Validation of the Boussinesq equation for use in traction field determination

Cell traction force plays an important role in many biological processes. Several traction force microscopy methods have been developed to determine cell traction forces based on the Boussinesq solution. This approach, however, is rooted in a half-space assumption. The purpose of this study was to determine the error induced in the half-space assumption using a finite element method (FEM). It demonstrates that displacement error between the FEM and the Boussinesq equation can be used to measure the accuracy of the Boussinesq equation, although singularity exists in the loading point. For one concentrated force, significant difference between the FEM and the Boussinesq equation occurs in the whole field; this difference decreases with an increase in the plate thickness. However, in the case of the balanced forces, the offset of the balanced forces decreases the errors in the middle area. Overall, this study demonstrates that increasing the thickness of the polyacrylamide gel is important for reducing the error of the Boussinesq equation when determining the displacement field of the gel under loads.     

MODEL DEVELOPMENT AND PROCESS OPTIMIZATION FOR SOLVENT EXTRACTION OF POLYPHENOLS FROM RED GRAPES USING BOX–BEHNKEN DESIGN

The objective of the present study is to find out the optimum extraction conditions for extraction of polyphenols from red grapes using Box–Behnken design. Red grapes polyphenols were extracted using acid–ethanol solvent at various extraction temperature (40–60°C), extraction time (20–100 min) and different solid–liquid ratio (1:5–1:15 g:ml). The effect (main and interactive) of extraction conditions on total anthocyanin, phenolic and flavonoid content were studied using Box–Behnken design (three factors at three levels). The results showed that the contribution of the quadratic model was significant for all the responses. Second-order mathematical regression models were developed and were found to fit well with observed data. Derringer's desirability function methodology was performed to find out the optimal conditions based on both individual and combinations of all responses (extraction temperature: 57°C, time: 61 min, and solid–liquid ratio: 1:8.7 g:ml) were established. At this optimal condition, the anthocyanin yield, total phenolic and flavonoid content were 73.92 mg/100 g, 221.4 mg GAE/100 g, and 79.08 mg CE/100 g, respectively. A desirability value of 0.902 was achieved at this point.     

Partial Purification and Characterization of Chromate Reductase of a Novel Ochrobactrum sp. Strain Cr-B4

Hexavalent chromium contamination is a serious problem due to its high toxicity and carcinogenic effects on the biological systems. The enzymatic reduction of toxic Cr(VI) to the less toxic Cr(III) is an efficient technology for detoxification of Cr(VI)-contaminated industrial effluents. In this regard, a chromate reductase enzyme from a novel Ochrobactrum sp. strain Cr-B4, having the ability to detoxify Cr(VI) contaminated sites, has been partially purified and characterized. The molecular mass of this chromate reductase was found to be 31.53 kD, with a specific activity 14.26 U/mg without any addition of electron donors. The temperature and pH optima for chromate reductase activity were 40°C and 8.0, respectively. The activation energy (E_a) for the chromate reductase was found to be 34.7 kJ/mol up to 40°C and the activation energy for its deactivation (E_d) was found to be 79.6 kJ/mol over a temperature range of 50–80°C. The frequency factor for activation of chromate reductase was found to be 566.79 s^?1, and for deactivation of chromate reductase it was found to be 265.66 × 10³ s^?1. The reductase activity of this enzyme was affected by the presence of various heavy metals and complexing agents, some of which (ethylenediamine tetraacetic acid [EDTA], mercaptoethanol, NaN₃, Pb²⁺, Ni²⁺, Zn²⁺, and Cd²⁺) inhibited the enzyme activity, while metals like Cu²⁺ and Fe³⁺ significantly enhanced the reductase activity. The enzyme followed Michaelis–Menten kinetics with K_m of 104.29 µM and a V_max of 4.64 µM/min/mg.     

A Leap-frog Algorithm for Stochastic Dynamics

Abstract

A third-order algorithm for stochastic dynamics (SD) simulations is proposed, identical to the powerful molecular dynamics leap-frog algorithm in the limit of infinitely small friction coefficient γ. It belongs to the class of SD algorithms, in which the integration time step Δt is not limited by the condition Δt ≤ γ^?1, but only by the properties of the systematic force. It is shown how constraints, such as bond length or bond angle constraints, can be incorporated in the computational scheme. It is argued that the third-order Verlet-type SD algorithm proposed earlier may be simplified without loosing its third-order accuracy. The leap-frog SD algorithm is proven to be equivalent to the verlet-type SD algorithm. Both these SD algorithms are slightly more economical on computer storage than the Beeman-type SD algorithm.     

Mixing of nanofluids: molecular dynamics simulations and modelling

In this paper we study a mixing scheme, which has recently been proposed for microfluids, on the nanoscale. We do this by performing a series of nonequilibrium molecular dynamics simulations. On the nanoscale the chaotic mixing regime is captured. We discover a new phenomenon where the two mixing fluids exchange positions after leaving the mixing intersection. The results from the molecular dynamics simulations also reveal complex spatio-temporal stream velocity profiles generated by the mixing device. We find that these profiles can be modelled through an approximate analytical solution to the Navier–Stokes equation.     

Monte Carlo Study of the Buckingham Exponential-six Fluid

Abstract

In this paper we report the results of extensive Monte Carlo simulations of a pure fluid of Buckingham modified exponential-six molecules. Data are presented for the configurational energy and pressure covering a wide range of temperatures and densities. These data are interpreted using the generalized van der Waals partition function with a novel separation into free volume and mean potential terms. We find, surprisingly, that the Buckingham fluid is described by a simple van der Waals-like equation of state provided that the b parameter is temperature dependent and chosen in a theoretically correct manner.     

Direct Evaluation of Vapour-Liquid Equilibria of Mixtures by Molecular Dynamics Using Gibbs-Duhem Integration

Abstract

We present an extension of the Gibbs-Duhem integration method that permits direct evaluation of vapour-liquid equilibria of mixtures by molecular dynamics. The Gibbs-Duhem integration combines the best elements of the Gibbs ensemble Monte Carlo technique and thermodynamic integration. Given conditions of coexistence of pure substances, simultaneous but independent molecular dynamics simulations of each phase at constant number of particles, constant pressure, constant temperature and constant fugacity fraction of species 2 are carried out in succession along coexistence lines. In each simulation, the coexistence pressure is adjusted to satisfy the Clapeyron-type equation. The Clapeyron-type equation is a first-order nonlinear differential equation that prescribes how the pressure must change with the fugacity fraction of species 2 to maintain coexistence at constant temperature. The Clapeyron-type equation is solved by the predictor-corrector method. Running averages of mole fraction and compressibility factor for the two phases are used to evaluate the right-hand side of the Clapeyron-type equation. The Gibbs-Duhem integration method is applied to three prototypes of binary mixtures of the two-centre Lennard-Jones fluid having various elongations. The starting points on the coexistence curve were taken from published data.     

避难所对七星瓢虫捕食桃蚜功能反应的影响

自然情况下的捕食是以植物为中介发生的。作者采用植物模型作为捕食环境,测试了单纯的物理因素(避难所)对七星瓢虫Coccinella septempunctata L.捕食桃蚜Myzus persicae(Sulzer)的功能反应的影响。结果表明,避难所的存在能造成七星瓢虫捕食量和捕食率极显著下降,对雄虫的影响显著比雌虫强,且在中等猎物密度时影响更为突出。Logistic回归分析发现,七星瓢虫雌虫和雄虫无论避难所是否存在,功能反应类型均为HollingⅡ型。避难所不存在的情况下,雌、雄成虫的圆盘方程分别为N a=1.0259 N0/(1+0.003078 N0)和N a=0.9246 N0/(1+0.002127 N0),避难所存在的情况下,其圆盘方程分别为N a=0.9500 N0/(1+0.00342 N0)和N a=0.6463N0/(1+0.002262 N0)。避难所的存在能导致两性成虫瞬时攻击率极显著下降,但仅雄虫处置时间极显著延长,说明雄虫在环境异质性较高时捕获猎物更困难。     

Life‐History Patterns of Cuban Poeciliid Fishes (Teleostei: Cyprinodontiformes)

The following work provides basic information about the life history of 10 Cuban species of the family Poeciliidae. Adult fish stocks were captured in their natural habitat, and litters obtained from them were raised and maintained in captivity for 19 weeks. For each species, we present the mean value of newborn length (TL_o), age at sexual maturity (AM), total length at sexual maturity (TLM), as well as the patterns of postnatal growth in aquarium conditions, which were described using size–age curves and nonlinear regression equations (Richards model). There are differences in growth dynamics among species. In general, growth rates differ for both sexes in all poeciliids studied, males maturing earlier than females, who reach higher values of total length at the 19th week (TL_f). Sexual size dimorphism could be explained by the specific roles of each sex (fecundity in females and early maturity in males) while differences in growth among species could be related to their distribution patterns in the wild. The data summarized in this contribution can be useful for the conservation of these fish species. Zoo Biol 32:251–256, 2013. © 2012 Wiley Periodicals, Inc.