Search results for "Free Energy"
showing 10 items of 170 documents
The effect of vertical ground movement on masonry walls simulated through an elastic–plastic interphase meso-model: a case study
2019
The present paper proposes an interphase model for the simulation of damage propagation in masonry walls in the framework of a mesoscopic approach. The model is thermodynamically consistent, with constitutive relations derived from a Helmholtz free potential energy. With respect to classic interface elements, the internal stress contribute is added to the contact stresses. It is considered that damage, in the form of loss of adhesion or cohesion, can potentially take place at each of the two blocks–mortar physical interfaces. Flow rules are obtained in the framework of the Theory of Plasticity, considering bilinear domains of ‘Coulomb with tension cut-off’ type. The model aims to be a first…
Redox potentials and acidity constants from density functional theory based molecular dynamics.
2014
CONSPECTUS: All-atom methods treat solute and solvent at the same level of electronic structure theory and statistical mechanics. All-atom computation of acidity constants (pKa) and redox potentials is still a challenge. In this Account, we review such a method combining density functional theory based molecular dynamics (DFTMD) and free energy perturbation (FEP) methods. The key computational tool is a FEP based method for reversible insertion of a proton or electron in a periodic DFTMD model system. The free energy of insertion (work function) is computed by thermodynamic integration of vertical energy gaps obtained from total energy differences. The problem of the loss of a physical refe…
On the divide between animate and inanimate
2015
Vitalism was abandoned already for a long time ago, yet the impression that animate beings differ in some fundamental way from inanimate objects continues to thrive. Here, we argue that scale free patterns, found throughout nature, present convincing evidence that this demarcation is only imaginary. Therefore, all systems ought to be regarded alike, i.e., all are consuming free energy in least time. This way evolutionary processes can be understood as a series of changes from one state to another, so that flows of energy themselves naturally select those ways and means, such as species and societies or gadgets and galaxies to consume free energy in the least time in quest of attaining therm…
Salinity gradient energy
2016
Abstract Beyond the most common renewable energy sources today exploited for the production of clean energy, salinity gradients power (SGP) has been attracting the increasing interest of scientists and companies involved in the field. This chapter provides an introduction to SGP, reporting a brief history of the technological developments throughout the years, from the beginning to present. A number of different SGP technologies have been developed in the last decades, all based on the concept of harvesting the energy from the controlled mixing of two solutions at different salinities. A theoretical analysis of the energy potential for SGP places this renewable source of energy among those …
Monotonicity and local uniqueness for the Helmholtz equation
2017
This work extends monotonicity-based methods in inverse problems to the case of the Helmholtz (or stationary Schr\"odinger) equation $(\Delta + k^2 q) u = 0$ in a bounded domain for fixed non-resonance frequency $k>0$ and real-valued scattering coefficient function $q$. We show a monotonicity relation between the scattering coefficient $q$ and the local Neumann-Dirichlet operator that holds up to finitely many eigenvalues. Combining this with the method of localized potentials, or Runge approximation, adapted to the case where finitely many constraints are present, we derive a constructive monotonicity-based characterization of scatterers from partial boundary data. We also obtain the local…
Electron-density critical points analysis and catastrophe theory to forecast structure instability in periodic solids
2018
The critical points analysis of electron density,i.e. ρ(x), fromab initiocalculations is used in combination with the catastrophe theory to show a correlation between ρ(x) topology and the appearance of instability that may lead to transformations of crystal structures, as a function of pressure/temperature. In particular, this study focuses on the evolution of coalescing non-degenerate critical points,i.e. such that ∇ρ(xc) = 0 and λ1, λ2, λ3≠ 0 [λ being the eigenvalues of the Hessian of ρ(x) atxc], towards degenerate critical points,i.e. ∇ρ(xc) = 0 and at least one λ equal to zero. The catastrophe theory formalism provides a mathematical tool to model ρ(x) in the neighbourhood ofxcand allo…
Ewald Hering und die Gegenfarbtheorie
1996
Ewald Hering's color-opponent-theory is still considered one of the foundations of the visual sciences. Prior to Hering, Hermann v. Helmholtz introduced a theory of color appearance, which was based primarily on the physical aspects of the stimulus. In contrast to Helmholtz, Hering's theory strongly emphasized the subject's perception of color. As a consequence, Hering considered Helmholtz' theory inadequate. Contrary to some historical accounts, he did not object to Helmholtz's three-receptor explanation for color-mixture. Instead of Helmholtz' fundamental colors red, green, and blue, Hering suggested that the colors possess opponent character: blue-yellow; red-green; and, black-white. Hel…
Metal complex-DNA binding: Insights from molecular dynamics and DFT/MM calculations.
2012
Molecular dynamics (MD) simulations, followed by density functional theory/molecular mechanics (DFT/MM) calculations, provided a detailed structure of the binding site between the cationic metallointercalator (dipyrido [3,2-a:2',3'-c]phenazine)(glycinato)copper(II), [Cu(gly)(dppz)](+), and the two dodeca-deoxynucleotide duplexes [dodeca(dG-dC)]2 and [dodeca(dA-dT)]2. Three simultaneous DNA binding types were detected in the fully optimized DFT/MM structures: 1) metal coordination through exocyclic oxygen atoms of nitrogen bases; 2) intercalation of the dppz chromophore between stacked Watson-Crick AT-AT and GC-GC bases; and 3) hydrogen bonding between the glycinato ligand and amine groups o…
Theoretical study of spiropyran-merocyanine thermal isomerization.
2004
Abstract Quantum mechanical computations at DFT level were carried out on the processes involved in the thermal reaction SP ⇆ ME, where SP is the nitro-substituted spirobenzopyran (1 ′ ,3 ′ -dihydro-1 ′ ,3 ′ ,3 ′ -trimethyl-6-nitro-spiro[2H-1-benzopyran-2,2 ′ - [2H]indole]) in the closed form and ME is the corresponding open form. A detailed theoretical description of the overall reaction is reported along with the thermodynamic parameters for all intermediates and transition states. The obtained activation energy value is in agreement with the available experimental data in solution.
Protein Conformational Landscapes and Catalysis. Influence of Active Site Conformations in the Reaction Catalyzed by L-Lactate Dehydrogenase
2015
In the past decade, L-Lactate Dehydrogenase (LDH) has become an extremely useful marker in both clinical diagnosis and in monitoring the course of many human diseases. It has been assumed since the 1980s that the full catalytic process of LDH starts with the binding of the cofactor and the substrate followed by the enclosure of the active site by a mobile loop of the protein before the reaction takes place. In this paper, we show that the chemical step of the LDH-catalyzed reaction can proceed within the open loop conformation, and the different reactivity of the different protein conformations would be in agreement with the broad range of rate constants measured in single-molecule spectrom…