Effects of lipid saturation on bicelle to vesicle transition of a binary phospholipid mixture: a molecular dynamics simulation study.

Controlling the transition from lipid bicelles to vesicles is essential for producing engineered vesicles. We perform coarse-grained molecular dynamics (CGMD) simulations of unsaturated/saturated lipid mixtures to clarify the effects of lipid unsaturation on vesiculation at the molecular scale. The results demonstrate that vesiculation depends on the concentration of unsaturated lipids and the degree of unsaturation. The probability of vesiculation increases linearly with the apparent unsaturated lipid concentration at a low degree of unsaturation. Higher degrees of unsaturation lead to phase segregation within the binary bicelles, reducing the probability of vesiculation. A comparison between CGMD simulations and the conventional theory of vesiculation shows that the theoretical predictions of binary lipid systems must explicitly include phase segregation effects. Furthermore, simulations with biased lipid distributions reveal that vesiculation is facilitated by the preconcentration of unsaturated lipids in the core region of the bicelle but is then temporally limited as the unsaturated lipids move to the bicelle edges. These findings advance theoretical and experimental studies on binary lipid systems and promote the development of tailor-made vesicles.

Changes in free energy barrier for water permeation by stretch-induced phase transitions in phospholipid/cholesterol bilayers.

Water permeation through phospholipid/cholesterol bilayers is the key to understanding tension-induced rupture of biological cell membranes. We performed molecular dynamics simulations of stretched phospholipid/cholesterol bilayers to investigate changes in the free energy profile of water molecules across the bilayer and the lipid structure responsible for water permeation. We modeled stretching of the bilayer by applying areal strain. In stretched phospholipid/cholesterol bilayers, the hydrophobic tail of the phospholipids became disordered and the free energy barrier to water permeation decreased. Upon exceeding the critical areal strain, a phase transition to an interdigitated gel phase occurred before rupture, and the hydrophobic tail ordering as well as the free energy barrier were restored. In pure phospholipid bilayers, we did not observe such recoveries. These transient recoveries in the phospholipid/cholesterol bilayer suppressed water permeation and membrane rupture, followed by an increase in the critical areal strain at which the bilayer ruptured. This result agrees with experimental results and provides a reasonable molecular mechanism for the toughness of phospholipid/cholesterol bilayers under tension.Communicated by Ramaswamy H. Sarma.

Shear-flow-induced negative tension of phospholipid bilayer: Molecular dynamics simulation.

Shear flow has been theoretically predicted to suppress the undulation of surfactant bilayers and generate negative tension, which is considered to be a driving force of the transition from the lamellar phase to the multilamellar vesicle phase in surfactant/water suspensions, the so-called onion transition. We performed coarse-grained molecular dynamics simulations of a single phospholipid bilayer under shear flow to clarify the relationship between the shear rate, bilayer undulation, and negative tension, providing molecular-level insight into the undulation suppression. An increasing shear rate suppressed bilayer undulation and increased negative tension; these results are consistent with theoretical predictions. The non-bonded forces between the hydrophobic tails facilitated negative tension, whereas the bonded forces within the tails suppressed it. The force components of the negative tension were anisotropic in the bilayer plane and prominently changed in the flow direction, although the resultant tension was isotropic. Our findings regarding a single bilayer will underlie further simulation studies of multilamellar bilayers, including inter-bilayer interactions and topological changes of bilayers under shear flow, which are essential for the onion transition and are unresolved in the theoretical and experimental studies.

Mathematical modeling of pulmonary acinus structure: Verification of acinar shape effects on pathway structure using rat lungs.

The pulmonary acinus is the gas exchange unit in the lung and has a very complex microstructure. The structure model is essential to understand the relationship between structural heterogeneity and mechanical phenomena at the acinus level with computational approaches. We propose an acinus structure model represented by a cluster of truncated octahedra in conical, double-conical, inverted conical, or chestnut-like conical confinement to accommodate recent experimental information of rodent acinar shapes. The basis of the model is the combined use of Voronoi and Delaunay tessellations and the optimization of the ductal tree assuming the number of alveoli and the mean path length as quantities related to gas exchange. Before applying the Voronoi tessellation, controlling the seed coordinates enables us to model acinus with arbitrary shapes. Depending on the acinar shape, the distribution of path length varies. The lengths are more widely spread for the cone acinus, with a bias toward higher values, while most of the lengths for the inverted cone acinus primarily take a similar value. Longer pathways have smaller tortuosity and more generations, and duct length per generation is almost constant irrespective of generation, which agrees well with available experimental data. The pathway structure of cone and chestnut-like cone acini is similar to the surface acini's features reported in experiments. According to space-filling requirements in the lung, other conical acini may also be acceptable. The mathematical acinus structure model with various conical shapes can be a platform for computational studies on regional differences in lung functions along the lung surface, underlying respiratory physiology and pathophysiology.

Kelvin-Helmholtz-like instability of phospholipid bilayers under shear flow: System-size dependence.

We performed a series of molecular dynamics (MD) simulations of phospholipid bilayers under shear flow to estimate the effect of the system size on Kelvin-Helmholtz (KH)-like instability of the bilayer at the molecular scale. To extend the estimation by the MD simulations to the microscale, we introduced linear stability analysis for the fluid-fluid interface consisting of a thin membrane. For both the MD simulations and theoretical model, the critical velocity difference across the bilayer, where instability occurs, decreased with increasing wavelength of the bilayer undulation λ, which corresponds to the system size. When λ was more than about ten times larger than the bilayer thickness, the critical velocity difference in the MD simulations was in quantitative agreement with that obtained by the theoretical model. This means that the theoretical model is applicable for the shear-induced KH-like instability of the bilayer for large λ. The theoretical model showed that the critical velocity difference for the KH-like instability was proportional to λ^{-3/2}. Based on these results, we discuss the implications of the shear-induced bilayer instability in the shear-induced cell damage observed in experiments.

Targeting inhaled fibers to the pulmonary acinus: Opportunities for augmented delivery from in silico simulations.

Non-spherical particles, and fibers in particular, are potentially attractive airborne carriers for pulmonary drug delivery. Not only do they exhibit a high surface-to-volume ratio relative to spherical aerosols, but their aerodynamic properties also enable them to reach deep into the lungs. Until present, however, our understanding of the deposition characteristics of inhaled aerosols in the distal acinar lung regions has been mostly limited to spheres. To shed light on the fate of elongated aerosols in the pulmonary depths, we explore through in silico numerical simulations the deposition and dispersion characteristics of ellipsoid-shaped fibers in a physiologically-realistic acinar geometry under oscillatory breathing flow conditions mimicking various inhalation maneuvers. The transient translation and rotational movement of micron-sized elongated particles under drag, lift, and gravitational forces are simulated as a function of size (dp) and aspect ratio (AR). Our findings underscore how acinar deposition characteristics are intimately linked to the geometrical combination of dp and AR under oscillatory flow conditions. Surprisingly, the elongation of the traditionally recommended size range of spherical particles (i.e., 2-3 µm) for acinar deposition may lead to a decrease in deposition efficiency and dispersion. Instead, our findings advocate how elongating particles (i.e., high AR) in the larger size range of 4-6 µm might be leveraged for improved targeted deposition to the acinar regions. Together, these results point to new windows of opportunities in selecting the shape and size of micron-sized fibers for targeted pulmonary deposition. Such in silico efforts represent an essential stepping stone in further exploring aerosol drug carrier designs for inhalation therapy to the deep lungs.

Bicelle-to-Vesicle Transition of a Binary Phospholipid Mixture Guided by Controlled Local Lipid Compositions: A Molecular Dynamics Simulation Study.

An essential step of nanoliposome formation in an aqueous lipid solution is the transition from discoidal lipid aggregate (bicelle) to vesicle. We investigate here the bicelle-to-vesicle transition of a binary lipid mixture of saturated and unsaturated phosphatidylcholine by performing nonequilibrium molecular dynamics simulations with the coarse-grained representation of di-palmitoyl-phosphatidyl-choline (DPPC) and di-linoleoyl-phosphatidyl-choline (DLiPC). When the DPPC molecules of a stable DPPC bicelle are randomly replaced with the DLiPC molecules, the transition occurs for higher apparent DLiPC concentrations. On the other hand, when the DPPC molecules only in the core region of the bicelle are replaced, the transition occurs even for lower apparent DLiPC concentrations. For the bicelle where the head and tail layers are pure DPPC and DLiPC monolayers, respectively, the side of the DLiPC monolayer becomes the concave surface of bending bicelle. Controlling the local lipid compositions in a binary lipid bicelle has the potential to determine the success of vesicle formation and the direction of bicelle bending. Our findings help explain nanoliposome formation with sonication and give useful information for controlling encapsulation efficiencies of nanoliposomes.

Heterogeneous structure and surface tension effects on mechanical response in pulmonary acinus: A finite element analysis.

BACKGROUND: The pulmonary acinus is a dead-end microstructure that consists of ducts and alveoli. High-resolution micro-CT imaging has recently provided detailed anatomical information of a complete in vivo acinus, but relating its mechanical response with its detailed acinar structure remains challenging. This study aimed to investigate the mechanical response of acinar tissue in a whole acinus for static inflation using computational approaches. METHODS: We performed finite element analysis of a whole acinus for static inflation. The acinar structure model was generated based on micro-CT images of an intact acinus. A continuum mechanics model of the lung parenchyma was used for acinar tissue material model, and surface tension effects were explicitly included. An anisotropic mechanical field analysis based on a stretch tensor was combined with a curvature-based local structure analysis. FINDINGS: The airspace of the acinus exhibited nonspherical deformation as a result of the anisotropic deformation of acinar tissue. A strain hotspot occurred at the ridge-shaped region caused by a rod-like deformation of acinar tissue on the ridge. The local structure becomes bowl-shaped for inflation and, without surface tension effects, the surface of the bowl-shaped region primarily experiences isotropic deformation. Surface tension effects suppressed the increase in airspace volume and inner surface area, while facilitating anisotropic deformation on the alveolar surface. INTERPRETATION: In the lungs, the heterogeneous acinar structure and surface tension induce anisotropic deformation at the acinar and alveolar scales. Further research is needed on structural variation of acini, inter-acini connectivity, or dynamic behavior to understand multiscale lung mechanics.

Stretch-Induced Interdigitation of a Phospholipid/Cholesterol Bilayer.

The interdigitated gel (LßI) phase is one of the membrane phases of phospholipid molecules in which the hydrophobic tails of the phospholipid molecules penetrate the opposite leaflet of the bilayer. Recent molecular dynamics (MD) simulations have shown that interdigitation can take place as a phase transition from the liquid-ordered (Lo) phase to the LßI phase under stretching. However, there is still no conclusive experimental evidence for this process, so its existence remains controversial. In this study, to explain the transition from energy balance, we propose a free-energy model. The model consists of three energy components: the elastic deformation energy, surface energy at the bilayer-water interface, and interphase boundary energy. To determine the parameters of the model, we perform MD simulations of a stretched 1,2-dipalmitoyl- sn-glycero-3-phosphocholine/cholesterol bilayer. The phase diagrams from our model are in good agreement with those obtained from MD simulations. The energy balance among the components in the stretched bilayer quantitatively explains the stretch-induced transition. In the model, increasing the system size to that used in experiments shows that interdigitation is favorable for rigid bilayers under stretching or in alcohol solutions. These results suggest that the stretch-induced interdigitation might be observed in microscopic experiments.

Morphological Characterization of Acinar Cluster in Mouse Lung Using a Multiscale-based Segmentation Algorithm on Synchrotron Micro-CT Images.

Understanding the three-dimensional morphology of pulmonary acini is essential when exploring the biomechanics of respiratory function. In this study, we characterized the morphology of individual acini and a cluster of acini stemming from the same terminal conducting airway using a quantitative approach based on the semi-automatic segmentation of synchrotron micro-CT images of mouse lung. The volume and surface area of five clusters of mouse acini including 50 individual acini were estimated based on the voxel and surface mesh of segmented acini at FRC. The pathway length and width were estimated for one cluster including 15 acini based on the skeleton of segmented acini. The acinar volume was 0.09 ± 0.07 mm(3) (mean ± SD), and the surface area was 6.82 ± 4.49 mm(2) , in agreement with previous studies. The volume of the acinar clusters was 0.89 ± 0.34 mm(3) , and the surface area was 68.18 ± 17.66 mm(2) . The largest volume acinus per cluster was found in the distal region of the terminal conducting airway, and apparent respiratory bronchioles were observed only in large-volume acini. The generation number of pathways per acinus was 8 ± 2 (range: 6-12). The pathway length at lower generations (generations 2-6) increased with the generation number in a single cluster, while did not significantly change at lower generations in some acinar groups. The pathway width increased with increasing generation numbers. Our approach characterized the quantitative morphology of pulmonary acinar clusters in mouse lung, and the results can be used in further biomechanical simulation studies. Anat Rec, 299:1424-1434, 2016. © 2016 Wiley Periodicals, Inc.

Collapse of a lipid-coated nanobubble and subsequent liposome formation.

We investigate the collapse of a lipid-coated nanobubble and subsequent formation of a lipid vesicle by coarse grained molecular dynamics simulations. A spherical nanobubble coated with a phospholipid monolayer in water is a model of an aqueous dispersion of phospholipids under negative pressure during sonication. When subjected to a positive pressure, the bubble shape deforms into an irregular spherical shape and the monolayer starts to buckle and fold locally. The local folds grow rapidly in multiple directions and forming a discoidal membrane with folds of various amplitudes. Folds of small amplitude disappear in due course and the membrane develops into a unilamellar vesicle via a bowl shape. Folds with large amplitude develop into a bowl shape and a multivesicular shape forms. The membrane shape due to bubble collapse can be an important factor governing the vesicular shape during sonication.

Effects of Stretching Speed on Mechanical Rupture of Phospholipid/Cholesterol Bilayers: Molecular Dynamics Simulation.

Rupture of biological cell membrane under mechanical stresses is critical for cell viability. It is triggered by local rearrangements of membrane molecules. We investigated the effects of stretching speed on mechanical rupture of phospholipid/cholesterol bilayers using unsteady molecular dynamics simulations. We focused on pore formation, the trigger of rupture, in a 40 mol% cholesterol-including bilayer. The unsteady stretching was modeled by proportional and temporal scaling of atom positions at stretching speeds from 0.025 to 30 m/s. The effects of the stretching speed on the critical areal strain, where the pore forms, is composed of two regimes. At low speeds (<1.0 m/s), the critical areal strain is insensitive to speed, whereas it significantly increases at higher speeds. Also, the strain is larger than that of a pure bilayer, regardless of the stretching speeds, which qualitatively agrees with available experimental data. Transient recovery of the cholesterol and phospholipid molecular orientations was evident at lower speeds, suggesting the formation of a stretch-induced interdigitated gel-like phase. However, this recovery was not confirmed at higher speeds or for the pure bilayer. The different responses of the molecular orientations may help explain the two regimes for the effect of stretching speed on pore formation.

Mathematical model of a heterogeneous pulmonary acinus structure.

The pulmonary acinus is a gas exchange unit distal to the terminal bronchioles. A model of its structure is important for the computational investigation of mechanical phenomena at the acinus level. We propose a mathematical model of a heterogeneous acinus structure composed of alveoli of irregular sizes, shapes, and locations. The alveoli coalesce into an intricately branched ductal tree, which meets the space-filling requirement of the acinus structure. Our model uses Voronoi tessellation to generate an assemblage of the alveolar or ductal airspace, and Delaunay tessellation and simulated annealing for the ductal tree structure. The modeling condition is based on average acinar and alveolar volume characteristics from published experimental information. By applying this modeling technique to the acinus of healthy mature rats, we demonstrate that the proposed acinus structure model reproduces the available experimental information. In the model, the shape and size of alveoli and the length, generation, tortuosity, and branching angle of the ductal paths are distributed in several ranges. This approach provides a platform for investigating the heterogeneous nature of the acinus structure and its relationship with mechanical phenomena at the acinus level.

Computational studies on strain transmission from a collagen gel construct to a cell and its internal cytoskeletal filaments.

We developed a mechanical tissue model containing a cell with cytoskeletal filaments inside to investigate how tissue deformation is reflected in the deformation of a cell and its internal cytoskeletal filaments. Tissue that assumes a collagen gel construct was depicted as an isotropic linear elastic material, and the cell was modeled as an assembly of discrete elements including a cell membrane, nuclear envelope, and cytoskeletal filaments. Mechanical behaviors were calculated based on the minimum energy principle. The results demonstrated the effects of the type of tissue deformation on deformations of cytoskeletal filaments. The distribution of strains of cytoskeletal filaments was skewed toward compression when a tissue was stretched, toward stretch when the tissue was compressed, and almost normal when the tissue was sheared. The results also addressed the dependency of deformations of a cell and cytoskeletal filaments on the ratio of the Young's modulus of a tissue to that of a cell. Upon tissue stretching, cell strain increased and the distribution of strains of cytoskeletal filaments broadened on both stretch and compression sides with an increase in the Young's modulus ratio. This suggested that the manner of tissue deformation and the tissue/cell Young's modulus ratio are reflected in the distribution pattern of strains of cytoskeletal filaments. The present model is valuable to understanding the mechanisms of cellular responses in a tissue.

Molecular dynamics simulations of pore formation in stretched phospholipid/cholesterol bilayers.

Molecular dynamics (MD) simulations of pore formation in stretched dipalmitoylphosphatidylcholine (DPPC) bilayers containing different concentrations of cholesterol (0, 20, 40, and 60 mol%) are presented. The stretched bilayers were simulated by constant NPZA||T MD simulations with various constant areas. The effects of the cholesterol concentration on pore formation are examined in terms of the critical areal strain where the pore is formed, the processes of pore formation, and the change in molecular orientation of the DPPC molecules by analyzing the order parameters and radial distribution functions of the DPPC molecules. With increasing cholesterol concentration, the critical areal strain initially increases, peaks at 40 mol%, and then decreases, which agrees well with the available experimental data. For the bilayers containing cholesterol, DPPC molecules become disordered at low areal strains, whereas the order slightly increases when the areal strain exceeds a certain value depending on the cholesterol concentration. For 40 mol% cholesterol, the two monolayers in the bilayer interpenetrate under high areal strains, inducing an increase of the order parameters and the peak positions of the radial distribution function compared with their states at low areal strains, indicating the formation of an interdigitated gel-phase-like structure. The transient increasing of the order of the molecular orientations may inhibit water penetration into the bilayer, resulting in increased critical areal strain in the phospholipid/cholesterol bilayers.

A semiautomatic segmentation algorithm for extracting the complete structure of acini from synchrotron micro-CT images.

Pulmonary acinus is the largest airway unit provided with alveoli where blood/gas exchange takes place. Understanding the complete structure of acinus is necessary to measure the pathway of gas exchange and to simulate various mechanical phenomena in the lungs. The usual manual segmentation of a complete acinus structure from their experimentally obtained images is difficult and extremely time-consuming, which hampers the statistical analysis. In this study, we develop a semiautomatic segmentation algorithm for extracting the complete structure of acinus from synchrotron micro-CT images of the closed chest of mouse lungs. The algorithm uses a combination of conventional binary image processing techniques based on the multiscale and hierarchical nature of lung structures. Specifically, larger structures are removed, while smaller structures are isolated from the image by repeatedly applying erosion and dilation operators in order, adjusting the parameter referencing to previously obtained morphometric data. A cluster of isolated acini belonging to the same terminal bronchiole is obtained without floating voxels. The extracted acinar models above 98% agree well with those extracted manually. The run time is drastically shortened compared with manual methods. These findings suggest that our method may be useful for taking samples used in the statistical analysis of acinus.

Molecular dynamics simulations of pore formation dynamics during the rupture process of a phospholipid bilayer caused by high-speed equibiaxial stretching.

Rupture of a phospholipid bilayer under mechanical stresses is triggered by pore formation in an intact bilayer. To understand the molecular details of the dynamics of pore formation we perform molecular dynamics simulations of a phospholipid bilayer under two different equibiaxial stretching conditions: first, unsteady stretching with various stretching speeds in the range of 0.1-1.0m/s, and second, quasistatic stretching. We analyze (i) patterns of pore formation, (ii) the critical area where a pore forms, (iii) the deformation of the bilayer, and (iv) the apparent breaking force. With stretching, the bilayer deforms anisotropically due to lipid chain packing and water penetrating into the hydrophilic region of the bilayer, and when the area exceeds a critical value, water filled pore structure penetrating the bilayer forms and develops into a large pore, resulting in rupture. For a high stretching speed, small pores (multipore) can temporarily form in a small area. It has been statistically determined that the probability of the multipore formation, the critical areal strain, and the apparent breaking force increase with the stretching speed in the range of 0-50%, 0.8-2.0, and 250-400 pN, respectively. The results qualitatively agree with the experimental and other simulation results, and rationalize the leakage of hemoglobin from erythrocytes in shock wave experiments.

Self-organization of a stable pore structure in a phospholipid bilayer.

We demonstrate the self-organization process of a stable pore structure in a phospholipid bilayer by unsteady and nonequilibrium molecular dynamics simulations. The simulation is started from an initial state including some amount of water molecules in its hydrophobic region, which is a model of a cell membrane stimulated by ultrasound radiation for the membrane permeabilization (sonoporation). We show that, in several nanoseconds, the bilayer-water system can spontaneously develop into a water-filled pore structure without any mechanical and electrical forcing from outside, when the initial number of water molecules in the hydrophobic region exceeds a critical value. The increase in the initial number of water molecules enhances the probability of pore formation, and sometimes induces the formation of transient micellelike structures of phospholipid molecules.

Molecular dynamics simulation of structural changes of lipid bilayers induced by shock waves: Effects of incident angles.

Unsteady and nonequilibrium molecular dynamics simulations of the response of dipalmitoylphosphatidylcholine (DPPC) bilayers to the shock waves of various incident angles are presented. The action of an incident shock wave is modeled by adding a momentum in an oblique direction to water molecules adjacent to a bilayer. We thereby elucidate the effects of incident shock angles on (i) collapse and rebound of the bilayer, (ii) lateral displacement of headgroups, (iii) tilts of lipid molecules, (iv) water penetration into the hydrophobic region of the bilayer, and (v) momentum transfer across the bilayer. The number of water molecules delivered into the hydrophobic region is found to be insensitive to incident shock angles. The most important structural changes are the lateral displacement of headgroups and tilts of lipid molecules, which are observed only in the half of the bilayer directly exposed to a shock wave for all incident shock angles studied here. As a result, only the normal component of the added oblique momentum is substantially transferred across the bilayer. This also suggests that the irradiation by shock waves may induce a jet-like streaming of the cytoplasm toward the nucleus.

A non-invasive tissue-specific molecular delivery method of cancer gene therapy.

A Japanese word, monozukuri (literally translated "making things") is the philosophy of first having the idea and then the faith in the technical expertise and experience to accomplish the result. We believe that the concept of engineering is monozukuri. Through the process of monozukuri, engineered natural science based on mathematics and physics has been developed. Medicine is the field of study which has been developed for maintaining daily healthy life with diagnosis, treatment, examination, and protection. Biomedical engineering is the interdisciplinary study of engineering and medicine, and should be developed based on monozukuri. In this particular research, we have developed a physical molecular delivery method for cancer gene therapy using nano/microbubbles and ultrasound. First, the behavior of cavitation bubbles and subsequent shock wave phenomena involved in the mechanism of molecular delivery were analyzed, combining theory and computer simulation. In a second step, the methodology was optimized in vitro and in vivo. Finally, the therapeutic potential of the method in pre-clinical models was evaluated using transgenes relevant to cancer gene therapy instead of reporter genes, and whole body, non-invasive imaging using single photon emission computed tomography (SPECT/CT) was used to evaluate the selectivity of gene delivery in vivo.