Finding the bulk viscosity of air from Rayleigh-Brillouin light scattering spectra.

Spectral line shape models can successfully reproduce experimental Rayleigh-Brillouin spectra, but they need knowledge about the bulk viscosity ηb. Light scattering involves GHz frequencies, but since ηb is only documented at low frequencies, ηb is usually left as a free parameter, which is determined by a fit of the model to an experimental spectrum. The question is whether models work so well because of this freedom. Moreover, for light scattering in air, spectral models view "air" as an effective molecule. We critically evaluate the use of ηb as a fit parameter by comparing ηb obtained from fits of the Tenti S6 model to the result of Direct Simulation Monte Carlo (DSMC) for a mixture of Nitrogen and Oxygen. These simulations are used to compute light scattering spectra, which are then compared to experiments. The DSMC simulation parameters are cross-checked with a molecular dynamics simulation based on intermolecular potentials. At large values of the uniformity parameter y, y ≈ 4, where the Brillouin contribution to spectra is large, fitted ηb are 20% larger than the ones from DSMC, while the quality of the simulated spectra is comparable to that of the Tenti S6 line shape model. At smaller y, the difference between fitted and simulated ηb can be as large as 100%. We hypothesize the breakdown of the bulk viscosity concept to be the cause of this fallacy.

Generalized Form for Finite-Size Corrections in Mutual Diffusion Coefficients of Multicomponent Mixtures Obtained from Equilibrium Molecular Dynamics Simulation.

The system-size dependence of computed mutual diffusion coefficients of multicomponent mixtures is investigated, and a generalized correction term is derived. The generalized finite-size correction term was validated for the ternary molecular mixture chloroform/acetone/methanol as well as 28 ternary LJ systems. It is shown that only the diagonal elements of the Fick matrix show system-size dependency. The finite-size effects of these elements can be corrected by adding the term derived by Yeh and Hummer (J. Phys. Chem. B 2004, 108, 15873-15879). By performing an eigenvalue analysis of the finite-size effects of the matrix of Fick diffusivities we show that the eigenvector matrix of Fick diffusivities does not depend on the size of the simulation box. Only eigenvalues, which describe the speed of diffusion, depend on the size of the system. An analytic relation for finite-size effects of the matrix of Maxwell-Stefan diffusivities was developed. All Maxwell-Stefan diffusivities depend on the system size, and the required correction depends on the matrix of thermodynamic factors.

Insights into deployment of DNA markers in plant variety protection and registration.

KEY MESSAGE: The efficiency of phenotype-based assessments of plant variety protection and registration could be improved by the integration of DNA-based testing. We review the current and proposed models in the era of next-generation breeding. The current plant variety protection system relies on morphological description of plant varieties. Distinctness, uniformity, and stability (DUS) assessments determine whether a new variety is distinguishable from common knowledge varieties and exhibits sufficient phenotypic uniformity and stability during two independent growing cycles. However, DUS assessment can be costly, time-consuming and often restricted to a relatively small number of traits that can be influenced by environmental conditions. This calls for the adoption of a DNA-based system which is endorsed by the International Union for the Protection of New Varieties of Plants (UPOV). This could enable examiners to deploy trait-specific DNA markers in DUS testing as well as using such genetic markers to manage reference collections. Within UPOV's system, breeders can freely use protected varieties in breeding programs. However, breeders of protected varieties may seek sharing in ownership of essentially derived varieties once it is proven that they, with the exception of a few distinctive DUS trait(s), conform to parental varieties in essential characteristics. As well as their complementary role in DUS testing, DNA markers have been known as a good replacement of morphological traits in defining boundaries between independently and essentially derived varieties. With the advent of new breeding technologies that allow minor modification in varieties with outcomes of specific merit or utility, detecting distinctness between varieties may become increasingly challenging. This, together with the ever-increasing number of varieties with which to compare new candidate varieties, supports the potential utility of using DNA-based approaches in variety description.

OCTP: A Tool for On-the-Fly Calculation of Transport Properties of Fluids with the Order- n Algorithm in LAMMPS.

We present a new plugin for LAMMPS for on-the-fly computation of transport properties (OCTP) in equilibrium molecular dynamics. OCTP computes the self- and Maxwell-Stefan diffusivities, bulk and shear viscosities, and thermal conductivities of pure fluids and mixtures in a single simulation. OCTP is the first implementation in LAMMPS that uses the Einstein relations combined with the order- n algorithm for the efficient sampling of dynamic variables. OCTP has low computational requirements and is easy to use because it follows the native input file format of LAMMPS. A tool for calculating the radial distribution function (RDF) of the fluid beyond the cutoff radius, while taking into account the system size effects, is also part of the new plugin. The RDFs computed from OCTP are needed to obtain the thermodynamic factor, which relates Maxwell-Stefan and Fick diffusivities. To demonstrate the efficiency of the new plugin, the transport properties of an equimolar mixture of water-methanol were computed at 298 K and 1 bar.

Optimizing Nonbonded Interactions of the OPLS Force Field for Aqueous Solutions of Carbohydrates: How to Capture Both Thermodynamics and Dynamics.

Knowledge on thermodynamic and transport properties of aqueous solutions of carbohydrates is of great interest for process and product design in the food, pharmaceutical, and biotechnological industries. Molecular simulation is a powerful tool to calculate these properties, but current classical force fields cannot provide accurate estimates for all properties of interest. The poor performance of the force fields is mainly observed for concentrated solutions, where solute-solute interactions are overestimated. In this study, we propose a method to refine force fields, such that solute-solute interactions are more accurately described. The OPLS force field combined with the SPC/Fw water model is used as a basis. We scale the nonbonded interaction parameters of sucrose, a disaccharide. The scaling factors are chosen in such a way that experimental thermodynamic and transport properties of aqueous solutions of sucrose are accurately reproduced. Using a scaling factor of 0.8 for Lennard-Jones energy parameters (ϵ) and a scaling factor of 0.95 for partial atomic charges ( q), we find excellent agreement between experiments and computed liquid densities, thermodynamic factors, shear viscosities, self-diffusion coefficients, and Fick (mutual) diffusion coefficients. The transferability of these optimum scaling factors to other carbohydrates is verified by computing thermodynamic and transport properties of aqueous solutions of d-glucose, a monosaccharide. The good agreement between computed properties and experiments suggests that the scaled interaction parameters are transferable to other carbohydrates, especially for concentrated solutions.

Shear Viscosity Computed from the Finite-Size Effects of Self-Diffusivity in Equilibrium Molecular Dynamics.

A method is proposed for calculating the shear viscosity of a liquid from finite-size effects of self-diffusion coefficients in Molecular Dynamics simulations. This method uses the difference in the self-diffusivities, computed from at least two system sizes, and an analytic equation to calculate the shear viscosity. To enable the efficient use of this method, a set of guidelines is developed. The most efficient number of system sizes is two and the large system is at least four times the small system. The number of independent simulations for each system size should be assigned in such a way that 50%-70% of the total available computational resources are allocated to the large system. We verified the method for 250 binary and 26 ternary Lennard-Jones systems, pure water, and an ionic liquid ([Bmim][Tf2N]). The computed shear viscosities are in good agreement with viscosities obtained from equilibrium Molecular Dynamics simulations for all liquid systems far from the critical point. Our results indicate that the proposed method is suitable for multicomponent mixtures and highly viscous liquids. This may enable the systematic screening of the viscosities of ionic liquids and deep eutectic solvents.

Absorption Refrigeration Cycles with Ammonia-Ionic Liquid Working Pairs Studied by Molecular Simulation.

For absorption refrigeration, it has been shown that ionic liquids have the potential to replace conventional working pairs. Due to the huge number of possibilities, conducting lab experiments to find the optimal ionic liquid is infeasible. Here, we provide a proof-of-principle study of an alternative computational approach. The required thermodynamic properties, i.e., solubility, heat capacity, and heat of absorption, are determined via molecular simulations. These properties are used in a model of the absorption refrigeration cycle to estimate the circulation ratio and the coefficient of performance. We selected two ionic liquids as absorbents: [emim][Tf2N], and [emim][SCN]. As refrigerant NH3 was chosen due to its favorable operating range. The results are compared to the traditional approach in which parameters of a thermodynamic model are fitted to reproduce experimental data. The work shows that simulations can be used to predict the required thermodynamic properties to estimate the performance of absorption refrigeration cycles. However, high-quality force fields are required to accurately predict the cycle performance.

Finite-Size Effects of Binary Mutual Diffusion Coefficients from Molecular Dynamics.

Molecular dynamics simulations were performed for the prediction of the finite-size effects of Maxwell-Stefan diffusion coefficients of molecular mixtures and a wide variety of binary Lennard-Jones systems. A strong dependency of computed diffusivities on the system size was observed. Computed diffusivities were found to increase with the number of molecules. We propose a correction for the extrapolation of Maxwell-Stefan diffusion coefficients to the thermodynamic limit, based on the study by Yeh and Hummer ( J. Phys. Chem. B , 2004 , 108 , 15873 - 15879 ). The proposed correction is a function of the viscosity of the system, the size of the simulation box, and the thermodynamic factor, which is a measure for the nonideality of the mixture. Verification is carried out for more than 200 distinct binary Lennard-Jones systems, as well as 9 binary systems of methanol, water, ethanol, acetone, methylamine, and carbon tetrachloride. Significant deviations between finite-size Maxwell-Stefan diffusivities and the corresponding diffusivities at the thermodynamic limit were found for mixtures close to demixing. In these cases, the finite-size correction can be even larger than the simulated (finite-size) Maxwell-Stefan diffusivity. Our results show that considering these finite-size effects is crucial and that the suggested correction allows for reliable computations.

Genetic Mapping of Quantitative Trait Loci for Yield-Affecting Traits in a Barley Doubled Haploid Population Derived from Clipper × Sahara 3771.

Many traits play essential roles in determining crop yield. Wide variation for morphological traits exists in Hordeum vulgare L., but the genetic basis of this morphological variation is largely unknown. To understand genetic basis controlling morphological traits affecting yield, a barley doubled haploid population (146 individuals) derived from Clipper × Sahara 3771 was used to map chromosome regions underlying days to awn appearance, plant height, fertile spike number, flag leaf length, spike length, harvest index, seed number per plant, thousands kernel weight, and grain yield. Twenty-seven QTLs for nine traits were mapped to the barley genome that described 3-69% of phenotypic variations; and some genomic regions harbor a given QTL for more than one trait. Out of 27 QTLs identified, 19 QTLs were novel. Chromosomal regions on 1H, 2H, 4H, and 6H associated with seed grain yield, and chromosome regions on 2H and 6H had major effects on grain yield (GY). One major QTL for seed number per plant was flanked by marker VRS1-KSUF15 on chromosome 2H. This QTL was also associated with GY. Some loci controlling thousands kernel weight (TKW), fertile spike number (FSN), and GY were the same. The major grain yield QTL detected on linkage PSR167 co-localized with TAM10. Two major QTLs controlling TKW and FSN were also mapped at this locus. Eight QTLs on chromosomes 1H, 2H, 3H, 4H, 5H, 6H, and 7H consistently affected spike characteristics. One major QTL (ANIONT1A-TACMD) on 4H affected both spike length (SL) and spike number explained 9 and 5% of the variation of SL and FSN, respectively. In conclusion, this study could cast some light on the genetic basis of the studied pivotal traits. Moreover, fine mapping of the identified major effect markers may facilitate the application of molecular markers in barley breeding programs.

Thermodynamic and Transport Properties of Crown-Ethers: Force Field Development and Molecular Simulations.

Crown-ethers have recently been used to assemble porous liquids (PLs), which are liquids with permanent porosity formed by mixing bulky solvent molecules (e.g., 15-crown-5 ether) with solvent-inaccessible organic cages. PLs and crown-ethers belong to a novel class of materials, which can potentially be used for gas separation and storage, but their performance for this purpose needs to be assessed thoroughly. Here, we use molecular simulations to study the gas separation performance of crown-ethers as the solvent of porous liquids. The TraPPE force field for linear ether molecules has been adjusted by fitting a new set of torsional potentials to accurately describe cyclic crown-ether molecules. Molecular dynamics (MD) simulations have been used to compute densities, shear viscosities, and self-diffusion coefficients of 12-crown-4, 15-crown-5, and 18-crown-6 ethers. In addition, Monte Carlo (MC) simulations have been used to compute the solubility of the gases CO2, CH4, and N2 in 12-crown-4 and 15-crown-5 ether. The computed properties are compared with available experimental data of crown-ethers and their linear counterparts, i.e., polyethylene glycol dimethyl ethers.

Identification and DUS Testing of Rice Varieties through Microsatellite Markers.

Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analysis based on Dice similarity coefficient and UPGMA algorithm, and, third, determining the ability of microsatellite markers to separate varieties utilizing the best combination of markers. For this research, 12 microsatellite markers were used. In total, 83 polymorphic alleles (6.91 alleles per locus) were found. In addition, the variation of PIC was calculated from 0.52 to 0.9. The results of cluster analysis showed the complete discrimination of varieties from each other except for IR58025A and IR58025B. Moreover, cluster analysis could detect the most of the improved varieties from local varieties. Based on the best combination of markers analysis, five pair primers together have shown the same results of all markers for detection among all varieties. Considering the results of this research, we can propose that microsatellite markers can be used as a complementary tool for morphological characteristics in DUS tests.