Ending the Energy-Poverty Nexus: An Ethical Imperative for Just Transitions.

Arguments for a just transition are integral to debates about climate change and the drive to create a carbon-neutral economy. There are currently two broad approaches rooted in ethics and justice for framing just energy transitions. The first can be described as internal to the transition and emphasizes the anticipation, assessment, and redressing of harms created by the transition itself and the inclusion in transition governance of groups or communities potentially harmed by its disruptions. In this article, we propose a second approach to ethics and justice in an energy transition, which we describe as systemic or societal in scope. This approach complements attention to the proximate dynamics and impacts of the transition process with a focus on the distant societal and economic outcomes the transition brings into being and how they compare to conditions prior to the transition. It poses the question: do the transformative social, economic, and technological changes wrought by energy systems create more just societies and economies, or do they instead reinforce or recreate long-standing injustices and inequalities? We illustrate this approach with an assessment of one of the most significant existing forms of energy injustice: the energy-poverty nexus. We argue that the energy-poverty nexus reflects configurations of socio-energy systems that create complex, extractive feedbacks between energy insecurity and economic insecurity and, over time, reinforce or exacerbate poverty. We further argue that just energy transitions should work to disentangle these configurations and re-design them so as to create generative rather than extractive feedbacks, thus ending the energy-poverty nexus and creating long-term outcomes that are more just, equitable, and fair.

Association of helical beta-peptides and their aggregation behavior from the potential of mean force in explicit solvent.

Helical beta-peptides have been shown to fold into well-defined structures. In aqueous solution, some beta-peptides self-assemble into nanoscale fibers, aggregates, and liquid crystalline phases. Molecular simulations, at an atomistic level, are used to examine, in a systematic manner, the interactions between distinct beta-peptide molecules. The relationship between side-chain chemistry (and position along the backbone) and, in particular, aggregation behaviors, is assessed by calculating the potential of mean force or dimerization free energy of two peptides in explicit water. The free energy profiles as a function of separation for helical, amphiphilic beta-peptides are consistent with experimental observations, and help explain the origins of aggregate or fiber formation in solution. Close examination of the energetic and entropic contributions to the free energy reveals that, depending on the position of certain side groups along the molecule, the tendency of two peptides to aggregate can be driven by entropy or by energy, respectively. In contrast to findings from previous works that employed a coarse representation of the solvent, it is shown that water-peptide interactions play key roles in the association behavior of beta-peptides.

Surface activity of amphiphilic helical beta-peptides from molecular dynamics simulation.

The surface activity of beta-peptides is investigated using molecular simulations. The type and display of hydrophobic and hydrophilic groups on helical beta-peptides is varied systematically. Peptides with 2/3 hydrophobic groups are found to be surface active, and to adopt an orientation parallel to the air-water interface. For select beta-peptides, we also determine the potential of mean force required to bring a peptide to the air-water interface. Facially amphiphilic helices with 2/3 hydrophobic groups are found to exhibit the lowest free energy of adsorption. The adsorption process is driven by a favorable energetic term and opposed by negative entropic changes. The temperature dependence of adsorption is also investigated; facially amphiphilic helices are found to adopt orientations that are largely independent of temperature, while nonfacially amphiphilic helices sample a broader range of interfacial orientations at elevated temperatures. The thermodynamics of adsorption of beta-peptides is compared to that of 1-octanol, a well-known surfactant, and ovispirin, a naturally occurring antimicrobial peptide. It is found that the essential difference lies in the sign of the entropy of adsorption, which is negative for beta- and alpha-peptides and positive for traditional surfactants such as octanol.

The effect of the water/methane interface on methane hydrate cages: the potential of mean force and cage lifetimes.

Molecular dynamics simulations were used to determine the influence of a methane-water interface on the position and stability of methane hydrate cages. A potential of mean force was calculated as a function of the separation of a methane hydrate cage and a methane-water interface. The hydrate cages are found to be strongly repelled from the methane gas into the water phase. At low enough temperatures, however, the most favorable location for the hydrate cage is at the interface on the water side. Cage lifetime simulations were performed in bulk water and near a methane-water interface. The methane-water interface increases the cage lifetime by almost a factor of 2 compared to cage lifetimes of cages in bulk water. The potential of mean force and the cage lifetime results give additional explanations for the proposed nucleation of gas hydrates at gas-water interfaces.

Dipole-induced self-assembly of helical beta-peptides.

In this work, the interactions between beta-peptides are investigated for helix-forming peptides using molecular simulation. The role of electrostatic interactions in the self-assembly of these peptides is studied by calculating the dipole moment of various 14-helical beta-peptides using molecular dynamics simulations. The stability of a beta-peptide that is known to form a liquid crystalline phase is determined by calculating the potential of mean force using the expanded ensemble density of states method. This peptide is found to form a mechanically stable 14-helix in an implicit solvent model. The interaction between two of these peptides is examined by calculating the potential of mean force between the two peptides in implicit solvent. The peptides are shown to favorably associate in an end-to-end manner, driven largely by dipolar interactions. In order to understand the possible structures that form when many peptides interact in solution, a coarse-grained model is developed. Brownian dynamics simulations of the coarse-grained model at intermediate concentrations (1-50 mM) are performed, and the aggregation behavior is understood by calculating the diffusivity and the radial distribution function. An analysis of the resultant structures reveals that the coarse-grained model of the peptide leads to the formation of spherical clusters.

Mechanical stability of helical beta-peptides and a comparison of explicit and implicit solvent models.

Synthetic beta-peptide oligomers have been shown to form stable folded structures analogous to those encountered in naturally occurring proteins. Literature studies have speculated that the conformational stability of beta-peptides is greater than that of alpha-peptides. Direct measurements of that stability, however, are not available. Molecular simulations are used in this work to quantify the mechanical stability of four helical beta-peptides. This is achieved by subjecting the molecules to tension. The potential of mean force associated with the resulting unfolding process is determined using both an implicit and an explicit solvent model. It is found that all four molecules exhibit a highly stable helical structure. It is also found that the energetic contributions to the potential of mean force do not change appreciably when the molecules are stretched in explicit water. In contrast, the entropic contributions decrease significantly. As the peptides unfold, a loss of intramolecular energy is compensated by the formation of additional water-peptide hydrogen bonds. These entropic effects lead in some cases to a loss of stability upon cooling the peptides, a phenomenon akin to the cold denaturing of some proteins. While the location of the free energy minimum and the structural helicity of the peptides are comparable in the implicit-solvent and explicit-water cases, it is found that, in general, the helical structure of the molecules is more stable in the implicit solvent model than in explicit water.

The effects of reversibility and noise on stochastic phosphorylation cycles and cascades.

The phosphorylation-dephosphorylation cycle is a common motif in cellular signaling networks. Previous work has revealed that, when driven by a noisy input signal, these cycles may exhibit bistable behavior. Here, a recently introduced theorem on network bistability is applied to prove that the existence of bistability is dependent on the stochastic nature of the system. Furthermore, the thermodynamics of simple cycles and cascades is investigated in the stochastic setting. Because these cycles are driven by the ATP hydrolysis potential, they may operate far from equilibrium. It is shown that sufficient high ATP hydrolysis potential is necessary for the existence of a bistable steady state. For the single-cycle system, the ensemble average behavior follows the ultrasensitive response expected from analysis of the corresponding deterministic system, but with significant fluctuations. For the two-cycle cascade, the average behavior begins to deviate from the expected response of the deterministic system. Examination of a two-cycle cascade reveals that the bistable steady state may be either propagated or abolished along a cascade, depending on the parameters chosen. Likewise, the variance in the response can be maximized or minimized by tuning the number of enzymes in the second cycle.