Chemical Potential,Partial Enthalpy and Partial Volume of Mixtures by NPT Molecular Dynamics

Abstract

Equilibrium NPT molecular dynamics computer simulations have been used to determine the chemical potential, partial enthalpy and partial volume of model Ar-Kr mixtures using newly devised non-intrusive particle insertion and particle swap techniques [P. Sindzingre et al. Chemical Physics, 129 (1989) 213]. In this report we examine, for the first time, in some detail the relative convergence statistics of the particle swap and particle insertion methods for these properties for binary Lennard-Jones (LJ) mixtures. Both species are represented by single-site Lennard-Jones pair potentials with Lorentz-Berthelot rules for the cross-species interactions. We show that, over the whole phase diagram and especially in the vicinity of the fluid-solid coexistence line, the particle swap method gives significantly better statistics than the particle insertion method for the difference in chemical potential of the two species, partial enthalpy and partial volume of each species. Also, we find that, using the particle swap method, the difference in the chemical potential converges more rapidly than the differences in the partial enthalpy and volume.     

The Influence of Charge Calculation on Molecular Dynamics Simulation of Adenine in Water

Abstract

Molecular dynamics simulations of an aqueous solution of adenine have been performed using different methods of charge calculation to evaluate the influence of the values of the atomic charges on the dynamical results and to incorporate new information about the interaction between adenine and water. Four sets of partial charges where computed using ab-initio methods. In all cases the hydration properties of adenine were similar. These results support the view that the simulations by molecular dynamics, at least for the regime of infinite dilution, are not sensitive with respect to the different sets of partial charges used. A net hydrophobic behavior of the adenine molecule, on the water was observed.     

Experimental and theoretical studies on TI+ interactions with the cation-selective channel of the sarcoplasmic reticulum

Summary This paper presents an experimental study and a theoretical interpretation of the effects of thallous ion on the electrical properties of the cation-selective channel of the sarcoplasmic reticulum (SR channel). The properties of this channel in solutions which do not contain thallous ion are consistent with the predictions of Läuger's theory for singly occupied pores (P. Läuger, 1973,Biochim. Biophys. Acta 311:423–441). However, this theory does not account for SR channel properties in mixtures containing thallous ion. SR channel conductance is less than predicted in mixed salt solutions of thallium with either potassium or ammonium (J. Fox, 1983,Biochim. Biophys. Acta 736:241–245), yet is greater than expected in mixtures of lithium and thallium. In a simple single-ion pore, the ratio of the products of the single-salt binding constants and maximum conductances is equal to the permeability ratio calculated from zero-current potential experiments under near equilibrium conditions. This is not found for the SR channel when thallous ion is present. SR channel properties in the presence of thallous ion can, however, be explained by a model which postulates the existence of two external modulatory sites on the channel, without implying double-occupancy in the permeation pathway. When thallous ion is bound to a modulatory site the maximum conductance of the channel to all permeating ions is altered (thallous included). Two other models (a three-barrier, two-internal-site pore which allows multiple occupancy, and a pore with fluctuating barriers) are discussed, but are found to be unable to fit our conductance data at different concentrations.     

6. The Sedimenting-Droplet Procedure for Measuring Fluid Densities

ABSTRACT

An apparatus is described which is used for the determination of velocities of falling droplets of small volumes (5/xl) through hydrophobic mixtures. From calibration curves with sodium chloride solutions of different molarities and specific gravities, the densities of the fluid in the droplets were obtained by interpolation. The density of the solutions of proteins may be determined and used in the calculation of partial specific volumes. The hydrophobic fluid used was a mixture of Dow Corning 200, kerosine to reduce the viscosity, and 1.2-dichlorobenzine to increase the specific gravity to approximately that of water.     

Physicochemical study of the protein–liposome interactions: influence of liposome composition and concentration on protein binding

Abstract

The aim of the present study is to investigate the interactions between liposomes and proteins and to evaluate the role of liposomal lipid composition and concentration in the formation of protein corona. Liposomes composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) or hydrogenated soybean phosphatidylcholine (HSPC) with 1,2-dipalmitoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (sodium salt) (DPPG), 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-3000] (DPPE-PEG 3000), cholesterol (CH) or mixtures of these lipids, were prepared at different concentrations by the thin-film hydration method. After liposomes were dispersed in HPLC-grade water and foetal bovine serum (FBS), their physicochemical characteristics, such as size, size distribution, and ζ-potential, were determined using dynamic and electrophoretic light scattering. Aggregation of DPPC, HSPC, DPPC:CH (9:1 molar ratio), and HSPC:CH (9:1 molar ratio) in FBS was observed. On the contrary, liposomes incorporating DPPG lipids and CH both in a molar ratio of 11% were found to be stable over time, while their size did not alter dramatically in biological medium. Liposomes containing CH and PEGylated lipids retain their size in the presence of serum as well as their physical stability. In addition, our results indicate that the protein binding depends on the presence of polyethylene glycol (PEG), CH, concentration and surface charge. In this paper, we introduce a new parameter, fraction of stealthiness (F_s), for investigating the extent of protein binding to liposomes. This parameter depends on the changes in size of liposomes after serum incubation, while liposomes have stealth properties when F_s is close to 1. Thus, we conclude that lipid composition and concentration affect the adsorption of proteins and the liposomal stabilization.     

A metabolite fingerprinting for the characterization of commercial botanical dietary supplements

Phytopharmaceuticals, phytomedicines and botanical dietary supplements are products of wide interest considering the increase of their use. The development of fast and effective analytical methods able to give a fingerprinting of the product, on the basis of the plant extracts declared to be contained in it, is surely of high interest. In a previous investigation electrospray mass spectrometry was proved to be effective for the characterization of plant extracts. The direct infusion of the samples and the analyses in both positive and negative ion mode lead to a clear differentiation of the different samples. To verify if the same approach can be effective also for mixtures of plant extracts, five different commercial dietary supplements [Sedivitax gocce (1), Finocarbo Plus opercoli (2), Sollievo Bio tavolette (3), MiniMas opercoli (4) and Ruscoven gocce (5), all products from Aboca S.p.A., Sansepolcro, Italy] were analyzed by ESI. In order to evaluate possible changes in the metabolic profile with respect to different years of production, ten different batches of the commercial dietary supplements were considered. The mass spectral data were evaluated by multivariate analysis and the obtained results suggest that the method allows a satisfactory and rapid characterization of complex mixtures of commercial dietary supplements.     

Molecular verification and characterization of BYDV-resistant germ plasms derived from hybrids of wheat with Thinopyrum ponticum and Th. intermedium

Twenty-five partial amphiploids (2n=8x=56), which were derived from hybrids of wheat (Triticum aestivum L.) with either Thinopyrum ponticum (Podpera) Liu & Wang, Th. intermedium (Host) Barkworth & D. Dewey, or Th. junceum (L.) A. Löve, were assayed for resistance to BYDV serotype PAV by slot-blot hybridization with viral cDNA of a partial coat protein gene. Three immune lines were found among seven partial amphiploids involving Th. ponticum. Seven highly resistant lines were found in ten partial amphiploids involving Th. intermedium. None of eight partial amphiploids or 13 addition lines of Chinese Spring — Th. junceum were resistant to BYDV. Genomic in situ hybridization demonstrated that all of the resistant partial amphiploids, except TAF46, carried an alien genome most closely related to St, whether it was derived from Th. ponticum or Th. intermedium. The two partial amphiploids carrying an intact E genome of Th. ponticum are very susceptible to BYDV-PAV. In TAF46, which contains three pairs of St- and four pairs of E-genome chromo somes, the gene for BYDV resistance has been located to a modified 7 St chromosome in the addition line L1. This indicates that BYDV resistance in perennial polyploid parents, i.e., Th. ponticum and Th. intermedium, of these partial amphiploids is probably controlled by a gene(s) located on the St-genome chromosome(s).     

公立医院内部绩效工资分配三阶段测算方法研究

目的 建立适应公立医院改革背景的医院内部绩效工资分配测算方法。方法 监控样本医院内部绩效工资分配的运行情况,梳理绩效工资分配测算方法的短板。进行文献研究、医务人员访谈,分析医务人员反馈意见。对绩效工资分配模拟测算结果进行对比分析。结果 建立了包含基础奖、完成率奖、超额奖的三阶段测算方法,依据科室在各阶段的贡献程度测算绩效工资。三阶段测算方法能有效实现医院控制内部绩效工资分配的效率与公平的平衡,方法运行稳健。结论 三阶段测算方法促进医院改进内部绩效工资分配工作的质量和效率。     

PCR-based assay for the rapid detection of fumonisin-producing Fusarium species in maize-based animal and poultry feeds in Karnataka,India

Abstract

One hundred and fourteen animal feedstuffs and eighty poultry feed mixtures commonly used for animal and poultry nutrition in Karnataka, India, were analysed for Fusarium contamination. The total counts of fusaria in animal feeds and poultry feed mixtures revealed a high incidence of F. verticillioides, being isolated from all positive samples. Most contaminated samples were maize pellets (71.4%), cotton seed (66.6%), maize powder (60%) and fine wheat bran (50%), respectively, while no Fusarium species was isolated from Bengal gram husk and wheat flakes. All the Fusarium species were identified by the PCR method using genus specific ITS and group specific FUM 1 primers. Of the 374 Fusarium isolates tested with ITS set of primers, all fusaria scored positive, whereas only 244 (65%) isolates tested positive with the FUM 1 set of primers. The specificity of the primers provides the basis for a simple, accurate and precise detection of Fusarium species that represents fumonisin producers, which are a considerable risk for animal, poultry and human health.     

Direct absorptiometric quantitation in high-performance liquid chromatography in the absence of concomitant reference standards

A method for absorptiometric quantification in high-performance liquid chromatography that utilizes the known molar absorption coefficients of the individual components of a mixture of analytes to enable a series of determinations to be carried out without the concomitant use of reference standards is described. An equation is derived that describes the dependence of the molar amount of a defined analyte on the parameters influencing the detector response and on the peak area of the analyte in the chromatogram. The equation can be used for the direct calculation ofthe molar amount of individual analytes in a well resolved mixture. A method for the analysis of two analytes, the peaks of which totally overlap but which differ by their molar absorption coefficients, is also described. The validity of the equations and the applicability of the proposed method was examined in the analysis of 5-(2-dimethylaminoethoxy)-7-oxo-7H-benzo [c]fluorene hydrochloride (benflurone) and its metabolites. Some examples of the application of this approach are considered.     

Diversity starts early: notharctid primates from the Sandcouleean (Early Eocene) of the Powder River Basin,Wyoming, USA

Abstract

Abundant specimens, mostly isolated teeth, of the Primate family Notharctidae occur in the Early Eocene rocks of the Powder River Basin of northeastern Wyoming, USA. Very early in the North American history of the family, the notharctid species diversified and this diversity may have been widespread, and not restricted to more southerly areas in the Rocky Mountains. The diversity is shown by detailed analysis of the molar dentition. Two new genera are established: Megaceralemur with Megaceralemur trigonodus as its type and Megaceralemur matthewi sp. nov. as a Sandcouleean species and Pinolophus, with Pinolophus meikei sp. nov. as its type, for a form with an entoconid notch on lower molar 1. Megaceralemur has a prominent nannopithex-fold which dominates the posterior cingulum of upper molars 1–2 and a cristid obliqua on lower molar 1 which attaches to the metaconid, not the metalophid as it does in Cantius and other genera. A small species, Cantius lohseorum sp. nov., is named for a derived lineage the size of Cantius torresi.

urn:lsid:zoobank.org:pub:066DC515-A2DD-40AF-AD8A-3834E2AFD0FB     

Long-Range Interactions between Ligands Bound to a DNA Molecule Give Rise to Adsorption with the Character of Phase Transition of the First Kind

Abstract

Influence of long-range interactions between ligands bound to DNA molecule on the character of their adsorption is studied using computer modeling. For this investigation, two calculation procedures are developed. They are based upon the method of the free energy minimum and on the partition function method. The both procedures demonstrate that in the case of a strong enough attraction between all the bound ligands their binding to DNA has the character of phase transition of the first kind. There is a break in the binding curve c(c₀) where c—relative concentration of bound ligands, c ₀—molar concentration of free ligands. The break occurs because there is an interval of central degrees of binding (～50% of the maximum c value) that are prohibited for individual DNA molecules. Such a transition might be caused by some types of DNA condensation. Attraction between the neighboring ligands only, adjacent or/and separated by double helix regions, does not cause this effect.     

多层生物介质传感器的特性研究（英文）

目的 多层生物介质的生物传感器被广泛应用于各大领域,其检测特性对于传感器优劣的评估尤为重要。本文目的在于量化表征多层生物介质的电学特征。方法 基于生物电阻抗谱技术来探究多层生物介质的电化学阻抗谱特性,并结合保角映射的方法来量化表征多层生物介质,阐明其对阻抗的影响规律,继而为生物传感器的研制与开发提供理论基础。有效提取各生物介质层修饰后电阻抗参数(Z^*),从而量化表征多层生物介质层的电阻抗谱特性。结果 对多层模型进行了理论计算并构建了相关试验测试系统,研究结果表明,随着生物介质层的逐步修饰,检测区域电阻抗参数(Z^*)在f=0.1～50 MHz下持续上升,理论计算结果趋势与试验结果趋势较好吻合,论证了此理论计算方法的正确性。结论 本文证实了可根据生物电阻抗谱和保角映射方法量化表征多层生物介质的电阻抗谱特性,对生物传感器的研制与开发有一定的实用价值。     

Arylpiperazinylalkyl derivatives of 8-amino-1,3-dimethylpurine-2,6-dione as novel multitarget 5-HT/D receptor agents with potential antipsychotic activity

A series of new 7-arylpiperazinylalkyl-1,3-dimethyl-purine-2,6-dione derivatives with diversified 8-amino substituent in 8 position was synthesized and their 5-HT_1A, 5-HT_2A, 5-HT₆, 5-HT₇, and D₂ receptor affinities were determined. The binding study allowed identifying some potent 5-HT_1A/5-HT_2A/5-HT₇/D₂ ligands. The most interesting because of their multireceptor profile were 8-piperidine (30–35) and 8-dipropylamine (45–47) analogs with four and five carbon aliphatic linkers. The selected compounds 24, 31, 34, 39, 41, 43, 45, and 46 in the functional in vitro evaluation for all targeted receptors showed significant partial D₂ agonist, partial 5-HT_1A agonist, and 5-HT_2A antagonist properties. The advantageous in vitro affinity of compound 34 for 5-HT_1A and D₂ receptors has been explained by means of molecular modeling, taking into consideration its partial agonist activity towards the latter one. In behavioral studies, compounds 32 and 34 revealed antipsychotic-like properties, significantly decreasing d-amphetamine-induced hyperactivity in mice.     

Shear Viscosity of Model Mixtures by Nonequilibrium Molecular Dynamics III. Effect of Quadrupolar Interactions

Abstract

We present new results for thermodynamic properties and viscosities of pure quadrupolar fluids, a pure dipolar quadrupolar fluid, nonquadrupolar/quadrupolar mixtures, and quadrupolar/quadrupolar mixtures. It is evident that, the addition of quadrupolar interactions to the pure Ar and the addition of quadrupolar interactions to the pure dipolar Ar, leads to higher viscosities as was observed in the addition of dipolar interactions to the pure Ar [Lee and Cummings, J. Chem. Phys., 105, 2044 (1996)]. The total energies and the mixture densities show a linear dependence for both nonquadrupolar Ar/quadrupolar Kr (case B) and quadrupolar Ar/quadrupolar Kr (case C), and the linearity of case C is better than that of case B. This is not consistent with the idea that in the cases of the dipolar mixtures, dipolar/dipolar and nondipolar/nondipolar mixture are likely to be more ideal than nondipolar/dipolar mixtures. This is mainly due to the weaker interaction of quadrupole-quadrupole than that of dipoledipole.     

Heritability: the link between development and the microevolution of molar tooth form

Abstract

The developmental gene expression, morphogenesis, and population variation in mammalian molar teeth has become increasingly well understood, providing a model system for synthesizing evolution and developmental genetics. In this study, we estimated additive genetic covariances in molar shape (G) using parent-offspring regression in Cryptotis parva, the Least Shrew. We found that crown shape had an overall h² value of 0.34 (±0.08), with higher heritabilities in molar cusps than notches. We compared the genetic covariances to phenotypic (P) and environmental (E) covariances, and to the covariances in crown features expected from the enamel knot developmental cascade (D). We found that G and D were not strongly correlated and that major axes of G (evolutionary lines of least resistance) are better predictors of evolutionary divergences in soricines than is D. We conclude that the enamel knot cascade does impose constraints on the evolution of molar shape, but that it is so permissive that the divergences among soricines (whose last common ancestor lived about 14 million years ago) do not fully explore its confines. Over tens of millions of years, G will be a better predictor of the major axes of evolution in molar shape than D.     

Refined homology model of cytochrome bcc complex B subunit for virtual screening of potential anti-tuberculosis agents

Abstract

Cytochrome bcc complex is important for ATP synthesis and cellular activity, as a crucial step in the terminal reduction of oxygen in aerobic electron transport chains. The b subunit of cytochrome bcc complex (QcrB) has been reported as a promising anti-tuberculosis target, with many novel anti-tuberculosis scaffolds reported. However, the 3D structure of mycobacterium tuberculosis (M. tuberculosis) QcrB has not been released, making it hard to understand the interactions between QcrB and its inhibitors as well as to develop novel anti-tuberculosis scaffolds. Herein we built the optimal homology model of M. tuberculosis QcrB using the M. smegmatis QcrB structure as template, which was refined through all-atom molecular dynamics simulation. Then, the binding modes of known inhibitors were predicted through molecular docking method, along with molecular dynamics simulation and binding free energy calculation to verify the accuracy of docking results and stability of the protein-inhibitor complexes. The informative key residues within QcrB site enabled us to perform structure-based virtual library screening to obtain potential M. tuberculosis QcrB inhibitors, which were validated through molecular dynamics simulation and MM-GBSA calculation and analyzed through pharmacokinetic properties prediction. Our research would provide a deeper insight into the interactions between M. tuberculosis QcrB and its inhibitors, which boosts to develop novel therapy against tuberculosis.

Communicated by Ramaswamy H. Sarma     

Monte Carlo-Self Consistent Field Study of the Symmetrical Models of Polyelectrolytes

Abstract

Time saving procedures unifying Monte Carlo and self consistent field approaches for the calculation of equilibrium potentials and density distributions of mobile ions around a polyion in a polyelectrolyte system are considered. In the final version of the method the region around the polyion is divided into two zones—internal and external; all the ions of the internal zone are accounted for explicitly in a Monte Carlo procedure, in the external zone the self consistent field approximation is applied with an exchange of ions between regions. Simulations are carried out for cylindrical and spherical polyions in solutions with mono-and divalent ions and their mixtures. The results are compared with Poisson—Boltzmann approximation and experimental data on intrinsic viscosity.     

Liposomes loaded with a dirhenium compound and cisplatin: preparation,properties and improved in vivo anticancer activity

Abstract

Liposomes loaded with the rhenium compound (bis-dimethylsulfoxido-cis-tetrachlorodi-μ-pivalatodirhenium(III) (cis–Re₂((CH₃)₃CCOO)₂Cl₄?2DMSO, I) and cisplatin in the molar ratio of 4:1 as well as those loaded only with I were synthesized and characterized by scanning electron microscopy, transmission electron microscopy, dynamic light scattering and electronic absorption spectroscopy. The relative stability of liposomes loaded with I is reflected by a minimal change in the electronic absorption spectra over a period of 8 days whereas the stability of those loaded with both drugs is lower, which we ascribe to the formation of new Re-Pt species inside the liposomes. Furthermore, the investigations of the co-encapsulation effects on the anticancer activity of the Re-Pt system were undertaken. Importantly, the co-encapsulated liposomes exhibit synergistic or additive anticancer activities in vivo, e.g. introduction of these liposomes into tumor-bearing rats demonstrated their antianemic, nephro- and hepato-protecting effects. These liposomes, which are active in cancer treatment, protect the dirhenium compounds from hydrolysis and preserve the biological properties of the Re-Pt hybrid. This study reveals the importance of combined therapy in nanotechnology and medicine.     

Molecular Dynamics as a Mathematical Mapping. I. Differentiable Force Functions

Abstract

The molecular dynamics technique can be viewed as a deterministic mathematical mapping between, on one side, the force field parameters that describe the potential energy interactions and the input macroscopic conditions, and, on the other, the calculated macroscopic properties of the bulk molecular system.

The differentiability of such a mapping in the conventional molecular dynamics calculations is affected by the discontinuities in particle positions introduced by the periodic boundary conditions and the discontinuities introduced by the minimum image convention and other methods commonly employed to approximate the calculation of interparticle potential and force.

This paper proposes an alternative molecular dynamics framework based on modified force functions which are almost everywhere continuous and differentiable, and exhibit a natural periodicity. These characteristics obviate the need for both the periodic boundary conditions and the minimum image convention, as well as for any corrections for long-range interactions. They also make it possible to apply standard methods of variational calculus for the computation of partial derivatives of the molecular dynamics mapping.

The modified framework is first introduced for the case of simple monoatomic fluids where the nature of the forces exerted between any pair of two particles is identical. A more general model describing the interactions of flexible molecules is then developed. We describe the application of this approach to mixtures of alkane molecules interacting via the NERD force field.