Energy Calculation Methods Research Articles

Hot spot profiles of SARS-CoV-2 and human ACE2 receptor protein protein interaction obtained by density functional tight binding fragment molecular orbital method

The prevalence of a novel β-coronavirus (SARS-CoV-2) was declared as a public health emergency of international concern on 30 January 2020 and a global pandemic on 11 March 2020 by WHO. The spike glycoprotein of SARS-CoV-2 is regarded as a key target for the development of vaccines and therapeutic antibodies. In order to develop anti-viral therapeutics for SARS-CoV-2, it is crucial to find amino acid pairs that strongly attract each other at the interface of the spike glycoprotein and the human angiotensin-converting enzyme 2 (hACE2) complex. In order to find hot spot residues, the strongly attracting amino acid pairs at the protein–protein interaction (PPI) interface, we introduce a reliable inter-residue interaction energy calculation method, FMO-DFTB3/D/PCM/3D-SPIEs. In addition to the SARS-CoV-2 spike glycoprotein/hACE2 complex, the hot spot residues of SARS-CoV-1 spike glycoprotein/hACE2 complex, SARS-CoV-1 spike glycoprotein/antibody complex, and HCoV-NL63 spike glycoprotein/hACE2 complex were obtained using the same FMO method. Following this, a 3D-SPIEs-based interaction map was constructed with hot spot residues for the hACE2/SARS-CoV-1 spike glycoprotein, hACE2/HCoV-NL63 spike glycoprotein, and hACE2/SARS-CoV-2 spike glycoprotein complexes. Finally, the three 3D-SPIEs-based interaction maps were combined and analyzed to find the consensus hot spots among the three complexes. As a result of the analysis, two hot spots were identified between hACE2 and the three spike proteins. In particular, E37, K353, G354, and D355 of the hACE2 receptor strongly interact with the spike proteins of coronaviruses. The 3D-SPIEs-based map would provide valuable information to develop anti-viral therapeutics that inhibit PPIs between the spike protein of SARS-CoV-2 and hACE2.

An Approach to Computing Solvent Reorganization Energy.

A method for accurate calculation of reorganization free energy of an explicit solvent solvating a solute molecule is presented. The method relies on the knowledge of solvation free energy known either from experimental measurement or from accurate calculation. An important part of this approach lies in the calculation of entropy in solute-solvent interaction free energy using the interaction entropy method, combined with the calculation of enthalpy of solvent reorganization based on a finite number of solvent molecules near the solute molecule. This interaction entropy-solvent reorganization or IESR method enables one to compute both enthalpy and entropy components of the solvent reorganization energy from MD simulation of the solvated system. The calculated results are determined by the molecular force field only without any empirical parameter. The current method is applied to computing the reorganization energies of water solvent solvating a wide range of solute molecules including both hydrophilic and hydrophobic ones. The accuracy of the approach is indirectly verified by the excellent agreement of individual enthalpies and entropies of the solvation energies between theory and experiment.

Adsorption-Induced Liquid-to-Solid Phase Transition of Cu Clusters in Catalytic Dissociation of CO2.

Sub-nanometer metal clusters widely existing in catalysts have a large ensemble of metastable isomers that can interconvert during catalytic reactions, exhibiting complex dynamical catalytic effects. In this work, we systematically investigate the temperature dependent structural dynamics of the Cu13 cluster in CO2 dissociation using ab initio molecular dynamics and the free energy calculation method. We find an abnormal entropic effect due to adsorption-induced liquid-to-solid phase transition of the cluster during the course of the elementary dissociation step at transition temperatures. In the dissociation product, the formation of a rigid Cu3O unit decreases the dynamical fluidity of the cluster and increases the melting temperature, causing a decrease in the entropy of the dissociation product. Our work demonstrates the nontrivial effects of surface adsorption on phase transition behaviors of dynamic clusters and offers a new perspective to dynamic catalysis.

Computational analysis of hereditary spastic paraplegia mutations in the kinesin motor domains of KIF1A and KIF5A

Hereditary spastic paraplegias (HSPs) are a genetically heterogeneous collection of neurodegenerative disorders categorized by progressive lower-limb spasticity and frailty. The complex HSP forms are characterized by various neurological features including progressive spastic weakness, urinary sphincter dysfunction, extra pyramidal signs and intellectual disability (ID). The kinesin superfamily proteins (KIFs) are microtubule-dependent molecular motors involved in intracellular transport. Kinesins directionally transport membrane vesicles, protein complexes, and mRNAs along neurites, thus playing important roles in neuronal development and function. Recent genetic studies have identified kinesin mutations in patients with HSPs. In this study, we used the computational approaches to investigate the 40 missense mutations associated with HSP and ID in KIF1A and KIF5A. We performed homology modeling to construct the structures of kinesin–microtubule binding domain and kinesin–tubulin complex. We applied structure-based energy calculation methods to determine the effects of missense mutations on protein stability and protein–protein interaction. The results revealed that the most of disease-causing mutations could change the folding free energy of kinesin motor domain and the binding free energy of kinesin–tubulin complex. We found that E253K associated with ID in KIF1A decrease the protein stability of kinesin motor domains. We showed that the HSP mutations located in kinesin–tubulin complex interface, such as K253N and R280C in KIF5A, can destabilize the kinesin–tubulin complex. The computational analysis provides useful information for understanding the roles of kinesin mutations in the development of ID and HSPs.

Research on the conversion of self-anchoring test data to static loading test data

Self-anchoring testing is a new method for testing the bearing capacity of pile foundations. This study compares the results of a self-anchoring test to that of an existing method, static loading testing, by examining the variation rules for the axial force, lateral resistance and Q–s curve of pile foundations using a model test. A non-linear fitting analysis of the pile–soil load transfer during a self-anchoring test was performed using the measured test data, and a new mathematical expression for the pile–soil load transfer was proposed. By drawing on the relationship between the pile body deformation energy and the external force, an energy calculation method was introduced as part of the numerical calculations for the self-anchoring test. By determining the difference in the pile body energy, a calculation method for pile behaviour was established to realise the conversion of self-anchoring test data to static loading test data. The results of an engineering example using the proposed calculation method were found to be basically consistent with the measured data. Therefore, the calculation method was shown to enable the conversion of results from a self-anchoring test to a static loading test.

In-Situ Determination of Buildings’ Thermo- Physical Characteristics: Method Development, Experimentation, and Computation

In-Situ Determination of Buildings’ Thermo- Physical Characteristics: Method Development, Experimentation, and Computation

Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy.

CREB-binding protein (CBP) is a multi-subunit scaffold protein complex in transcription regulation process, binding and interacting with ligands such as mixed-lineage leukemia (MLL) and c-Myb allosterically. Here in this study, we have revisited the concept of allostery in CBP via residue-based interaction energy calculation based on molecular dynamics (MD) simulations. To this end, we conducted MD simulations of KIX:MLL:c-Myb ternary complex, its binary components and kinase-inducible domain (KID) interacting domain (KIX) backbone. Interaction energy profiles and cross correlation analysis were performed and the results indicated that KIX:MLL and KIX:c-Myb:MLL complexes demonstrate significant similarities according to both analysis methods. Two regions in the KIX backbone were apparent from the interaction energy and cross correlation maps that hold a key to allostery phenomena observed in CBP. While one of these regions are related to the ligand binding residues, the other comprises of L12-G2 loop and α3 helix regions that have been found to have a significant role in allosteric signal propagation. All in all, residue-based interaction energy calculation method is demonstrated to be a valuable calculation technique for the detection of allosteric signal propagation and ligand interaction regions.

Breakdown of the Use of Energy in Common Areas of Residential Buildings in Chile

In the last 15 years the population of the Metropolitan Region has increased by 16.10%. Due to this greater densification, many people have had to live in residential buildings. By accepting this condition, residents have also accepted a monthly payment of common expenses. The reality shows that the latter are unpredictable prior to the operation of the building and once in operation their distribution and origin, allowing for the planning of resources, is not known. Based on the foregoing, we propose an energy calculation method to estimate the electricity and gas consumption of hot water for both domestic use and heating of the facilities present in the common areas of buildings. The method was applied in 2 residential buildings in Santiago with similar characteristics in order to compare the results obtained with the calculation method versus the actual consumption information. The results show that the most consumed basic services correspond to gas used for boilers at 67.5% and electricity at 29%. Regarding electricity, cold water pumps generated the highest energy consumption followed by lighting of parking areas. The percentage difference between the estimated monthly expenditure and the monthly expense charged for electricity was 11.50% and 9.19% for Building A and B, respectively. Moreover, in the case of gas, the difference was 21.10% for Building A and 17.09% for Building B.

Learning EEG topographical representation for classification via convolutional neural network

Electroencephalography (EEG) topographical representation (ETR) can monitor regional brain activities and is emerging as a successful technique for causally exploring cortical mechanisms and connections. However, it is a challenge to find a robust method supporting high-dimensional EEG data with low signal-to-noise ratios from multiple objects and multiple channels. To address this issue, a new ETR energy calculation method for learning the EEG patterns of brain activities using a convolutional neural network is reported. It is able to customize temporal ETR training and recognize multiple objects within a common learning model. Specifically, an open-access dataset from the 2008 Brain-Computer Interface (BCI) Competition IV-2a is used for classification of five classes containing four Motor Imagery actions and one relax action. The proposed classification framework outperforms the best state-of-the-art classification method by 10.11% in average subject accuracy. Furthermore, by studying the ETR parameter optimization, a user interface for BCI applications is obtained and a real-time method implemented.

A review of operational energy consumption calculation method for urban buildings

Rapid urbanization has driven economic and social development, but it has also led to continued growth in building energy consumption. It is of great significance to ensure the user comfort while controlling the growth of building energy use. Accurate quantification of urban buildings' energy demand can support energy efficient and sustainable community design, assist urban morphology generation and optimization, building layout optimization, building shape and construction design, HVAC system optimization, assessment of the energy program and policy. In recent years, researchers worldwide have carried out research of urban scale energy consumption calculation methods from different perspectives, and encountered different technical difficulties. This paper provides a critical review on the energy modeling methods at urban neighborhood scale from the following three aspects: database, models and platforms. Through literature review, the authors indicate the advantages and limitations of current urban building energy calculation methods and tools, and propose the following possible approaches to improve the operational energy consumption calculation method for urban buildings: (1) develop micro-environment data generation methods that can be directly applied to energy consumption calculation of urban buildings; (2) improve the capabilities to collect, filter and convert the building information data by introducing the data mining technique; (3) introduce the cluster analysis and artificial intelligence technology to improve the speed of energy consumption calculation; (4) develop a visualization platform to realize real-time editing and calculating of urban design.

An Oscillation Energy Calculation Method Suitable for the Disturbance Source Location of Generator Control Systems

Low frequency power oscillation threatens the secure and stable operation of power systems. Since the appearance of low frequency oscillation there are lots of approaches to analyze this problem. The oscillation source location method based on oscillation energy is adopted to find the cause of the oscillation, and to locate the oscillation source. Forced power oscillation is a kind of low frequency oscillation based on resonance mechanism, and the key is to quickly locate and remove the disturbance source. Aiming at the shortcomings of the existing disturbance source location methods, an oscillation energy calculation method suitable for the generator control systems level location is proposed. With the rich acquisition of generator data by means of phasor measurement unit (PMU), this method has the advantage of not relying on generator parameters. Taking the forced power oscillation caused by the abnormality of the governor system as an example, the superiority of the method is verified.

Implementation of adaptive integration method for free energy calculations in molecular systems.

Estimating free energy differences by computer simulation is useful for a wide variety of applications such as virtual screening for drug design and for understanding how amino acid mutations modify protein interactions. However, calculating free energy differences remains challenging and often requires extensive trial and error and very long simulation times in order to achieve converged results. Here, we present an implementation of the adaptive integration method (AIM). We tested our implementation on two molecular systems and compared results from AIM to those from a suite of other methods. The model systems tested here include calculating the solvation free energy of methane, and the free energy of mutating the peptide GAG to GVG. We show that AIM is more efficient than other tested methods for these systems, that is, AIM results converge to a higher level of accuracy and precision for a given simulation time.

Accurate Calculation Method for Mechanical Specific Energy of Horizontal Well

The existing drilling efficiency-monitoring model based on the theory of mechanical specific energy is only applicable to vertical wells. When it is used to monitor the drilling efficiency of horizontal wells, the impact of high friction in horizontal wells is not considered, so the monitored specific energy of the machine is not real Specific energy of horizontal wells. Based on the previous research results, this dissertation uses the micro-element method to segment the drill string into micro-elements, and considers the influence of the friction torque of the horizontal well. For the existing horizontal wells, rotary drilling, sliding drilling and the characteristics of compound drilling have derived the mechanical specific energy calculation models of horizontal wells based on these three different drilling conditions for real-time monitoring of drilling efficiency of horizontal wells.

First-principles calculation of excited states of diatomic molecules: a benchmark for the Gutzwiller conjugate gradient minimisation method

We recently proposed the Gutzwiller conjugate gradient minimisation (GCGM) method for efficient and accurate calculation of the ground state total energy of molecular and bulk systems. The GCGM method is developed under the framework of Gutzwiller wave function but goes beyond the commonly adopted Gutzwiller approximation to improve the accuracy and flexibility in treating the correlation effects. In this conference proceeding, we benchmark the GCGM method with the calculation of excited state potential energy curves of three diatomic molecules, namely H2, N2, and O2. Our calculations demonstrate the flexibility and reasonable accuracy of the method.

Study on energy consumption index system and calculation method of highway transportation infrastructure in Qinghai Province

In view of the lack of mandatory statistics on energy consumption of transportation infrastructure at the national level, the energy consumption index system of Qinghai highway transportation infrastructure was established based on the analytic hierarchy process by using fuzzy synthetic evaluation method. And the calculation method of Qinghai highway transportation infrastructure was established based on the calculation results of the unit energy consumption coefficient of each classification index. This work offers reference for the rapid evaluation of the energy consumption of Qinghai highway transportation infrastructure.

The influence of two calculation methods on relative energy contribution of men's wheelchair racing T54 events

To study whether the two methods of energy calculation affects the value of relative energy contribution in men's T54 wheelchair racing events. Ten men's T54 wheelchair racers (age (22.9±5.2) yrs、sitting height (90.9±3.2) cm、body mass (59.3±8.3) kg) participate in 1 incremental test and 4 time trials (400 m、800 m、1 500 m、5 000 m). A portable gas analyzer, polar heart rate belt and a blood lactate analyzer were used to measure VO2 at every breath, HR and blood lactate changes. The energetic contribution was measured with phosphocreatine-lactate-oxygen(PCr-La-O2) and maximal accumulated oxygen deficit(MAOD) methods. The anaerobic and total energy portions from MAOD were lower than those from PCr-La-O2 ( especially in 400 m: WTOT (50.8 ±12.7) KJ vs (65.2±13.5) KJ、WANA (31.0±9.0) KJ vs (45.4±11.4) KJ, P＜0.05), resulting in WAER% calculated by MAOD was generally higher than PCr-La-O2 method (especially in 400 m : WAER% 39.0% ±1.2% vs 30.4%±8.4 %,P＜0.05). The study proves that the two-calculation method causes WAER% difference. MAOD method does lead to an overestimate of WAER%. Recommend to use the same calculation method for diagnosis and monitoring in the longitudinal study of long-term scientific research (such as the 4-year Olympic Games),to avoiding the difference in results caused by different calculation methods, which will further influence the development of coaches' training plans and training implementation effect.

Proposed Method for Probabilistic Energy Simulations for Multi-Family Dwellings

As regulations regarding energy use and emissions of CO2 equivalents in buildings become more stringent, the need for more accurate tools and improved methods for predicting these parameters in building performance simulations increases. In the first part of this project, a probabilistic method was developed and applied to the transient energy calculations and evaluated using a single-family dwelling case study. The method was used to successfully predict the variation of the energy use in 26 houses built in the same residential area and with identical building characteristics and services. This project continues the development and testing of the probabilistic method for energy calculations by applying it to a multi-family building. The complexity of the building model increases as the multi-family model consists of 52 zones, compared to the single-zone model used for the single-family dwelling. The multi-family model also includes additional parameters that are evaluated, such as the domestic hot water circulation losses. This paper presents the probabilistic method applied to the building performance simulations used to predict the energy use for the multi-family building and discusses the differences between the previous and new method used in this study.

A novel method for calculating the light energy distribution in building space

In lighting design in buildings, the conventional algorithms may cause significant calculation error of light energy distribution and may not ensure illumination uniformity. In this paper, the radiation method in computer graphics is studied, combined with formula derivation, two kinds of light energy calculation methods based on Lambert reflection model and non-Lambert reflection model are investigated, and two models: model 1 and model 2, are established for interior space of non-uniform height and non-rectangular interior space respectively. Comparing simulation results of the models with existing models in a DIALux environment, the illumination uniformity calculation error of model 1 is 30%, and the calculation error of model 2 is within 5%. In addition, parameters of the models are modulated by experiments, in order to improve the accuracy of the models. Although model 1 based on Lambert's reflection model runs fast, its accuracy needs to be improved. In the case of high simulation accuracy of spatial light environment, model 2 based on the non-Lambert reflection model is the better choice. At the same time, it is proved that the improved radiation method is feasible in calculating the light energy of interior spaces with non-uniform height and non-rectangular shape.

Nearly zero energy renovation concepts for apartment buildings

Revised EPBD directive has set ambitious targets for renovation. It is stated that Member States shall establish a long-term strategy facilitating the cost-effective transformation of existing buildings into nearly-zero energy buildings. The long-term strategy should set out a roadmap with a view to the long-term 2050 goal of reducing greenhouse gas emissions in the European Union. This creates the need for cost-efficient renovation solutions which can be implemented in large scale. The impact assessment shows that roughly a doubled renovation rate of 3 % would be needed to accomplish the energy efficiency ambitions in a cost-effective manner. The objective of this study is to specify renovation concepts with adequate heating and ventilation, based on Estonian and German apartment buildings and corresponding local solutions. Energy performance and sizing analyses were conducted for selected multifamily apartment buildings typical for 1960-70es with three different renovation concepts. Energy calculations were conducted with national energy calculation methods and national energy requirements for major renovation. In the renovation, the building envelope insulation, air tightness, and heating and ventilation systems were improved so that the renovated building complies with national nearly zero-energy requirement for major renovation.

In-Situ Determination of Buildings’ Thermo- Physical Characteristics

In-Situ Determination of Buildings’ Thermo- Physical Characteristics