Light scattering by an elongated particle: spheroid versus infinite cylinder

Using the method of separation of variables and a new approach to calculations of the prolate spheroidal wave functions, we study the optical properties of very elongated (cigar-like) spheroidal particles. A comparison of extinction efficiency factors of prolate spheroids and infinitely long circular cylinders is made. For the normal and oblique incidence of radiation, the efficiency factors for spheroids converge to some limiting values with an increasing aspect ratio a/b provided particles of the same thickness are considered. These values are close to, but do not coincide with the factors for infinite cylinders. The relative difference between factors for infinite cylinders and elongated spheroids (a/b \ga 5) usually does not exceed 20 % if the following approximate relation between the angle of incidence $\alpha (in degrees)$ and the particle refractive index m=n+ki takes the place: \alpha \ga 50 |m-1| + 5 where 1.2 \la n \la 2.0 and k \la 0.1. We show that the quasistatic approximation can be well used for very elongated optically soft spheroids of large sizes.Comment: 12 pages, 7 figures, Accepted by Measurement Science and Technology (special OPC issue

Using of parallel computing for the quasi-static analysis of microstrip filters topology

An algorithm for calculation of multiconductor microstrip devices implemented on a substrate with slots in the ground plane using a quasistatic methods has been developed. Analysis of techniques for constructing a parallel algorithm for finding the inverse matrices for quasi-static calculation of microstrip filters was carried ou

Details of charge distribution in stable viral capsid

We present the results of Molecular Dynamics simulations of a viral capsid with the aim to analyse ion distribution on the capsid's surface that defines its stability. Two systems were modelled, a stable capsid with neutralising number of ions and an unstable capsid with low number of ions. For the ion distribution analysis the capsid's structure was identical and fixed in both simulations. It was then released for the stability analysis. The ion distribution demonstrated two types of the local regions on the inner surface of the capsid's wall: highly occupied with chloride ions in both systems despite a largely uniform electrostatic potential everywhere on the surface, and the regions that loose almost all chloride ions in the unstable capsid. The latter regions are located close to the cracks that are formed when the capsid is destabilised and thus could initiate the collapse of the capsid

Study of the effectiveness of various cannabinoid receptor 1 (CB1) agonists using molecular docking and molecular dynamics modeling

The binding of a series of small organic molecules, acting as agonists of the cannabinoid receptor CB1, was investigated by means of three methods of computational chemistry. Binding modes were predicted by means of molecular docking, and binding free energy was estimated via docking, molecular-mechanics Poisson-Boltzmann surface area method, and multistate Bennett acceptance ratio. No evident correlation was observed for the molecules between the experimental characteristics of affinity and three computed binding free energy estimates. The reasons for the discrepancy were discussed

Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density

It is very difficult to reconstruct computationally a large biomolecular complex in its biological entirety from experimental data. The resulting atomistic model should not contain gaps structurally and it should yield stable dynamics. We, for the first time, reconstruct from published incomplete cryo-EM density a complete MS2 virus at atomistic resolution, that is, the capsid with the genome, and validate the result by all-atom Molecular Dynamics with explicit water. The available experimental data includes a high resolution protein capsid and an inhomogeneously resolved genome map. For the genomic RNA, apart from 16 hairpins with atomistic resolution, the strands near the capsid’s inner surface were resolved up to the nucleic backbone level, and the innermost density was completely unresolved. As a result, only 242 nucleotides (out of 3569) were positioned, while only a fragmented backbone was outlined for the rest of the genome, making a detailed model reconstruction necessary. For model reconstruction, in addition to the available atomistic structure information, we extensively used the predicted secondary structure of the genome (base pairing). The technique was based on semi-automatic building of relatively large strands of RNA with subsequent manual positioning over the traced backbone. The entire virus structure (capsid+genome) was validated by a Molecular Dynamics run in physiological solution with ions at standard conditions confirming the stability of the model

Utilization of the wastes of vital activity

The recycling of wastes from the biological complex for use in life-support systems is discussed. Topics include laboratory equipment, heat treatment of waste materials, mineralization of waste products, methods for production of ammonium hydroxide and nitric acid, the extraction of sodium chloride from mineralized products, and the recovery of nutrient substances for plants from urine

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported

Рубцеве травлення телят за дії пробіотиків

The influence of probiotics Lactobacillus spp. and Bacillus Subtilis on the activity of cicatricial microorganisms in 30-day-old calves of the Volyn beef breed. Three (control and two experimental) groups of animals were formed, each with 8 heads. By drinking, the calves of the first experimental group received Bacillus Subtilis, II – Lactobacillus spp. The rumen content in experimental animals was studied using the fistula method. The research results showed that the mass of cicatricial bacteria and ciliates changed under the influence of probiotics in the experimental groups compared to the control group. There were also changes in the biochemical indicators of the rumen; in particular, the content of ammonia from bacteria and ciliates was likely to decrease (Р < 0.05), and the amount of volatile fatty acids was possible to increase (Р < 0.05). It has been established that probiotic supplements contribute to the accelerated formation of cicatricial microflora and its ability to break down fiber. For example, the probiotic Lactobacillus spp. has a more significant stimulating effect on forming LFA bacteria, and Bacillus Subtilis has a more significant stimulating effect on the LFA of infusoria. Ammonia formation of bacteria and ciliates was lowest under the action of Lactobacillus spp. Probiotics have a positive impact on nitrogen metabolism in the rumen, which contributes to a decrease in the concentration of lactic acid, stimulates the growth of anaerobic bacteria (cellulolytic, lactic acid, and proteolytic), increases digestive processes, and destroys intermediate products of metabolism. Under the action of probiotics, the content of cellulolytic microorganisms in the I and II experimental groups was 1.2 and 1.3 times higher; the number of lactic acid bacteria was 1.7 times higher in both I and II experimental groups, and the number of proteolytic bacteria is 1.5 and 1.3 times higher compared to the control group.Досліджували вплив пробіотиків Lactobacillus spp. і Bacillus Subtilis на активність рубцевих мікроорганізмів 30-добових телят волинської м’ясної породи. Сформовано три (контрольна і дві дослідні) групи тварин, по 8 голів у кожній. Шляхом випоювання телята І дослідної групи отримували Bacillus Subtilis, ІІ – Lactobacillus spp. Вміст рубця у піддослідних тварин досліджували фістульним методом. Результати проведених досліджень показали, що за впливу пробіотиків у дослідних групах, порівняно з контрольною, змінювалась маса рубцевих бактерій та інфузорій. Також відбувалися зміни у біохімічних показниках рубця, зокрема вміст аміаку від бактерій та інфузорій вірогідно знижувався (Р < 0,05), а кількість летких жирних кислот – вірогідно зростала (Р < 0,05). Встановлено, що пробіотичні добавки сприяють прискореному формуванню рубцевої мікрофлори та її здатності розщеплювати клітковину. Так, на утворення ЛЖК бактерій більша стимулююча дія виявлена у пробіотика Lactobacillus spp., а на ЛЖК інфузорій – Bacillus Subtilis. Утворення аміаку як бактерій, так і інфузорій було найнижчим за дії Lactobacillus spp. Виявлено позитивний вплив пробіотиків на обмін азоту в рубці, що сприяє зниженню концентрації молочної кислоти, стимулює зростання анаеробних бактерій (целюлозолітичних, молочнокислих і протеолітичних), відбувається посилення травних процесів та руйнування проміжних продуктів обміну речовин. За дії пробіотиків у І та ІІ дослідних групах вміст целюлозолітичних мікроорганізмів  був в 1,2 та 1,3 раза вищим; кількість молочнокислих бактерій – в 1,7 раза більша як І, так і ІІ дослідних групах, а кількість протеолітичних бактерій – в 1,5 та в 1,3 раза більшою порівняно з контрольною групою