Fractal and complex network analyses of protein molecular dynamics

Based on protein molecular dynamics, we investigate the fractal properties of energy, pressure and volume time series using the multifractal detrended fluctuation analysis (MF-DFA) and the topological and fractal properties of their converted horizontal visibility graphs (HVGs). The energy parameters of protein dynamics we considered are bonded potential, angle potential, dihedral potential, improper potential, kinetic energy, Van der Waals potential, electrostatic potential, total energy and potential energy. The shape of the h(q)h(q) curves from MF-DFA indicates that these time series are multifractal. The numerical values of the exponent h(2)h(2) of MF-DFA show that the series of total energy and potential energy are non-stationary and anti-persistent; the other time series are stationary and persistent apart from series of pressure (with H≈0.5H≈0.5 indicating the absence of long-range correlation). The degree distributions of their converted HVGs show that these networks are exponential. The results of fractal analysis show that fractality exists in these converted HVGs. For each energy, pressure or volume parameter, it is found that the values of h(2)h(2) of MF-DFA on the time series, exponent λλ of the exponential degree distribution and fractal dimension dBdB of their converted HVGs do not change much for different proteins (indicating some universality). We also found that after taking average over all proteins, there is a linear relationship between 〈h(2)〉〈h(2)〉 (from MF-DFA on time series) and 〈dB〉〈dB〉 of the converted HVGs for different energy, pressure and volume.

Design a zero energy house in Brisbane, Australia

Due to the increasing energy demand and global warming effects, energy efficient buildings have become increasingly important in the modern construction industry. This research is conducted to evaluate the energy performance, financial feasibility and potential energy savings of zero energy houses. Through the use of building computer simulation technique, a 5 stars energy rated house was modelled and validated by comparing the energy performance of a base case scenario to a typical house in Brisbane. By integrating energy reduction strategies and utilizing onsite renewable energy such as solar energy, zero energy performance is achieved. It is found that approximately 66 % energy savings can be achieved in the household annual energy usage by focusing on maximizing the thermal performance of building envelope, minimizing the energy requirements and incorporating solar energy technologies.

Studies involving electrostatic potential of valinomycin

The electrostatic potential of valinomycin in various conformations as obtained by the crystal structures (uncomplexed, complexed) and theoretical considerations have been evaluated and compared. The potential energy profiles along the æ axis of the bracelet-like structures show a systematic variation from the uncomplexed to the complexed structure. This type of conformational change and the potential variation are probably associated with different states of ion transport, like the capture and release of ions by the ionophore. Also, the asymmetry of the molecule due to D-HyIV on one side and L-Lac on the other side is reflected in the potential values along the Z-axis, the magnitude of which, is considerable in the uncomplexed structure. The evaluation of the potential at the ab-initio level on smaller fragments indicate that the order of liganding capacity of oxygen is amide ether ester. Also, the inductive effects due to alkyl substitution is negligible as evidenced by the potential studies on the substituted amides and esters.

Open-circuit potential-time transient of the magnesium anode

On interrupting polarisation, the magnesium anode exhibits a negative overshoot in potential followed by a slow recovery to a steady state value. A model has been proposed to explain the opencircuit potential-time transient in terms of a spontaneous passivation of the metal and the consequent changes in the corrosion potential. Theoretical expressions have been derived for the timedependence of the open-circuit electrode potential. Calculated, potential-time curves thus obtained are in qualitative agreement with experimental data. A possible application of this phenomenon to develop non-destructive quality control tests of Mg, Li and Al-based dry cells has been pointed out.

Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen

Gas fermentation using acetogenic bacteria offers a promising route for the sustainable production of low carbon fuels and commodity chemicals from abundant, inexpensive C1 feedstocks including industrial waste gases, syngas, reformed methane or methanol. Clostridium autoethanogenum is a model gas fermenting acetogen that produces fuel ethanol and 2,3-butanediol, a precursor for nylon and rubber. Acetogens have already been used in large scale industrial fermentations, they are ubiquitous and known to play a prominent role in the global carbon cycle. Still, they are considered to live on the thermodynamic edge of life and potential energy constraints when growing on C1 gases pose a major challange for the commercial production of fuels and chemicals. We have developed a systematic platform to investigate acetogenic energy metabolism, exemplified here by experiments contrasting heterotrophic and autotrophic metabolism. The platform is built from complete omics technologies, augmented with genetic tools and complemented by a manually curated genome-scale mathematical model. Together the tools enable the design and development of new, energy efficient pathways and strains for the production of chemicals and advanced fuels via C1 gas fermentation. As a proof-of-platform, we investigated heterotrophic growth on fructose versus autotrophic growth on gas that demonstrate the role of the Rnf complex and Nfn complex in maintaining growth using the Wood–Ljungdahl pathway. Pyruvate carboxykinase was found to control the rate-limiting step of gluconeogenesis and a new specialized glyceraldehyde-3-phosphate dehydrogenase was identified that potentially enhances anabolic capacity by reducing the amount of ATP consumed by gluconeogenesis. The results have been confirmed by the construction of mutant strains.

Energy landscape view of phase transitions and slow dynamics in thermotropic liquid crystals

Thermotropic liquid crystals are known to display rich phase behavior on temperature variation. Although the nematic phase is orientationally ordered but translationally disordered, a smectic phase is characterized by the appearance of a partial translational order in addition to a further increase in orientational order. In an attempt to understand the interplay between orientational and translational order in the mesophases that thermotropic liquid crystals typically exhibit upon cooling from the high-temperature isotropic phase, we investigate the potential energy landscapes of a family of model liquid crystalline systems. The configurations of the system corresponding to the local potential energy minima, known as the inherent structures, are determined from computer simulations across the mesophases. We find that the depth of the potential energy minima explored by the system along an isochor grows through the nematic phase as temperature drops in contrast to its insensitivity to temperature in the isotropic and smectic phases. The onset of the growth of the orientational order in the parent phase is found to induce a translational order, resulting in a smectic-like layer in the underlying inherent structures; the inherent structures, surprisingly, never seem to sustain orientational order alone if the parent nematic phase is sandwiched between the high-temperature isotropic phase and the low-temperature smectic phase. The Arrhenius temperature dependence of the orientational relaxation time breaks down near the isotropic-nematic transition. We find that this breakdown occurs at a temperature below which the system explores increasingly deeper potential energy minima.

Dynamic security assessment of power systems using structure-preserving energy functions

An application of direct methods to dynamic security assessment of power systems using structure-preserving energy functions (SPEF) is presented. The transient energy margin (TEM) is used as an index for checking the stability of the system as well as ranking the contigencies based on their severity. The computation of the TEM requires the evaluation of the critical energy and the energy at fault clearing. Usually this is done by simulating the faulted trajectory, which is time-consuming. In this paper, a new algorithm which eliminates the faulted trajectory estimation is presented to calculate the TEM. The system equations and the SPEF are developed using the centre-of-inertia (COI) formulation and the loads are modelled as arbitrary functions of the respective bus voltages. The critical energy is evaluated using the potential energy boundary surface (PEBS) method. The method is illustrated by considering two realistic power system examples.

Energy absorption behaviours of CSM-based GFRC plates with hemispherical features

In the present study, the mechanical behaviour of CSM (chopped strand mat)-based GFRC (glass fibre-reinforced composite) plates with single and multiple hemispheres under compressive loads has been investigated both experimentally and numerically. The basic stress-strain behaviours arc identified with quasi-static tests on two-ply coupon laminates and short cylinders, and these are followed up with compressive tests in a UTM (universal testing machine) on single- and multiple-hemisphere plates. The ability of an explicit LS-DYNA solver in predicting the complex material behaviour of composite hemispheres, including failure, is demonstrated. The relevance and scalability of the present class of structural components as `force-multipliers' and `energy-multipliers' have been justified by virtue of findings that as the number of hemispheres in a panel increased from one to four, peak load and average absorbed energy rose by factors of approximately four and six, respectively. The performance of a composite hemisphere has been compared to similar-sized steel and aluminium hemispheres, and the former is found to be of distinctly higher specific energy than the steel specimen. A simulation-based study has also been carried out on a composite 2 x 2-hemisphere panel under impact loads and its behaviour approaching that of an ideal energy absorber has been predicted. In summary, the present investigation has established the efficacy of composite plates with hemispherical force multipliers as potential energy-absorbing countermeasures and the suitability of CAE (computer-aided engineering) for their design.

Relationship between entropy and diffusion: A statistical mechanical derivation of Rosenfeld expression for a rugged energy landscape

Diffusion-a measure of dynamics, and entropy-a measure of disorder in the system are found to be intimately correlated in many systems, and the correlation is often strongly non-linear. We explore the origin of this complex dependence by studying diffusion of a point Brownian particle on a model potential energy surface characterized by ruggedness. If we assume that the ruggedness has a Gaussian distribution, then for this model, one can obtain the excess entropy exactly for any dimension. By using the expression for the mean first passage time, we present a statistical mechanical derivation of the well-known and well-tested scaling relation proposed by Rosenfeld between diffusion and excess entropy. In anticipation that Rosenfeld diffusion-entropy scaling (RDES) relation may continue to be valid in higher dimensions (where the mean first passage time approach is not available), we carry out an effective medium approximation (EMA) based analysis of the effective transition rate and hence of the effective diffusion coefficient. We show that the EMA expression can be used to derive the RDES scaling relation for any dimension higher than unity. However, RDES is shown to break down in the presence of spatial correlation among the energy landscape values. (C) 2015 AIP Publishing LLC.

Energy Principle And Nonlinear Electric-Mechanical Behavior Of Ferroelectric Ceramics

Many experimental observations have shown that a single domain in a ferroelectric material switches by progressive movement of domain walls, driven by a combination of electric field and stress. The mechanism of the domain switch involves the following steps: initially, the domain has a uniform spontaneous polarization; new domains with the reverse polarization direction nucleate, mainly at the surface, and grow though the crystal thickness; the new domain expands sideways as a new domain continues to form; finally, the domain switch coalesces to complete the polarization reversal. According to this mechanism, the volume fraction of the domain switching is introduced in the constitutive law of the ferroelectric material and used to study the nonlinear constitutive behavior of a ferroelectric body in this paper. The principle of stationary total potential energy is put forward in which the basic unknown quantities are the displacement u(i), electric displacement D-i and volume fraction rho(I) of the domain switching for the variant I. The mechanical field equation and a new domain switching criterion are obtained from the principle of stationary total potential energy. The domain switching criterion proposed in this paper is an expansion and development of the energy criterion established by Hwang et al. [ 1]. Based on the domain switching criterion, a set of linear algebraic equations for determining the volume fraction rho(I) of domain switching is obtained, in which the coefficients of the linear algebraic equations only contain the unknown strain and electric fields. If the volume fraction rho(I) of domain switching for each domain is prescribed, the unknown displacement and electric potential can be obtained based on the conventional finite element procedure. It is assumed that a domain switches if the reduction in potential energy exceeds a critical energy barrier. According to the experimental results, the energy barrier will strengthen when the volume fraction of the domain switching increases. The external mechanical and electric loads are increased step by step. The volume fraction rho(I) of domain switching for each element obtained from the last loading step is used as input to the constitutive equations. Then the strain and electric fields are calculated based on the conventional finite element procedure. The finite element analysis is carried out on the specimens subjected to uniaxial coupling stress and electric field. Numerical results and available experimental data are compared and discussed. The present theoretic prediction agrees reasonably with the experimental results.

A surface energy model and application to mechanical behavior analysis of single crystals at sub-micron scale

Size effects of mechanical behaviors of materials are referred to the variation of the mechanical behavior due to the sample sizes changing from macroscale to micro-/nanoscales. At the micro-/nanoscale, since sample has a relatively high specific surface area (SSA) (ratio of surface area to volume), the surface although it is often neglected at the macroscale, becomes prominent in governing the energy effect, although it is often neglected at the macroscale, becomes prominent in governing the mechanical behavior. In the present research, a continuum model considering the surface energy effect is developed through introducing the surface energy to total potential energy. Simultaneously, a corresponding finite element method is developed. The model is used to analyze the axial equilibrium strain problem for a Cu nanowire at the external loading-free state. As another application of the model, from dimensional analysis, the size effects of uniform compression tests on the microscale cylinder specimens for Ni and Au single crystals are analyzed and compared with experiments in literatures. (C) 2009 Elsevier B.V. All rights reserved.

Spring-to-Spring Balancing as Energy-Free Adjustment Method in Gravity Equilibrators

Generally, adjustment of gravity equilibrator to a new payload requires energy, e.g. to increase the pre-load of the balancing spring. A novel way of energy-free adjustment of gravity equilibrators is possible by introducing the concept of a storage spring. The storage spring supplies or stores the energy necessary to adjust the balancer spring of the gravity equilibrator. In essence the storage spring mechanism maintains a constant potential energy within the spring mechanism; energy is exchanged between the storage and balancer spring when needed. Various conceptual designs using both zero-free-length springs and regular extension springs are proposed. Two models were manufactured demonstrating the practical embodiments and functionality.

Gaussian Approximation Potential: an interatomic potential derived from first principles Quantum Mechanics

Simulation of materials at the atomistic level is an important tool in studying microscopic structure and processes. The atomic interactions necessary for the simulation are correctly described by Quantum Mechanics. However, the computational resources required to solve the quantum mechanical equations limits the use of Quantum Mechanics at most to a few hundreds of atoms and only to a small fraction of the available configurational space. This thesis presents the results of my research on the development of a new interatomic potential generation scheme, which we refer to as Gaussian Approximation Potentials. In our framework, the quantum mechanical potential energy surface is interpolated between a set of predetermined values at different points in atomic configurational space by a non-linear, non-parametric regression method, the Gaussian Process. To perform the fitting, we represent the atomic environments by the bispectrum, which is invariant to permutations of the atoms in the neighbourhood and to global rotations. The result is a general scheme, that allows one to generate interatomic potentials based on arbitrary quantum mechanical data. We built a series of Gaussian Approximation Potentials using data obtained from Density Functional Theory and tested the capabilities of the method. We showed that our models reproduce the quantum mechanical potential energy surface remarkably well for the group IV semiconductors, iron and gallium nitride. Our potentials, while maintaining quantum mechanical accuracy, are several orders of magnitude faster than Quantum Mechanical methods.

First principles interatomic potential for tungsten based on Gaussian process regression

An accurate description of atomic interactions, such as that provided by first principles quantum mechanics, is fundamental to realistic prediction of the properties that govern plasticity, fracture or crack propagation in metals. However, the computational complexity associated with modern schemes explicitly based on quantum mechanics limits their applications to systems of a few hundreds of atoms at most. This thesis investigates the application of the Gaussian Approximation Potential (GAP) scheme to atomistic modelling of tungsten - a bcc transition metal which exhibits a brittle-to-ductile transition and whose plasticity behaviour is controlled by the properties of $\frac{1}{2} \langle 111 \rangle$ screw dislocations. We apply Gaussian process regression to interpolate the quantum-mechanical (QM) potential energy surface from a set of points in atomic configuration space. Our training data is based on QM information that is computed directly using density functional theory (DFT). To perform the fitting, we represent atomic environments using a set of rotationally, permutationally and reflection invariant parameters which act as the independent variables in our equations of non-parametric, non-linear regression. We develop a protocol for generating GAP models capable of describing lattice defects in metals by building a series of interatomic potentials for tungsten. We then demonstrate that a GAP potential based on a Smooth Overlap of Atomic Positions (SOAP) covariance function provides a description of the $\frac{1}{2} \langle 111 \rangle$ screw dislocation that is in agreement with the DFT model. We use this potential to simulate the mobility of $\frac{1}{2} \langle 111 \rangle$ screw dislocations by computing the Peierls barrier and model dislocation-vacancy interactions to QM accuracy in a system containing more than 100,000 atoms.

Separation of potential and kinetic electron emission from Si and W induced by multiply charged neon and argon ions

T he total secondary electron emission yields, gamma(T), induced by impact of the fast ions Neq+ (q = 2-8) and Arq+ (q = 3-12) on Si and Neq+ (q = 2-8) on W targets have been measured. It was observed that for a given impact energy, gamma(T) increases with the charge of projectile ion. By plotting gamma(T) as a function of the total potential energy of the respective ion, true kinetic and potential electron yields have been obtained. Potential electron yield was proportional to the total potential energy of the projectile ion. However, decrease in potential electron yield with increasing kinetic energy of Neq+ impact on Si and W was observed. This decrease in potential electron yield with kinetic energy of the ion was more pronounced for the projectile ions having higher charge states. Moreover, kinetic electron yield to energy-loss ratio for various ion-target combinations was calculated and results were in good agreement with semi-empirical model for kinetic electron emission.