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Electrophoretic mobilization in capillary isoelectric focusing by a weak acid or an acidic ampholyte as catholyte assessed by computer simulation

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ELECTROPHORESIS 2023年第7-8期44卷 656-666页

作者： Thormann, Wolfgang Univ Bern Inst Infect Dis Bern Switzerland Univ Bern Inst Infect Dis CH-3008 Bern Switzerland

Capillary isoelectric focusing (CIEF) with cationic electrophoretic mobilization induced via replacing the catholyte with the anolyte or a solution of another acid or amino acid was investigated by computer simulation for a wide range pH gradient bracketed between two amphoteric spacers and short electrode vials with a higher id than the capillary. Dynamic simulations provide insight into the complexity of the mobilizing process in a hitherto inaccessible way. The electrophoretic mobilizing process begins with the penetration of the mobilizing compound through the entire capillary, is followed by a gradual or steplike decrease of pH, and ends in an environment with a non-homogenous solution of the mobilizer. Analytes do not necessarily pass the point of detection in the order of decreasing pI values. Cationic mobilization encompasses an inherent zone dispersing and refocusing process toward the capillary end. This behavior is rather strong with phosphoric acid and citric acid, moderate with aspartic acid, glutamic acid (GLU), formic acid, and acetic acid and less pronounced in the absence of the cathodic spacer. The data reveal that optical detectors should not be placed before 90% of capillary length. Aspartic acid, GLU, formic acid, and acetic acid provide an environment with a continuously decreasing pH that explains their successful use in optimized two-step CIEF protocols.

关键词： capillary isoelectric focusing chemical mobilization computer simulation electrophoretic mobilization

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Reflection of Light Ions from a Solid Surface: Analytical Model and computer simulation

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JOURNAL OF SURFACE INVESTIGATION 2023年第1期17卷 78-83页

作者： Afanas'ev, V. P. Lobanova, L. G. Shulga, V. I. Natl Res Univ MPEI Moscow 111250 Russia Moscow MV Lomonosov State Univ Skobeltsyn Inst Nucl Phys Moscow 119991 Russia

An analytical solution to the equation for the distribution of the flux density of reflected light ions over the path length and energy losses in the target is obtained. It is based on the solution of boundary problems for the transport equation using the invariant imbedding method in the small-angle approximation. In the case of proton reflection from copper and tungsten targets, the analytical results are compared with computer-simulation data obtained using the OKSANA program, as well as with experimental data. The possibility of verifying the stopping power of the target material based on the created methodology is noted.

关键词： reflection of light ions analytical model invariant imbedding method small-angle approximation computer simulation stopping power

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Developing radio frequency (RF) heating protocol in packed tofu processing by computer simulation

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CURRENT RESEARCH IN FOOD SCIENCE 2023年 6卷 100474页

作者： Cui, Baozhong Ye, Pengfei Wang, Ke Sun, Yanan Mao, Chao Pang, Huiyun Fu, Hongfei Wang, Yequn Chen, Xiangwei Wang, Yunyang Northwest A&F Univ Coll Food Sci & Engn Yangling 712100 Shaanxi Peoples R China

Packed tofu was produced by reheating the mixture of preheated soymilk and coagulant in a sealed container. This study aimed to replace the conventional heating method with RF heating during the reheating of soymilk for packed tofu production. In this study, dielectric properties (DPs), thermal properties (TPs), and rheological properties of soymilk were determined. A mathematical model was developed to simulate the RF heating process of soymilk to determine the appropriate packaging geometry. Water holding capacity (WHC), texture analysis, color measurement, and microstructure observation were performed to evaluate the quality of RF-heated packed tofu. Results showed that soymilk added with Glucono-Delta-Lactone (GDL) coagulated at the temperature above 60. C, and the loss factor ( e'') was slightly reduced when soymilk was converted to tofu at coagulation temperature. Based on the simulation results, the cylindrical vessel (phi 50 mm x 100 mm) was chosen as the soymilk container for desired heating rate (5.9. C/min) and uniformity (lambda = 0.0065, 0.0069, 0.0016 for top, middle, and bottom layers). The texture analysis revealed that the hardness and chewiness of packed tofu prepared by RF heating were enhanced (maximum 1.36 times and 1.21 times) compared with commercial packed tofu, while the springiness were not significantly changed. Furthermore, the denser network structure was observed inside RFheated packed tofu by SEM. These results indicated that packed tofu prepared by RF heating was of higher gel strength and sensory quality. RF heating has the potential to be applied in packed tofu production.

关键词： RF heating Packed tofu computer simulation Reheating of soymilk Coagulation Quality evaluation

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"Half-wet-half-dry": an innovation in undergraduate laboratory classes to generate transgenic mouse models using CRISPR/Cas9 and computer simulation

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JOURNAL OF BIOLOGICAL EDUCATION 2023年第5期57卷 1083-1091页

作者： Li, Linpeng Song, Chao Ma, Yi Zou, Yi Jinan Univ Natl Demonstrat Ctr Expt Educ Life Sci & Technol Guangzhou Peoples R China

Animal models are widely used in laboratory practicals in biomedical disciplines. However, experiments involving animal work are usually time-and-labor consuming. It is also costly to run an animal lab and the animal caring/holding request special training. Here we present a laboratory course design that provides students with wet lab experience in gene editing in mouse stem cell lines using CRSISPR/Cas9 and dry lab experience in generating transgenic mouse models using computer simulation. This workshop is for senior undergraduates as well as graduate students and is designed to help them understand the application of gene editing in biomedical research. The virtual simulation is incorporated as a computer-based alternative to using mice for embryo transplantation, breeding, and characterization. The integrated curriculum of wet and dry laboratories enabled us to complete this complicate multi-disciplinary experiment in one semester. In addition, the computer-based alternatives reduce the unnecessary animal tests down to zero and errors during practice are well-tolerated without raising any ethical issues. The survey and student's feedback showed overall satisfaction in their learning experiences and learning benefits. The evaluation of the outcomes of learning objectives on the completion of this course revealed positive achievements in bioinformatics, molecular biology, and in general animal work

关键词： Transgenic mouse models CRISPR Cas9 computer simulation

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Evaluation of lesion characteristics and baseline impedance on high-power short-duration radiofrequency catheter ablation using computer simulation

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HEART AND VESSELS 2023年第12期38卷 1459-1467页

作者： Sun, Yao Zhu, Xin Nakamura, Keijiro Wang, Shuyu Univ Aizu Grad Sch Comp Sci & Engn Aizu Wakamatsu Japan Toho Univ Ohashi Med Ctr Div Cardiovasc Med Meguro Tokyo 1538515 Japan

Myocardium baseline impedance (BI) is an important factor in ablation effectiveness. This study examined the performance of low-power and long-duration (LPLD), high-power and short-duration (HPSD) ablation at different BIs by computer simulation. A 3D model of the ablation region was constructed for simulation, and in vitro experiments were performed to validate the simulation. Three ablation power and duration configurations of 30 W/30 s, 50 W/10 s, and 90 W/5 s were used for simulation with BI values of 90, 100, 110, 120, 130, and 140 O. Roll-off time and ablation volume were measured to evaluate ablation results. The simulation is consistent with the in vitro experiments. When BI is changed from 90 Omega to 140 Omega, the lesion volume over 50 degrees C with BI of 140 Omega was reduced by 6.3%, 6.7%, and 7.3% for 30 W/30 s, 50 W/10 s, and 90 W/5 s configurations, respectively, and the lesion volume over 100 degrees C was reduced by 62.8%, 49.7%, and 22.5% under 30 W/30 s, 50 W/10 s, and 90 W/5 s, respectively. simulation results revealed that HPSD (vHPSD) and LPLD ablation were more affected by changes in BI in the lesion volumes over 50 degrees C and 100 degrees C, respectively, and demonstrated that resistive and conductive heating were the main heating effects in HPSD (vHPSD) and LPLD, respectively.

关键词： Baseline impedance computer simulation High-power Short-duration Radiofrequency ablation

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Estimation of Deformation Site Parameters for Symmetric and Asymmetric Rolling of a Strip Using computer simulation

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RUSSIAN METALLURGY 2023年第13期2023卷 2005-2011页

作者： Kozhevnikov, A. V. Skripalenko, M. M. Kozhevnikova, I. A. Skripalenko, M. N. Sidorov, A. A. Semenov, A. A. Romantsev, B. A. Yusupov, V. S. Cherepovets State Univ Cherepovets 162600 Vologda Oblast Russia Natl Univ Sci & Technol MISIS Moscow 119049 Russia LLC Tesis Moscow 105062 Russia Russian Acad Sci Baikov Inst Met & Mat Sci Moscow 119334 Russia

computer simulation of longitudinal rolling is performed for different combinations of the diameters of the upper and lower rolls: 600-600, 590-600, 570-600, and 300-600 mm. The rolling for each variant of combinations of working roll diameters has been carried out in three passes (the initial strip thickness is 2 mm;the gap between the rolls is 1.4 mm in the first pass, 0.98 mm in the second pass, and 0.66 mm in the third pass. The methods have been proposed for determining the lengths of the arc of contact and of the actual deformation site, and the lengths of external zones have been estimated.

关键词： asymmetric rolling computer simulation actual deformation site length of the arc of contact external zones

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Negative Polarization of Celestial Bodies: Review and computer simulation

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SOLAR SYSTEM RESEARCH 2023年第2期57卷 143-160页

作者： Petrov, D. V. Kiselev, N. N. Savushkin, A. A. Zhuzhulina, E. A. Russian Acad Sci Crimean Astrophys Observ Crimea 298409 Russia

A brief review of the main causes of a negative degree of linear polarization of radiation scattered by regolith surfaces of atmosphereless cosmic bodies and ensembles of particles in the opposition region is presented. The results of computer simulation are provided, which made it possible to calculate the polarization degree of light scattered by pairs of irregular particles. The distance between the particles changed, which made it possible to obtain a visual representation of the total effect of the nature of negative polarization in the case of two-particle scattering (scattering in which two particles participate). Previously, a similar study was carried out for the case of two spherical particles, and showed that two-particle scattering by spheres only changes the degree of linear polarization in absolute value. We showed that two-particle scattering by irregular particles has a variable effect on the degree of linear polarization, both increasing and decreasing it. We also demonstrated that two-particle scattering by irregular particles can form a negative polarization even if the light scattered by a single particle is positively polarized. Therefore, in theoretical studies of the appearance of negative polarization, it is important to take into account two-particle scattering.

关键词： light scattering degree of linear polarization mechanisms of negative polarization computer simulation

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Biomechanical Comparison of Kinematic and Mechanical Knee Alignment Techniques in a computer simulation Medial Pivot Total Knee Arthroplasty Model

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JOURNAL OF KNEE SURGERY 2023年第6期36卷 596-604页

作者： Song, Young Dong Nakamura, Shinichiro Kuriyama, Shinichi Nishitani, Kohei Ito, Hiromu Morita, Yugo Yamawaki, Yusuke Matsuda, Shuichi Kyoto Univ Grad Sch Med Dept Orthopaed Surg Kyoto Japan Kyoto Univ Grad Sch Med Dept Adv Med Rheumat Dis Kyoto Japan

Several concepts may be used to restore normal knee kinematics after total knee arthroplasty. One is a kinematically aligned (KA) technique, which restores the native joint line and limb alignment, and the other is the use of a medial pivot knee (MPK) design, with a ball and socket joint in the medial compartment. This study aimed to compare motions, contact forces, and contact stress between mechanically aligned (MA) and KA (medial tilt 3 degrees [KA3] and 5 degrees [KA5]) models in MPK. An MPK design was virtually implanted with MA, KA3, and KA5 in a validated musculoskeletal computer model of a healthy knee, and the simulation of motion and contact forces was implemented. Anteroposterior (AP) positions, mediolateral positions, external rotation angles of the femoral component relative to the tibial insert, and tibiofemoral contact forces were evaluated at different knee flexion angles. Contact stresses on the tibial insert were calculated using finite element analysis. The AP position at the medial compartment was consistent for all models. From 0 degrees to 120 degrees, the femoral component in KA models showed larger posterior movement at the lateral compartment (0.3, 6.8, and 17.7 mm in MA, KA3, and KA5 models, respectively) and larger external rotation (4.2 degrees, 12.0 degrees, and 16.8 degrees in the MA, KA3, and KA5 models, respectively) relative to the tibial component. Concerning the mediolateral position of the femoral component, the KA5 model was positioned more medially. The contact forces at the lateral compartment of all models were larger than those at the medial compartment at >60 degrees of knee flexion. The peak contact stresses on the tibiofemoral joint at 90 degrees and 120 degrees of knee flexion were higher in the KA models. However, the peak contact stresses of the KA models at every flexion angle were <20 MPa. The KA technique in MPK can successfully achieve near-normal knee kinematics;however, there may be a concern for higher contact st

关键词： total knee arthroplasty computer simulation medial pivot knee kinematics contact stresses

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Nitric oxide binding to ferrous nitrobindins: A computer simulation investigation

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JOURNAL OF INORGANIC BIOCHEMISTRY 2023年第1期248卷 112336页

作者： Messias, Andresa Pasquadibisceglie, Andrea Armino, Diego Alonso de De Simone, Giovanna Polticelli, Fabio Coletta, Massimo Ascenzi, Paolo Estrin, Dario A. Univ Buenos Aires Fac Ciencias Exactas & Nat Dept Quim Inorgan Analit & Quim Fis Intendente Guiraldes 2160C1428EHA Buenos Aires Argentina Univ Buenos Aires CONICET Inst Quim Fis Mat Medio Ambiente & Energia INQUIMA Ciudad Univ Pabellon 2C1428EHA Buenos Aires Argentina Roma Tre Univ Dept Sci Viale G Marconi 446 I-00146 Rome Italy IRCCS Fdn Bietti I-00198 Rome Italy Acad Nazl Lincei Via Lungara 10 I-00165 Rome Italy

Nitrobindins (Nbs) represent an evolutionary conserved all-beta-barrel heme-proteins displaying a highly solvent-exposed heme-Fe(III) atom, coordinated by a proximal His residue. Interestingly, even if the distal side is exposed to the solvent, the value of the second order rate constants for ligand binding to the ferrous derivative is almost one order of magnitude lower than those reported for myoglobins (Mbs). Noteworthy, nitric oxide binding to the sixth coordination position of the heme-Fe(II)-atom causes the cleavage or the severe weakening of the proximal His-Fe(II) bond. Here, we provide a computer simulation investigation to shed light on the molecular basis of ligand binding kinetics, by dissecting the ligand binding process into the ligand migration and the bond formation steps. Classical molecular dynamics simulations were performed employing a steered molecular dy-namics approach and the Jarzinski equality to obtain ligand migration free energy profiles. The formation of the heme-Fe(II)-NO bond took into consideration the iron atom displacement from the heme plane. The ligand migration is almost unhindered, and the low rate constant for NO binding is due to the large displacement of the Fe(II) atom with respect to the heme plane responsible for the barrier for the Fe(II)-NO bond formation. In addition, we investigated the weakening and breaking of the proximal His-Fe(II) bond, observed experimentally upon NO binding, by means of a combination of classical molecular dynamics simulations and quantum-classical (QM-MM) optimizations. In both human and M. tuberculosis Nbs, a stable alternative conformation of the proximal His residue interacting with a network of water molecules was observed.

关键词： computer simulation Heme-proteins Nitric oxide Nitrobindin QM/MM

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Synthesis and Antiaggregant and Anticoagulant Activity of Amino-Acid Salts and computer simulation of the Interaction of Their Structures with the Surface of Cyclooxygenase

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PHARMACEUTICAL CHEMISTRY JOURNAL 2023年第11期56卷 1451-1456页

作者： Gurevich, K. G. Urakov, A. L. Purygin, P. P. Abzalilov, T. A. Garaev, T. M. Zarubin, Yu. P. Afanasiev, V. A. Sakaev, V. E. Samoredov, A. V. Pavlov, V. N. Lovtsova, L. V. A I Evdokimov Moscow State Med & Dent Univ Minist Hlth Russian Federat 20-1 Delegatskaya St Moscow 127473 Russia Izhevsk State Med Acad Minist Hlth Russian Federat 281 Kommunarov St Izhevsk 426034 Russia Samara Natl Res Univ Inst Nat Sci 34 Moskovskoe Shosse Samara 443086 Russia Bashkir State Med Univ Minist Hlth Russian Federat 5 Lenina St Ufa 450008 Russia Microbiol named Honorary Acad N F Gamaleya N F Gamalei Natl Res Ctr Epidemiol Minist Hlth Russian Federat 18 Gamalei St Moscow 123098 Russia Privolzhsky Res Med Univ Minist Hlth Russian Federat 10-1 Minina Pozharskogo Sq Nizhnii Novgorod 603005 Russia

Effective drugs with antiaggregant and anticoagulant activity are known to possess side effects. It was hypothesized that compounds synthesized from natural amino acids would possess these pharmacological activities without many of the side effects. In this regard, a number of amino-acid salts of alkali and alkaline-earth metals were synthesized and studied. The newly synthesized compounds were identified using PMR spectra, IR spectroscopy, and elemental analysis. Laboratory studies carried out with isolated blood of healthy volunteers identified seven compounds exhibiting antiaggregant properties. The antiaggregant effects of these compounds on the maximum amplitude of aggregation was comparable to that of acetylsalicylic acid and exceeded it in terms of inhibition of the platelet release reaction. computer simulation of the interaction of the most active amino-acid salts with the surface of cyclooxygenase confirmed their possible participation in the inhibition of this enzyme.

关键词： amino acids salts synthesis antiaggregant activity anticoagulant activity cyclooxygenase computer simulation

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