interior solution, respectively, corresponding to endo- and exocytosis. Thus, for partial engulfment, endocytic particles undergo biased diffusion towards the membrane segments with the lowest membrane curvature, whereas exocytic particles move towards segments with the highest curvature. The curvature-induced forces are also effective for Janus particles with one adhesive and one non-adhesive surface domain. In fact, Janus particles with a strongly adhesive surface domain are always partially engulfed which implies that they provide

  20. How dominant is the most efficient pathway through the potential energy landscape of a slowly diffusing disordered system?

    PubMed

    Nguyen, Crystal N; Isaacson, Joseph I; Shimmyo, Kayoko Beth; Chen, Andersen; Stratt, Richard M

    2012-05-14

    It has been suggested that the most-efficient pathway taken by a slowly diffusing many-body system is its geodesic path through the parts of the potential energy landscape lying below a prescribed value of the potential energy. From this perspective, slow diffusion occurs just because these optimal paths become particularly long and convoluted. We test this idea here by applying it to diffusion in two kinds of well-studied low-dimensional percolation problems: the 2d overlapping Lorentz model, and square and simple-cubic bond-dilute lattices. Although the most efficient path should be at its most dominant with the high-dimensional landscapes associated with many-body problems, it is useful to examine simpler, low-dimensional, constant-potential-energy problems such as these ones, both because the simpler models lend themselves to more accurate geodesic-path-finding approaches, and because they offer a significant contrast to many of the models used in the traditional energy-landscape literature. Neither the continuum nor the lattice percolation examples are adequately described by our geodesic-path formalism in the weakly disordered (relatively-fast-diffusion) limit, but in both cases the formalism successfully predicts the existence of the percolation transition and (to a certain extent) the slow diffusion characteristic of near-percolation behavior. The numerical results for these models are not nearly accurate enough near their transitions to describe critical exponents, but the models do showcase the qualitative validity of the geodesic perspective in that they allow us to see explicitly how tortuous and sparse the optimal pathways become as the diffusion constants begin to vanish.

  1. Density functional theory study of dopant effect on formation energy of intrinsic point defects in germanium crystals

    NASA Astrophysics Data System (ADS)

    Yamaoka, S.; Kobayashi, K.; Sueoka, K.; Vanhellemont, J.

    2017-09-01

    During the last decade the use of single crystal germanium (Ge) layers and structures in combination with silicon (Si) substrates has led to a revival of defect research on Ge. Ge is used because of the much higher carrier mobility compared to Si, allowing to design devices operating at much higher frequencies. A major issue for the use of Ge single crystal wafers is the fact that all Czochralski-grown Ge (CZ-Ge) crystals are vacancy-rich and contain vacancy clusters that are much larger than the ones in Si. In contrast to Si, control of intrinsic point defect concentrations has not yet been realized at the same level in Ge crystals due to the lack of experimental data especially on dopant effects. In this study, we have evaluated with density functional theory (DFT) calculations the dopant effect on the formation energy (Ef) of the uncharged vacancy (V) and self-interstitial (I) in Ge and compared the results with those for Si. The dependence of the total thermal equilibrium concentrations of point defects (sum of free V or I and V or I paired with dopant atoms) at melting temperature on the type and concentration of various dopants is obtained. It was found that (1) Ge crystals will be more V-rich by Tl, In, Sb, Sn, As and P doping, (2) Ge crystals will be more I-rich by Ga, C and B doping, (3) Si doping has negligible impact. The dopant impact on Ef of V and I in Ge has a narrower range and is smaller than that in Si. The obtained results are useful to control grown-in V and I concentrations, and will perhaps also allow to develop defect-free ;perfect; Ge crystals.

  2. Land cover change in the zone of sporadic permafrost causes shift in landscape-scale turbulent energy fluxes

    NASA Astrophysics Data System (ADS)

    Helbig, M.; Wischnewski, K.; Kljun, N.; Chasmer, L.; Quinton, W. L.; Detto, M.; Sonnentag, O.

    2015-12-01

    current heterogeneous to a homogeneous bog landscape could lead to a decrease in the maximum PBL height by about 700 m and to a decrease in regional Ta by 1 to 2 K. Our results show clearly that permafrost degradation and forest cover shifts will affect local and regional surface energy balances in the boreal zone and could represent important modifiers of future climates.

  3. The Potential and Flux Landscape Theory of Ecology

    PubMed Central

    Zhang, Kun; Wang, Erkang; Wang, Jin

    2014-01-01

    The species in ecosystems are mutually interacting and self sustainable stable for a certain period. Stability and dynamics are crucial for understanding the structure and the function of ecosystems. We developed a potential and flux landscape theory of ecosystems to address these issues. We show that the driving force of the ecological dynamics can be decomposed to the gradient of the potential landscape and the curl probability flux measuring the degree of the breaking down of the detailed balance (due to in or out flow of the energy to the ecosystems). We found that the underlying intrinsic potential landscape is a global Lyapunov function monotonically going down in time and the topology of the landscape provides a quantitative measure for the global stability of the ecosystems. We also quantified the intrinsic energy, the entropy, the free energy and constructed the non-equilibrium thermodynamics for the ecosystems. We studied several typical and important ecological systems: the predation, competition, mutualism and a realistic lynx-snowshoe hare model. Single attractor, multiple attractors and limit cycle attractors emerge from these studies. We studied the stability and robustness of the ecosystems against the perturbations in parameters and the environmental fluctuations. We also found that the kinetic paths between the multiple attractors do not follow the gradient paths of the underlying landscape and are irreversible because of the non-zero flux. This theory provides a novel way for exploring the global stability, function and the robustness of ecosystems. PMID:24497975

  4. The potential and flux landscape theory of ecology.

    PubMed

    Xu, Li; Zhang, Feng; Zhang, Kun; Wang, Erkang; Wang, Jin

    2014-01-01

    The species in ecosystems are mutually interacting and self sustainable stable for a certain period. Stability and dynamics are crucial for understanding the structure and the function of ecosystems. We developed a potential and flux landscape theory of ecosystems to address these issues. We show that the driving force of the ecological dynamics can be decomposed to the gradient of the potential landscape and the curl probability flux measuring the degree of the breaking down of the detailed balance (due to in or out flow of the energy to the ecosystems). We found that the underlying intrinsic potential landscape is a global Lyapunov function monotonically going down in time and the topology of the landscape provides a quantitative measure for the global stability of the ecosystems. We also quantified the intrinsic energy, the entropy, the free energy and constructed the non-equilibrium thermodynamics for the ecosystems. We studied several typical and important ecological systems: the predation, competition, mutualism and a realistic lynx-snowshoe hare model. Single attractor, multiple attractors and limit cycle attractors emerge from these studies. We studied the stability and robustness of the ecosystems against the perturbations in parameters and the environmental fluctuations. We also found that the kinetic paths between the multiple attractors do not follow the gradient paths of the underlying landscape and are irreversible because of the non-zero flux. This theory provides a novel way for exploring the global stability, function and the robustness of ecosystems.

  5. Nitrogen rate and landscape impacts on life cycle energy use and emissions from switchgrass-derived ethanol

    SciTech Connect

    Mbonimpa, Eric G.; Kumar, Sandeep; Owens, Vance N.; Chintala, Rajesh; Sieverding, Heidi L.; Stone, James J.

    2015-08-24

    Switchgrass-derived ethanol has been proposed as an alternative to fossil fuels to improve sustainability of the US energy sector. In this study, life cycle analysis (LCA) was used to estimate the environmental benefits of this fuel. To better define the LCA environmental impacts associated with fertilization rates and farm-landscape topography, results from a controlled experiment were analyzed. Data from switchgrass plots planted in 2008, consistently managed with three nitrogen rates (0, 56, and 112 kg N ha–1), two landscape positions (shoulder and footslope), and harvested annually (starting in 2009, the year after planting) through 2014 were used as input into the Greenhouse gases, Regulated Emissions and Energy use in transportation (GREET) model. Simulations determined nitrogen (N) rate and landscape impacts on the life cycle energy and emissions from switchgrass ethanol used in a passenger car as ethanol–gasoline blends (10% ethanol:E10, 85% ethanol:E85s). Results indicated that E85s may lead to lower fossil fuels use (58 to 77%), greenhouse gas (GHG) emissions (33 to 82%), and particulate matter (PM2.5) emissions (15 to 54%) in comparison with gasoline. However, volatile organic compounds (VOCs) and other criteria pollutants such as nitrogen oxides (NOx), particulate matter (PM10), and sulfur dioxides (SOx) were higher for E85s than those from gasoline. Nitrogen rate above 56 kg N ha–1 yielded no increased biomass production benefits; but did increase (up to twofold) GHG, VOCs, and criteria pollutants. Lower blend (E10) results were closely similar to those from gasoline. The landscape topography also influenced life cycle impacts. Biomass grown at the footslope of fertilized plots led to higher switchgrass biomass yield, lower GHG, VOCs, and criteria pollutants in comparison with those at the shoulder position. Lastly, results also showed that replacing switchgrass before maximum stand life (10–20 years.) can

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

    USGS Publications Warehouse

    Biewick, Laura R.H.

    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.

  7. Defining and quantifying frustration in the energy landscape: Applications to atomic and molecular clusters, biomolecules, jammed and glassy systems

    NASA Astrophysics Data System (ADS)

    de Souza, V. K.; Stevenson, J. D.; Niblett, S. P.; Farrell, J. D.; Wales, D. J.

    2017-03-01

    The emergence of observable properties from the organisation of the underlying potential energy landscape is analysed, spanning a full range of complexity from self-organising to glassy and jammed systems. The examples include atomic and molecular clusters, a β-barrel protein, the GNNQQNY peptide dimer, and models of condensed matter that exhibit structural glass formation and jamming. We have considered measures based on several different properties, namely, the Shannon entropy, an equilibrium thermodynamic measure that uses a sample of local minima, and indices that require additional information about the connections between local minima in the form of transition states. A frustration index is defined that correlates directly with key properties that distinguish relaxation behaviour within this diverse set. The index uses the ratio of the energy barrier to the energy difference with reference to the global minimum. The contributions for each local minimum are weighted by the equilibrium occupation probabilities. Hence we obtain fundamental insight into the connections and distinctions between systems that cover the continuum from efficient structure-seekers to landscapes that exhibit broken ergodicity and rare event dynamics.

  8. Origin of the Fragile-to-Strong Crossover in Liquid Silica as Expressed by its Potential-Energy Landscape

    NASA Astrophysics Data System (ADS)

    Saksaengwijit, A.; Reinisch, J.; Heuer, A.

    2004-12-01

    The origin of the fragile-to-strong crossover in liquid silica is characterized in terms of properties of the potential-energy landscape (PEL). Using the standard BKS model [B. W. H. van Beest, G. J. Kramer, and R. A. van Santen,

    Phys. Rev. Lett. 64, 1955 (1990)
    ] of silica we observe a low-energy cutoff of the PEL. It is shown that this feature of the PEL is responsible for the occurrence of the fragile-to-strong crossover and may also explain the avoidance of the Kauzmann paradox. The number of defects, i.e., deviations from the ideal tetrahedral structure, vanishes for configurations with energies close to this cutoff. This suggests a structural reason for this cutoff.

  9. Water-regolith-energy Interaction in Landscape Evolution and Its Influence on Forming Asymmetric Landscape: An Example from the Shale Hills Critical Zone Observatory of Central Pennsylvania

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Slingerland, R. L.; Shi, Y.; Duffy, C.; West, N.

    2015-12-01

    Shale Hills Critical Zone Observatory (SSHCZO) is a 0.08 km2 first order experimental research catchment with relatively homogeneous bedrock, regolith and tectonic uplift, but with an asymmetric slope and thickness of regolith on the north- and south-facing hillslopes. In this paper, we use a hydrological-morphodynamic model (LE-PIHM), which links bedrock, soil, surface and subsurface water flow, plant, energy, and seasonal climate, to address the influence of water-regolith-energy interaction on soil creep process, the possible factors causing slope asymmetry and the spatial distribution of regolith transport at the SSHCZO. Two non-dimensional parameters were used to explore the competitive relationship between regolith diffusion and advection forming self-organized channel spacing, relief and slope length at steady state. Model simulation under seasonal meteorological forcing shows spatial variations of hillslope sediment fluxes. An experimental study using Beryllium 10 at the SSHCZO (West et al 2013) showed that a south-facing planar slope had a greater diffusion flux rate than a planar on north-facing slope. The model confirms this relationship in general although there are significant local variations. The largest regolith transport rate by overland flow (advection) occurs at the junctions of main channel and swales. The model simulation further suggests that north-south differences in diffusive flux may be a result of asymmetric solar insolation which affects freeze-thaw frequency and sediment transport through the process of soil creep. This study demonstrates the value of physically-based distributed landscape evolution model on estimating spatial distribution of regolith transport and highlights the critical transition zone.

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

    USGS Publications Warehouse

    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

  11. Effect of Grain size on the Giant Intrinsic Coercivity of High-Energy Milled Sm(Co,Cu,Fe)5 Alloys

    NASA Astrophysics Data System (ADS)

    Sultana, Dilara; Gabay, Alexandar; Hadjipanayis, George

    2008-03-01

    The giant intrinsic magnetic hardness of Sm(Co,Cu)5 alloys have been known for a long time [1]. Previous studies suggested that this behavior is due to the crystal site disorder [2]. Our previous work has explained that the room-temperature intrinsic coercivity of 37 kOe after low-temperature aging is rather due to the intrinsic change in the Co atomic site occupation [3]. In this study, we investigated the effect of grain refinement through the high energy milling on the intrinsic coercivity of the Sm(Co,Cu,Fe)5 alloys. We have found that grain refinement does not affect the high coercivity of homogenized alloys, but strongly influences the onset of the giant coercivity during low-temperature aging. The microstructures of the samples are examined with TEM. [1] E.A. Nesbitt, R.H. Willens, R.C. Sherwood, E. Buehler, J.H. Wernick 1968 Appl.. Phys. Lett. 12, 361. [2] H. Oesterrier , F.T. Parker, M. Misroach 1979 J. Appl. Phys. 50, 4273. [3] A.M. Gabay, P. Larson, I.I. Manzin, G.C. Hadjipanayis 2005, J. Phys. D: Appl. Phys. 38, 1.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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

  14. Fugitive methane emissions from natural, urban, agricultural, and energy-production landscapes of eastern Australia

    NASA Astrophysics Data System (ADS)

    Kelly, Bryce F. J.; Iverach, Charlotte P.; Lowry, Dave; Fisher, Rebecca E.; France, James L.; Nisbet, Euan G.

    2015-04-01

    Modern cavity ringdown spectroscopy systems (CRDS) enable the continuous measurement of methane concentration. This allows for improved quantification of greenhouse gas emissions associated with various natural and human landscapes. We present a subset of over 4000 km of continuous methane surveying along the east coast of Australia, made using a Picarro G2301 CRDS, deployed in a utility vehicle with an air inlet above the roof at 2.2 mAGL. Measurements were made every 5 seconds to a precision of <0.5 ppb for CH4. These surveys were undertaken during dry daytime hours and all measurements were moisture corrected. We compare the concentration of methane in the near surface atmosphere adjacent to open-cut coal mines, unconventional gas developments (coal seam gas; CSG), and leaks detected in cities and country towns. In areas of dryland crops the median methane concentration was 1.78 ppm, while in the irrigation districts located on vertisol soils the concentration was as low as 1.76 ppm, which may indicate that these soils are a sink for methane. In the Hunter Valley, New South Wales, open-cut coal mining district we mapped a continuous 50 km interval where the concentration of methane exceeded 1.80 ppm. The median concentration in this interval was 2.02 ppm. Peak readings were beyond the range of the reliable measurement (in excess of 3.00 ppm). This extended plume is an amalgamation of plumes from 17 major pits 1 to 10 km in length. Adjacent to CSG developments in the Surat Basin, southeast Queensland, only small anomalies were detected near the well-heads. Throughout the vast majority of the gas fields the concentration of methane was below 1.80 ppm. The largest source of fugitive methane associated with CSG was off-gassing methane from the co-produced water holding ponds. At one location the down wind plume had a cross section of approximately 1 km where the concentration of methane was above 1.80 ppm. The median concentration within this section was 1.82 ppm

  15. Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions.

    PubMed

    Wojtas-Niziurski, Wojciech; Meng, Yilin; Roux, Benoit; Bernèche, Simon

    2013-04-09

    The potential of mean force describing conformational changes of biomolecules is a central quantity that determines the function of biomolecular systems. Calculating an energy landscape of a process that depends on three or more reaction coordinates might require a lot of computational power, making some of multidimensional calculations practically impossible. Here, we present an efficient automatized umbrella sampling strategy for calculating multidimensional potential of mean force. The method progressively learns by itself, through a feedback mechanism, which regions of a multidimensional space are worth exploring and automatically generates a set of umbrella sampling windows that is adapted to the system. The self-learning adaptive umbrella sampling method is first explained with illustrative examples based on simplified reduced model systems, and then applied to two non-trivial situations: the conformational equilibrium of the pentapeptide Met-enkephalin in solution and ion permeation in the KcsA potassium channel. With this method, it is demonstrated that a significant smaller number of umbrella windows needs to be employed to characterize the free energy landscape over the most relevant regions without any loss in accuracy.

  16. Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions

    PubMed Central

    Wojtas-Niziurski, Wojciech; Meng, Yilin; Roux, Benoit; Bernèche, Simon

    2013-01-01

    The potential of mean force describing conformational changes of biomolecules is a central quantity that determines the function of biomolecular systems. Calculating an energy landscape of a process that depends on three or more reaction coordinates might require a lot of computational power, making some of multidimensional calculations practically impossible. Here, we present an efficient automatized umbrella sampling strategy for calculating multidimensional potential of mean force. The method progressively learns by itself, through a feedback mechanism, which regions of a multidimensional space are worth exploring and automatically generates a set of umbrella sampling windows that is adapted to the system. The self-learning adaptive umbrella sampling method is first explained with illustrative examples based on simplified reduced model systems, and then applied to two non-trivial situations: the conformational equilibrium of the pentapeptide Met-enkephalin in solution and ion permeation in the KcsA potassium channel. With this method, it is demonstrated that a significant smaller number of umbrella windows needs to be employed to characterize the free energy landscape over the most relevant regions without any loss in accuracy. PMID:23814508

  17. Condensation transition and forced unravelling of DNA-histone H1 toroids: a multi-state free energy landscape

    NASA Astrophysics Data System (ADS)

    Mack, A. H.; Schlingman, D. J.; Salinas, R. D.; Regan, L.; Mochrie, S. G. J.

    2015-02-01

    DNA is known to condense with multivalent cations and positively charged proteins. However, the properties and energetics of DNA superstructures, such as chromatin, are poorly understood. As a model system, we investigate histone H1 condensation of DNA with tethered particle motion and force-extension measurements. We show that after the addition of H1 to DNA, a concentration dependent lag time is followed by the DNA spontaneously condensing. The trigger for this condensation phase transition can be modeled as sufficient H1s having bound to the DNA, providing insight into the 30 nm fiber condensation upon H1 binding. Furthermore, optical tweezers force-extension measurements of histone H1 condensed DNA reveals a sequence of state transitions corresponding to the unwinding of superhelical turns. We determine the complete, experimental, multi-state free energy landscape for the complex using Crooks fluctuation theorem. The measured force-versus-extension and free energy landscape are compared to predictions from a simple, theoretical model. This work encourages the theoretical description of DNA/protein structure and energetics and their role in chromatin and other, more complex, systems.

  18. Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.

    PubMed

    Higo, Junichi; Dasgupta, Bhaskar; Mashimo, Tadaaki; Kasahara, Kota; Fukunishi, Yoshifumi; Nakamura, Haruki

    2015-07-30

    A novel enhanced conformational sampling method, virtual-system-coupled adaptive umbrella sampling (V-AUS), was proposed to compute 300-K free-energy landscape for flexible molecular docking, where a virtual degrees of freedom was introduced to control the sampling. This degree of freedom interacts with the biomolecular system. V-AUS was applied to complex formation of two disordered amyloid-β (Aβ30-35 ) peptides in a periodic box filled by an explicit solvent. An interpeptide distance was defined as the reaction coordinate, along which sampling was enhanced. A uniform conformational distribution was obtained covering a wide interpeptide distance ranging from the bound to unbound states. The 300-K free-energy landscape was characterized by thermodynamically stable basins of antiparallel and parallel β-sheet complexes and some other complex forms. Helices were frequently observed, when the two peptides contacted loosely or fluctuated freely without interpeptide contacts. We observed that V-AUS converged to uniform distribution more effectively than conventional AUS sampling did.

  19. Using the optical-klystron effect to increase and measure the intrinsic beam energy spread in free-electron-laser facilities

    NASA Astrophysics Data System (ADS)

    Prat, Eduard; Ferrari, Eugenio; Reiche, Sven; Schietinger, Thomas

    2017-04-01

    We present a setup based on the optical klystron concept, consisting of two undulator modules separated by a magnetic chicane, that addresses two issues in free-electron-laser (FEL) facilities. On the one hand, it allows increasing the intrinsic energy spread of the beam at the source, which is useful to counteract the harmful microbunching instability. This represents an alternative method to the more conventional laser heater with the main advantage that no laser system is required. On the other hand, the setup can be used to reconstruct the initial beam energy spread, whose typical values in FEL injectors around 1 keV are very difficult to measure with standard procedures.

  20. Managing riverine landscapes as meta-ecosystems

    NASA Astrophysics Data System (ADS)

    Tockner, K.

    2014-12-01

    Aquatic and terrestrial ecosystems are tightly linked through energy, material, information, and organism flows. At the landscape scale, these reciprocal flows are controlled by the composition, configuration, boundary conditions and linkage of individual ecosystem types, thereby forming so-called meta-ecosystems. The relative importance of individual ecosystem types depends on the intrinsic properties (so-called "ecosystem traits"), the setting within the landscape, and the characteristics of interfaces that control cross-system fluxes. For example, the juxtaposition of particular ecosystem types (i.e. their composition and configuration) may alter the magnitude of landscape processes as well as the directions of flow among ecosystem types. Therefore, the meta-ecosystem concept provides a framework to quantify ecosystem diversity, a neglected component of biodiversity, and to test its effects on genetic and species diversity as well as the functional performance in coupled ecosystems. Given their topographic position at the lowest point in the landscape, aquatic ecosystems are particularly susceptible to influences exerted by their surrounding terrestrial environment, both the immediately adjacent riparian zones and the entire catchment that they drain. Questions that need to be tackled may include: What are the consequences of exchange pulses between aquatic and terrestrial ecosystems on the functional performance of individual ecosystems? What are the mechanisms and processes underlying structural and functional biodiversity at aquatic-terrestrial interfaces? In this respect, the meta-ecosystem concept might be very helpful in landscape management and in ecosystem design and engineering.

  1. A study of intrinsic statistical variation for low-energy nuclear recoils in liquid xenon detector for dark matter searches

    NASA Astrophysics Data System (ADS)

    Wang, Lu; Wei, Wenzhao; Mei, Dongming; Cubed Collaboration

    2015-10-01

    Noble liquid xenon experiments, such as XENON100, LUX, XENON 1-Ton, and LZ are large dark matter experiments directly searches for weakly interacting massive particles (WIMPs). One of the most important features is to discriminate nuclear recoils from electronic recoils. Detector response is generally calibrated with different radioactive sources including 83mKr, tritiated methane, 241AmBe, 252Cf, and DD-neutrons. The electronic recoil and nuclear recoil bands have been determined by these calibrations. However, the width of nuclear recoil band needs to be fully understood. We derive a theoretical model to understand the correlation of the width of nuclear recoil band and intrinsic statistical variation. In addition, we conduct experiments to validate the theoretical model. In this paper, we present the study of intrinsic statistical variation contributing to the width of nuclear recoil band. DE-FG02-10ER46709 and the state of South Dakota.

  2. Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes.

    PubMed

    Das, Payel; Matysiak, Silvina; Clementi, Cecilia

    2005-07-19

    Coarse-grained models have been extremely valuable in promoting our understanding of protein folding. However, the quantitative accuracy of existing simplified models is strongly hindered either from the complete removal of frustration (as in the widely used Gō-like models) or from the compromise with the minimal frustration principle and/or realistic protein geometry (as in the simple on-lattice models). We present a coarse-grained model that "naturally" incorporates sequence details and energetic frustration into an overall minimally frustrated folding landscape. The model is coupled with an optimization procedure to design the parameters of the protein Hamiltonian to fold into a desired native structure. The application to the study of src-Src homology 3 domain shows that this coarse-grained model contains the main physical-chemical ingredients that are responsible for shaping the folding landscape of this protein. The results illustrate the importance of nonnative interactions and energetic heterogeneity for a quantitative characterization of folding mechanisms.

  3. Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes

    PubMed Central

    Das, Payel; Matysiak, Silvina; Clementi, Cecilia

    2005-01-01

    Coarse-grained models have been extremely valuable in promoting our understanding of protein folding. However, the quantitative accuracy of existing simplified models is strongly hindered either from the complete removal of frustration (as in the widely used Gō-like models) or from the compromise with the minimal frustration principle and/or realistic protein geometry (as in the simple on-lattice models). We present a coarse-grained model that “naturally” incorporates sequence details and energetic frustration into an overall minimally frustrated folding landscape. The model is coupled with an optimization procedure to design the parameters of the protein Hamiltonian to fold into a desired native structure. The application to the study of src-Src homology 3 domain shows that this coarse-grained model contains the main physical-chemical ingredients that are responsible for shaping the folding landscape of this protein. The results illustrate the importance of nonnative interactions and energetic heterogeneity for a quantitative characterization of folding mechanisms. PMID:16006532

  4. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.

    PubMed

    Lei, Hongxing; Wu, Chun; Liu, Haiguang; Duan, Yong

    2007-03-20

    High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica exchange molecular dynamics for 200 ns each and three sets of conventional microsecond-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation model. The protein folded consistently to the native state; the lowest C(alpha)-rmsd from the x-ray structure was 0.46 A, and the C(alpha)- rmsd of the center of the most populated cluster was 1.78 A at 300 K. ab initio simulations have previously not reached this level. The folding landscape of HP35 can be partitioned into the native, denatured, and two intermediate-state regions. The native state is separated from the major folding intermediate state by a small barrier, whereas a large barrier exists between the major folding intermediate and the denatured states. The melting temperature T(m) = 339 K extracted from the heat-capacity profile was in close agreement with the experimentally derived T(m) = 342 K. A comprehensive picture of the kinetics and thermodynamics of HP35 folding emerges when the results from replica exchange and conventional molecular dynamics simulations are combined.

  5. The Folding Energy Landscape of the Dimerization Domain of E. coli Trp Repressor: A Joint Experimental and Theoretical Investigation

    PubMed Central

    Simler, B. Robert; Levy, Yaakov; Onuchic, José N.; Matthews, C. Robert

    2007-01-01

    Enhanced structural insights into the folding energy landscape of the N-terminal dimerization domain of E. coli tryptophan repressor, [2-66]2 TR, were obtained from a combined experimental and theoretical analysis of its equilibrium folding reaction. Previous studies have shown that the three intertwined helices in [2-66]2 TR are sufficient to drive the formation of a stable dimer for the full-length protein, [2-107]2 TR. The monomeric and dimeric folding intermediates that appear during the folding reactions of [2-66]2 TR have counterparts in the folding mechanism of the full-length protein. The equilibrium unfolding energy surface on which the folding and dimerization reactions occur for [2-66]2 TR was examined with a combination of native-state hydrogen exchange analysis, pepsin digestion and MALDI mass spectrometry performed at several protein and denaturant concentrations. Peptides corresponding to all three helices in [2-66]2 TR show multi-layered protection patterns consistent with the relative stabilities of the dimeric and monomeric folding intermediates. The observation of protection exceeding that offered by the dimeric intermediate in segments from all three helices implies that a segment-swapping mechanism may be operative in the monomeric intermediate. Protection greater than that expected from the global stability for a single amide hydrogen in a peptide from the A-helix and another from the C-helix may reflect non-random structure, possibly a pre-cursor for segment swapping, in the urea-denatured state. Native topology-based model simulations that correspond to a funnel energy landscape capture both the monomeric and dimeric intermediates suggested by the HX-MS data and provide a rationale for the progressive acquisition of secondary structure in their conformational ensembles. PMID:16956620

  6. Curl flux, coherence, and population landscape of molecular systems: nonequilibrium quantum steady state, energy (charge) transport, and thermodynamics.

    PubMed

    Zhang, Zhedong; Wang, Jin; Zhang, Z D; Wang, J

    2014-06-28

    We established a theoretical framework in terms of the curl flux, population landscape, and coherence for non-equilibrium quantum systems at steady state, through exploring the energy and charge transport in molecular processes. The curl quantum flux plays the key role in determining transport properties and the system reaches equilibrium when flux vanishes. The novel curl quantum flux reflects the degree of non-equilibriumness and the time-irreversibility. We found an analytical expression for the quantum flux and its relationship to the environmental pumping (non-equilibriumness quantified by the voltage away from the equilibrium) and the quantum tunneling. Furthermore, we investigated another quantum signature, the coherence, quantitatively measured by the non-zero off diagonal element of the density matrix. Populations of states give the probabilities of individual states and therefore quantify the population landscape. Both curl flux and coherence depend on steady state population landscape. Besides the environment-assistance which can give dramatic enhancement of coherence and quantum flux with high voltage at a fixed tunneling strength, the quantum flux is promoted by the coherence in the regime of small tunneling while reduced by the coherence in the regime of large tunneling, due to the non-monotonic relationship between the coherence and tunneling. This is in contrast to the previously found linear relationship. For the systems coupled to bosonic (photonic and phononic) reservoirs the flux is significantly promoted at large voltage while for fermionic (electronic) reservoirs the flux reaches a saturation after a significant enhancement at large voltage due to the Pauli exclusion principle. In view of the system as a quantum heat engine, we studied the non-equilibrium thermodynamics and established the analytical connections of curl quantum flux to the transport quantities such as energy (charge) transfer efficiency, chemical reaction efficiency, energy

  7. Unraveling energy conversion modeling in the intrinsic persistent upconverted luminescence of solids: a study of native point defects in antiferromagnetic Er2O3.

    PubMed

    Huang, Bolong

    2016-05-11

    We investigated the mechanism of the intrinsic persistent luminescence of Er2O3 in the A-type lattice based on first-principles calculations. We found that the native point defects were engaged in mutual subtle interactions in the form of chemical reactions between different charge states. The release of energy related to lattice distortion facilitates the conversion of energy for electrons to be transported between the valence band and the trap levels or even between the deep trap levels so as to generate persistent luminescence. The defect transitions that take place along the zero-phonon line release energy to enable optical transitions, with the exact amount of negative effective correlation energy determined by the lattice distortions. Our calculations on the thermodynamic transition levels confirm that both the visible and NIR experimentally observed intrinsic persistent luminescence (phosphor or afterglow) are related to the thermodynamic transition levels of oxygen-related defects, and the thermodynamic transition levels within different charge states for these defects are independent of the chemical potentials of the given species. Lattice distortion defects such as anion Frenkel (a-Fr) pair defects play an important role in transporting O-related defects between different lattice sites. To obtain red persistent luminescence that matches the biological therapeutic window, it is suggested to increase the electron transition levels between high-coordinated O vacancies and related metastable a-Fr defects; a close-packed core-shell structure is required to quench low-coordinated O-related defects so as to reduce the green band luminescence. We further established a conversed chain reaction (CCR) model to interpret the energy conversion process of persistent luminescence in terms of the inter-reactions of native point defects between different charge states. It is advantageous to use the study of defect levels combined with formation energies to suggest limits

  8. Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations

    PubMed Central

    Chang, Le; Takada, Shoji

    2016-01-01

    Histone tail acetylation is a key epigenetic marker that tends to open chromatin folding and activate transcription. Despite intensive studies, precise roles of individual lysine acetylation in chromatin folding have only been poorly understood. Here, we revealed structural dynamics of tri-nucleosomes with several histone tail acetylation states and analyzed histone tail interactions with DNA by performing molecular simulations at an unprecedentedly high resolution. We found versatile acetylation-dependent landscapes of tri-nucleosome. The H4 and H2A tail acetylation reduced the contact between the first and third nucleosomes mediated by the histone tails. The H3 tail acetylation reduced its interaction with neighboring linker DNAs resulting in increase of the distance between consecutive nucleosomes. Notably, two copies of the same histone in a single nucleosome have markedly asymmetric interactions with DNAs, suggesting specific pattern of nucleosome docking albeit high inherent flexibility. Estimated transcription factor accessibility was significantly high for the H4 tail acetylated structures. PMID:27698366

  9. Covariant energy density functionals: The assessment of global performance across the nuclear landscape

    SciTech Connect

    Afanasjev, A. V.

    2015-10-15

    The assessment of the global performance of the state-of-the-art covariant energy density functionals and related theoretical uncertainties in the description of ground state observables has recently been performed. Based on these results, the correlations between global description of binding energies and nuclear matter properties of covariant energy density functionals have been studied in this contribution.

  10. Global and local aspects of the surface potential landscape for energy level alignment at organic-ZnO interfaces

    NASA Astrophysics Data System (ADS)

    Stähler, Julia; Rinke, Patrick

    2017-03-01

    Hybrid systems of organic and inorganic semiconductors are a promising route for the development of novel opto-electronic and light-harvesting devices. A key ingredient for achieving a superior functionality by means of a hybrid system is the right relative position of energy levels at the interfaces of the two material classes. In this Perspective, we address the sensitivity of the potential energy landscape at various ZnO surfaces, a key ingredient for interfacial energy level alignment, by combining one- and two-photon photoelectron spectroscopy with density-functional theory calculations (DFT). We show that even very large work function changes (>2.5 eV) do not necessarily have to be accompanied by surface band bending in ZnO. Band bending - if it does occur - may be localized to few Å or extend over hundreds of nanometers with very different results for the surface work function and energy level alignment. Managing the delicate balance of different interface manipulation mechanisms in organic-inorganic hybrid systems will be a major challenge towards future applications.

  11. Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the