Molecular mechanics modeling of azobenzene-based photoswitches

We present an extension of the generalized amber force field to allow the modeling of azobenzenes by means of classical molecular mechanics. TD-DFT calculations were employed to derive different interaction models for 4-hydroxy-4'-methyl-azobenzene, including the ground (S(0)) and S(1) excited state. For both states, partial charges and the -N = N- torsion potentials were characterized. On this basis, we pave the way to large-scale model simulations involving azobenzene molecular switches. Using the example of an isolated molecule, the mechanics of cyclic switching processes are demonstrated by classical molecular dynamics simulations.     

The mechanics of neutrophils: synthetic modeling of three experiments

Much experimental data exist on the mechanical properties of neutrophils, but so far, they have mostly been approached within the framework of liquid droplet models. This has two main drawbacks: 1), It treats the cytoplasm as a single phase when in reality, it is a composite of cytosol and cytoskeleton; and 2), It does not address the problem of active neutrophil deformation and force generation. To fill these lacunae, we develop here a comprehensive continuum-mechanical paradigm of the neutrophil that includes proper treatment of the membrane, cytosol, and cytoskeleton components. We further introduce two models of active force production: a cytoskeletal swelling force and a polymerization force. Armed with these tools, we present computer simulations of three classic experiments: the passive aspiration of a neutrophil into a micropipette, the active extension of a pseudopod by a neutrophil exposed to a local stimulus, and the crawling of a neutrophil inside a micropipette toward a chemoattractant against a varying counterpressure. Principal results include: 1), Membrane cortical tension is a global property of the neutrophil that is affected by local area-increasing shape changes. We argue that there exists an area dilation viscosity caused by the work of unfurling membrane-storing wrinkles and that this viscosity is responsible for much of the regulation of neutrophil deformation. 2), If there is no swelling force of the cytoskeleton, then it must be endowed with a strong cohesive elasticity to prevent phase separation from the cytosol during vigorous suction into a capillary tube. 3), We find that both swelling and polymerization force models are able to provide a unifying fit to the experimental data for the three experiments. However, force production required in the polymerization model is beyond what is expected from a simple short-range Brownian ratchet model. 4), It appears that, in the crawling of neutrophils or other amoeboid cells inside a micropipette, measurement of velocity versus counterpressure curves could provide a determination of whether cytoskeleton-to-cytoskeleton interactions (such as swelling) or cytoskeleton-to-membrane interactions (such as polymerization force) are predominantly responsible for active protrusion.     

A cell-based framework for modeling cardiac mechanics

Cardiomyocytes are the functional building blocks of the heart—yet most models developed to simulate cardiac mechanics do not represent the individual cells and their surrounding matrix. Instead, they work on a homogenized tissue level, assuming that cellular and subcellular structures and processes scale uniformly. Here we present a mathematical and numerical framework for exploring tissue-level cardiac mechanics on a microscale given an explicit three-dimensional geometrical representation of cells embedded in a matrix. We defined a mathematical model over such a geometry and parametrized our model using publicly available data from tissue stretching and shearing experiments. We then used the model to explore mechanical differences between the extracellular and the intracellular space. Through sensitivity analysis, we found the stiffness in the extracellular matrix to be most important for the intracellular stress values under contraction. Strain and stress values were observed to follow a normal-tangential pattern concentrated along the membrane, with substantial spatial variations both under contraction and stretching. We also examined how it scales to larger size simulations, considering multicellular domains. Our work extends existing continuum models, providing a new geometrical-based framework for exploring complex cell–cell and cell–matrix interactions.

     

Multiscale modeling and mechanics of filamentous actin cytoskeleton

The adaptive structure and functional changes of the actin cytoskeleton are induced by its mechanical behavior at various temporal and spatial scales. In particular, the mechanical behaviors at different scales play important roles in the mechanical functions of various cells, and these multiscale phenomena require clarification. To establish a milestone toward achieving multiscale modeling and simulation, this paper reviews mathematical analyses and simulation methods applied to the mechanics of the filamentous actin cytoskeleton. The actin cytoskeleton demonstrates characteristic behaviors at every temporal and spatial scale, and mathematical models and simulation methods can be applied to each level of actin cytoskeletal structure ranging from the molecular to the network level. This paper considers studies on mathematical models and simulation methods based on the molecular dynamics, coarse-graining, and continuum dynamics approaches. Every temporal and spatial scale of actin cytoskeletal structure is considered, and it is expected that discrete and continuum dynamics ranging from functional expression at the molecular level to macroscopic functional expression at the whole cell level will be developed and applied to multiscale modeling and simulation.     

Homogenization modeling for the mechanics of perfused myocardium

Altered coronary perfusion can change the apparent diastolic stiffness of ventricular myocardium--the ‘garden hose’ effect. Our recent findings showed that myocardial strains are reduced during ventricular filling, primarily along the directions transverse to the coronary microvessels. In this article, we review hypotheses and theoretical models regarding the role that regional wall stress plays in the mechanical interaction between myocardium and coronary circulation. Various mechanisms have been used to explain the effects of the tissue stress on coronary flow, as well as the effect of coronary dynamics on myocardial mechanics. Many models of coronary pressure-flow relations using lumped parameter circuit analogs. Poroelasticity and swelling theories have been used to model the mechanics of perfused muscle. Here, we describe a new mathematical model of the mechanics of perfused myocardium derived using homogenization theory. In this model, perfused myocardium is treated as a nonlinear anisotropic elastic solid embedded with cylindrical vessels of known distensibility. The solid compartment is incompressible but the vascular compartment may change volume according to a simple relation between vessel diameter and perfusion pressure. The work done by the perfusion pressure in changing vascular volume contributes to the macroscopic strain energy and hence affects the stress and stiffness of the composite. Conversely, the stress in the tissue affects microvessel diameter and volume, since tractions transverse to the vessel axis oppose the internal blood pressure. Finite element simulations of passive filling show good agreement of model with experimental results.     

Muscle and prosthesis contributions to amputee walking mechanics: A modeling study

Unilateral, below-knee amputees have altered gait mechanics, which can significantly affect their mobility. Below-knee amputees lose the functional use of the ankle muscles, which are critical during walking to provide body support, forward propulsion, leg-swing initiation and mediolateral balance. Thus, either muscles must compensate or the prosthesis must provide the functional tasks normally provided by the ankle muscles. Three-dimensional (3D) forward dynamics simulations of amputee and non-amputee walking were generated to identify muscle and prosthesis contributions to amputee walking mechanics, including the subtasks of body support, forward propulsion, leg-swing initiation and mediolateral balance. Results showed that the prosthesis provided body support in the absence of the ankle muscles. The prosthesis contributed to braking from early to mid-stance and propulsion in late stance. The prosthesis also functioned like the uniarticular soleus muscle by transferring energy from the residual leg to the trunk to provide trunk propulsion. The residual-leg vasti and rectus femoris reduced their contributions to braking in early stance, which mitigated braking from the prosthesis during this period. The prosthesis did not replace the function of the gastrocnemius, which normally generates energy to the leg to initiate swing. As a result, lower overall energy was delivered to the residual leg. The prosthesis also acted to accelerate the body laterally in the absence of the ankle muscles. These results provide further insight into muscle and prosthesis function in below-knee amputee walking and can help guide rehabilitation methods and device designs to improve amputee mobility.     

Explicit finite element modeling of total knee replacement mechanics

Joint kinematics and contact mechanics dictate the success of current total knee replacement (TKR) devices. Efficient computer models present an effective way of evaluating these characteristics. Predicted contact stress and area due to articulations at the tibio-femoral and patello-femoral interfaces indicate potential clinical performance. Previous finite element (FE) knee models have generally been used to predict contact stresses and/or areas during static or quasi-static loading conditions. Explicit dynamic FE analyses have recently been used to efficiently predict TKR kinematics and contact mechanics during dynamic loading conditions. The objective of this study was to develop and experimentally validate an explicit FE TKR model that incorporates tibio-femoral and patello-femoral articulations. For computational efficiency, we developed rigid body analyses that can reasonably reproduce the kinematics, contact pressure distribution, and contact area of a fully deformable system. Results from the deformable model showed that the patello-femoral and tibio-femoral kinematics were in good agreement with experimental knee simulator measurements. Kinematic results from the rigid body analyses were nearly identical to those from the fully deformable model, and the contact pressure and contact area correlation was acceptable given the great reduction in analysis time. Component mesh density studied had little effect on the predicted kinematics, particularly for the patellar component, and small effects on the predicted contact pressure and area. These analyses have shown that, at low computational cost, a force-control dynamic simulation of a gait cycle can yield useful and predictable results.     

Structural mechanics modeling reveals stress-adaptive features of cutaneous scars

Biomechanics and Modeling in Mechanobiology - The scar is a predominant outcome of adult mammalian wound healing despite being associated with partial function loss. Here in this paper, we have...     

Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling

Soluble epoxide hydrolase (sEH) is an enzyme involved in drug metabolism that catalyzes the hydrolysis of epoxides to form their corresponding diols. sEH has a broad substrate range and shows high regio- and enantioselectivity for nucleophilic ring opening by Asp333. Epoxide hydrolases therefore have potential synthetic applications. We have used combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations (at the AM1/CHARMM22 level) and high-level ab initio (SCS-MP2) QM/MM calculations to analyze the reactions, and determinants of selectivity, for two substrates: trans-stilbene oxide (t-SO) and trans-diphenylpropene oxide (t-DPPO). The calculated free energy barriers from the QM/MM (AM1/CHARMM22) umbrella sampling MD simulations show a lower barrier for phenyl attack in t-DPPO, compared with that for benzylic attack, in agreement with experiment. Activation barriers in agreement with experimental rate constants are obtained only with the highest level of QM theory (SCS-MP2) used. Our results show that the selectivity of the ring-opening reaction is influenced by several factors, including proximity to the nucleophile, electronic stabilization of the transition state, and hydrogen bonding to two active site tyrosine residues. The protonation state of His523 during nucleophilic attack has also been investigated, and our results show that the protonated form is most consistent with experimental findings. The work presented here illustrates how determinants of selectivity can be identified from QM/MM simulations. These insights may also provide useful information for the design of novel catalysts for use in the synthesis of enantiopure compounds.     

Fracture mechanics modeling of popping event during daughter cell separation

Most bacteria cells divide by binary fission which is part of a bacteria cell cycle and requires tight regulations and precise coordination. Fast separation of Staphylococcus Aureus (S. Aureus) daughter cells, named as popping event, has been observed in recent experiments. The popping event was proposed to be driven by mechanical crack propagation in the peripheral ring which connected two daughter cells before their separation. It has also been shown that after the fast separation, a small portion of the peripheral ring was left as a hinge. In the article, we develop a fracture mechanics model for the crack growth in the peripheral ring during S. Aureus daughter cell separation. In particular, using finite element analysis, we calculate the energy release rate associated with the crack growth in the peripheral ring, when daughter cells are inflated by a uniform turgor pressure inside. Our results show that with a fixed inflation of daughter cells, the energy release rate depends on the crack length non-monotonically. The energy release rate reaches a maximum value for a crack of an intermediate length. The non-monotonic relationship between the energy release rate and crack length clearly indicates that the crack propagation in the peripheral ring can be unstable. The computed energy release rate as a function of crack length can also be used to explain the existence of a small portion of peripheral ring remained as hinge after the popping event.     

Integrating GIS and remote sensing for vegetation analysis and modeling: methodological issues

Abstract. GIS and remote sensing have emerged as distinct spatial data handling technologies with their own methods of data representation and analysis. Combining them as tools to support vegetation analysis and modeling thus presents a number of challenges. The paper begins by describing the major data sources, applications, and software characteristics of each technology, and then compares them within a consistent terminological framework that emphasizes the digital representation of continuously varying spatial data. Because the spatial continuum can be discretized in many different ways, and because each can only approximate the truth, both GIS and remote sensing are subject to error and uncertainty. Integration, and subsequent analysis and modeling, require that explicit attention be directed to uncertainty. The paper reviews the models of error that have been developed in recent years for spatial data and examines their use in the interface between GIS and remote sensing. The paper looks at the functional requirements of modeling, and includes discussion of error propagation.     

Selecting near-native conformations in homology modeling: the role of molecular mechanics and solvation terms

A free energy function, combining molecular mechanics energy with empirical solvation and entropic terms, is used for ranking near-native conformations that occur in the conformational search steps of homology modeling, i.e., side-chain search and loop closure calculations. Correlations between the free energy and RMS deviation from the X-ray structure are established. It is shown that generally both molecular mechanics and solvation/entropic terms should be included in the potential. The identification of near-native backbone conformations is accomplished primarily by the molecular mechanics term that becomes the dominant contribution to the free energy if the backbone is even slightly strained, as frequently occurs in loop closure calculations. Both terms become equally important if a sufficiently accurate backbone conformation is found. Finally, the selection of the best side-chain positions for a fixed backbone is almost completely governed by the solvation term. The discriminatory power of the combined potential is demonstrated by evaluating the free energies of protein models submitted to the first meeting on Critical Assessment of techniques for protein Structure Prediction (CASP1), and comparing them to the free energies of the native conformations.     

An inverse modeling approach for semilunar heart valve leaflet mechanics: exploitation of tissue structure

Determining the biomechanical behavior of heart valve leaflet tissues in a noninvasive manner remains an important clinical goal. While advances in 3D imaging modalities have made in vivo valve geometric data available, optimal methods to exploit such information in order to obtain functional information remain to be established. Herein we present and evaluate a novel leaflet shape-based framework to estimate the biomechanical behavior of heart valves from surface deformations by exploiting tissue structure. We determined accuracy levels using an “ideal” in vitro dataset, in which the leaflet geometry, strains, mechanical behavior, and fibrous structure were known to a high level of precision. By utilizing a simplified structural model for the leaflet mechanical behavior, we were able to limit the number of parameters to be determined per leaflet to only two. This approach allowed us to dramatically reduce the computational time and easily visualize the cost function to guide the minimization process. We determined that the image resolution and the number of available imaging frames were important components in the accuracy of our framework. Furthermore, our results suggest that it is possible to detect differences in fiber structure using our framework, thus allowing an opportunity to diagnose asymptomatic valve diseases and begin treatment at their early stages. Lastly, we observed good agreement of the final resulting stress–strain response when an averaged fiber architecture was used. This suggests that population-averaged fiber structural data may be sufficient for the application of the present framework to in vivo studies, although clearly much work remains to extend the present approach to in vivo problems.     

MRI-based modeling for radiocarpal joint mechanics: validation criteria and results for four specimen-specific models

The objective of this study was to validate the MRI-based joint contact modeling methodology in the radiocarpal joints by comparison of model results with invasive specimen-specific radiocarpal contact measurements from four cadaver experiments. We used a single validation criterion for multiple outcome measures to characterize the utility and overall validity of the modeling approach. For each experiment, a Pressurex film and a Tekscan sensor were sequentially placed into the radiocarpal joints during simulated grasp. Computer models were constructed based on MRI visualization of the cadaver specimens without load. Images were also acquired during the loaded configuration used with the direct experimental measurements. Geometric surface models of the radius, scaphoid and lunate (including cartilage) were constructed from the images acquired without the load. The carpal bone motions from the unloaded state to the loaded state were determined using a series of 3D image registrations. Cartilage thickness was assumed uniform at 1.0 mm with an effective compressive modulus of 4 MPa. Validation was based on experimental versus model contact area, contact force, average contact pressure and peak contact pressure for the radioscaphoid and radiolunate articulations. Contact area was also measured directly from images acquired under load and compared to the experimental and model data. Qualitatively, there was good correspondence between the MRI-based model data and experimental data, with consistent relative size, shape and location of radioscaphoid and radiolunate contact regions. Quantitative data from the model generally compared well with the experimental data for all specimens. Contact area from the MRI-based model was very similar to the contact area measured directly from the images. For all outcome measures except average and peak pressures, at least two specimen models met the validation criteria with respect to experimental measurements for both articulations. Only the model for one specimen met the validation criteria for average and peak pressure of both articulations; however the experimental measures for peak pressure also exhibited high variability. MRI-based modeling can reliably be used for evaluating the contact area and contact force with similar confidence as in currently available experimental techniques. Average contact pressure, and peak contact pressure were more variable from all measurement techniques, and these measures from MRI-based modeling should be used with some caution.     

Brain temperature and limits on transcranial cooling in humans: quantitative modeling results

Selective brain cooling (SBC) of varying strengths has been demonstrated in a number of mammals and appears to play a role in systemic thermoregulation. Although primates lack obvious specialization for SBC, the possibility of brain cooling in humans has been debated for many years. This paper reports on the use of mathematical modeling to explore whether surface cooling can control effectively the temperature of the human cerebrum. The brain was modeled as a hemisphere with a volume of 1.33 1 and overlying layers of cerebrospinal fluid, skull, and scalp. Each component was assigned appropriate dimensions, physical properties and physiological characteristics that were determined from the literature. The effects of blood flow and of thermal conduction were modeled using the steady-state form of the bio-heat equation. Input parameters included core (arterial) temperature: normal (37°C) or hyperthermic (40°C), air temperature: warm (30°C) or hot (40°C), and sweat evaporation rate: 0, 0.25, or 0.50 l · m⁻² · h⁻¹. The resulting skin temperatures of the model ranged from 31.8°C to 40.2°C, values which are consistent with data obtained from the literature. Cerebral temperatures were generally insensitive to surface conditions (air temperature and evaporation rate), which affected only the most superficial level of the cerebrum (≤1.5 mm) The remaining parenchymal temperatures were 0.2–0.3°C above arterial temperatures, regardless of surface conditions. This held true even for the worst-case conditions combining core hyperthermia in a hot environment with zero evaporative cooling. Modeling showed that the low surface-to-volume ratio, low tissue conductivity, and high rate of cerebral perfusion combine to minimize the potential impact of surface cooling, whether by transcranial venous flow or by conduction through intervening layers to the skin or mucosal surfaces. The dense capillary network in the brain assures that its temperature closely follows arterial temperature and is controlled through systemic thermoregulation independent of head surface temperature. A review of the literature reveals several independent lines of evidence which support these findings and indicate the absence of functionally significant transcranial venous flow in either direction. Given the fact that humans sometimes work under conditions which produce face and scalp temperatures that are above core temperature, a transcranial thermal link would not necessarily protect the brain, but might instead increase its vulnerability to environmentally induced thermal injury. Accepted: 11 March 1998     

Brain functional network modeling and analysis based on fMRI: a systematic review

In recent years, the number of patients with neurodegenerative diseases (i.e., Alzheimer’s disease, Parkinson’s disease, mild cognitive impairment) and mental disorders (i.e., depression, anxiety and schizophrenia) have increased dramatically. Researchers have found that complex network analysis can reveal the topology of brain functional networks, such as small-world, scale-free, etc. In the study of brain diseases, it has been found that these topologies have undergoed abnormal changes in different degrees. Therefore, the research of brain functional networks can not only provide a new perspective for understanding the pathological mechanism of neurological and psychiatric diseases, but also provide assistance for the early diagnosis. Focusing on the study of human brain functional networks, this paper reviews the research results in recent years. First, this paper introduces the background of the study of brain functional networks under complex network theory and the important role of topological properties in the study of brain diseases. Second, the paper describes how to construct a brain functional network using neural image data. Third, the common methods of functional network analysis, including network structure analysis and disease classification, are introduced. Fourth, the role of brain functional networks in pathological study, analysis and diagnosis of brain functional diseases is studied. Finally, the paper summarizes the existing studies of brain functional networks and points out the problems and future research directions.     

A porous-medium approach for modeling heart mechanics. I. theory

A method is developed for evaluating the distribution of the blood pressure, stresses and strains of the muscle fibers, and motion of the cardiac wall due to the cyclic contractions of the heart. The cardiac system is subdivided into two media: the chambers and the wall; the latter is enclosed by two impermeable surfaces (with one interface separating the two media and the other confining the wall). The momentum balance equation for the blood in the (two) cardiac ventricles is averaged, yielding a modification of Forchheimer's law, namely inclusion of the time derivative of the flux. The contracting muscle provides the driving force for the blood flow, and the endocardial velocity is thus taken as identical to that of the blood in the cavity next to the wall. Translation of the endocardium is governed by the blood pressure gradients in the ventricles. The blood pressure and stress-strain pattern in the myocardium are analyzed by applying concepts of the theory of mixtures to the blood and to the saturated solid matrix. With the blood pressure simulated by a modified Darcy law with relative fluid-solid velocity, fiber stresses and strains can be assessed with the aid of appropriate constitutive and compatibility laws.     

Quantitative modeling identifies critical cell mechanics driving bile duct lumen formation

Biliary ducts collect bile from liver lobules, the smallest functional and anatomical units of liver, and carry it to the gallbladder. Disruptions in this process caused by defective embryonic development, or through ductal reaction in liver disease have a major impact on life quality and survival of patients. A deep understanding of the processes underlying bile duct lumen formation is crucial to identify intervention points to avoid or treat the appearance of defective bile ducts. Several hypotheses have been proposed to characterize the biophysical mechanisms driving initial bile duct lumen formation during embryogenesis. Here, guided by the quantification of morphological features and expression of genes in bile ducts from embryonic mouse liver, we sharpened these hypotheses and collected data to develop a high resolution individual cell-based computational model that enables to test alternative hypotheses in silico. This model permits realistic simulations of tissue and cell mechanics at sub-cellular scale. Our simulations suggest that successful bile duct lumen formation requires a simultaneous contribution of directed cell division of cholangiocytes, local osmotic effects generated by salt excretion in the lumen, and temporally-controlled differentiation of hepatoblasts to cholangiocytes, with apical constriction of cholangiocytes only moderately affecting luminal size.