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1.
In this study, the homogenized anisotropic elastic properties of single bone lamellae are computed using a finite element unit cell method. The resulting stiffness tensor is utilized to calculate indentation moduli for multiple indentation directions in the lamella plane which are then related to nanoindentation experiments. The model accounts for different fibril orientation patterns in the lamellae—the twisted and orthogonal plywood pattern, a 5-sublayer pattern and an X-ray diffraction-based pattern. Three-dimensional sectional views of each pattern facilitate the comparison to transmission electron (TEM) images of real lamella cuts. The model results indicate, that the 5-sublayer- and the X-ray diffraction-based patterns cause the lamellae to have a stiffness maximum between 0° and 45° to the osteon axis. Their in-plane stiffness characteristics are qualitatively matching the experimental findings that report a higher stiffness in the osteon axis than in the circumferential direction. In contrast, lamellae owning the orthogonal or twisted plywood fibril orientation patterns have no preferred stiffness alignment. This work shows that the variety of fibril orientation patterns leads to qualitative and quantitative differences in the lamella elastic mechanical behavior. The study is a step toward a deeper understanding of the structure—mechanical function relationship of bone lamellae.  相似文献   

2.
The existence and role of prestress in the various hierarchical structures of long bone are long standing questions. In this study, the prestress and associated strain that exist in a component of human bone microstructure, circularly fibered osteonic lamella, are estimated. Such estimates allow the formulation of hypotheses on prestress formation and lamellar stiffness. Dimensional measurements were obtained for eight fully calcified lamellae. These dimensions, before isolation from the surrounding alternate osteon and after strain relief by isolation and axial sectioning, furnish data upon which a geometric lamellar model is constructed. A material model is based on the most likely hypothesis as to lamellar structure. This geometric-material model allows estimation of the preexisting strain. The largest strains occur in shear circumferential-axial and normal axial strain directions, averaging 0.08 and 0.05, respectively. The geometric-material model expresses prestress in terms of as yet unknown elastic moduli. The average prestress magnitude is the largest in shear circumferential-axial direction, compensating for alternate osteon weakness in this direction. The estimated axial prestress confirms long hypothesized alternate osteon precompression, which impedes fractures of areas of collagen bundles transverse to the osteon axis at low stresses. The results of the model support the formulation of the following biological hypotheses: (a) lamellar prestress occurs at a supra-molecular level, namely through collagen bundles which are themselves likely to be prestressed; (b) collagen bundles oblique to the lamellar axis are responsible for shear prestress; (c) prestress ranges up to 0.11 GPa; and (d) the lamella is less stiff than alternate osteon.  相似文献   

3.
Mineralized collagen fibrils have been usually analyzed like a two-phase composite material where crystals are considered as platelets that constitute the reinforcement phase. Different models have been used to describe the elastic behavior of the material. In this work, it is shown that when Halpin–Tsai equations are applied to estimate elastic constants from typical constituent properties, not all crystal dimensions yield a model that satisfy thermodynamic restrictions. We provide the ranges of platelet dimensions that lead to positive definite stiffness matrices. On the other hand, a finite element model of a mineralized collagen fibril unit cell under periodic boundary conditions is analyzed. By applying six canonical load cases, homogenized stiffness matrices are numerically calculated. Results show a monoclinic behavior of the mineralized collagen fibril. In addition, a 5-layer lamellar structure is also considered where crystals rotate in adjacent layers of a lamella. The stiffness matrix of each layer is calculated applying Lekhnitskii transformations, and a new finite element model under periodic boundary conditions is analyzed to calculate the homogenized 3D anisotropic stiffness matrix of a unit cell of lamellar bone. Results are compared with the rule-of-mixtures showing in general good agreement.  相似文献   

4.
The effects of collagen fiber orientation and osteon geometry on the mechanical properties of secondary osteons under axial compression/tension and combined loadings (compression, bending and torsion) were investigated using a composite-beam finite-element model. Three cross-sectional shapes of secondary osteons were studied to show the effect of geometry. The results of stiffness are presented using the tension and compression properties for each lamella. The model shows that the mechanical properties of osteons are enhanced in bending and torsion when collagen fibers are oriented within 30 degrees of the loading axis. Osteons with alternating lamellar orientation are not well adapted to resist torsional moments, but alternate collagen fiber orientation has virtually no effect on the bending stiffness of osteons. Fiber orientation affects the mechanical properties less significantly when osteons are non-circular. Collagen fiber orientation and osteon geometry interact to determine the mechanical behavior of the osteon, and may act in a compensatory manner in the adaptive process.  相似文献   

5.
Micromechanical estimates of the elastic constants for a single bone osteonal lamella and its substructures are reported. These estimates of elastic constants are accomplished at three distinct and organized hierarchical levels, that of a mineralized collagen fibril, a collagen fiber, and a single lamella. The smallest collagen structure is the collagen fibril whose diameter is the order of 20 nm. The next structural level is the collagen fiber with a diameter of the order of 80 nm. A lamella is a laminate structure, composed of multiple collagen fibers with embedded minerals and consists of several laminates. The thickness of one laminate in the lamella is approximately 130 nm. All collagen fibers in a laminate in the lamella are oriented in one direction. However, the laminates rotate relative to the adjacent laminates. In this work, all collagen fibers in a lamella are assumed to be aligned in the longitudinal direction. This kind of bone with all collagen fibers aligned in one direction is called a parallel fibered bone. The effective elastic constants for a parallel fibered bone are estimated by assuming periodic substructures. These results provide a database for estimating the anisotropic poroelastic constants of an osteon and also provide a database for building mathematical or computational models in bone micromechanics, such as bone damage mechanics and bone poroelasticity.  相似文献   

6.
The crystal structure and texture of the monodisperse periodic polypeptide [(AG)3EG(GA)3EG]10 (poly(±AG)3EG; A=alanine, G=glycine, E=glutamic acid) were analyzed by X-ray diffraction, Fourier transform infrared spectroscopy, and electron microscopy. Structure determination was aided by comparison with the recently described structure for the related periodic polypeptide [(AG)3EG]36 by Krejchi et al. (Macromolecules 1997;30:5012). Texture-oriented samples of poly(±AG)3EG were obtained by crystallization of the polymer from aqueous formic acid solution. The evidence supports an antiparallel (ap) β-sheet protein structure and the X-ray diffraction signals index on an orthorhombic unit cell with parameters: a=0.950 nm (hydrogen-bond direction), b=1.052 nm (apβ-sheet stacking direction), c=6.95 nm (chain direction). The absence of the (010) diffraction signal, a prominent signal in the poly(AG)3EG diffraction pattern, implies that the apβ-sheets are ‘apolar', i.e. both surfaces are equally populated with alanyl methyl groups. Selective line broadening of wide-angle diffraction signals with ℓ≠0 gives an estimated crystal size of 4 nm in the chain direction. This observation, coupled with the appearance of low-angle particle interference peaks, indicates a crystal thickness considerably less than the chain length and suggests an adjacent-re-entry chain-folded lamellar structure incorporating the apβ-sheet architecture. The polypeptide folds through γ-turns, in-phase with the pseudo-octapeptide repeat; the glutamic acid residues occur on the lamellar surfaces. These results and those from the crystalline lamellae of poly(AG)3EG suggest that β-turns are not compatible with these repetitively stacked apβ-sheet structures. This implies that intersheet interactions of alanyl methyl groups and glycyl -protons are not sufficiently strong to dictate the folding geometry in these structures.  相似文献   

7.
Berlin K  O'Leary DP  Fushman D 《Proteins》2011,79(7):2268-2281
We present and evaluate a rigid-body, deterministic, molecular docking method, called ELMDOCK, that relies solely on the three-dimensional structure of the individual components and the overall rotational diffusion tensor of the complex, obtained from nuclear spin-relaxation measurements. We also introduce a docking method, called ELMPATIDOCK, derived from ELMDOCK and based on the new concept of combining the shape-related restraints from rotational diffusion with those from residual dipolar couplings, along with ambiguous contact/interface-related restraints obtained from chemical shift perturbations. ELMDOCK and ELMPATIDOCK use two novel approximations of the molecular rotational diffusion tensor that allow computationally efficient docking. We show that these approximations are accurate enough to properly dock the two components of a complex without the need to recompute the diffusion tensor at each iteration step. We analyze the accuracy, robustness, and efficiency of these methods using synthetic relaxation data for a large variety of protein-protein complexes. We also test our method on three protein systems for which the structure of the complex and experimental relaxation data are available, and analyze the effect of flexible unstructured tails on the outcome of docking. Additionally, we describe a method for integrating the new approximation methods into the existing docking approaches that use the rotational diffusion tensor as a restraint. The results show that the proposed docking method is robust against experimental errors in the relaxation data or structural rearrangements upon complex formation and is computationally more efficient than current methods. The developed approximations are accurate enough to be used in structure refinement protocols.  相似文献   

8.
Fabric and compliance tensors of a cube of cancellous bone with a complicated three-dimensional trabecular structure were obtained for trabecular surface remodeling by using a digital image-based model combined with a large-scale finite element method. Using mean intercept length and a homogenization method, the fabric and compliance tensors were determined for the trabecular structure obtained in the computer remodeling simulation. The tensorial quantities obtained indicated that anisotropic structural changes occur in cancellous bone adapting to the compressive loading condition. There were good correlations between the fabric tensor, bone volume fraction, and compliance tensor in the remodeling process. The result demonstrates that changes in the structural and mechanical properties of cancellous bone are essentially anisotropic and should be expressed by tensorial quantities.  相似文献   

9.
A method has been developed for the calculation of the enantioselectivity of chymotrypsin catalysed hydrolytic reactions using molecular mechanics and molecular dynamics. Nine different ester substrates, which are hydrolysed by the enzyme over a wide range of reaction rates have been studied. Models of the transition state of the ester hydrolysis were built using computer aided molecular modelling. The energies of the transition state models were calculated by molecular mechanics and molecular dynamics methods. The point charges of the substrates were modelled from known force field parameters and by semiempirical methods. The difference in free energy of activation between the enantiomers of each substrate were compared with experimental values. The calculations approximated the experimental results. The calculated structure of the transition state model of the chymotrypsin catalysed hydrolysis of acetyl-phenylalanine ester was virtually the same as the published crystal structure of a chymotrypsin-trifluoromethyl ketone inhibitor complex (Brady et al., Biochemistry 29: 7600-7607, 1990).  相似文献   

10.
Using primers derived from a region of the Candida albicans CDR1 (Candida drug resistance) gene that is conserved in other ABC (ATP-binding cassette) transporters, a DNA fragment from a previously unknown CDR gene was obtained by polymerase chain reaction (PCR). After screening a C. albicans genomic library with this fragment as a probe, the complete CDR4 gene was isolated and sequenced. CDR4 codes for a putative ABC transporter of 1490 amino acids with a high degree of homology to Cdr1p, Cdr2p and Cdr3p from C. albicans (62, 59 and 57% amino acid sequence identity, respectively). Cdr4p has a predicted structure typical for cluster I.1 of yeast ABC transporters, characterized by two homologous halves, each comprising an N-terminal hydrophilic domain with consensus sequences for ATP binding and a C-terminal hydrophobic domain with six transmembrane helices. In contrast to the CDR1/CDR2 genes, the genetic structure of the CDR4 gene was conserved in 59 C. albicans isolates from six different patients. Northern hybridization analysis showed that the CDR4 gene was expressed in most isolates, but no correlation between CDR4 mRNA levels and the degree of fluconazole resistance of the isolates was found. In addition, a C. albicans mutant in which both copies of the CDR4 gene were disrupted by insertional mutagenesis was not hypersusceptible to fluconazole as compared to the parent strain. Unlike CDR1 and CDR2, CDR4 does not, therefore, seem to be involved in fluconazole resistance in C. albicans.  相似文献   

11.
聚四氟乙烯(PTFE)塑料管研磨法是测定植物碳同位素比率(δ13C)值常用的前处理方法。该方法处理样品高效快捷,但对植物δ13C可能存在污染。本研究利用人工气候室开展双因素交互试验,包括空气相对湿度(50%和80%)和空气δ13C(13C富集和贫化的空气)两个因素,对比了PTFE塑料管研磨法和不锈钢管研磨法处理C4植物糙隐子草δ13C的结果。结果表明: 在相同湿度条件下,不同空气δ13C处理的植物13C分馏值(Δ13C,矫正了光合作用底物的δ13C差异)原本可以视为重复,但由于PTFE塑料颗粒的混入,相同湿度不同13C丰度空气培养下植物叶片Δ13C平均差值为4.8‰。该污染效应导致单个叶片δ13C测定的误差高达8‰。考虑到C4植物的Δ13C较低(通常为1‰~8‰),这种污染效应已经超出了可以接受的误差范围。通过建立类似Keeling曲线的二元混合模型对误差进行了有效消除,并准确估算了植物样品和污染物的δ13C。说明广泛采用的PTFE管研磨方法对研究C4植物Δ13C并不适用,将导致较大的误差。对精度要求较高的研究内容建议使用不锈钢瓶进行研磨。  相似文献   

12.
赵磊  刘淑艳 《菌物学报》2019,38(9):1457-1469
白粉菌是一类植物专性寄生真菌,广泛分布于世界各地,可引起多种植物白粉病。开展白粉菌交配型基因研究可以为全面认识白粉菌的生活史循环和系统演化提供证据。本研究以子囊菌中已报道的10种MAT基因和4种侧翼基因的氨基酸序列为种子序列,采用生物信息学方法在21个白粉菌基因组中进行氨基酸同源性分析,探索MAT基因及其侧翼基因的种类和线性排布。结果表明,21个白粉菌基因组中有10个属于MAT1-1型,包含MAT1-1-1MAT1-1-3两种基因;10个属于MAT1-2型,仅包含MAT1-2-1基因;在Erysiphe pulchra的基因组中同时存在MAT1-1-1MAT1-1-3MAT1-2-1;而4种侧翼基因SLA2APC5APN2CoxVia在21个白粉菌基因组中均存在。21个菌株中有两个菌株Blumeria graminis f. sp. hordei RACE1和Golovinomyces orontiiMAT基因和4种侧翼基因分布在同一个scaffold,其余菌株MAT基因和侧翼基因均不在同一scaffold出现。本研究分别分析了具有MAT1-1MAT1-2的菌株中MAT基因和4种侧翼基因的排列关系,同时根据9个菌株的MAT基因注释信息,推测了其他菌株的MAT基因结构。结果表明,同属白粉菌的MAT基因结构相同,属间MAT基因结构差异明显。以从白粉菌基因组中获得的MAT1-1-1MAT1-1-3MAT1-2-1 3种MAT基因序列分别构建系统发育树,发现布氏白粉菌属Blumeria、白粉菌属Erysiphe和戈洛文白粉菌属Golovinomyces分别形成独立分枝,且白粉菌属与戈洛文白粉菌属形成姊妹群,这与前人对白粉菌系统发育关系的研究结果一致。本研究得到的白粉菌MAT基因种类、分布及其结构的相关结果为进一步实验提供了理论依据,为探究白粉菌的系统发育提供了新的思路。  相似文献   

13.
At its highest level of microstructural organization—the mesoscale or millimeter scale—cortical bone exhibits a heterogeneous distribution of pores (Haversian canals, resorption cavities). Multi-scale mechanical models rely on the definition of a representative volume element (RVE). Analytical homogenization techniques are usually based on an idealized RVE microstructure, while finite element homogenization using high-resolution images is based on a realistic RVE of finite size. The objective of this paper was to quantify the size and content of possible cortical bone mesoscale RVEs. RVE size was defined as the minimum size: (1) for which the apparent (homogenized) stiffness tensor becomes independent of the applied boundary conditions or (2) for which the variance of elastic properties for a set of microstructure realizations is sufficiently small. The field of elastic coefficients and microstructure in RVEs was derived from one acoustic microscopy image of a human femur cortical bone sample with an overall porosity of 8.5%. The homogenized properties of RVEs were computed with a finite element technique. It was found that the size of the RVE representative of the overall tissue is about 1.5 mm. Smaller RVEs (~0.5 mm) can also be considered to estimate local mesoscopic properties that strongly depend on the local pores volume fraction. This result provides a sound basis for the application of homogenization techniques to model the heterogeneity of cortical microstructures. An application of the findings to estimate elastic properties in the case of a porosity gradient is briefly presented.  相似文献   

14.
李国春  宋华东  李琦  卜书海 《生态学杂志》2017,28(11):3487-3493
采用单变量和双变量O-ring函数对太白山大熊猫栖息地巴山冷杉林主要树种的空间分布格局、种间关联性及其与林下开花箭竹的空间关联性进行了多尺度分析.结果表明: 巴山冷杉林中,巴山冷杉数量最多,但种群结构衰退,白桦种群相对年轻,种群结构稳定,红桦种群也呈衰退趋势;3个主要树种在小尺度上呈聚集分布,随尺度增加,逐渐表现为随机分布.3个树种的空间关联性主要表现在小尺度范围内,随尺度增加,空间分布格局逐渐表现为不关联;巴山冷杉和白桦与开花秦岭箭竹在大、中尺度内呈现正相关,而红桦与开花秦岭箭竹在大、中尺度上表现出负相关.大熊猫栖息地内乔木和林下秦岭箭竹共同推动森林的动态演替和发展,进而影响秦岭大熊猫栖息地的环境变化.  相似文献   

15.
Ionic and neutral polysaccharides with well-defined structures were chosen to investigate the mechanism of water sorption at different relative humidities. From an experimental point of view, the freezing water was determined by DSC when the total sorbed water was obtained from thermogravimetry. The isotherms of sorption and enthalpies of interaction were determined using the combination of a microbalance and a microcalorimeter. It is shown that freezing water appears for P/P0 > 0.85 especially with the neutral polymers. The differential molar enthalpy of interaction is higher for P/P0 < 0.85 corresponding to the fixation of two water molecules forming double H-bonds; this result is confirmed by molecular modelling; saturation is obtained experimentally for 4 water molecules interacting per glucose unit. On ionic polymers, the water retention increases especially over P/P0 0.8 and the enthalpy of interaction is higher for the first water molecules sorbed. For P/P0 0.8, the numbers of bound water molecules found are 2 per glucopyranosyl unit for neutral polysaccharides, 5 for glucuronan and 9–10 for carboxymethylcellulose (CMC) of D = 2 and hyaluronan (HA)  相似文献   

16.
Background: Ab initio protein structure prediction is to predict the tertiary structure of a protein from its amino acid sequence alone. As an important topic in bioinformatics, considerable efforts have been made on designing the ab initio methods. Unfortunately, lacking of a perfect energy function, it is a difficult task to select a good near-native structure from the predicted decoy structures in the last step. Methods: Here we propose an ensemble clustering method based on k-medoids to deal with this problem. The k-medoids method is run many times to generate clustering ensembles, and then a voting method is used to combine the clustering results. A confidence score is defined to select the final near-native model, considering both the cluster size and the cluster similarity. Results: We have applied the method to 54 single-domain targets in CASP-11. For about 70.4% of these targets, the proposed method can select better near-native structures compared to the SPICKER method used by the I-TASSER server. Conclusions: The experiments show that, the proposed method is effective in selecting the near-native structure from decoy sets for different targets in terms of the similarity between the selected structure and the native structure.  相似文献   

17.
金针菇栽培通过提高栽培室CO2浓度来抑制菌盖生长,提高商品质量。碳酸酐酶能调节CO2/HCO3 -在细胞内的平衡,它可能是响应CO2胁迫的关键酶。本研究利用我们已完成的金针菇Flammulina filiformis的基因组测序数据,以双色蜡蘑碳酸酐酶家族基因为参照,通过本地BLAST,得到7个金针菇碳酸酐酶家族的基因,分别命名为CA-1CA-2CA-3CA-4CA-5CA-6CA-7。基因结构、保守结构域和系统进化分析结果均支持这7个序列是碳酸酐酶家族的编码基因。高浓度CO2胁迫处理金针菇子实体12h,CA-1CA-2表达量与CO2浓度正相关,CA-5负相关,CA-3CA-4CA-6没有响应,CA-7无明显规律。据此推测,CA-1CA-2CA-5可能是金针菇响应CO2胁迫的关键基因之一,参与调控菌盖生长发育。  相似文献   

18.
依据吉林省长白山胡桃楸天然次生混交林12个典型区域的坡向、坡位分布,结合胡桃楸龄级,布设样地109块,以年龄-树高数据为材料,编制了吉林省东部山区胡桃楸天然次生混交林立地指数表.结果表明: 应用3倍树高标准差法剔除异常数据,最终得到80块379对胡桃楸不同龄级的年龄与树高数据,运用7个数学模型进行比较,确定了单形立地指数导向曲线方程式: H=28.0181(1-e-0.0341A)1.0503,决定系数R2为0.85,残差平方和为0.89,基准年龄为50年,指数级距为2 m,得到了16~28 m的7条立地指数曲线.根据不同立地类型,建立了多形立地指数模型,幂函数拟合效果较好,即H=B0tB1,其中B0=10-9e0.9213SI,B1=-0.2139SI+5.6183,最终得到了多形立地指数模型方程式H=10-9e0.9213SIt-0.2139SI+5.6183.指数级差法和落点检验法对2种立地指数模型的精度检验表明,多形立地指数的精确度较高,能够准确地反映胡桃楸不同立地类型间树高生长的差异,可用于吉林省长白山区胡桃楸天然次生混交林立地质量评价.  相似文献   

19.
Fabric and compliance tensors of a cube of cancellous bone with a complicated three-dimensional trabecular structure were obtained for trabecular surface remodeling by using a digital image-based model combined with a large-scale finite element method. Using mean intercept length and a homogenization method, the fabric and compliance tensors were determined for the trabecular structure obtained in the computer remodeling simulation. The tensorial quantities obtained indicated that anisotropic structural changes occur in cancellous bone adapting to the compressive loading condition. There were good correlations between the fabric tensor, bone volume fraction, and compliance tensor in the remodeling process. The result demonstrates that changes in the structural and mechanical properties of cancellous bone are essentially anisotropic and should be expressed by tensorial quantities.  相似文献   

20.
申惠翡  赵冰  徐静静 《生态学杂志》2016,27(12):3895-3904
以15个杜鹃花品种为试材,利用扫描电镜观察叶片17项解剖结构,应用变异系数、相关分析和聚类分析对叶片解剖结构进行筛选,采用隶属函数对各品种的耐热性进行综合评价,探讨杜鹃花叶片解剖结构与植株耐热性的关系,为杜鹃花耐热品种选育、引种栽培及栽培区划分提供细胞学理论依据.结果表明: 杜鹃花叶片为典型的异面叶,表皮细胞垂周壁略呈波浪状,气孔为无规则形,仅分布于下表皮,品种之间有16项解剖结构指标差异达到极显著水平,仅下表皮厚度为显著水平;叶片角质层厚度、气孔密度、气孔宽度、栅栏组织厚度和组织结构疏松度是影响耐热性的主要叶片解剖结构性状,而叶片厚度、气孔长度、孔径、气孔开度、海绵组织厚度、栅海比、上下表皮细胞长度和厚度、组织结构疏松度、中脉厚度与植株耐热性的关系不大.15个品种杜鹃花耐热性存在一定差异,其强弱顺序为:松江大桃红>状元红>绿色光辉>粉珍珠>外国红>蓝茵>笔止>大和之春>国旗红>玉玲珑>红珊瑚>宁波红>套瓣朱砂>爱丁堡>琉球红.15个品种杜鹃花抗热性可划分为4类:松江大桃红、状元红和绿色光辉为抗热类型;粉珍珠、外国红、蓝茵、笔止、大和之春、国旗红和玉玲珑为中度抗热类型;红珊瑚、宁波红、套瓣朱砂和爱丁堡为低抗热类型;琉球红为不抗热类型.杜鹃花耐热性的准确评价需参考形态结构、生理生化、遗传等因素,以及杜鹃花高温受害及受害后恢复状况.  相似文献   

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