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

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.

Peptide Power: Mechanistic Insights into the Effect of Mitochondria-Targeted Tetrapeptides on Membrane Electrostatics from Molecular Simulations

Mitochondrial dysfunction is implicated in nine of the ten leading causes of death in the US, yet there are no FDA-approved therapeutics to treat it. Synthetic mitochondria-targeted peptides (MTPs), including the lead compound SS-31, offer promise, as they have been shown to restore healthy mitochondrial function and treat a variety of common diseases. At the cellular level, research has shown that MTPs accumulate strongly at the inner mitochondrial membrane (IMM), slow energy sinks (e.g., proton leaks), and improve ATP production. Modulation of electrostatic fields around the IMM has been implicated as a key aspect in the mechanism of action (MoA) of these peptides; however, molecular and mechanistic details have remained elusive. In this study, we employed all-atom molecular dynamics simulations (MD) to investigate the interactions of four MTPs with lipid bilayers and calculate their effect on structural and electrostatic properties. In agreement with previous experimental findings, we observed the modulation of the membrane surface and dipole potentials by MTPs. The simulations reveal that the MTPs achieve a reduction in the dipole potential by acting to disorder both lipid head groups and water layers proximal to the bilayer surface. We also find that MTPs decrease the bilayer thickness and increase the membrane's capacitance. These changes suggest that MTPs may enhance how much potential energy can be stored across the IMM at a given transmembrane potential difference. The MTPs also displace cations away from the bilayer surface, modulating the surface potential and offering an alternative mechanism for how these MTPs reduce mitochondrial energy sinks like proton leaks and mitigate Ca2+ accumulation stress. In conclusion, this study highlights the therapeutic potential of MTPs and underlines how interactions of MTPs with lipid bilayers serve as a fundamental component of their MoA.

Cell-scale hemolysis evaluation of intervenient ventricular assist device based on dissipative particle dynamics

Most of the existing hemolysis mechanism studies are carried out on the macro flow scale. They assume that the erythrocyte membranes with different loads will suffer the same damage, which obviously has limitations. Thus, exploring the hemolysis mechanism through the macroscopic flow field information is a tough challenge. In order to further understand the non-physiological shear hemolysis phenomenon at the cell scale, this study used the coarse-grained erythrocytes damage model at the mesoscopic scale based on the transport dissipative particle dynamics (tDPD) method. Combined with computational fluid dynamics the hemolysis of scalarized shear stress (τ) in the clearance of "Impella 5.0" was evaluated under the Lagrange perspective and Euler perspective. The results from the Lagrange perspective showed that the change rate of scaled shear stress (τ˙) was the most critical factor in damaging RBCs in the rotor region of "Impella 5.0"and other transvalvular micro-axial blood pumps. Then, we propose a dimensionless number Dk with time integration based on τ˙ to evaluate hemolysis. The Dissipative particle dynamics simulation results are consistent with the Dk evaluation results, so τ˙ may be an important factor in the hemolysis of VADs. Finally, we tested the hemolysis of 30% hematocrit whole blood in the "Impella 5.0" shroud clearance from the Euler perspective. Relevant results indicate that because of the wall effect, the RBCs near the impeller side are more prone to damage, and most of the cytoplasm is also gathered at the rotor side.

Development of a charged model of the SARS-CoV-2 viral surface

A recent study provided experimental evidence of inactivation of viral activity after radio-frequency (RF) exposures in the 6-12 GHz band that was hypothesized to be caused by vibrations of an acoustic dipole mode in the virus that excited the viral membrane to failure. Here, we develop an atomic-scale molecular dynamics (MD) model of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral surface to estimate the electric fields necessary to rupture the viral membrane via dipole shaking of the virus. We computed the absorption spectrum of the system via unbiased MD simulations and found no particular strong absorption in the GHz band. We investigated the mechanical resiliency of the viral membrane by introducing uniaxial strains in the system and observed no pore formation in the membrane for strains up to 50%. Because the computed absorption spectrum was found to be essentially flat, and the strain required to break the viral membrane was >0.5, the field strength associated with rupture of the virus was greater than the dielectric breakdown value of air. Thus, RF disinfection of enveloped viruses would occur only once sufficient heat was transferred to the virus via a thermal mechanism and not by direct action (shaking) of the RF field oscillations on the viral membrane.

Extreme Membrane Tensile Loads Induce Half-Activation of the Thermosensitive TRPV1 Channel

Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels convert a wide range of physical and chemical stimuli into channel opening is essential to understanding their normal function. Here, half-activation of thermosensitive TRPV1 channel under extreme membrane stretching from blast loads was provided by molecular dynamics simulations. The results show that such extreme membrane stretch loading will only lead to half-activation of the TRPV1 channel: that is, the upper gate is open for high-speed stretching (>15m/s), but the lower gate is still closed. The corresponding activation threshold also depends on both the tensile speed and the area strain. This means that the direct mechanical gating of TRP channels in one step is unlikely to occur.

Development of a mesoscopic framework spanning nanoscale protofibril dynamics to macro-scale fibrin clot formation

Thrombi form a micro-scale fibrin network consisting of an interlinked structure of nanoscale protofibrils, resulting in haemostasis. It is theorized that the mechanical effect of the fibrin clot is caused by the polymeric protofibrils between crosslinks, or to their dynamics on a nanoscale order. Despite a number of studies, however, it is still unknown, how the nanoscale protofibril dynamics affect the formation of the macro-scale fibrin clot and thus its mechanical properties. A mesoscopic framework would be useful to tackle this multi-scale problem, but it has not yet been established. We thus propose a minimal mesoscopic model for protofibrils based on Brownian dynamics, and performed numerical simulations of protofibril aggregation. We also performed stretch tests of polymeric protofibrils to quantify the elasticity of fibrin clots. Our model results successfully captured the conformational properties of aggregated protofibrils, e.g., strain-hardening response. Furthermore, the results suggest that the bending stiffness of individual protofibrils increases to resist extension.

Impact of Lipid Peroxidation on the Response of Cell Membranes to High-Speed Equibiaxial Stretching: A Computational Study

The difference between diseased and healthy cellular membranes in response to mechanical stresses is crucial for biology, as well as in the development of medical devices. However, the biomolecular mechanisms by which mechanical stresses interact with diseased cellular components remain largely unknown. In this work, we focus on the response of diseased cellular membranes with lipid peroxidation to high-speed tensile loadings. We find that the critical areal strain (ξ_c, when the pore forms) is highly sensitive to lipid peroxidation. For example, ξ_c of a fully oxidized bilayer is only 64 and 69% of the nonoxidized one at the stretching speed of 0.1 and 0.6 m/s, respectively. ξ_c decreases with the increase in the oxidized lipid ratio, regardless of the speeds. Also, the critical rupture tension of membranes exhibits a similar change. It is obvious that the oxidized membranes are more easily damaged than normal ones by high-speed stretching, which coincides with experimental findings. The reason is that peroxidation introduces a polar group to the tail of lipids, increases the hydrophilicity of tails, and warps the tails to the membrane-water interface, which causes loose accumulation and disorder of lipid tails. This can be deduced from the variation in the area per lipid and order parameter. In addition, the lowering stretching modulus and line tension of membranes (i.e., softening) after lipid peroxidation is also a significant factor. We reveal the difference between the peroxidized (diseased) and normal membrane in response to high-speed stretching, give the ξ_c value in the pore formation of membranes and analyze the influence of the stretching speed, peroxidation ratio, and molecular structure of phospholipids. We hope that the molecular-level information will be useful for the development of biological and medical devices in the future.

Numerical simulation of intracellular drug delivery via rapid squeezing

Intracellular drug delivery by rapid squeezing is one of the most recent and simple cell membrane disruption-mediated drug encapsulation approaches. In this method, cell membranes are perforated in a microfluidic setup due to rapid cell deformation during squeezing through constricted channels. While squeezing-based drug loading has been successful in loading drug molecules into various cell types, such as immune cells, cancer cells, and other primary cells, there is so far no comprehensive understanding of the pore opening mechanism on the cell membrane and the systematic analysis on how different channel geometries and squeezing speed influence drug loading. This article aims to develop a three-dimensional computational model to study the intracellular delivery for compound cells squeezing through microfluidic channels. The Lattice Boltzmann method, as the flow solver, integrated with a spring-connected network via frictional coupling, is employed to capture compound capsule dynamics over fast squeezing. The pore size is proportional to the local areal strain of triangular patches on the compound cell through mathematical correlations derived from molecular dynamics and coarse-grained molecular dynamics simulations. We quantify the drug concentration inside the cell cytoplasm by introducing a new mathematical model for passive diffusion after squeezing. Compared to the existing models, the proposed model does not have any empirical parameters that depend on operating conditions and device geometry. Since the compound cell model is new, it is validated by simulating a nucleated cell under a simple shear flow at different capillary numbers and comparing the results with other numerical models reported in literature. The cell deformation during squeezing is also compared with the pattern found from our compound cell squeezing experiment. Afterward, compound cell squeezing is modeled for different cell squeezing velocities, constriction lengths, and constriction widths. We reported the instantaneous cell center velocity, variations of axial and vertical cell dimensions, cell porosity, and normalized drug concentration to shed light on the underlying physics in fast squeezing-based drug delivery. Consistent with experimental findings in the literature, the numerical results confirm that constriction width reduction, constriction length enlargement, and average cell velocity promote intracellular drug delivery. The results show that the existence of the nucleus increases cell porosity and loaded drug concentration after squeezing. Given geometrical parameters and cell average velocity, the maximum porosity is achieved at three different locations: constriction entrance, constriction middle part, and outside the constriction. Our numerical results provide reasonable justifications for experimental findings on the influences of constriction geometry and cell velocity on the performance of cell-squeezing delivery. We expect this model can help design and optimize squeezing-based cargo delivery.

Efficient encapsulation of functional proteins into erythrocytes by controlled shear-mediated membrane deformation

Red blood cells (RBCs) are attractive carriers of biomolecular payloads due to their biocompatibility and the ability to shelter their encapsulated cargo. Commonly employed strategies to encapsulate payloads into RBCs, such as hypotonic shock, membrane fusion or electroporation, often suffer from low throughput and unrecoverable membrane impairment. This work describes an investigation of a method to encapsulate protein payloads into RBCs by controlling membrane deformation either transiently or extendedly in a microfluidic channel. Under the optimized conditions, the loading efficiency of enhanced green fluorescent protein into mouse RBCs increased was about 2.5- and 4-fold compared to that with osmotic entrapment using transient and extended deformation, respectively. Significantly, mouse RBCs loaded with human arginase exhibit higher enzymatic activity and membrane integrity compared to their counterparts loaded by osmotic entrapment. These features together with the fact that this shear-mediated encapsulation strategy allows loading with physiological buffers highlight the key advantages of this approach compared to traditional osmotic entrapment.

Mechanics of Bacterial Interaction and Death on Nanopatterned Surfaces

Nanopatterned surfaces are believed to kill bacteria through physical deformation, a mechanism that has immense potential against biochemical resistance. Because of its elusive nature, this mechanism is mostly understood through biophysical modeling. Problematically, accurate descriptions of the contact mechanics and various boundary conditions involved in the bacteria-nanopattern interaction remain to be seen. This may underpin conflicting predictions, found throughout the literature, regarding two important aspects of the mechanism-that is, its critical action site and relationship with geometry. Herein, a robust computational analysis of bacteria-nanopattern interaction is performed using a three-dimensional finite element modeling that incorporates relevant continuum mechanical properties, multilayered envelope structure, and adhesion interaction conditions. The model is applied to more accurately study the elusory mechanism and its enhancement via nanopattern geometry. Additionally, micrographs of bacteria adhered on a nanopatterned cicada wing are examined to further inform and verify the major modeling predictions. Together, the results indicate that nanopatterned surfaces do not kill bacteria predominantly by rupture in between protruding pillars as previously thought. Instead, nondevelopable deformation about pillar tips is more likely to create a critical site at the pillar apex, which delivers significant in-plane strains and may locally rupture and penetrate the cell. The computational analysis also demonstrates that envelope deformation is increased by adhesion to nanopatterns with smaller pillar radii and spacing. These results further progress understanding of the mechanism of nanopatterned surfaces and help guide their design for enhanced bactericidal efficiency.

Coarse-Grained Modeling of Pore Dynamics on the Red Blood Cell Membrane under Large Deformations

Transient pore formation on the membrane of red blood cells (RBCs) under high mechanical tensions is of great importance in many biomedical applications, such as RBC damage (hemolysis) and mechanoporation-based drug delivery. The dynamic process of pore formation, growth, and resealing is hard to visualize in experiments. We developed a mesoscale coarse-grained model to study the characteristics of transient pores on a patch of the lipid bilayer that is strengthened by an elastic meshwork representing the cytoskeleton. Unsteady molecular dynamics was used to study the pore formation and reseal at high strain rates close to the physiological ranges. The critical strain for pore formation, pore characteristics, and cytoskeleton effects were studied. Results show that the presence of the cytoskeleton increases the critical strain of pore formation and confines the pore growth. Moreover, the pore recovery process under negative strain rates (compression) is analyzed. Simulations show that pores can remain open for a long time during the high-speed tank-treading induced stretching and compression process that a patch of the RBC membrane usually experiences under high shear flow. Furthermore, complex loading conditions can affect the pore characteristics and result in denser pores. Finally, the effects of strain rate on pore formation are analyzed. Higher rate stretching of membrane patch can result in a significant increase in the critical areal strain and density of pores. Such a model reveals the dynamic molecular process of RBC damage in biomedical devices and mechanoporation that, to our knowledge, has not been reported before.

Ultrasound-Responsive Cavitation Nuclei for Therapy and Drug Delivery

Therapeutic ultrasound strategies that harness the mechanical activity of cavitation nuclei for beneficial tissue bio-effects are actively under development. The mechanical oscillations of circulating microbubbles, the most widely investigated cavitation nuclei, which may also encapsulate or shield a therapeutic agent in the bloodstream, trigger and promote localized uptake. Oscillating microbubbles can create stresses either on nearby tissue or in surrounding fluid to enhance drug penetration and efficacy in the brain, spinal cord, vasculature, immune system, biofilm or tumors. This review summarizes recent investigations that have elucidated interactions of ultrasound and cavitation nuclei with cells, the treatment of tumors, immunotherapy, the blood-brain and blood-spinal cord barriers, sonothrombolysis, cardiovascular drug delivery and sonobactericide. In particular, an overview of salient ultrasound features, drug delivery vehicles, therapeutic transport routes and pre-clinical and clinical studies is provided. Successful implementation of ultrasound and cavitation nuclei-mediated drug delivery has the potential to change the way drugs are administered systemically, resulting in more effective therapeutics and less-invasive treatments.

Multiscale modeling of hemolysis during microfiltration

In this paper, we propose a multiscale numerical algorithm to simulate the hemolytic release of hemoglobin (Hb) from red blood cells (RBCs) flowing through sieves containing micropores with mean diameters smaller than RBCs. Analyzing the RBC damage in microfiltration is important in the sense that it can quantify the sensitivity of human erythrocytes to mechanical hemolysis while they undergo high shear rate and high deformation. Here, the numerical simulations are carried out via lattice Boltzmann method and spring connected network (SN) coupled by an immersed boundary method. To predict the RBC sublytic damage, a sub-cellular damage model derived from molecular dynamic simulations is incorporated in the cellular solver. In the proposed algorithm, the local RBC strain distribution calculated by the cellular solver is used to obtain the pore radius on the RBC membrane. Index of hemolysis (IH) is calculated by resorting to the resulting pore radius and solving a diffusion equation considering the effects of steric hinderance and increased hydrodynamic drag due to the size of the hemoglobin molecule. It should be mentioned that current computational hemolysis models usually utilize empirical fitting of the released free hemoglobin (Hb) in plasma from damaged RBCs. These empirical correlations contain ad hoc parameters that depend on specific device and operating conditions, thus cannot be used to predict hemolysis under different conditions. In contrast to the available hemolysis model, the proposed algorithm does not have any empirical parameters. Therefore, it can predict the IH in microfilter with different sieve pore sizes and filtration pressures. Also, in contrast to empirical correlations in which the Hb release is related to shear stress and exposure time without considering the physical processes, the proposed model links flow-induced deformation of the RBC membrane to membrane permeabilization and hemoglobin release. In this paper, the cellular solver is validated by simulating optical tweezers experiment, shear flow experiment as well as an experiment to measure RBC deformability in a very narrow microchannel. Moreover, the shape of a single RBC at the rupture moment is compared with corresponding experimental data. Finally, to validate the damage model, the results obtained from our parametric study on the role of filtration pressure and sieve pore size in Hb release are compared with experimental data. Numerical results are in good agreement with experimental data. Similar to the corresponding experiment, the numerical results confirm that hemolysis increases with increasing the filtration pressure and reduction in pore size on the sieve. While in experiment, the RBC pore size cannot be measured, the numerical results can quantify the RBC pore size. The numerical results show that at the sieve pore size of 2.2 μm above 25 cm Hg, RBC pore size is above 75 nm and RBCs experience rupture. More importantly, the results demonstrate that the proposed approach is independent from the operating conditions and it can estimate the hemolysis in a wide range of filtration pressure and sieve pore size with reasonable accuracy.

Prediction of mechanical hemolysis in medical devices via a Lagrangian strain-based multiscale model

This work introduces a new Lagrangian strain-based model to predict the shear-induced hemolysis in biomedical devices. Current computational models for device-induced hemolysis usually utilize empirical fitting of the released free hemoglobin (Hb) in plasma from damaged red blood cells (RBCs). These empirical correlations contain parameters that depend on specific device and operating conditions, thus cannot be used to predict hemolysis in a general device. The proposed algorithm does not have any empirical parameters, thus can presumably be used for hemolysis prediction in various blood-wetting medical devices. In contrast to empirical correlations in which the Hb release is related to the shear stress and exposure time without considering the physical processes, the proposed model links flow-induced deformation of the RBC membrane to membrane permeabilization and Hb release. In this approach, once the steady-state numerical solution of blood flow in the device is obtained under a prescribed operating condition, sample path lines are traced from the inlet of the device to the outlet to calculate the history of the shear stress tensor. In solving the fluid flow, it is assumed that RBCs do not have any influence on the flow pattern. Along each path line, shear stress tensor will be input into a coarse-grained (CG) RBC model to calculate the RBC deformation. Then the correlations obtained from molecular dynamics (MD) simulations are applied to relate the local areal RBC deformation to the perforated area on the RBC membrane. Finally, Hb released out of transient pores is calculated over each path line via a diffusion equation considering the effects of the steric hindrance and increased hydrodynamic drag due to the size of the Hb molecule. The total index of hemolysis (IH) is calculated by integration of released Hb over all the path lines in the computational domain. Hemolysis generated in the Food and Drug Administration (FDA) nozzle and two blood pumps, that is, a CentriMag blood pump (a centrifugal pump) and HeartMate II (an axial pump), for different flow regimes including the laminar and turbulent flows are calculated via the proposed algorithm. In all the simulations, the numerical predicted IH is close to the range of experimental data. The results promisingly indicate that this multiscale approach can be used as a tool for predicting hemolysis and optimizing the hematologic design of other types of blood-wetting devices.

Modeling thermal inkjet and cell printing process using modified pseudopotential and thermal lattice Boltzmann methods

Pseudopotential lattice Boltzmann methods (LBMs) can simulate a phase transition in high-density ratio multiphase flow systems. If coupled with thermal LBMs through equation of state, they can be used to study instantaneous phase transition phenomena with a high-temperature gradient where only one set of formulations in an LBM system can handle liquid, vapor, phase transition, and heat transport. However, at lower temperatures an unrealistic spurious current at the interface introduces instability and limits its application in real flow system. In this study, we proposed new modifications to the LBM system to minimize a spurious current which enables us to study nucleation dynamic at room temperature. To demonstrate the capabilities of this approach, the thermal ejection process is modeled as one example of a complex flow system. In an inkjet printer, a thermal pulse instantly heats up the liquid in a microfluidic chamber and nucleates bubble vapor providing the pressure pulse necessary to eject droplets at high speed. Our modified method can present a more realistic model of the explosive vaporization process since it can also capture a high-temperature/density gradient at nucleation region. Thermal inkjet technology has been successfully applied for printing cells, but cells are susceptible to mechanical damage or death as they squeeze out of the nozzle head. To study cell deformation, a spring network model, representing cells, is connected to the LBM through the immersed boundary method. Looking into strain and stress distribution of a cell membrane at its most deformed state, it is found that a high stretching rate effectively increases the rupture tension. In other words, membrane deformation energy is released through creation of multiple smaller nanopores rather than big pores. Overall, concurrently simulating multiphase flow, phase transition, heat transfer, and cell deformation in one unified LB platform, we are able to provide a better insight into the bubble dynamic and cell mechanical damage during the printing process.

Molecular dynamics simulations of heterogeneous cell membranes in response to uniaxial membrane stretches at high loading rates

The chemobiomechanical signatures of diseased cells are often distinctively different from that of healthy cells. This mainly arises from cellular structural/compositional alterations induced by disease development or therapeutic molecules. Therapeutic shock waves have the potential to mechanically destroy diseased cells and/or increase cell membrane permeability for drug delivery. However, the biomolecular mechanisms by which shock waves interact with diseased and healthy cellular components remain largely unknown. By integrating atomistic simulations with a novel multiscale numerical framework, this work provides new biomolecular mechanistic perspectives through which many mechanosensitive cellular processes could be quantitatively characterised. Here we examine the biomechanical responses of the chosen representative membrane complexes under rapid mechanical loadings pertinent to therapeutic shock wave conditions. We find that their rupture characteristics do not exhibit significant sensitivity to the applied strain rates. Furthermore, we show that the embedded rigid inclusions markedly facilitate stretch-induced membrane disruptions while mechanically stiffening the associated complexes under the applied membrane stretches. Our results suggest that the presence of rigid molecules in cellular membranes could serve as “mechanical catalysts” to promote the mechanical destructions of the associated complexes, which, in concert with other biochemical/medical considerations, should provide beneficial information for future biomechanical-mediated therapeutics.

Molecular dynamics simulations indicate that deoxyhemoglobin, oxyhemoglobin, carboxyhemoglobin, and glycated hemoglobin under compression and shear exhibit an anisotropic mechanical behavior

We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior; however, this study investigates the mechanical behavior of hemoglobin, a major constituent of red blood cells, using steered molecular dynamics (SMD) simulations to obtain anisotropic mechanical behavior under compression and shear loading conditions. Four different configurations of hemoglobin molecules were considered: deoxyhemoglobin (deoxyHb), oxyhemoglobin (HbO₂), carboxyhemoglobin (HbCO), and glycated hemoglobin (HbA_1C). The SMD simulations were performed on the hemoglobin variants to estimate their unidirectional stiffness and shear stiffness. Although hemoglobin is structurally denoted as a globular protein due to its spherical shape and secondary structure, our simulation results show a significant variation in the mechanical strength in different directions (anisotropy) and also a strength variation among the four different hemoglobin configurations studied. The glycated hemoglobin molecule possesses an overall higher compressive mechanical stiffness and shear stiffness when compared to deoxyhemoglobin, oxyhemoglobin, and carboxyhemoglobin molecules. Further results from the models indicate that the hemoglobin structures studied possess a soft outer shell and a stiff core based on stiffness.

A Cellular Model of Shear-Induced Hemolysis

A novel model is presented to study red blood cell (RBC) hemolysis at cellular level. Under high shear rates, pores form on RBC membranes through which hemoglobin (Hb) leaks out and increases free Hb content of plasma leading to hemolysis. By coupling lattice Boltzmann and spring connected network models through immersed boundary method, we estimate hemolysis of a single RBC under various shear rates. First, we use adaptive meshing to find local strain distribution and critical sites on RBC membranes, and then we apply underlying molecular dynamics simulations to evaluate damage. Our approach comprises three sub-models: defining criteria of pore formation, calculating pore size, and measuring Hb diffusive flux out of pores. Our damage model uses information of different scales to predict cellular level hemolysis. Results are compared with experimental studies and other models in literature. The developed cellular damage model can be used as a predictive tool for hydrodynamic and hematologic design optimization of blood-wetting medical devices.

IMPETUS - Interactive MultiPhysics Environment for Unified Simulations

We introduce IMPETUS - Interactive MultiPhysics Environment for Unified Simulations, an object oriented, easy-to-use, high performance, C++ program for three-dimensional simulations of complex physical systems that can benefit a large variety of research areas, especially in cell mechanics. The program implements cross-communication between locally interacting particles and continuum models residing in the same physical space while a network facilitates long-range particle interactions. Message Passing Interface is used for inter-processor communication for all simulations.

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.

Membrane pore formation in atomistic and coarse-grained simulations

Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

The Interaction between Influenza HA Fusion Peptide and Transmembrane Domain Affects Membrane Structure

Viral glycoproteins, such as influenza hemagglutinin (HA) and human immunodeficiency virus gp41, are anchored by a single helical segment transmembrane domain (TMD) on the viral envelope membrane. The fusion peptides (FP) of the glycoproteins insert into the host membrane and initiate membrane fusion. Our previous study showed that the FP or TMD alone perturbs membrane structure. Interaction between the influenza HA FP and TMD has previously been shown, but its role is unclear. We used PC spin labels dipalmitoylphospatidyl-tempo-choline (on the headgroup), 5PC and 14PC (5-C and 14-C positions on the acyl chain) to detect the combined effect of FP-TMD interaction by titrating HA FP to TMD-reconstituted 1,2-dimyristoyl-sn-glycero-3-phosphocholine/1,2-dimyristoyl-sn-glycero-3-phospho-(1'-rac-glycerol)/cholesterol lipid bilayers using electron spin resonance. We found that the FP-TMD increases the lipid order at all positions, which has a greater lipid ordering effect than the sum of the FP or TMD alone, and this effect reaches deeper into the membranes. Although HA-mediated membrane fusion is pH dependent, this combined effect is observed at both pH 5 and pH 7. In addition to increasing lipid order, multiple components are found for 5PC at increased concentration of FP-TMD, indicating that distinct domains are induced. However, the mutation of Gly1 in the FP and L187 in the TMD eliminates the perturbations, consistent with their fusogenic phenotypes. Electron spin resonance on spin-labeled peptides confirms these observations. We suggest that this interaction may provide a driving force in different stages of membrane fusion: initialization, transition from hemifusion stalk to transmembrane contact, and fusion pore formation.

Damage in spherical cellular membrane generated by the shock waves: coarse-grained molecular dynamics simulation of lipid vesicle

Traumatic Brain Injury is a major health issue that is hard to diagnose since it often occurs without signs of external injuries. While it is well known that exposure of biological cells to shock waves causes damage to the cell membrane, it is currently unknown by which mechanisms damage is caused, and how it depends on physical parameters such as shock wave velocity, shock pulse duration, or shock pulse shape. In this computational study, we use a coarse-grained model of the lipid vesicle as a generic model of a cell membrane to elucidate the general principles of the cellular damage induced by the shock wave direct passage through the cranium. Results indicate that the extent of the liposome compression does not strongly depend on the pressure pulse and that liposome extension is very sensitive to the change in the negative pressure phase. The structural integrity of the vesicle is altered as pores form in the lipid membrane at overall pressure impulses generated by supersonic shock waves, which are greater than 5 Pa·s at single or repetitive exposure. Consequently, these permeability changes may lead to changes in the influx of sodium, potassium, and calcium ions.

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.

Lipid membranes in external electric fields: kinetics of large pore formation causing rupture

About 40 years ago, Helfrich introduced an elastic model to explain shapes and shape transitions of cells (Z Naturforsch C, 1973; 28:693). This seminal article stimulated numerous theoretical as well as experimental investigations and created new research fields. In particular, the predictive power of his approach was demonstrated in a large variety of lipid model system. Here in this review, we focus on the development with respect to planar lipid membranes in external electric fields. Stimulated by the early work of Helfrich on electric field forces acting on liposomes, we extended his early approach to understand the kinetics of lipid membrane rupture. First, we revisit the main forces determining the kinetics of membrane rupture followed by an overview on various experiments. Knowledge on the kinetics of defect formation may help to design stable membranes or serve for novel mechanism for controlled release.

Analysis of red blood cell deformation under fast shear flow for better estimation of hemolysis

We examined the deformation behavior of a red blood cell (RBC) in various flow fields to determine whether the extent of RBC deformation is correlated with the shear stress used as a hemolysis index. The RBC model was introduced to a simple shear flow (Couette flow) and to slightly complex flows (unsteady shear flows and stenosed flows). The RBC deformation was assessed by the maximum first principal strain over the RBC membrane and compared with the shear stress. Although the results were consistent under steady Couette flow, this was not the case under unsteady Couette flow or stenosed flow due to the viscoelastic nature of the RBC deformation caused by fluid forces. These results suggest that there is a limitation in accurately estimating the mechanical damage of RBCs solely from a macroscopic flow field, indicating the necessity of taking into account the dynamic deformation of RBCs to provide a better estimation of hemolysis.

Stability of Newton black films under mechanical stretch--a molecular dynamics study

The stability of Newton black films (NBFs) under lateral mechanical stretch was investigated by nonequilibrium molecular dynamics (NEMD) simulations using force field parameters validated by accurate prediction of surface tensions. The applied strains accelerated film ruptures, enabling efficient measurements of the critical thicknesses of the films. Two representative surfactants, sodium dodecyl sulfate (SDS) for ionic surfactant and pentaethylene glycol monododecyl ether (C12EO5H) for nonionic surfactant, were investigated and compared. The predicted critical thickness of C12EO5H-coated film is smaller than that of the SDS-coated film, which is consistent with previously reported experimental observations. Our simulation results show that while the two surfactant-coated films exhibit similar dynamic properties attributed to the Marangoni-Gibbs effect, their surface structural characteristics are quite different. Consequently the two films demonstrate distinct rupture mechanisms in which rupture starts at uncovered water domains in the SDS-coated film, but at lateral surfactant/water interfaces in the C12EO5H-coated film. Our findings provide new insights into the stabilization mechanisms of NBFs and will facilitate the design and development of new films with improved properties.