Computational Identification of a New Form of Li2MnSiO4 for Battery Applications

2017 ◽  
Vol 263 ◽  
pp. 160-164
Author(s):  
Maxim Arsentev ◽  
Marina Kalinina ◽  
Petr Tikhonov ◽  
Anastasia Shmigel ◽  
Nadezhda Kovalko ◽  
...  
Keyword(s):  
Phase Transformations ◽  
Three Dimensional ◽  
High Capacity ◽  
Dimensional Structure ◽  
Practical Application ◽  
Computational Identification ◽  
New Form ◽  
The Stability ◽  
Inorganic Framework ◽  
Computer Studies

The reversibility of phase transformations in Li2MnSiO4 and related materials during charge/discharge of the material is an important factor to enable the practical application of the cathode materials. However, the stability of this material is still unattainable. Here we report the computational identification of a new form of Li2MnSiO4 as a stable candidate with acceptable characteristics. The stability could arise due to the presence of the three-dimensional structure of the inorganic framework. The presence of a structure with a compact unit cell forms the basis for high capacity. Surprisingly it was found to have a stable analogue occurring in nature – Na2CaSiO4 with the same structure. Using this information the possible routes of obtaining such material are presented. The prediction of such material has been not found in the literature previously. Of course the problems such as phase transformations upon delithiation may exist, and to check the data the experimental and computer studies needed.

Protein intrachain contact prediction with most interacting residues (MIR)

2014 ◽  
Vol 10 (4) ◽  
Author(s):  
Ruben Acuña ◽  
Zoé Lacroix ◽  
Nikolaos Papandreou ◽  
Jacques Chomilier
Keyword(s):  
Structural Changes ◽  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Accessible Surface Area ◽  
Dimensional Structure ◽  
Closed Loops ◽  
Folding Process ◽  
Folding Nucleus ◽  
Accessible Surface ◽  
The Stability

AbstractThe transition state ensemble during the folding process of globular proteins occurs when a sufficient number of intrachain contacts are formed, mainly, but not exclusively, due to hydrophobic interactions. These contacts are related to the folding nucleus, and they contribute to the stability of the native structure, although they may disappear after the energetic barrier of transition states has been passed. A number of structure and sequence analyses, as well as protein engineering studies, have shown that the signature of the folding nucleus is surprisingly present in the native three-dimensional structure, in the form of closed loops, and also in the early folding events. These findings support the idea that the residues of the folding nucleus become buried in the very first folding events, therefore helping the formation of closed loops that act as anchor structures, speed up the process, and overcome the Levinthal paradox. We present here a review of an algorithm intended to simulate in a discrete space the early steps of the folding process. It is based on a Monte Carlo simulation where perturbations, or moves, are randomly applied to residues within a sequence. In contrast with many technically similar approaches, this model does not intend to fold the protein but to calculate the number of non-covalent neighbors of each residue, during the early steps of the folding process. Amino acids along the sequence are categorized as most interacting residues (MIRs) or least interacting residues. The MIR method can be applied under a variety of circumstances. In the cases tested thus far, MIR has successfully identified the exact residue whose mutation causes a switch in conformation. This follows with the idea that MIR identifies residues that are important in the folding process. Most MIR positions correspond to hydrophobic residues; correspondingly, MIRs have zero or very low accessible surface area. Alongside the review of the MIR method, we present a new postprocessing method called smoothed MIR (SMIR), which refines the original MIR method by exploiting the knowledge of residue hydrophobicity. We review known results and present new ones, focusing on the ability of MIR to predict structural changes, secondary structure, and the improved precision with the SMIR method.

Three-Dimensional Velocity and Droplet Size Measurements of Spray Flow (Keynote Paper)

2003 ◽  
Author(s):  
Yoshio Zama ◽  
Masaaki Kawahashi ◽  
Hiroyuki Hirahara
Keyword(s):  
Velocity Distribution ◽  
Droplet Size ◽  
Measurement Technique ◽  
Three Dimensional ◽  
High Density ◽  
Dimensional Structure ◽  
Practical Application ◽  
Droplet Motion ◽  
Observation Area ◽  
Spray Field

The present investigation describes an application of a novel technique of simultaneous measurement of droplet size and three-dimensional components of velocity in a high density spray with swirl. The spray has a complicated and three-dimensional structure caused by mixing with surrounding airflow entrained by high speed fuel jet issuing from a nozzle. The breakup process of fuel film to fine-droplet-cloud, the droplet size dispersion and the velocity distribution of droplets are important factors in practical application of fuel spray for combustors. The conventional technique can be applied to local measurement of droplet speed and size. Recent methods, based on optical and image processing techniques, provide measurement of the velocity and droplet size distribution in observation area or volume. Maeda et al. proposed an excellent measurement technique of the size and the velocity distribution of droplet in spray based on interferometric laser imaging in which the fringe pattern is generated at the out of focus plane by interference between 0th order and 1st order refractions of droplet illuminated by high power laser light sheet. And also, in this technique, the separation of overlapping droplets image has been successfully done by optical method. As a practical application, the size and velocity distributions of droplets in a high density spray without swirl have been measured by this technique. In general, the droplet motion in a spray field is highly three-dimensional. Especially, a spray generated by a swirl nozzle shows complicated droplet motion in the three-dimensional field. In order to analyze the configuration of a complicated spray field, three-dimensional velocity measurement of droplets must be required. In the present paper, a combined measurement technique of the size and three velocity components of droplets in three-dimensional spray field based on doublet imaging technique of droplets and stereoscopic PIV method has been developed. And its feasibility and applicability was confirmed by practical application to measurements of spray fields induced by a swirl jet nozzle using in gas turbine.

scholarly journals Nanoparticles Mediated Protein Stability in Comparison with Osmolytes: in vivo Approach

2021 ◽  
Vol 33 (6) ◽  
pp. 1433-1438
Author(s):  
R. Verma ◽  
N. Singh ◽  
P. Chaudhuri (Chattopadhyay)
Keyword(s):  
Gold Nanoparticles ◽  
Dihydrofolate Reductase ◽  
Three Dimensional ◽  
Cellular Level ◽  
Dimensional Structure ◽  
Important Group ◽  
Unfolded State ◽  
The Status ◽  
The Stability

The native three-dimensional structure of protein is quite unstable under critical destabilizing conditions. In order to enhance the stability and activity for a proper folded environment of a protein, many stabilizing materials are added such as nanoparticles and osmolytes to an unfolded state of protein. Osmolytes are the important group of molecules which are engaged by the cell as an adaption in the severe conditions. In this communication, a comparative in vivo study is reported for imparting the status of stability and folding ability of zebrafish dihydrofolate reductase (zDHFR) protein with gold nanoparticles and various osmolytes (glycerol, glucose and betain). Present observations revealed that the interaction of gold nanoparticles (AuNPs) with bacteria at the cellular level helps in maintaining the stability of protein more effectively than osmolytes which could be used for many biological and pharmacological approaches although glycerol as an osmolyte also stabilizes the protein at a significant level.

scholarly journals SE-OnionNet: A Convolution Neural Network for Protein–Ligand Binding Affinity Prediction

2021 ◽  
Vol 11 ◽  
Author(s):  
Shudong Wang ◽  
Dayan Liu ◽  
Mao Ding ◽  
Zhenzhen Du ◽  
Yue Zhong ◽  
...  
Keyword(s):  
Neural Network ◽  
Binding Affinity ◽  
Three Dimensional ◽  
Model Performance ◽  
Protein Molecule ◽  
Stochastic Gradient Descent ◽  
Dimensional Structure ◽  
Scoring Functions ◽  
Ligand Complex ◽  
The Stability

Deep learning methods, which can predict the binding affinity of a drug–target protein interaction, reduce the time and cost of drug discovery. In this study, we propose a novel deep convolutional neural network called SE-OnionNet, with two squeeze-and-excitation (SE) modules, to computationally predict the binding affinity of a protein–ligand complex. The OnionNet is used to extract a feature map from the three-dimensional structure of a protein–drug molecular complex. The SE module is added to the second and third convolutional layers to improve the non-linear expression of the network to improve model performance. Three different optimizers, stochastic gradient descent (SGD), Adam, and Adagrad, were also used to improve the performance of the model. A majority of protein–molecule complexes were used for training, and the comparative assessment of scoring functions (CASF-2016) was used as the benchmark. Experimental results show that our model performs better than OnionNet, Pafnucy, and AutoDock Vina. Finally, we chose the macrophage migration inhibitor factor (PDB ID: 6cbg) to test the stability and robustness of the model. We found that the prediction results were not affected by the docking position, and thus, our model is of acceptable robustness.

scholarly journals Nonorthogonal Aerial Optoelectronic Platform Based on Triaxial and Control Method Designed for Image Sensors

Sensors ◽  
2019 ◽  
Vol 20 (1) ◽  
pp. 10
Author(s):  
Quanchao Li ◽  
Shuyan Xu ◽  
Yulei Xu ◽  
Lei Li ◽  
Liu Zhang
Keyword(s):  
Optical Sensors ◽  
Control Method ◽  
Three Dimensional ◽  
Voice Coil Motor ◽  
Image Sensor ◽  
Dimensional Structure ◽  
Internal Space ◽  
Drive Control ◽  
The Stability ◽  
Better Than

A traditional aerial optoelectronic platform consists of inside and outside multilayer gimbals, while an internal gimbal and drive components occupy the internal space where optical sensors are located. In order to improve the replaceability of optical sensors and to increase their available space, this paper introduces a nonorthogonal aerial optoelectronic platform based on three axes; we carried out research on its drive control method. A three-dimensional structure of an aerial optoelectronic platform was designed. A noncontact drive of a linear voice coil motor was introduced, and a drive control scheme of a proportional integral and a disturbance observer was adopted. Finally, simulations and experiments were carried out. Results showed that the aerial optoelectronic platform could effectively release three times the image sensor space, and the servo bandwidth was 60.2 Hz, which was much better than that of traditional two-axis and four-gimbal platforms. The stability accuracy of the system reached 4.9958 micron rad, which was obviously better than that of traditional gimbals. This paper provides a reference for the design of new optoelectronic platforms.

scholarly journals Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251751
Author(s):  
Siti Nor Hasmah Ishak ◽  
Nor Hafizah Ahmad Kamarudin ◽  
Mohd Shukuri Mohamad Ali ◽  
Adam Thean Chor Leow ◽  
Fairolniza Mohd Shariff ◽  
...  
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Substrate Preference ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Docking Analysis ◽  
Three Dimensional Structure ◽  
Ion Interactions ◽  
The Stability

5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl–esters.

scholarly journals Heat and SDS insensitive NDK dimers are largely stabilised by hydrophobic interaction to form functional hexamer in Mycobacterium smegmatis.

2013 ◽  
Vol 60 (2) ◽  
Author(s):  
Muthu Arumugam ◽  
Parthasarathi Ajitkumar
Keyword(s):  
Hydrophobic Interaction ◽  
Hydrophobic Interactions ◽  
Three Dimensional ◽  
Nucleoside Diphosphate Kinase ◽  
Dimensional Structure ◽  
Recombinant Enzymes ◽  
Basic Subunit ◽  
Oligomeric Form ◽  
The Stability ◽  
And Function

The primary structure and function of nucleoside diphosphate kinase (NDK), a substrate non-specific enzyme involved in the maintenance of nucleotide pools is also implicated to play pivotal roles in many other cellular processes. NDK is conserved from bacteria to human and forms a homotetramer or hexamer to exhibit its biological activity. However, the nature of the functional oligomeric form of the enzyme differs among different organisms. The functional form of NDKs from many bacterial systems, including that of the human pathogen, Mycobacterium tuberculosis (MtuNDK), is a hexamer, although some bacterial NDKs are tetrameric in nature. The present study addresses the oligomeric property of MsmNDK and how a dimer, the basic subunit of a functional hexamer, is stabilized by hydrogen bonds and hydrophobic interactions. Homology modeling was generated using the three-dimensional structure of MtuNDK as a template; the residues interacting at the monomer-monomer interface of MsmNDK were mapped. Using recombinant enzymes of wild type, catalytically inactive mutant, and monomer-monomer interactive mutants of MsmNDK, the stability of the dimer was verified under heat, SDS, low pH, and methanol. The predicted residues (Gln17, Ser24 and Glu27) were engaged in dimer formation, however the mutated proteins retained the ATPase and GTPase activity even after introducing single (MsmNDK- Q17A, MsmNDK-E27A, and MsmNDK-E27Q) and double (MsmNDK-E27A/Q17A) mutation. However, the monomer-monomer interaction could be abolished using methanol, indicating the stabilization of the monomer-monomer interaction by hydrophobic interaction.

Insights into the structural evolution and electronic properties of deficient-electron sodium chloride clusters

2020 ◽  
Vol 10 (9) ◽  
pp. 1404-1411
Author(s):  
Shihui Guo ◽  
Yu Zhang ◽  
Ping Wang ◽  
Huang Tang ◽  
Wei Dai ◽  
...  
Keyword(s):  
Sodium Chloride ◽  
Electronic Properties ◽  
Three Dimensional ◽  
Magic Number ◽  
Structural Evolution ◽  
Linear Structure ◽  
Dimensional Structure ◽  
Three Stages ◽  
The Stability ◽  
Cluster Series

We have explored the structural evolution and electronic properties of cationic sodium chloride (NaCl)+n (n = 1–8) clusters. The global minimum of cationic (NaCl)+n clusters have been extensively searched using CALYPSO method combined with DFT calculations. The structural evolution of (NaCl)+n clusters can be divided into three stages: linear structure, planar ring-like structure and three-dimensional structure. It is worth to note that cuboid structure is more common in the cluster series as the cluster size increases. (NaCl)+4 clusters is identified as "magic number" clusters by means of the relative stabilities analyses. The following chemical bonding analysis indicate that the stability of (NaCl)+ 4cluster mainly comes from the interaction between Na 3s and Cl 3p atomic orbitals.

Roles of the procollagen C-propeptides in health and disease

2019 ◽  
Vol 63 (3) ◽  
pp. 313-323 ◽  
Author(s):  
David J.S. Hulmes
Keyword(s):  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Missense Mutations ◽  
Detailed Model ◽  
Morphogenetic Protein ◽  
Collagen Molecules ◽  
Health And Disease ◽  
The Stability ◽  
New Interactions

AbstractThe procollagen C-propeptides of the fibrillar collagens play key roles in the intracellular assembly of procollagen molecules from their constituent polypeptides chains, and in the extracellular assembly of collagen molecules into fibrils. Here we review recent advances in understanding the molecular mechanisms controlling C-propeptide trimerization which have revealed the importance of inter-chain disulphide bonding and a small number of charged amino acids in the stability and specificity of different types of chain association. We also show how the crystal structure of the complex between the C-propeptide trimer of procollagen III and the active fragment of procollagen C-proteinase enhancer-1 leads to a detailed model for accelerating release of the C-propeptides from procollagen by bone morphogenetic protein-1 and related proteinases. We then discuss the effects of disease-related missense mutations in the C-propeptides in relation to the sites of these mutations in the three-dimensional structure. While in general there is a good correlation between disease severity and structure-based predictions, there are notable exceptions, suggesting new interactions involving the C-propeptides yet to be characterized. Mutations affecting proteolytic release of the C-propeptides from procollagen are discussed in detail. Finally, the roles of recently discovered interaction partners for the C-propeptides are considered during fibril assembly and cross-linking.

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