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This study investigated the effects of Science, Technology, Engineering, Art, and Mathematics (STEAM) learning to student's achievement in chemistry learning of molecular models topic. The quantitative method of true experimental design was implemented in this study. The random sampling required 80 students in two classes with STEAM learning and the other class with the inquiry. Student's achievements were obtained after the learning process using the essay test. The essay test was consist of seven structured questions that valid and reliable. The findings showed that there were no significant differences in the post-test score between STEAM and inquiry classes. The average score of the STEAM post-test was 44.28 while the inquiry class is 43.65. Statistical test results with t-test also show no difference between STEAM and inquiry classes. Both STEAM learning and inquiry give the same result of students' achievement on the molecular models subject. [ABSTRACT FROM AUTHOR]

The effect of molecular models on viscosity and thermal conductivity calculations is investigated. The Direct Simulation Monte Carlo (DSMC) method for rarefied gas flows is used to simulate Couette and Fourier flows as a means of obtaining the transport coefficients. Experimental measurements for argon (Ar) provide a baseline for comparison over a wide temperature range of 100-1,500 K. The variable hard sphere (VHS), variable soft sphere (VSS), and Lennard-Jones (L-J) molecular models have been implemented into a parallel version of Bird's one-dimensional DSMC code, DSMC1, and the model parameters have been recalibrated to the current experimental data set. While the VHS and VSS models only consider the short-range, repulsive forces, the L-J model also includes constributions from the long-range, dispersion forces. Theoretical results for viscosity and thermal conductivity indicate the L-J model is more accurate than the VSS model; with maximum errors of 1.4% and 3.0% in the range 300-1,500 K for L-J and VSS models, respectively. The range of validity of the VSS model is extended to 1,650 K through appropriate choices for the model parameters. [ABSTRACT FROM AUTHOR]

Setting up molecular models for the prediction of fluid phase behavior rests on an interdisciplinary basis of foundation, of which quantum mechanics and statistical mechanics are particularily relevant. Quantum mechanics provides molecular properties such as the geometry, multiple moments and polarizabilities or alternative formulations of the molecular charge distribution, which are required to calculate the energy of a molecular system. Statistical mechanics provides relationships between the molecular energy of the system and the macroscopic fluid phase behavior. Solving the statistical mechanical equations for the general case is possible by computer simulation. Due to the excessive amount of computer time required for the execution of such calculations this route is restricted to particular applications and to model development. For practical purposes solutions using simplifications tailored to the application under consideration are established. This paper reviews the field from an application oriented perspective. [ABSTRACT FROM AUTHOR]

The direct simulation Monte Carlo (DSMC) method is applied here to model the electron-beam (e-beam) physical vapor deposition of copper thin films. A suitable molecular model for copper-copper interactions have been determined based on comparisons with experiments for a 2D slit source. The model for atomic copper vapor is then used in axi-symmetric DSMC simulations for analysis of a typical e-beam metal deposition system with a cup crucible. The dimensional and non-dimensional mass fluxes obtained are compared for two different deposition configurations with non-uniformity as high as 40% predicted from the simulations. [ABSTRACT FROM AUTHOR]

In this paper we discuss the state of the art of modelling of liquid crystals at molecular resolution level, showing their evolution from simple uniaxial to more complex mono-site and multi-site models. We then introduce “decorated” models, where specific molecular details, e.g. electrostatic charge distributions are added to allow the computer simulation of more realistic and more specific features and briefly show some of their applications. [ABSTRACT FROM AUTHOR]

A Quantum Chemical study of the Raman spectra of several Polycyclic Aromatic Hydrocarbons (PAHs) with different sizes and symmetries was carried out with gradient corrected Density Functional Theory. The analysis of the computed Raman Intensities, in terms of local valence parameters, allows to identify a peculiar physical mechanism associated with the confinement of π electrons in finite size domains of condensed six-membered rings. This involves a rearrangement of the electronic structure accompanied by a relaxation of the nuclear geometry. It is shown that the same mechanism allows to rationalize the Raman features observed in the spectra of nanostructured carbon materials. [ABSTRACT FROM AUTHOR]

Mutations in the FHL1 gene can cause X-linked hereditary myopathy, which causes one of the rarest intractable diseases. The age of the disease onset is quite variable from early infancy to adulthood, and the patients show progressive muscle weakness and atrophy. The FHL1 protein is constituted by four and a half LIM domains. Each LIM domain contains two zinc fingers, which contribute to the structural stability of the LIM domain. A change in the cysteine or histidine residues in the 2nd LIM domain (LIM2) is closely associated with the disease severity. Therefore, LIM2 is suggested to have an essential role in maintaining the structure of FHL1. In this study, molecular dynamics simulation was performed on molecular models consisting of LIM1 and LIM2 of wild and mutant FHL1. We calculated the extent of distortion of zinc finger structure and measured the distance between zinc atom and Cα atom of zinc-coordinated residues. Our analysis showed that the correlation between these two quantities is larger in the mutants associated with severe myopathy. [ABSTRACT FROM AUTHOR]

Thiocyanate dehydrogenase (TcDH) and thioredoxin like protein (TLP) play an important role in metabolism of some sulfur-oxidizing bacteria (SOB). TcDH catalyzes oxidative thiocyanate conversion into cyanate, elemental sulfur, and two reducing equivalents without involvement of molecular oxygen. The gene of thioredoxin-like protein (TLP) can be found adjacent to the gene of TcDH for some SOB. The co-evolving residues (correlating mutations) for TcDH and TLP sequences for these SOB were determined using bioinformatic analysis. The models of TcDH and TLP from Thiohalobacter thiocyanaticus HRh1 were obtained by homology modeling. Macromolecular docking of the TcDH and TLP models confirmed the positions of some co-evolving residues in interacting interfaces. Analysis of the protein complexes revealed the 2 possible binding sites involved in interaction between TcDH and TLP. We identified the specific residues in TcDH and TLP that stabilize the interactions. [ABSTRACT FROM AUTHOR]

A simple mathematical model of UN, U2N3, and UN2 crystals is used for reconstructing the pair potentials of interaction of the nearest neighbors and subsequent molecular dynamics simulation. The corresponding parameters of the U−N potential in U2N3 and UN2 crystals are obtained from the experimental values of the lattice constant and the bulk moduli of UN, U2N3, UN2 at room temperature. The linear expansion coefficients of U2N3 and UN2 crystals, as well as the U2N3 bulk modulus are estimated within the harmonic approximation. The dependences of the U2N3 and UN2 lattice constants on temperature are calculated by the molecular dynamics method. [ABSTRACT FROM AUTHOR]

This paper presents the results of the study of the effect of structural modifications of carbon nanotubes on the surface adsorption of the main elements of the products of the shot of the non-corrosive shock composition of the igniter. Carbon single-layer nanotubes of types «armchair» (6,6), «chiral» (3,6) and «zig-zag» (0,10) have been considered. The calculations are performed in the framework of molecular cluster model using semiempirical PM3 scheme. [ABSTRACT FROM AUTHOR]

2-(2-(4-(3-Carboxy-1-ethyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)piperazin-1-yl)-2-oxoethyl)-2- hydroxysuccinic acid (2) and 3-(4-(3-carboxy-1-ethyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)piperazine-1-carbonyl)- 3-hydroxypentanedioic acid (3) derivatives, a class of norfloxacin analogues of dimethyl citrate conjugates have been synthesized. They were synthesized and characterized by 1H NMR, 13C NMR, IR, Mass, elemental analysis and their molecular modeling studies, antibacterial and anticancer activities have been assessed. Screening results indicate that compound 2 possess good antibacterial activity against several microorganisms, with MIC values in the range of 0.16-0.35 mg/mL and MBCs in the range of 0.55‒0.84 mg/mL. Experiments indicated that 3, the regioisomer of 2 demonstrated the most significant activity towards the human colon cancer cell line (HCT‒15) with IC50 value 8.2 and against human colorectal adenocarcinoma cell line (HT‒29) with IC50 8.9. Fascinated by the results, the title compounds were designed and evaluated for molecular and pharmacokinetic properties prediction, drug-likeness model scores by using Molinspiration-2008 and MolSoft-2007. The regioisomeric citrate conjugates followed Lipinski's 'Rule of five' and can be considered as potential antibacterial and anticancer bioavailable oral leads. [ABSTRACT FROM AUTHOR]

The applicability of UV spectroscopy to the quantitative determination of ribavirin in aqueous solutions was demonstrated. The existence of a third conformational form of ribavirin was found, and the optimization of three ribavirin conformers was performed using the nonempirical Kohn–Sham method. It was found that, regardless of the confirmation of ribavirin molecules, the absorption maximum of its aqueous solution corresponds to 206 nm. [ABSTRACT FROM AUTHOR]

Coumarins and their derivatives have biological activities such as anti-microbial, anticancer, antioxidant and anti-HIV properties. Molecular modeling using Quantitative Structure and Activity Relationship (QSAR) has been performed on a series of diiodocoumarin derivatives as effective antimicrobial agent. This research focus on a set of experimetally inhibition-zone diameter (mm/mg sample) value data of 5diiodocoumarin derivatives, that is 6,8-diiodocoumarin-3-carboxylate, 6,8-diiodocoumarin-3-carboxylic acid, 6,8-diiodocoumarin-3-carbonylchloride, N-(4-(2-Hydroxyethyl)phenyl)-6,8-diiodocoumarin-3-carboxamide, and N-(4-Hydroxyphenyl)-6,8-diiodocoumarin-3-carboxamide. The mathematical method multi linear regression calculation was used to build the QSAR model. QSAR analysis was employed on fitting subset using log (1/inhibition-zone diameter) as dependent variable and atomic net charges, dipole moment and partition coefficient in n-octanol/water as independent variables. The parameterized Model number 3 (PM3) method was carried out to calculate the quantum chemical descriptors, chosen to represent the electronic descriptors of molecular structures. The relationship between log (1/inhibition-zone diameter) and the descriptors was described by resulted QSAR model. The resulted QSAR model for caffeic acid derivatives as anti-microbial is presented below: 8.051 + 32.24 C 5 + 27.24 O 7 + 0.021 log P R = 1 ; R 2 = 0.999 ; SE = 0.008 ; Sig = 0.038 QSAR model for diiodocoumarin derivatives showed partition coefficient of n-octanol/water and atom charge in C5 and O7 gave significant effect as descriptors to the anti-microbial activity.N-(4-(2-Hydroxyethyl)phenyl)-6,8-diiodocoumarin-3carboxamide and N-(4-Hydroxyphenyl)-6,8-diiodocoumarin-3-carboxamide have higher anti-microbial activity because the presence of hydroxyphenylgroup increases the electron density value of O7 and C5. The calculated PRESS (Predicted Residual Error Sum of Square) value was 7.13E-05 which indicates the calculated log (1/inhibition-zone diameter) using QSAR Hansch Model of diiodocoumarinderivativesis similar with experimental data. [ABSTRACT FROM AUTHOR]

We have developed an efficient and versatile model to describe warm and hot dense matter that couples an average atom model with the integral fluid equations for the ion correlations. This model provides all bound and free electronic states and wave functions, the interaction potentials and all correlation functions without adjustable parameters. The electrons can be described quantum mechanically (Schrödinger equation) or semi-classically with the Thomas-Fermi model. The ion-ion pair potential can be used in a classical molecular dynamics simulation to yield equation of state and dynamic properties of dense plasmas, including mixtures. This "pseudo-atom molecular dynamics" model, or PAMD, is more approximate than ab initio methods but presents distinct computational advantages. Extensions of the model allow the calculation of diffusion coefficients, viscosity, X-ray Thomson Scattering spectra, DC conductivities and opacities. LA-UR-19-27814 [ABSTRACT FROM AUTHOR]

The paper presents the review of works on modeling the interaction of photosynthetic proteins using the multiparticle Brownian dynamics method developed at the Department of Biophysics, Biological Faculty, Lomonosov Moscow State University. The method describes the displacement of individual macromolecules – mobile electron carriers, and their electrostatic interactions between each other and with pigment-protein complexes embedded in photosynthetic membrane. Three-dimensional models of the protein molecules were constructed on the basis of the data from the Protein Data Bank. We applied the Brownian methods coupled to molecular dynamic simulations to reveal the role of electrostatic interactions and conformational motions in the transfer of an electron from the cytochrome complex Cyt b6f) membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and to the molecule of the mobile carrier plastocyanin (Pc) in plants, green algae and cyanic bacteria. Taking into account the interior of photosynthetic membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and Cyt b6f, embedded in photosynthetic membrane, electron transfer and complex dissociation. Multiparticle Brownian simulation method can be used to consider the processes of protein interactions in subcellular systems in order to clarify the role of individual stages and the biophysical mechanisms of these processes. [ABSTRACT FROM AUTHOR]

The algebraic molecular model is used in 12C to construct densities and transition densities connecting low-lying states of the rotovibrational spectrum, first and foremost those belonging to the rotational bands based on the ground and the Hoyle states. These densities are then used as basic ingredients to calculate, besides electromagnetic transition probabilities, nuclear potentials and formfactors to describe elastic and inelastic α+12C scattering processes. The calculated densities and transition densities are also compared with those obtained by directly solving the problem of three interacting alpha’s within a three-body approach where continuum effects, relevant in particular for the Hoyle state, are properly taken into account. [ABSTRACT FROM AUTHOR]