scholarly journals Geometric Simulation Approach for Grading and Assessing the Thermostability of CALBs

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
B. Senthilkumar ◽  
D. Meshachpaul ◽  
R. Rajasekaran
Keyword(s):  
Surface Area ◽  
Structural Parameters ◽  
Conformational Sampling ◽  
Docking Analysis ◽  
Computational Docking ◽  
Highly Active ◽  
Structural Rigidity ◽  
Biodiesel Synthesis ◽  
The Stability ◽  
Thermostable Lipases

Candida antarcticalipase B (CALB) is a known stable and highly active enzyme used widely in biodiesel synthesis. In this work, the stability of native (4K6G) and mutant (4K5Q) CALB was studied through various structural parameters using conformational sampling approach. The contours of polar surface area and surface area of mutant CALB were 11357.67 Å2and 30007.4 Å2, respectively, showing an enhanced stability compared to native CALB with a statistically significantPvalue of < 0.0001. Moreover, simulated thermal denaturation of CALB, a process involving dilution of hydrogen bond, significantly shielded against different intervals of energy application in mutant CALB revealing its augmentation of structural rigidity against native CALB. Finally, computational docking analysis showed an increase in the binding affinity of CALB and its substrate (triglyceride) in mutant CALB with Atomic Contact Energy (ACE) of −91.23 kcal/mol compared to native CALB (ACE of −70.3 kcal/mol). The computational observations proposed that the use of mutant CALB (4K5Q) could serve as a best template for production of biodiesel in the future. Additionally, it can also be used as a template to identify efficient thermostable lipases through further mutations.

Selection of oxypeucedanin as a potential antagonist from molecular docking analysis of HSP90

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Joshua Oluwasegun Bamidele ◽  
George Oche Ambrose ◽  
Oluwaseun Suleiman Alakanse
Keyword(s):  
Molecular Docking ◽  
Liver Toxicity ◽  
Docking Study ◽  
Docking Studies ◽  
Molecular Docking Study ◽  
Docking Analysis ◽  
Computational Docking ◽  
Drug Candidates ◽  
Expression Rate ◽  
Client Proteins

AbstractHSP90 is observed as one of the copious molecular chaperones that play a key role in mediating appropriate folding, maturation, and firmness of many client proteins in cells. The expression rate of HSP90 in cancer cells is at a level of 2- to 10-fold higher than the 1- to 2-fold of its unstressed and healthy ones. To combat this, several inhibitors to HSP90 protein have been studied (such as geldanamycin and its derivative 17-AAG and 17-DMAG) and have shown some primary side effects including plague, nausea, vomiting, and liver toxicity, hence the search for the best-in-class inhibitor for this protein through in silico. This study is aimed at analyzing the inhibitory potency of oxypeucedanin-a furocoumarin derivations, which have been reported to have antipoliferative activity in human prostrate carcinoma DN145 cells, and three other drug candidates retrieved from the literature via computational docking studies. The results showed oxypeucedanin as the compound with the highest binding energy of −9.2 kcal/mol. The molecular docking study was carried out using PyRx, Auto Dock Vina option, and the target was validated to confirm the proper target and the docking procedure employed for this study.

Numerical and Experimental Approaches to Investigate the Stability of a Motorcycle Vehicle

2006 ◽  
Author(s):  
Federico Cheli ◽  
Marco Bocciolone ◽  
Marco Pezzola ◽  
Elisabetta Leo
Keyword(s):  
Degrees Of Freedom ◽  
Structural Parameters ◽  
Experimental Tests ◽  
Roll Angle ◽  
Longitudinal Motion ◽  
Reference Trajectory ◽  
Steering Angle ◽  
Steady State Condition ◽  
The Stability ◽  
Linearized Model

The study of motorcycle’s stability is an important task for the passenger’s safety. The range of frequencies involved for the handling stability is lower than 10 Hz. A numerical model was developed to access the stability of a motorcycle vehicle in this frequency range. The stability is analysed using a linearized model around the straight steady state condition. In this condition, the vehicle’s vertical and longitudinal motion are decoupled, hence the model has only four degrees of freedom (steering angle, yaw angle, roll angle and lateral translation), while longitudinal motion is imposed. The stability was studied increasing the longitudinal speed. The input of the model can be either a driver input manoeuvre (roll angle) or a transversal component of road input able to excite the vibration modes. The driver is introduced in the model as a steering torque that allows the vehicle to follow a reference trajectory. To validate the model, experimental tests were done. To excite the vehicle modes, the driver input was not taken into account considering both the danger for the driver and the repeatability of the manoeuvre. Two different vehicle configurations were tested: vehicle 1 is a motorcycle [7] and vehicle 2 is a scooter. Through the use of the validated model, a sensitivity analysis was done changing structural (for example normal trail, steering angle, mass) and non structural parameters (for example longitudinal speed).

On the stability of a mathematical model for HIV(AIDS) - cancer dynamics

2021 ◽  
Vol 8 (4) ◽  
pp. 783-796
Author(s):  
H. W. Salih ◽  
◽  
A. Nachaoui ◽  
Keyword(s):  
Mathematical Model ◽  
Highly Active Antiretroviral Therapy ◽  
Lyapunov Method ◽  
Equilibrium Points ◽  
Hiv Treatment ◽  
Biochemical Processes ◽  
Highly Active ◽  
Biological Phenomena ◽  
The Stability ◽  
The Impact

In this work, we study an impulsive mathematical model proposed by Chavez et al. [1] to describe the dynamics of cancer growth and HIV infection, when chemotherapy and HIV treatment are combined. To better understand these complex biological phenomena, we study the stability of equilibrium points. To do this, we construct an appropriate Lyapunov function for the first equilibrium point while the indirect Lyapunov method is used for the second one. None of the equilibrium points obtained allow us to study the stability of the chemotherapeutic dynamics, we then propose a bifurcation of the model and make a study of the bifurcated system which contributes to a better understanding of the underlying biochemical processes which govern this highly active antiretroviral therapy. This shows that this mathematical model is sufficiently realistic to formulate the impact of this treatment.

Adhesion of Partially and Fully Collapsed Nanotubes

2018 ◽  
Vol 86 (1) ◽  
Author(s):  
Ming Li ◽  
Hao Li ◽  
Fengwei Li ◽  
Zhan Kang
Keyword(s):  
Finite Deformation ◽  
Adhesion Energy ◽  
Van Der Waals Interactions ◽  
Critical Conditions ◽  
Nano Composites ◽  
Deformation Model ◽  
Analysis And Design ◽  
Structural Rigidity ◽  
Multiwall Nanotubes ◽  
The Stability

The competition between the structural rigidity and the van der Waals interactions may lead to collapsing of aligned nanotubes, and the resulting changes of both configurations and properties promise the applications of nanotubes in nano-composites and nano-electronics. In this paper, a finite-deformation model is applied to study the adhesion of parallel multiwall nanotubes with both partial and full collapsing, in which the noncontact adhesion energy is analytically determined. The analytical solutions of both configurations and energies of collapsed nanotubes are consistent with the molecular dynamics (MD) results, demonstrating the effectiveness of the finite-deformation model. To study the critical conditions of generating the partially and fully collapsed multiwall nanotubes, our analytical model gives the predictions for both the geometry- and energy-related critical diameters, which are helpful for the stability analysis and design of nanotube-based nano-devices.

scholarly journals Engineering Mesoporous NiO with Enriched Electrophilic Ni3+ and O− toward Efficient Oxygen Evolution

Catalysts ◽  
2018 ◽  
Vol 8 (8) ◽  
pp. 310 ◽  
Author(s):  
Xiu Liu ◽  
Zhi-Yuan Zhai ◽  
Zhou Chen ◽  
Li-Zhong Zhang ◽  
Xiu-Feng Zhao ◽  
...  
Keyword(s):  
Surface Area ◽  
Oxygen Evolution ◽  
Low Cost ◽  
Large Surface Area ◽  
Nucleophilic Attack ◽  
Title Reaction ◽  
Highly Active ◽  
Decomposition Of Water ◽  
Uniform Mesopores

Tremendous efforts have been devoted to develop low-cost and highly active electrocatalysts for oxygen evolution reaction (OER). Here, we report the synthesis of mesoporous nickel oxide by the template method and its application in the title reaction. The as-prepared mesoporous NiO possesses a large surface area, uniform mesopores, and rich surface electrophilic Ni3+ and O− species. The overpotential of meso-NiO in alkaline medium is 132 mV at 10 mA cm−1 and 410 mV at 50 mA cm−1, which is much smaller than that of the other types of NiO samples. The improvement in the OER activity can be ascribed to the synergy of the large surface area and uniform mesopores for better mass transfer and high density of Ni3+ and O− species favoring the nucleophilic attack by OH− to form a NiOOH intermediate. The reaction process and the role of electrophilic Ni3+ and O− were discussed in detail. This results are more conducive to the electrochemical decomposition of water to produce hydrogen fuel as a clean and renewable energy.

scholarly journals The assessment of the stability of the corneal structure after LASIK correction of myopia by different optical zone diameters

2016 ◽  
Vol 73 (6) ◽  
pp. 572-576 ◽  
Author(s):  
Milorad Milivojevic ◽  
Vladimir Petrovic ◽  
Miroslav Vukosavljevic ◽  
Ivan Marjanovic ◽  
Mirko Resan
Keyword(s):  
Structural Parameters ◽  
Preoperative Assessment ◽  
Laser In Situ Keratomileusis ◽  
Group I ◽  
Significant Difference ◽  
Optical Zone ◽  
Corneal Structure ◽  
The Stability ◽  
Corneal Thinning

Background/Aim. Enlargement of optical zone (OZ) diameter during laser in situ keratomileusis (LASIK) correction of myopia postoperatively improves the optical outcome, however, it also leads to the increased stroma tissue consumption - progressive corneal thinning. The aim of this investigation was to present the possibility of safe OZ enlargement without impairing the structural stability of the cornea, while obtaining an improved optical outcome with LASIK treatment of shortsightedness. Methods. Preoperative assessment of the cornea structure and prediction of the ablated stroma tissue consumption was conducted in 37 patients (74 eyes) treated for shortsightedness by means of the LASIK method. With the eyes that, according to their cornea structure, had the capacity for OZ diameter enlargement of 0.5 mm, LASIK treatment was performed within the wider OZ diameter of 7.0 mm compared to the standard 6.5 mm. The following two groups were formed, depending on the diameter of the utilized OZ: the group I (the eyes treated with the OZ 6.5 mm, n = 37) and the group II (the eyes treated with the OZ 7.0 mm, n = 37). Results. No significant difference in the observed structural parameters of the cornea was detected between the groups of patients treated with different OZ diameters. The values of all the parameters were significantly bellow the threshold values for the development of postoperative ectasia. Conclusion. Diameter enlargement of the treated OZ, if there is a preoperative cornea capacity for such enlargement, will not impair the postoperative stability of the cornea structure, and will significantly improve the optical outcome.

scholarly journals Structural and fractal characterization of adsorption pores of middle–high rank coal reservoirs in western Yunnan and eastern Guizhou: An experimental study of coals from the Panguan syncline and Laochang anticline

2018 ◽  
Vol 37 (1) ◽  
pp. 251-272 ◽  
Author(s):  
Junjian Zhang ◽  
Chongtao Wei ◽  
Gaoyuan Yan ◽  
Guanwen Lu
Keyword(s):  
Specific Surface ◽  
Surface Area ◽  
Specific Surface Area ◽  
Pore Volume ◽  
Pore Diameter ◽  
Structural Parameters ◽  
Total Pore Volume ◽  
Type A ◽  
Type B ◽  
Type C

To better understand the structural characteristic of adsorption pores (pore diameter < 100 nm) of coal reservoirs around the coalbed methane production areas of western Yunnan and eastern Guizhou, we analyzed the structural and fractal characteristics of pore size range of 0.40–2.0 nm and 2–100 nm in middle–high rank coals ( Ro,max = 0.93–3.20%) by combining low-temperature N2/CO2 adsorption tests and surface/volume fractal theory. The results show that the coal reservoirs can be divided into three categories: type A ( Ro,max < 2.15%), type B (2.15% <  Ro,max <2.50%), and type C ( Ro,max > 2.15%). The structural parameters of pores in the range from 2 to 100 nm are influenced by the degree of coal metamorphism and the compositional parameters (e.g., ash and volatile matter). The dominant diameters of the specific surface areas are 10–50 nm, 2–50 nm, and 2–10 nm, respectively. The pores in the range from <2 nm provide the largest proportion of total specific surface area (97.22%–99.96%) of the coal reservoir, and the CO2-specific surface area and CO2-total pore volume relationships show a positive linear correlation. The metamorphic degree has a much greater control on the pores (pore diameter less than 2 nm) structural parameters than those of the pore diameter ranges from 2 to 100 nm. Dv1 and Dv2 can characterize the structure of 2–100 nm adsorption pores, and Dv1 (volume heterogeneity) has a positive correlation with the pore structural parameters such as N2-specific surface area and N2-total pore volume. This parameter can be used to characterize volume heterogeneity of 2–10 nm pores. Dv2 (surface heterogeneity) showed type A > type B > type C and was mainly affected by the metamorphism degree. Ds2 can be used to characterize the pore surface heterogeneity of micropores in the range of 0.62–1.50 nm. This parameter has a good correlation with the pore parameters (CO2-total pore volume, CO2-specific surface area, and average pore size) and is expressed as type C < type B < type A. In conclusion, the heterogeneity of the micropores is less than that of the meso- and macropores (2–100 nm). Dv1, Dv2, and Ds2 can be used as effective parameters to characterize the pore structure of adsorption pores. This result can provide a theoretical basis for studying the pore structure compatibility of coal reservoirs in the region.

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