Concept Of Energy Landscape Research Articles

Energy-based corridor identification for mammals between protected areas in Iran.

Body mass plays a crucial role in determining the mass-specific energy expenditure during terrestrial locomotion across diverse animal taxa, affecting locomotion patterns. The energy landscape concept offers a framework to explore the relationship between landscape characteristics and energy expenditure, enhancing our understanding of animal movement. Although the energy landscape approach solely considers the topographic obstacles faced by animals, its suitability compared to previous methods for constructing resistance maps and delineating corridors has not been comprehensively examined. In this study, we utilized the enerscape R package to generate resistance maps in kilocalories (kcal) by incorporating digital elevation models (DEMs) and body size data (kg). We assigned body sizes ranging from 0.5 to 100 kg to encompass a wide range of small and large mammals in Iran, adjusting maximum dispersal distances accordingly from 50 to 200 km. By analyzing these scenarios, we produced four resistance maps for each body size. Next, we identified potential corridors between terrestrial protected areas in Iran using the Linkage Mapper toolkit and examined barriers and pinch-points along these paths. Our study revealed significant findings regarding the shared corridors between small and large mammals in Iran's landscape. Despite their differing body sizes and energy requirements, many corridors were found to be utilized by both small and large mammal species. For example, we identified 206 corridors for mammals weighing 500 g, which were also recognized as the least-cost paths for 100 kg mammals. Thus, embracing a comprehensive method in resistance map creation, one that incorporates species-specific traits and human infrastructure becomes imperative for accurately identifying least-cost paths and consequently pinpointing pinch points and barriers.

Entropy of metallic glasses and the size effect on glass transition

A statistical description of metallic glasses is proposed based on evaluation of an entropy and using the concept of potential energy landscape (PEL). The PEL is probed using nano-indentation, assuming that serrations observed are related to local energy levels. Serrations sizes follow a Poisson distribution consistent with, that their formation is a rare events. An entropy is derived revealing parameters characterizing the glass structure. The relevance of the approach is tested on the size effect on mechanical properties of metallic glass. It is noticed that the relations explain the effect of film thickness on the glass transition temperature observed for glass polymers.

Liquid-Liquid Crossover in Water Model: Local Structure vs Kinetics of Hydrogen Bonds.

In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase diagram of the water model, the thermodynamic region corresponding to the equilibrium liquid phase is divided by a line of the smooth liquid-liquid crossover. In the case of the water model TIP4P/2005, this crossover is revealed by various local order parameters and corresponds to pressures on the order of 3150 ± 350 atm at ambient temperature. In the vicinity of the crossover, the dynamics of water molecules change significantly, which is reflected, in particular, in the fact that the self-diffusion coefficient reaches its maximum values. In addition, changes in the structure also manifest themselves in changes in the kinetics of hydrogen bonding, which are captured by values of such quantities as the average lifetime of hydrogen bonding, the average lifetimes of different local coordination numbers, and the frequencies of changes in different local coordination numbers. An interpretation of the hydrogen bond kinetics in terms of the free energy landscape concept in the space of possible coordination numbers is proposed.

Correlation between fragility and surface glass transition temperature of polymers

The fragility of glass describes how rapidly its molecules slow down as it is cooled near its glass transition temperature. In nanoscale films, polymer glasses with higher fragility experience larger reductions in their Tg compared to those with lower fragility. We investigated whether this is due to the free surface of the polymers, which can cause the surface Tg (Tgsurf) to decrease relative to the bulk Tg. By measuring Tgsurf of various polymers, we found that the shift in Tgsurf relative to the bulk Tg increased with fragility. This suggests that more fragile polymers are more susceptible to the free surface effect. We explain this using the concept of energy landscape, as it is used to explain the different slowdown rates between strong and fragile glass formers at Tg.

Decolonizing energy justice from the ground up: Political ecology, ontology, and energy landscapes

The purpose of the paper is to expand the concept of energy justice by considering the struggles over coloniality and cultural identity in the Global South and their interactions with the spatial and historical development of energy systems and the ongoing forms of energy transitions. The article argues that the current conceptualizations of energy justice cannot be separated from the politics of incumbency as, without a decolonial critique, they tend to reproduce rather than transform hegemonic power relations. To be transformative, energy justice must be articulated from the politics of actually existing unsustainability. In other words, the starting position for energy justice must be that energy injustices are already embedded in existing energy systems and energy policies. Drawing on Latin-American decolonial thought, and the work of political ecologists around energy, this article advocates looking beyond a universalized conception of justice towards an approach where justice is based on a sense of place and is informed by the community’s relationship with the land. Using the concept of energy landscapes, the article puts forth an alternative way of understanding energy systems and conceptualizations of justice in decolonial settings.

Energy landscapes of perfect and defective solids: from structure prediction to ion conduction

The energy landscape concept is increasingly valuable in understanding and unifying the structural, thermodynamic and dynamic properties of inorganic solids. We present a range of examples which include (i) structure prediction of new bulk phases including carbon nitrides, phosphorus carbides, LiMgF3 and low-density, ultra-flexible polymorphs of B2O3, (ii) prediction of graphene and related forms of ZnO, ZnS and other compounds which crystallise in the bulk with the wurtzite structure, (iii) solid solutions, (iv) understanding grossly non-stoichiometric oxides including the superionic phases of δ-Bi2O3 and BIMEVOX and the consequences for the mechanisms of ion transport in these fast ion conductors. In general, examination of the energy landscapes of disordered materials highlights the importance of local structural environments, rather than sole consideration of the average structure.

Sacrifice zones and the construction of urban energy landscapes in Concepción, Chile

This article examines how national energy policies in Chile constitute urban energy landscapes characterized by environmental and spatial inequalities. The concept of urban energy landscapes is deployed to explain the spatial patterns resulting from energy governance and energy conflicts in the metropolitan area of Concepción, a metropolitan region of strategic importance in the configuration of national energy policy. These urban energy landscapes result from the constitution of 'sacrifice zones' that reflect an extractivist model of energy production. The combination of qualitative interviews and transect walks reveals different aspects of a dual arrangement of energy infrastructure and urbanization. The city's fragmented landscapes emerge from the coexistence of energy infrastructure and associated industries, with daily activities of communities that have little to do with these industries but live in their shadow. Conflicts in these urban energy landscapes are intense, with every inch of space contested by competing modes of 'being urban.' The urban energy landscape in Concepción is an expression of a clash of social and economic power with local priorities.Keywords: urban energy landscapes, industrial landscapes, sacrifice zones, energy conflicts, coal energy, Chile

Dynamics of the energy seascape can explain intra-specific variations in sea-crossing behaviour of soaring birds.

Thermal soaring birds extract energy from the atmosphere to achieve energetically low-cost movement. When encountering regions that are energetically costly to fly over, such as open seas, they should attempt to adjust the spatio-temporal pattern of their passage to maximize energy extraction from the atmosphere over these ecological barriers. We applied the concept of energy landscapes to investigate the spatio-temporal dynamics of energy availability over the open sea for soaring flight. We specifically investigated how the 'energy seascape' may shape age-specific sea-crossing behaviour of European honey buzzards, Pernis apivorus, over the Mediterranean Sea in autumn. We found uplift potential over the sea to be the main determinant of sea-crossing distance, rather than wind conditions. Considering this variable as a proxy for available energy over the sea, we constructed the energy seascape for the autumn migration season using 40 years of temperature data. Our results indicate that early-migrating adult buzzards are likely to encounter adverse energy subsidence over the Mediterranean, whereas late-migrating juveniles face less adverse flight conditions, and even conditions conducive to soaring flight. Our study provides evidence that the dynamics of the energy landscape can explain intra-specific variation in migratory behaviour also at sea.

Theorizing energy landscapes for energy transition management: Insights from a socioecological history of energy transitions in Bermuda

Energy production systems all over the world are in the early stages of a structural shift from below ground fossil fuels toward above ground energy flows – i.e., solar, wind, biomass, and other forms of renewable energy. In other words, the energy transition implies a profound landscape transformation. Theories and practices in energy transition management are currently underpinned by ‘society-technology’ or sociotechnical perspectives drawn from sustainability transition studies, which foreground political-economic rhythms and institutions that contribute to infrastructure lock-in and path dependence. The significance of these dominant views notwithstanding, they are inattentive to the challenges of landscape transformation and often relegate geographic space to a backdrop upon which sociotechnical transitions take place. The purpose of this paper is to foreground a ‘society-environment’ or socioecological perspective of energy transition and, in so doing, begin to take seriously its spatial dimensions. Our approach brings the energy landscape concept into dialogue with ideas about the production of space and materiality in order to conceptualize the ways in which an energy transition is intertwined with material landscapes (e.g., landscape aesthetics and land-use patterns), territorial structures acting upon landscapes (e.g., land-use planning policy), and social values drawn from and embedded in those landscapes (e.g., emotional attachments and livelihood strategies). We apply this approach to an analysis of energy transitions on the British overseas territory of Bermuda from circa 1819 to present day. The research highlights the broader landscape transformations throughout the island's efforts to establish itself as a British Royal Navy coaling station and then as a tourist destination, and links these histories to the contemporary political ecological factors shaping renewable energy deployment on the island. Conceptually, the paper attends to the influence of society-environment relations in shaping the articulation of technological transitions in particular places and times. More specifically, the research identifies how land-use systems and landscape values contribute to ‘lock-in’ and ‘path dependency’ that must be destabilized in order to facilitate energy transitions. Practically, the paper highlights the need to integrate energy planning with collaborative land-use planning as part of energy transition management.

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

Energy transition is an encompassing process which not only involves the energy system but also the landscape in which the energy system is embedded. Renewable energy is triggering new interactions with local landscapes in physical, socio-economic and institutional senses. We capture these interactions using the energy landscape concept, which expresses the interdependence of the energy system with the landscape. We aim to understand whether and how local energy initiatives facilitate this interdependency so as to see if local energy initiatives can be considered focal points in energy transition. We analyse how emerging local energy initiatives link different interests, land uses and activities within their energy practices and show how these facilitate interactions between various physical and social systems across multiple spatial scales. The paper concludes with several suggestions on how spatial planners and policy-makers can use the insights from the findings to support energy transition.

Thermodynamic projection of the antibody interaction network: The fountain energy landscape of molecular interaction systems

The adaptive humoral immune system of vertebrates functions by evolving a huge repertoire of binding proteins, which target potentially all molecules that come into contact with developing B cells. The key to endowing these binders with immunological activity is the adjustment of antibody structure and affinity against molecular targets. As a result, antibodies with a wide range of affinities and specificities evolve during the lifetime of an individual. A recently developed a quantitative model for the description of antibody homeostasis suggests that a quantitative network can describe the dynamic antibody-antigen interaction space. Here, this molecular interaction space is projected onto an energy landscape defined by entropy and free energy of binding. I introduce the concept of binding fountain energy landscape, which allows the thermodynamic representation of binding events and evolution of binding paths of multiple interactions. I further show that the hypersurface of the binding fountain corresponds to the antibody-antigen interaction network. The binding energy landscape identifies unique properties of B1 cells and natural antibodies, and distinct patterns of thymus independent and thymus dependent antibody responses. Overall, the fountain energy landscape concept of molecular interactions allows a systems biological, thermodynamic perception and description of the functioning of the clonal humoral immune system and generally describes protein evolution in thermodynamic space.

Role of conformational dynamics in the evolution of novel enzyme function.

The free energy landscape concept that describes enzymes as an ensemble of differently populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme activity, enantioselectivity, and specificity. Mutations introduced in the enzyme sequence can alter the populations of the pre-existing conformational states, thus strongly modifying the enzyme ability to accommodate alternative substrates, revert its enantiopreferences, and even increase the activity for some residual promiscuous reactions. In this feature article, we present an overview of the current experimental and computational strategies to explore the conformational free energy landscape of enzymes. We provide a series of recent publications that highlight the key role of conformational dynamics for the enzyme evolution towards new functions and substrates, and provide some perspectives on how conformational dynamism should be considered in future computational enzyme design protocols.

Thermodynamic projection of the antibody interaction network: The fountain energy landscape of molecular interaction systems

The adaptive humoral immune system of vertebrates functions by evolving a huge repertoire of binding proteins, which target potentially all molecules that come into contact with developing B cells. The key to endowing these binders with immunological activity is the adjustment of antibody structure and affinity against molecular targets. As a result, antibodies with a wide range of affinities and specificities evolve during the lifetime of an individual. I recently developed a quantitative model for the description of antibody homeostasis and suggested that a quantitative network can describe the dynamic antibody-antigen interaction space. Here, I project this molecular interaction space onto an energy landscape defined by conformational entropy and free energy of binding. I introduce the concept of binding fountain energy landscape, which allows the thermodynamic representation of binding events and paths of multiple interactions. I further show that the hypersurface of the binding fountain corresponds to the antibody-antigen interaction network. I propose that thymus independent and thymus dependent antibody responses show distinct patterns of changes in the energy landscape. Overall, the fountain energy landscape concept of molecular interactions allows a systems biological, thermodynamic perception and description of the functioning of the clonal humoral immune system.

Experimental creation and characterization of random potential-energy landscapes exploiting speckle patterns

The concept of potential energy landscapes is applied in many areas of science. We experimentally realize a random potential energy landscape (rPEL) to which colloids are exposed. This is achieved exploiting the interaction of matter with light. The optical set-up is based on a special diffuser, which creates a top-hat beam containing a speckle pattern. This is imposed on colloids. The effect of the speckle pattern on the colloids can be described by a rPEL. The speckle pattern as well as the rPEL are quantitatively characterized. The distributions of both, intensity and potential energy values, can be approximated by Gamma distributions. They can be tuned from exponential to approximately Gaussian with variable standard deviation, which determines the contrast of the speckles and the roughness of the rPEL. Moreover, the characteristic length scales, e.g. the speckle size, can be controlled. By rotating the diffuser, furthermore, a flat potential can be created and hence only radiation pressure exerted on the particles.

ChemInform Abstract: Conceptual Inorganic Materials Discovery — A Road Map

AbstractReview: 107 refs.

Conceptual inorganic materials discovery - a road map.

Synthesis of novel solids, which is a pivotal starting point in innovative materials research, is markedly impeded by the lack of predictability. A conception is presented that enables syntheses of new materials to be rationally planned. The approach is based on the atomic configuration space, and the potential energies associated to the atomic arrangements. Each minimum of the respective hyperspace of potential energy corresponds to a chemical compound capable of existence. Thus the whole realm of known and not-yet-known chemical compounds is represented in virtuo on that energy landscape. From this view it follows further that the full sets of the corresponding materials' properties are pre-determined. Within the scope of the "Energy Landscape Concept of Chemical Matter" presented, targets for synthesis are identified in a rational manner by searching the underlying potential energy landscapes for (meta)stable candidates computationally. Subsequently, the gained information are transferred to finite temperatures, which enables phase diagrams to be calculated, including metastable manifestations of matter, from first principles. The subsequent steps in materials discovery, e.g., assessing the properties and the impact of defects on the performance of the solids predicted are addressed briefly. The approach presented is complete and physically consistent; its feasibility has been proven and validated experimentally.

Size-dependent pressure-induced amorphization: a thermodynamic panorama.

Below a critical particle size, some pressurized compounds (e.g. TiO2, Y2O3, PbTe) undergo a crystal-to-amorphous transformation instead of a polymorphic transition. This effect reflects the greater propensity of nanomaterials for amorphization. In this work, a panorama of thermodynamic interpretations is given: first, a descriptive analysis based on the energy landscape concept gives a general comprehension of the balance between thermodynamics and kinetics to obtain an amorphous state. Then, a formal approach based on Gibbs energy to describe the thermodynamics and phase transitions in nanoparticles gives a basic explanation of size-dependent pressure-induced amorphization. The features of this transformation (amorphization occurs at pressures lower than the polymorphic transition pressure!) and the nanostructuration can be explained in an elaborated model based on the Ginzburg-Landau theory of phase transition and on percolation theory. It is shown that the crossover between polymorphic transition and amorphization is highly dependent on the defect density and interfacial energy, i.e., on the synthesis process. Their behavior at high pressure is a quality control test for the nanoparticles.

The energy landscape concept and its implications for synthesis planning

AbstractSynthesis of novel solids, in a chemical sense, is one of the spearheads of innovation in materials research. However, such an undertaking is substantially impaired by lack of control and predictability. We present a concept that points the way towards rational planning of syntheses in solid state and materials chemistry. The foundation of our approach is the representation of the whole material world, i.e., the known and not-yet-known chemical compounds, on an energy landscape, which implies information about the free energies of these configurations. From this it follows at once that all chemical compounds capable of existence (both thermodynamically stable and metastable ones) are already present in virtuo in this landscape. For the first step of synthesis planning, i.e., the identification of candidates that are capable of existence, we computationally search the respective potential energy landscapes for (meta)stable structure candidates. Recently we have extended our techniques to finite temperatures and pressures and calculated phase diagrams, including metastable manifestations of matter, without resorting to any experimental pre-information. The conception developed is physically consistent, and its feasibility has been proven. Applying appropriate experimental tools has enabled us to realize, e.g., elusive Na3N, including almost all of its predicted polymorphs, many years after the predictions were published.

Evolution of order in amorphous-to-crystalline phase transformation of MgF2

Structural disorder and distortion play a significant role in phase transformations. Experimentally, electron diffraction in the transmission electron microscope offers the ability to characterize disorderviathe pair distribution function (PDF) at high spatial resolution. In this work, energy-filteredin situelectron diffraction is applied to measure PDFs of different phases of MgF2from the amorphous deposit through metastable modifications to the thermodynamically stable phase. Despite the restriction of thick specimens resulting in multiple electron scattering, elaborate data analysis enabled experimental and molecular dynamics simulation data to be matched, thus allowing analysis of the evolution of short-range ordering. In particular, it is possible to explain the theoretically not predicted existence of a metastable phase by the presence of atomic disorder and distortion. The short-range ordering in the amorphous and crystalline phases is elucidated as three steps: (i) an initial amorphous phase exhibiting CaCl2-type short-range order which acts as a crystallization nucleus to guide the phase transformation to the metastable CaCl2-type phase and thus suppresses the direct appearance of the rutile-type phase; (ii) a metastable CaCl2-type phase containing short-range structural features of the stable rutile type; and (iii) the formation of a large volume fraction of disordered intergranular regions which stabilize the CaCl2-type phase. The structure evolution is described within the energy landscape concept.

Free Energy Landscapes of Ion Coordination in Aqueous Solution

We show how the fruitful concept of free energy landscape, as invoked in the description of complex biological systems, can be rather easily extended to build up a simple and accurate picture about solvent coordination around ions. This may represent a revealing key element for the qualitative and quantitative physical-chemical interpretation of a large number of phenomena occurring in solution, such as water exchange mechanisms, ion mobility, solvation dynamics, ion channel selectivity, and so on. In particular, using a computational approach rooted into molecular dynamics simulations and enhanced sampling techniques, we show how the free energy landscapes of ion coordination in solution can be very easily and accurately obtained in a number of illustrative examples.