The free energy of a reaction coordinate at multiple constraints: a concise formulation

The free energy as a function of the reaction coordinate (rc) is the key quantity for the computation of equilibrium and kinetic quantities. When it is considered as the potential of mean force, the problem is the calculation of the mean force for given values of the rc. We reinvestigate the PMCF (potential of mean constraint force) method which applies a constraint to the rc to compute the mean force as the mean negative constraint force and a metric tensor correction. The latter allows for the constraint imposed to the rc and possible artefacts due to multiple constraints of other variables which for practical reasons are often used in numerical simulations. Two main results are obtained that are of theoretical and practical interest. First, the correction term is given a very concise and simple shape which facilitates its interpretation and evaluation. Secondly, a theorem describes various rcs and possible combinations with constraints that can be used without introducing any correction to the constraint force. The results facilitate the computation of free energy by molecular dynamics simulations.     

Tacit collusion games in pool-based electricity markets under transmission constraints

Harrington et al. (Math Program Ser B 104:407–435, 2005) introduced a general framework for modeling tacit collusion in which producing firms collectively maximize the Nash bargaining objective function, subject to incentive compatibility constraints. This work extends that collusion model to the setting of a competitive pool-based electricity market operated by an independent system operator. The extension has two features. First, the locationally distinct markets in which firms compete are connected by transmission lines. Capacity limits of the transmission lines, together with the laws of physics that guide the flow of electricity, may alter firms’ strategic behavior. Second, in addition to electricity power producers, other market participants, including system operators and power marketers, play important roles in a competitive electricity market. The new players are included in the model in order to better represent real-world markets, and this inclusion will impact power producers’ strategic behavior as well. The resulting model is a mathematical program with equilibrium constraints (MPEC). Properties of the specific MPEC are discussed and numerical examples illustrating the impacts of transmission congestion in a collusive game are presented.     

From point defects to plate tectonic faults

Understanding and explaining emergent constitutive laws in the multi-scale evolution from point defects, dislocations and two-dimensional defects to plate tectonic scales is an arduous challenge in condensed matter physics. The Earth appears to be the only planet known to have developed stable plate tectonics as a means to get rid of its heat. The emergence of plate tectonics out of mantle convection appears to rely intrinsically on the capacity to form extremely weak faults in the top 100?km of the planet. These faults have a memory of at least several hundred millions of years, yet they appear to rely on the effects of water on line defects. This important phenomenon was first discovered in laboratory and dubbed “hydrolytic weakening”. At the large scale it explains cycles of co-located resurgence of plate generation and consumption (the Wilson cycle), but the exact physics underlying the process itself and the enormous spanning of scales still remains unclear. We present an attempt to use the multi-scale non-equilibrium thermodynamic energy evolution inside the deforming lithosphere to move phenomenological laws to laws derived from basic scaling quantities, develop self-consistent weakening laws at lithospheric scale and give a fully coupled deformation-weakening constitutive framework. At meso- to plate scale we encounter in a stepwise manner three basic domains governed by the diffusion/reaction time scales of grain growth, thermal diffusion and finally water mobility through point defects in the crystalline lattice. The latter process governs the planetary scale and controls the stability of its heat transfer mode.     

Effects of Medium Permeability Anisotropy on Chemical-Dissolution Front Instability in Fluid-Saturated Porous Media

This paper deals with the theoretical aspects of chemical-dissolution front instability problems in two-dimensional fluid-saturated porous media including medium anisotropic effects. Since a general anisotropic medium can be described as an orthotropic medium in the corresponding principal directions, a two-dimensional orthotropic porous medium is considered to derive the analytical solution for the critical condition, which is used to judge whether or not the chemical dissolution front can become unstable during its propagation. In the case of the mineral dissolution ratio (that is defined as the ratio of the dissolved-mineral equilibrium concentration in the pore-fluid to the molar concentration of the dissolvable mineral in the solid matrix of the fluid-saturated porous medium) approaching zero, the corresponding critical condition has been mathematically derived when medium permeability anisotropic effects are considered. As a complementary tool, the computational simulation method is used to simulate the morphological evolution of chemical dissolution fronts in two-dimensional fluid-saturated porous media including medium anisotropic effects. The related theoretical and numerical results demonstrated that: (1) a decrease in the medium anisotropic permeability factor (or ratio), which is defined as the ratio of the principal permeability in the transversal direction to that in the longitudinal direction parallel to the pore-fluid inflow direction, can stabilize the chemical dissolution front so that it becomes more difficult for a planar chemical-dissolution front to evolve into different morphologies in the chemical dissolution system; (2) the medium anisotropic permeability ratio can have significant effects on the morphological evolution of the chemical dissolution front. When the Zhao number of the chemical dissolution system is greater than its critical value, the greater the medium anisotropic permeability ratio, the faster the irregular chemical-dissolution front grows.     

Origin of p(2 x 1) phase on Si(001) by noncontact atomic force microscopy at 5 k

The controversial issue of the origin of the p(2 x 1) reconstruction of the Si(001) surface observed in recent low temperature scanning tunneling microscopy experiments is clarified here using 5 K noncontact atomic force microscopy. The c(4 x 2) phase is observed at separations corresponding to weak tip-surface interactions, confirming that it is the ground state of the surface. At larger frequency shifts the p(2 x 1) phase of symmetric dimers is observed. By studying the interaction of a reactive Si tip with the c(4 x 2) Si(001) surface using an ab initio method, we find that the observed change in the surface reconstruction is an apparent effect caused by tip induced dimer flipping resulting in a modification of the surface structure and appearance of the p(2 x 1) phase in the image. Using an appropriate scanning protocol, one can manipulate the surface reconstruction at will, which has significance in nanotechnology.     

Synthesis and stereochemical assignment of endo-7-phenyl-2,5-dioxabicyclo[4.1.0]heptane

The synthesis and stereochemical assignment of endo-7-phenyl-2,5-dioxabicyclo[4.1.0]heptane is reported. The stereochemical assignment was made based on both spectral and chemical data.