Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF

Abstract

The function of nanomaterials and biomaterials greatly depends on understanding nanoscale recognition mechanisms, crystal growth and surface reactions. The Interface Force Field (IFF) and surface model database are the first collection of transferable parameters for inorganic and organic compounds that can be universally applied to all materials. IFF uses common energy expressions and achieves best accuracy among classical force fields due to rigorous validation of structural and energetic properties of all compounds in comparison to perpetually valid experimental data. This paper summarises key aspects of parameterisation, including atomic charges and transferability of parameters and current coverage. Examples of biomolecular recognition at metal and mineral interfaces, surface reactions of alloys, as well as new models for graphitic materials and pi-conjugated molecules are described. For several metal–organic interfaces, a match in accuracy of computed binding energies between of IFF and DFT results is demonstrated at ten million times lower computational cost. Predictive simulations of biomolecular recognition of peptides on phosphate and silicate surfaces are described as a function of pH. The use of IFF for reactive molecular dynamics is illustrated for the oxidation of Mo₃Si alloys at high temperature, showing the development of specific porous silica protective layers. The introduction of virtual pi electrons in graphite and pi-conjugated molecules enables improvements in property predictions by orders of magnitude. The inclusion of such molecule-internal polarity in IFF can reproduce cation–pi interactions, pi-stacking in graphite, DNA bases, organic semiconductors and the dynamics of aqueous and biological interfaces for the first time.     

Self-aggregation of trehalose in the mixed solvents of 1,3-dimethylimidazolium ionic liquid and water

Abstract

Conformational variations of solvated trehaloses in binary mixtures of 1,3-dialkylimidazolium ([dmim]Cl) ionic liquids and trehalose as well as ternary mixtures of trehalose, [dmim]Cl and water have been studied by molecular dynamics (MD) simulations with and without polarisable force fields. The interaction energy between anion Cl^? and water is stronger than that between water itself in the [dmim]Cl-water mixtures. Isolated water clusters were found in the binary [dmim]Cl-water mixtures with 60.0 and 75.0% mole fraction of water, but a continuous water network appears when the concentration of the mixture increases to 99.9%. In the case of binary mixtures of trehalose and [dmim]Cl, both non-polarisable and polarisable models demonstrated that the pyranose rings of trehalose displayed chair conformations. MD simulations with polarisation model could sample larger conformation space than that with non-polarisable model. A self-aggregation behaviour of trehalose was found in the ternary trehalose-[dmim]Cl-water mixtures, which can be rationalised by the stronger non-bonded interaction energy between trehalose molecules and anion Cl^? than that between trehalose molecules and water.     

Indirect sinusoidal vibrations induces an acute increase in explosive strength

The purpose of this study was to examine the acute effect of indirect vibration on neuromuscular responses and fatigue resistance (electromyographic activity - EMG and force) during isometric exercise. Nineteen healthy men (age = 22.4 ± 2.7 years; body mass = 76.4 ± 12.9 kg, height = 175 ± 6.7 cm) performed isometric elbow flexion exercises in three experimental treatments: only isometric exercise (control - CON); isometric exercise with the addition of sinusoidal vibrations (SVE₁; frequency = 20 Hz, displacement = 3.55 ± 0.54 mm); and isometric exercise with the addition of sinusoidal vibrations with frequency variation (SVE₂; frequency = 20 ± 3 Hz, displacement = 3.6 ± 0.8 mm). The peak of the rate of EMG rise (RER) and the root mean square of biceps brachii during the first 200 ms (RMS200bic) were significantly higher in SVE₁ (RMS200bic, 25.57 ± 11.70%MVC; RER, 266.91 ± 130.16%MVC s⁻¹) than CON (RMS200bic, 19.31 ± 8.19%MVC; RER, 169.15 ± 65.98%MVC s⁻¹). Regarding force, in SVE₁, compared to CON, significant increases were observed in peak of rate of force development (CON, 643.96 ± 192.57 N/s; SVE₁, 845.54 ± 292.84 N/s), rate of force development in the first 200 ms (CON, 382.92 ± 138,63 N/s; SVE₁, 501.09 ± 147.46 N/s), and impulse in 200 ms (CON, 8.56 ± 3.56 N s; SVE₁, 11.67 ± 4.45 N s). The addition of indirect sinusoidal vibrations during exercise induced increases in the rate of force development (explosive strength), without affecting the peak force (maximal strength) and the ability to sustain strength production.     

云南西双版纳蝙蝠咬合力及生态位分化

咬合力与动物咀嚼系统的形态特征以及食物硬度有关,是评价动物取食行为的重要指标之一。本文于2012年4月在云南西双版纳对食果、食蜜和食虫3种食性的12种蝙蝠咬合力进行研究,使用咬合力探测仪测量蝙蝠手持状态下的咬合力,分析不同食性蝙蝠咬合力的差异,并与其体型（体重、前臂长、头长）进行相关分析。结果表明,3种食性蝙蝠的咬合力存在显著差异,食果蝙蝠咬合力最大,其次为食蜜蝙蝠,食虫蝙蝠咬合力最小;但是去除体重因素的影响之后,不同食性蝙蝠的咬合力则差异不显著。蝙蝠咬合力与体重、前臂长、头长均呈显著正相关。本文研究结果表明,体重是影响蝙蝠咬合力的主要因素,食性在一定程度上也对咬合力产生影响,食蜜蝙蝠吻部延长,头长上的特化导致其咬合力的减弱。     

Evaluation of a fast implicit solvent model for molecular dynamics simulations.

A solvation term based on the solvent accessible surface area (SASA) is combined with the CHARMM polar hydrogen force field for the efficient simulation of peptides and small proteins in aqueous solution. Only two atomic solvation parameters are used: one is negative for favoring the direct solvation of polar groups and the other positive for taking into account the hydrophobic effect on apolar groups. To approximate the water screening effects on the intrasolute electrostatic interactions, a distance-dependent dielectric function is used and ionic side chains are neutralized. The use of an analytical approximation of the SASA renders the model extremely efficient (i.e., only about 50% slower than in vacuo simulations). The limitations and range of applicability of the SASA model are assessed by simulations of proteins and structured peptides. For the latter, the present study and results reported elsewhere show that with the SASA model it is possible to sample a significant amount of folding/unfolding transitions, which permit the study of the thermodynamics and kinetics of folding at an atomic level of detail.     

Hydrodynamic Analysis of C-start in Crucian Carp

The kinematics of turning maneuvers of startled Crucian Carp (Carassius auratus) are presented. All escape response observed are C-type fast-starts. The position of the center of mass and the me,merit of inertia of the fish are calculated. The results show that the position of the center of mass is always at 35% of the length of the fish from the head and the position of the center of mass and rroment of inertia can be considered unchanged during C-start of Crucian Carp. Hydro-dynamic analysis of the C-start is given based on the kinematics data from our experiments. The C-start consists of three stages. In stage 1, the tail fin of fish rapidly flaps in one direction, and a large moment acts on the fish‘s body, which rotates around the center of mass with an angular acceleration. In stage 2, the tail fin flaps more slowly in the opposite direction at slower speed, the fish‘s body rotates around the center of mass with angular deceleration and the center of mass of the fish moves along an are. In stage 3, the moment approximately equals zero, the fish‘s body stops rotating and the center of mass the moves along a straight line.     

Evolution of bite performance in turtles

Abstract Among vertebrates, there is often a tight correlation between variation in cranial morphology and diet. Yet, the relationships between morphological characteristics and feeding performance are usually only inferred from biomechanical models. Here, we empirically test whether differences in body dimensions are correlated with bite performance and trophic ecology for a large number of turtle species. A comparative phylogenetic analysis indicates that turtles with carnivorous and durophagous diets are capable of biting harder than species with other diets. This pattern is consistent with the hypothesis that an evolutionary increase in bite performance has allowed certain turtles to consume harder or larger prey. Changes in carapace length tend to be associated with proportional changes in linear head dimensions (no shape change). However, maximum bite force tends to change in proportion to length cubed, rather than length squared, implying that changes in body size are associated with changes in the design of the jaw apparatus. After the effect of body size is accounted for in the analysis, only changes in head height are significantly correlated with changes in bite force. Additionally, our data suggest that the ability to bite hard might trade off with the ability to feed on fast agile prey. Rather than being the direct result of conflicting biomechanical or physiological demands for force and speed, this trade‐off may be mediated through the constraints imposed by the need to retract the head into the shell for defensive purposes.     

Energized Uptake of Sugars from the Apoplast of Leaves: A Study of Some Plants Possessing Different Minor Vein Anatomy

Solutions of sucrose, glucose, raffinose, and stachyose were fed via the petiole to detached leaves of plant species known to transfer sugars during photosynthesis into the phloem using either the apoplastic or the symplastic pathway of phloem loading. Symplastic phloem loaders, which translocate raffinose-type oligosaccharides and sucrose in the phloem, and apoplastic plants, translocating exclusively sucrose, were selected for this study. As the sugars arrived with the transpiration stream in the leaf blade within little more than a minute, dark respiration increased. Almost simultaneously, fluorescence of a potential-indicating dye, which had been infiltrated into the leaves, indicated membrane depolarization. Another fluorescent dye used to record the apoplastic pH revealed apoplastic alkalinization that occurred with a slight lag phase after respiration and membrane depolarization responses. Occasionally, alkalinization was preceded by transient apoplastic acidification. Whereas membrane depolarization and apoplastic acidification are interpreted as initial responses of the proton motive force across the plasma membrane to the advent of sugars in the leaf apoplast, the following apoplastic alkalinization showed that sugars were taken up from the apoplast into the symplast in cotransport with protons. This was true not only for glucose and sucrose, but also for raffinose and stachyose. Similar observations were made for sugar uptake not only in leaves of plants known to export sugars by symplastic phloem loading but also of plants using the apoplastic pathway. Increased respiration during sugar uptake revealed tight coupling between respiratory ATP production and ATP consumption by proton-translocating ATPase of the plasma membrane, which exports protons into the apoplast, thereby compensating for the proton loss in the apoplast when protons are transported together with sugars into the symplast. The extent of stimulation of respiration by sugars indicated that sugar uptake was not limited to phloem tissue. Ratios of the extra CO₂ released during sugar uptake to the amounts of sugars taken up were variable, but lowest values were lower than 0.2. When a ratio of 0.2 is taken as a basis to calculate rates of sugar uptake from observed maxima of sugar-dependent increases in respiration, rates of sugar uptake approached 350 nmol/(m² leaf surface s). Sugar uptake rates were half-saturated at sugar concentrations in the feeding solutions of about 10–25 mM indicating a low in vivo affinity of sugar uptake systems for sugars.