A hybrid approach to theoretical analysis of bovine pancreatic trypsin inhibitor.

A static analysis of bovine pancreatic trypsin inhibitor (BPTI) is presented based on a new discrete/continuum approach to modeling the dynamics of biomolecules. This hybrid method utilizes knowledge of the intramolecular potential and molecular configuration to generate a field of elastic modulus tensors. These tensors, which relate the local stress and strain for each atom in the biomolecule, can be used to judge the local rigidity as well as indicate regions of high stress. Comparing the tensor fields for an unrelaxed and a relaxed configuration, the microscopic structure of BPTI is found to be anisotropic and to have regions of stress even when it is relaxed in the potential field. However, when these fields are averaged over the whole protein or over individual residues the structure becomes more isotropic and the stressed regions vanish. Using these averaged tensors, we calculated bulk properties such as Young's modulus and the Lamé constants and they agreed with previously reported values.     

Investigation of asphalt aging behaviour due to oxidation using molecular dynamics simulation

An attempt is made to connect the link between internal chemical and molecular mechanical property change and external physical, rheological and mechanical property change for asphalt before and after oxidative aging using molecular dynamics (MD) simulation. Intermolecular interactions, density, bulk modulus and zero shear viscosity changes of model asphalt systems before and after oxidative aging and mechanical property changes of the asphalt systems under different compressive and tensile stress rates are investigated at room temperature (298 K). Simulation results demonstrate that oxidised functional groups in asphalt molecules increase the strength of intermolecular bonds and the bulk modulus of asphalt, which further contribute to the hardening of the oxidised asphalt. The internal property change is consistent with the external physical and rheological property change after oxidation, which is revealed by the increase of density and viscosity. In addition, both the unoxidised and oxidised asphalts deform more and fail faster with an increase in both compressive and tensile stress rates, especially under tensile stresses. The oxidised asphalt is stiffer than the unoxidised asphalt, which shows less deformation.     

Stress and strain analysis of contractions during ramp distension in partially obstructed guinea pig jejunal segments

Previous studies have demonstrated morphological and biomechanical remodeling in the intestine proximal to an obstruction. The present study aimed to obtain stress and strain thresholds to initiate contraction and the maximal contraction stress and strain in partially obstructed guinea pig jejunal segments. Partial obstruction and sham operations were surgically created in mid-jejunum of male guinea pigs. The animals survived 2, 4, 7 and 14 days. Animals not being operated on served as normal controls. The segments were used for no-load state, zero-stress state and distension analyses. The segment was inflated to 10 cmH(2)O pressure in an organ bath containing 37°C Krebs solution and the outer diameter change was monitored. The stress and strain at the contraction threshold and at maximum contraction were computed from the diameter, pressure and the zero-stress state data. Young's modulus was determined at the contraction threshold. The muscle layer thickness in obstructed intestinal segments increased up to 300%. Compared with sham-obstructed and normal groups, the contraction stress threshold, the maximum contraction stress and the Young's modulus at the contraction threshold increased whereas the strain threshold and maximum contraction strain decreased after 7 days obstruction (P<0.05 and 0.01). In conclusion, in the partially obstructed intestinal segments, a larger distension force was needed to evoke contraction likely due to tissue remodeling. Higher contraction stresses were produced and the contraction deformation (strain) became smaller.     

Cell wall elasticity: I. A critique of the bulk elastic modulus approach and an analysis using polymer elastic principles

The traditional bulk elastic modulus approach to plant cell pressure-volume relations is inconsistent with its definition. The relationship between the bulk modulus and Young's modulus that forms the basis of their usual application to cell pressure-volume properties is demonstrated to be physically meaningless. The bulk modulus describes stress/strain relations of solid, homogeneous bodies undergoing small deformations, whereas the plant cell is best described as a thin-shelled, fluid-filled structure with a polymer base. Because cell walls possess a polymer structure, an alternative method of mechanical analysis is presented using polymer elasticity principles. This initial study presents the groundwork of polymer mechanics as would be applied to cell walls and discusses how the matrix and microfibrillar network induce nonlinear stress/strain relationships in the cell wall in response to turgor pressure. In subsequent studies, these concepts will be expanded to include anisotropic expansion as regulated by the microfibrillar network.     

Effect of long-term anemia and retransfusion on central circulation during exercise

The bulk modulus and the shear modulus describe the capacity of material to resist a change in volume and a change of shape, respectively. The values of these elastic coefficients for air-filled lung parenchyma suggest that there is a qualitative difference between the mechanisms by which the parenchyma resists expansion and shear deformation; the bulk modulus changes roughly exponentially with the transpulmonary pressure, whereas the shear modulus is nearly a constant fraction of the transpulmonary pressure for a wide range of volumes. The bulk modulus is approximately 6.5 times as large as the shear modulus. In recent microstructural modeling of lung parenchyma, these mechanisms have been pictured as being similar to the mechanisms by which an open cell liquid foam resists deformations. In this paper, we report values for the bulk moduli and the shear moduli of normal air-filled rabbit lungs and of air-filled lungs in which alveolar surface tension is maintained constant at 16 dyn/cm. Elevating surface tension above normal physiological values causes the bulk modulus to decrease and the shear modulus to increase. Furthermore, the bulk modulus is found to be sensitive to a dependence of surface tension on surface area, but the shear modulus is not. These results agree qualitatively with the predictions of the model, but there are quantitative differences between the data and the model.     

Homogeneous non-equilibrium molecular dynamics simulations of viscous flow: techniques and applications

We provide a review of the literature for non-equilibrium molecular dynamics (NEMD) simulations of homogeneous fluids. Our review focuses on techniques for simulations of shear and elongational flows in viscous fluids and covers the formulation and application of NEMD algorithms for atomic and molecular fluids. We provide a set of expositions that can be effectively used as guidelines to formulate the relevant equations of motion, periodic boundary conditions and thermostats. We also provide a survey of applications in a convenient tabular form as an aid to researchers who wish to use NEMD to study transport phenomena.     

The dynamics of a hydrogel strip.

A hydrogel strip relaxes when it is stretched. The decay in tensile stress can be ascribed primarily to strain-induced swelling of the polymer network--a result that follows from a continuum model of the gel-solvent system. An equation of motion and a linear constitutive law of the polymer network, Darcy's law, and the conservation of mass of the network and interstitial fluid are solved with boundary and initial conditions appropriate for a stress-relaxation experiment. This model predicts that the time constant of decay depends inversely upon the square of the thickness of the sample. This result is confirmed by experiments. In addition, the network shear modulus, mu, bulk modulus, k, and hydraulic permeability, 1/f, which are estimated by non-linear regression, all agree with measurements obtained using other methods.     

Effects of age on elastic moduli of human lungs.

The model of the lung as an elastic continuum undergoing small distortions from a uniformly inflated state has been used to describe many lung deformation problems. Lung stress-strain material properties needed for this model are described by two elastic moduli: the bulk modulus, which describes a uniform inflation, and the shear modulus, which describes an isovolume deformation. In this study we measured the bulk modulus and shear modulus of human lungs obtained at autopsy at several fixed transpulmonary pressures (Ptp). The bulk modulus was obtained from small pressure-volume perturbations on different points of the deflation pressure-volume curve. The shear modulus was obtained from indentation tests on the lung surface. The results indicated that, at a constant Ptp, both bulk and shear moduli increased with age, and the increase was greater at higher Ptp values. The micromechanical basis for these changes remains to be elucidated.     

NpH-MD-Simulations of the Elastic Moduli of Cellulose II at Room Temperatue

We have used molecular dynamics modeling to investigate the stucture and mechanical properties of regenerated cellulose fibres. This work is motivated by continued interest in replacing the environmentally hazardous viscose process by alternative spinning methods. An important input parameter for any realistic model of the elastic properties is the stiffness tensor of the crystalline constituent, cellulose II. Conventional molecular mechanics techniques can be used to estimate the elastic reaction of a material with respect to small external stresses or strains, i.e. the compliance and stiffness tensors, and the elastic moduli derived therefrom, at zero temperature. In order to access non-zero temperatures, it is necessary to use either the quasi-harmonic approximation for the vibrational free energy or molecular dynamics (MD) simulations. In the present work, Parrinello-Rahman constant-stress MD was performed to generate trajectories in constant particle number (N), constant external stress tensor (p or t) and constant enthalpy H (NpH or HtN) ensemble. This was found to be less time consuming than working with isothermal conditions, as done by other authors. The fluctuations in kinetic energy and MD cell vectors were then used to calculate adiabatic elastic constants, thermal expansion coefficients and heat capacity. The isothermal elastic constants were found by applying a standard thermodynamic relation. The Youngs modulus along the chain direction, E_l, was determined to be 155 GPa, whereas the values in the perpendicular directions vary between 51 and 24 GPa. These results are of the same order of magnitude as those obtained by Tashiro and Kobayashi [1] with the static (T = 0K) method, but our value of E_l is 5% lower and, unexpectedly, the lateral values are up to six times higher. A strong anisotropy is found for shear along the chains in planes containing the chain axis, the shear modulus ranging from 5 to 20 GPa. Convergence was achieved in the simulations, to the extend that the elastic constants become stationary, but significant internal stresses remain, pointing to shortcomings in the software used. Further work is necessary to resolve these problems, although the major conclusions should be unaffected.     

Coupling field theory with mesoscopic dynamical simulations of multicomponent lipid bilayers

A method for simulating a two-component lipid bilayer membrane in the mesoscopic regime is presented. The membrane is modeled as an elastic network of bonded points; the spring constants of these bonds are parameterized by the microscopic bulk modulus estimated from earlier atomistic nonequilibrium molecular dynamics simulations for several bilayer mixtures of DMPC and cholesterol. The modulus depends on the composition of a point in the elastic membrane model. The dynamics of the composition field is governed by the Cahn-Hilliard equation where a free energy functional models the coupling between the composition and curvature fields. The strength of the bonds in the elastic network are then modulated noting local changes in the composition and using a fit to the nonequilibrium molecular dynamics simulation data. Estimates for the magnitude and sign of the coupling parameter in the free energy model are made treating the bending modulus as a function of composition. A procedure for assigning the remaining parameters in the free energy model is also outlined. It is found that the square of the mean curvature averaged over the entire simulation box is enhanced if the strength of the bonds in the elastic network are modulated in response to local changes in the composition field. We suggest that this simulation method could also be used to determine if phase coexistence affects the stress response of the membrane to uniform dilations in area. This response, measured in the mesoscopic regime, is already known to be conditioned or renormalized by thermal undulations.     

Study of semiconducting nanomaterials under pressure

The pressure induced structural and mechanical properties of nanocrystalline ZnO, ZnS, ZnSe, GaN, CoO, CdSe, CeO(2), SnO(2), SiC, c-BC(2)N, and β-Ga(2)O(3) with different grain sizes have been analyzed under high pressures. The molecular dynamics simulation model has been used to compute isothermal equation of state, volume collapse and bulk modulus of these materials in nano and bulk phases at ambient and high pressures and compared with the experimental data. It is evident from these calculations that the change in particle size affects directly the phase transition pressure and bulk modulus. The values of phase transition pressure and bulk modulus increase with decrease in grain size of the material. The equilibrium cell volume and volume collapse in parent phase is directly proportional to the grain size of the materials. Present results are in good agreement with experimental data. The model is able to explain these thermodynamic properties at varying temperatures and pressures successfully.     

The mechanical behaviour of intracondylar cancellous bone of the femur at different loading rates

The compressive properties of human cancellous bone of the distal intracondylar femur in its wet condition were determined. Specimens were obtained from six cadaveric femora and were tested at a strain rate of 0.002, 0.10 and 9.16 sec⁻¹. It was found that the compressive strength decreases with an increasing vertical distance from the joint. The highest compressive strength level was recorded in the posterior medial condyle. Correlations among the mechanical properties, the bulk specimen density and the bone mineral content yield (i) highly significant correlations between the compressive strength and the elastic modulus (ii) highly significant correlations between the compressive strength or the modulus of elasticity and the bulk specimen density (iii) a doubtful correlation between the compressive strength and the bone mineral content. All recorded graphs of the impact loaded specimens displayed several well defined stress peaks, unlike the graphs recorded at low loading rates. It can be concluded that upon impact loading the localized trabecular failure which is associated with each peak, does not affect the spongy bone's stress capacity in a detrimental way.     

Worms under Pressure: Bulk Mechanical Properties of C. elegans Are Independent of the Cuticle

The mechanical properties of cells and tissues play a well-known role in physiology and disease. The model organism Caenorhabditis elegans exhibits mechanical properties that are still poorly understood, but are thought to be dominated by its collagen-rich outer cuticle. To our knowledge, we use a novel microfluidic technique to reveal that the worm responds linearly to low applied hydrostatic stress, exhibiting a volumetric compression with a bulk modulus, κ = 140 ± 20 kPa; applying negative pressures leads to volumetric expansion of the worm, with a similar bulk modulus. Surprisingly, however, we find that a variety of collagen mutants and pharmacological perturbations targeting the cuticle do not impact the bulk modulus. Moreover, the worm exhibits dramatic stiffening at higher stresses—behavior that is also independent of the cuticle. The stress-strain curves for all conditions can be scaled onto a master equation, suggesting that C. elegans exhibits a universal elastic response dominated by the mechanics of pressurized internal organs.     

Leucine 41 is a gate for water entry in the reduction of Clostridium pasteurianum rubredoxin

Biological electron transfer is an efficient process even though the distances between the redox moieties are often quite large. It is therefore of great interest to gain an understanding of the physical basis of the rates and driving forces of these reactions. The structural relaxation of the protein that occurs upon change in redox state gives rise to the reorganizational energy, which is important in the rates and the driving forces of the proteins involved. To determine the structural relaxation in a redox protein, we have developed methods to hold a redox protein in its final oxidation state during crystallization while maintaining the same pH and salt conditions of the crystallization of the protein in its initial oxidation state. Based on 1.5 A resolution crystal structures and molecular dynamics simulations of oxidized and reduced rubredoxins (Rd) from Clostridium pasteurianum (Cp), the structural rearrangements upon reduction suggest specific mechanisms by which electron transfer reactions of rubredoxin should be facilitated. First, expansion of the [Fe-S] cluster and concomitant contraction of the NH...S hydrogen bonds lead to greater electrostatic stabilization of the extra negative charge. Second, a gating mechanism caused by the conformational change of Leucine 41, a nonpolar side chain, allows transient penetration of water molecules, which greatly increases the polarity of the redox site environment and also provides a source of protons. Our method of producing crystals of Cp Rd from a reducing solution leads to a distribution of water molecules not observed in the crystal structure of the reduced Rd from Pyrococcus furiosus. How general this correlation is among redox proteins must be determined in future work. The combination of our high-resolution crystal structures and molecular dynamics simulations provides a molecular picture of the structural rearrangement that occurs upon reduction in Cp rubredoxin.     

Implications of an Absolute Simultaneity Theory for Cosmology and Universe Acceleration

An alternate Lorentz transformation, Absolute Lorentz Transformation (ALT), has similar kinematics to special relativity yet maintains absolute simultaneity in the context of a preferred reference frame. In this study, it is shown that ALT is compatible with current experiments to test Lorentz invariance only if the proposed preferred reference frame is locally equivalent to the Earth-centered non-rotating inertial reference frame, with the inference that in an ALT framework, preferred reference frames are associated with centers of gravitational mass. Applying this theoretical framework to cosmological data produces a scenario of universal time contraction in the past. In this scenario, past time contraction would be associated with increased levels of blueshifted light emissions from cosmological objects when viewed from our current perspective. The observation that distant Type Ia supernovae are dimmer than predicted by linear Hubble expansion currently provides the most direct evidence for an accelerating universe. Adjusting for the effects of time contraction on a redshift–distance modulus diagram produces a linear distribution of supernovae over the full redshift spectrum that is consistent with a non-accelerating universe.     

Contractility,differential tension and membrane removal lead zebrafish epiboly biomechanics

Precise tissue remodeling during development is essential for shaping embryos and optimal organ function. Epiboly is an early gastrulation event by which the blastoderm expands around the yolk to engulf it. Three different layers are involved in this process, an epithelial layer (the enveloping layer, EVL), the embryo proper, constituted by the deep cells (DCs), and the yolk cell. Although teleost epiboly has been studied for many years, a clear understanding of its mechanics was still missing. Here we present new information on the cellular, molecular and mechanical elements involved in epiboly that, together with some other recent data and upon comparison with previous biomechanical models, lets conclude that the expansion of the epithelia is passive and driven by active cortical contraction and membrane removal in the adjacent layer, the External Yolk Syncytial Layer (E-YSL). The isotropic actomyosin contraction of the E-YSL cortex generates an anisotropic stress pattern and a directional net movement consequence of the differences in the deformation response of the 2 opposites adjacent domains (EVL and the Yolk Cytoplasmic Layer - YCL). Contractility is accompanied by the local formation of membrane folds and its removal by Rab5ab dependent macropinocytosis. The increase in area of the epithelia during the expansion is achieved by cell-shape changes (flattening) responding to spherical geometrical cues. The counterbalance between the geometry of the embryo and forces dissipation among different elements is therefore essential for epiboly global coordination.     

The application of a homogeneous half-space model in the analysis of endothelial cell micropipette measurements

Experimental studies have shown that endothelial cells which have been exposed to shear stress maintain a flattened and elongated shape after detachment. Their mechanical properties, which are studied using the micropipette experiments, are influenced by the level as well as the duration of the shear stress. In the present paper, we analyze these mechanical properties with the aid of two mathematical models suggested by the micropipette technique and by the geometry peculiar to these cells in their detached post-exposure state. The two models differ in their treatment of the contact zone between the cell and the micropipette. The main results are expressions for an effective Young's modulus for the cells, which are used in conjunction with the micropipette data to determine an effective Young's modulus for bovine endothelial cells, and to discuss the dependence of this modulus upon exposure to shear stress.     

Rheology of fibrin clots: III. Shear creep and creep recovery of fine ligated and coarse unligated clots

Creep and creep recovery of human fibrin clots in small shearing deformations have been investigated over a time scale from 24 to 10⁴ s. Coarse, unligated dots and fine dots ligated by fibrinoligase in the presence of calcium ions were studied to suppllement previous data on coarse ligated and fine unligated clots. Stress was found to be proportional to strain up to at least a maximum shear strain (in torsion geometry) of 2.6%. The initial modulus (25 s after imposition of stress) is proportional to approximately the 1.5 power of concentration for fine ligated and coarse unligated clots. For fine unligated clots, there is comparatively little creep subsequent to the initial deformation; ligation (in this case involving mostly the γ chains) reduces the creep to nearly zero. For coarse unligated dots, there is substantially more creep under constant stress, and creep recovery is not complete. legation (in this casa involving both γ and α chains) largely suppresses the creep and causes the recovery to be complete. If the structure is fully formed before creep begins, tests of creep recovery by the Boltzmann superposition principle show adherence to linear viscoelastic behavior for all four clot types. Otherwise, the Boltzmann test fails and the recovery is much less than calculated. For fine ligated clots, the observed recovery agrees well with that calculated on the basis of a dual structure model in which an additional independent structure is built up in the deformed state, so that the state of ease after removal of stress is a balance between two structures deformed in opposite senses, it is postulated that the coherence and elastic modulus of the fine ligated dot are largely due to steric blocking of long protofibrils with a high flexural stiffness. In the coarse clot, it is proposed that the structure involves extensive branching of thick bundles of protofibrils, which become permanently secured by the ligation of the α chains of the fibrin.     

Vibrational frequency shifts as a probe of hydrogen bonds: thermal expansion and glass transition of myoglobin in mixed solvents

The contribution of hydrogen bonds to protein-solvent interactions and their impact on structural flexibility and dynamics of myoglobin are discussed. The shift of vibrational peak frequencies with the temperature of myoglobin in sucrose/water and glycerol/water solutions is used to probe the expansion of the hydrogen bond network. We observe a characteristic change in the temperature slope of the O–H stretching frequency at the glass transition which correlates with the discontinuity of the thermal expansion coefficient. The temperature-difference spectra of the amide bands show the same tendency, indicating that stronger hydrogen bonding in the bulk affects the main-chain solvent interactions in parallel. However, the hydrogen bond strength decreases relative to the bulk solvent with increasing cosolvent concentration near the protein surface, which suggests preferential hydration. Weaker and/or fewer hydrogen bonds are observed at low degrees of hydration. The central O–H stretching frequency of protein hydration water is red-shifted by 40 cm^–1 relative to the bulk. The shift increases towards lower temperatures, consistent with contraction and increasing strength of the protein-water bonds. The temperature slope shows a discontinuity near 180 K. The contraction of the network has reached a critical limit which leads to frozen-in structures. This effect may represent the molecular mechanism underlying the dynamic transition observed for the mean square displacements of the protein atoms and the heme iron of myoglobin. Received: 10 July 1996 / Accepted: 10 April 1997