Effect of Shock-Induced Cavitation Bubble Collapse on the damage in the Simulated Perineuronal Net of the Brain

Effect of Shock-Wave-Mediated Collapse on Nanobubble Characteristics

To enhance the comprehension of the cavitation mechanism and explore its practical use in industrial production, this study developed models involving oxygen, varying bubble radii, and bubble quantities. This study uses molecular dynamics simulations coupled with the momentum mirror method to examine the collapse characteristics of bubbles during ultrasonic cavitation. The investigation uncovers patterns in the fluctuation of the maximum local density of water molecules, released pressure, and temperature. The findings demonstrate that, when oxygen-containing bubbles collapse at identical radii, the local density is notably higher and diminishes more rapidly. Moreover, the changes in the shape exhibit greater regularity. During the bubble collapse, a depression forms on the bubble's surface, coinciding with a notable surge in local density around the depression. As bubble radii and quantities increase, so does the local density along with a concurrent rise in the maximum pressure. Intriguingly, the model demonstrates the lowest pressure at Z = 35 Å accompanied by the emergence of a small crescent-shaped region with a reduced density. Throughout the pressure ascension phase, the rate of the maximum pressure change escalates with an increase in the number of bubbles. Conversely, during the pressure descent phase, the rate of the maximum pressure change diminishes with a growing number of bubbles. However, it is important to note that the maximum pressure does not exhibit a direct correlation with the number of bubbles. Ultimately, this study provides valuable technical guidance and a theoretical foundation for the integration of ultrasonic cavitation in industrial production processes.

Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes

This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other hyaluronan and hyaluronan-containing systems. Advances in accurate molecular mechanics force fields, simulation methods and software, and computer hardware have supported a recent flourish in such simulations, such that the simulation publications now outnumber the structural biology publications by an order of magnitude. In addition to supplementing the experimental structural biology with computed dynamic and thermodynamic information, the molecular dynamics studies provide a wealth of atomic-resolution information on hyaluronan-containing systems for which there is no atomic-resolution structural biology either available or possible. Examples of these summarized in this review include hyaluronan pairing with other hyaluronan molecules and glycosaminoglycans, with ions, with proteins and peptides, with lipids, and with drugs and drug-like molecules. Despite limitations imposed by present-day computing resources on system size and simulation timescale, atomic-resolution explicit-solvent molecular dynamics simulations have been able to contribute significant insight into hyaluronan's flexibility and capacity for intra- and intermolecular non-covalent interactions.

Degradation Mechanism of Micro-Nanobubble Technology for Organic Pollutants in Aqueous Solutions

Micro-nanobubbles (MNBs) technology has emerged as an effective means of sewage treatment, while the molecular mechanism for its pollutant degradation is still unknown. In this paper, the reactive molecular dynamics simulation technique is used to study the degradation mechanism of pollutants caused by shock-induced nanobubble collapse. We first demonstrate that the propagating shock wave can induce nanobubble collapse, and the collapsing nanobubble has the ability to focus mechanical energy via the converging motion of liquid in the interior of the bubble, leading to the formation of a high-speed jet with a much higher energy density. We also unveil the mechanical nature of long-chain pollutant degradation and the mechanism of free radical generation. Due to the impacting jet, the high-gradient flow has the ability to stretch the long-chain molecule and cause mechanical scission of the molecule in a homolytic manner. Finally, our simulation results reveal that adding ozone molecules to the collapsing bubble would introduce an additional dehydrogenation mechanism.

Cavitation nucleation and its ductile-to-brittle shape transition in soft gels under translational mechanical impact

Cavitation bubbles in the human body, when subjected to impact, are being increasingly considered as a possible brain injury mechanism. However, the onset of cavitation and its complex dynamics in biological materials remain unclear. Our experimental results using soft gels as a tissue simulant show that the critical acceleration (a_cr) at cavitation nucleation monotonically increases with increasing stiffness of gelatin A/B, while a_cr for agarose and agar initially increases but is followed by a plateau or even decrease after stiffness reach to ∼100 kPa. Our image analyses of cavitation bubbles and theoretical work reveal that the observed trends in a_cr are directly linked to how bubbles grow in each gel. Gelatin A/B, regardless of their stiffness, form a localized damaged zone (tens of nanometers) at the gel-bubble interface during bubble growth. In contrary, the damaged zone in agar/agarose becomes significantly larger (> 100 times) with increasing shear modulus, which triggers the transition from formation of a small, damaged zone to activation of crack propagation. STATEMENT OF SIGNIFICANCE: We have studied cavitation nucleation and bubble growth in four different types of soft gels (i.e., tissue simulants) under translational impact. The critical linear acceleration for cavitation nucleation has been measured in the simulants by utilizing a recently developed method that mimics acceleration profiles of typical head blunt events. Each gel type exhibits significantly different trends in the critical acceleration and bubble shape (e.g., A gel-specific sphere-to-saucer transition) with increasing gel stiffness. Our theoretical framework, based on the concepts of a damaged zone and crack propagation in each gel, explains underlying mechanisms of the experimental observations. Our in-depth studies shed light on potential links between traumatic brain injuries and cavitation bubbles induced by translational acceleration, the overlooked mechanism in the literature.

Shock-Induced Damage Mechanism of Perineuronal Nets

The perineuronal net (PNN) region of the brain’s extracellular matrix (ECM) surrounds the neural networks within the brain tissue. The PNN is a protective net-like structure regulating neuronal activity such as neurotransmission, charge balance, and action potential generation. Shock-induced damage of this essential component may lead to neuronal cell death and neurodegenerations. The shock generated during a vehicle accident, fall, or improvised device explosion may produce sufficient energy to damage the structure of the PNN. The goal is to investigate the mechanics of the PNN in reaction to shock loading and to understand the mechanical properties of different PNN components such as glycan, GAG, and protein. In this study, we evaluated the mechanical strength of PNN molecules and the interfacial strength between the PNN components. Afterward, we assessed the PNN molecules’ damage efficiency under various conditions such as shock speed, preexisting bubble, and boundary conditions. The secondary structure altercation of the protein molecules of the PNN was analyzed to evaluate damage intensity under varying shock speeds. At a higher shock speed, damage intensity is more elevated, and hyaluronan (glycan molecule) is most likely to break at the rigid junction. The primary structure of the protein molecules is least likely to fail. Instead, the molecules’ secondary bonds will be altered. Our study suggests that the number of hydrogen bonds during the shock wave propagation is reduced, which leads to the change in protein conformations and damage within the PNN structure. As such, we found a direct connection between shock wave intensity and PNN damage.

Effects of Focal Axonal Swelling Level on the Action Potential Signal Transmission

Focal axon swelling refers to localized swelling in axons that may occur because of trauma (e.g., traumatic brain injury) or neurodegenerative diseases (e.g., Alzheimer's disease). Since the swelling region can be many times larger than its original axon size, many researchers hypothesize that the swelling can alter the action potential (AP) signal. This article discusses the results of a series of newly developed computational studies to elucidate the possible intervention or blockage of AP signals due to swelling in the brain. We argue that the spherical geometry of the swelling site with its enlarged conducting interior causes the entering electric currents to spread evenly over the entire swelled membrane. As such, when the swelled surface becomes larger than the threshold size, the electric current will spread too thin to trigger the AP to spike. In this study, we have used a hybrid membrane model to simulate AP propagation across axons of different radii and swelling radii. We used an integrated model where a cylindrical symmetric 2D model is used to examine the electric current inside a spherical swelling site. In addition, two 1D models are used to capture the current flows along the upstream and downstream stretch before and after the swelling site. The parameters for this model are obtained from literature dedicated to modeling the experimental outcomes of mammal neurons. We observed two factors, which simultaneously affect AP transmission across a swelled axon: a) the axon radius and b) the ratio of the swelled and unswelled axon radii. In general, a thicker axon needs a smaller swelling size and axon ratio to block AP transmission. On the other hand, a thinner axon will reach the threshold at a larger swelling size and axon ratio. When only swelling size is considered, then thinner axons will block AP transmission at a smaller swelling radius. The AP transmission delay inside the swelled region determines whether the AP transmits forward or not. Notably, the blockage is worse if the AP fires at a high frequency. An increase in the charging and reset time due to swelling appears to be the main reason for the variation in axonal response.

Impact of Shock-Induced Cavitation Bubble Collapse on the Damage of Cell Membranes with Different Lipid Peroxidation Levels

Although the interaction mechanism between shock waves and cells is critical for advancing the medical applications of shock waves, we still have little understanding about it. This work aims to study the response of diseased cells subjected to lipid peroxidation to the nanojet from shock wave-induced bubble collapse by using the coarse-grained molecular dynamics simulation. Factors considered in the simulations include the shock velocity (up), movement time of piston (τp), bubble size (R), and peroxidation level of membranes. Here, we mainly focus on the role of peroxidation levels, that is, the degree (%) and the distribution of oxidized lipids in membranes. The results indicate that the shock damage threshold (up at which the pore in membranes is formed) of peroxidation membranes is less than that of normal membranes and decreases with the peroxidation degree. Importantly, the distribution of oxidized lipids has more effect on the damage threshold than the peroxidation degree. The threshold of membrane with 33% localized oxidized lipids is lower than that of membrane with 50% average oxidized lipids. The results can be explained by the stretching modulus (κs) and bending modulus (κb) of cell membranes. For example, the κb value (4.3 × 10-20 J) of 100% peroxidation membrane is about half of that (8.4 × 10-20 J) of a membrane without peroxidation. A lower modulus means high deformation under the same impact. Further analysis shows that peroxidation introduces a polar hydrophobic group to the tail of phospholipids that increases the hydrophilicity of tails and warps the tail of phospholipids toward the membrane-water interface, resulting in looser accumulation. This can be confirmed by the increased average phospholipid area with peroxidation levels. Indeed, most of the pores formed during the shock can heal. However, the permeation of water molecules across the healing membrane still increased. All these membrane-level information obtained from this study will be useful for improving the biomedical applications of shock waves.

Mechanically Induced Cavitation in Biological Systems

Cavitation bubbles form in soft biological systems when subjected to a negative pressure above a critical threshold, and dynamically change their size and shape in a violent manner. The critical threshold and dynamic response of these bubbles are known to be sensitive to the mechanical characteristics of highly compliant biological systems. Several recent studies have demonstrated different biological implications of cavitation events in biological systems, from therapeutic drug delivery and microsurgery to blunt injury mechanisms. Due to the rapidly increasing relevance of cavitation in biological and biomedical communities, it is necessary to review the current state-of-the-art theoretical framework, experimental techniques, and research trends with an emphasis on cavitation behavior in biologically relevant systems (e.g., tissue simulant and organs). In this review, we first introduce several theoretical models that predict bubble response in different types of biological systems and discuss the use of each model with physical interpretations. Then, we review the experimental techniques that allow the characterization of cavitation in biologically relevant systems with in-depth discussions of their unique advantages and disadvantages. Finally, we highlight key biological studies and findings, through the direct use of live cells or organs, for each experimental approach.

Cerebrospinal Fluid Cavitation as a Mechanism of Blast-Induced Traumatic Brain Injury: A Review of Current Debates, Methods, and Findings

Cavitation has gained popularity in recent years as a potential mechanism of blast-induced traumatic brain injury (bTBI). This review presents the most prominent debates on cavitation; how bubbles can form or exist within the cerebrospinal fluid (CSF) and brain vasculature, potential mechanisms of cellular, and tissue level damage following the collapse of bubbles in response to local pressure fluctuations, and a survey of experimental and computational models used to address cavitation research questions. Due to the broad and varied nature of cavitation research, this review attempts to provide a necessary synthesis of cavitation findings relevant to bTBI, and identifies key areas where additional work is required. Fundamental questions about the viability and likelihood of CSF cavitation during blast remain, despite a variety of research regarding potential injury pathways. Much of the existing literature on bTBI evaluates cavitation based off its prima facie plausibility, while more rigorous evaluation of its likelihood becomes increasingly necessary. This review assesses the validity of some of the common assumptions in cavitation research, as well as highlighting outstanding questions that are essential in future work.

Damage to Polystyrene Polymer Film by Shock Wave Induced Bubble Collapse

Metallic surfaces that are in contact with solutions are commonly used in numerous applications where these surfaces can be damaged by shock wave induced bubble collapse. Use of polymer films that coat such surfaces to prevent them from damage requires a better understanding of how much harm collapsing bubbles produce in the films. In this study, we report the results from coarse-grained molecular dynamics simulations to study the damage to polystyrene (PS) films coating a hard surface. The damage was caused by a collapsing nanobubble located in the proximity of the film and interacting with an impinging shock wave. This collapse produces a high-speed water jet that impacts the PS film with a greater force than the shock front and creates cavities/pits in the PS film. We observed that polymer molecules located in the jet vicinity undergo conformational extension in the direction perpendicular to the jet motion, while chain molecules in the rest of the film undergo compression. We also observed that damage to the film is sensitive to the strength of the shock wave.

On the Molecular Level Cavitation in Soft Gelatin Hydrogel

We have studied the molecular level cavitation mechanisms and bubble growth kinetics in soft gelatin hydrogel and water. The apparent difference in cavitation threshold pressure between that generates in pure water and that in gelatin hydrogel is considered. Gelatin, which is derived from collagen, is frequently used as a brain simulant material. In liquid, cavitation bubble is created when surrounding pressure drops below the saturation vapor pressure. In principle, a cavitation bubble should continue to grow as long as tensile pressure continues to increase in the system. In our study, using molecular dynamics simulation, we have investigated the pressure requirement for a nanoscale cavitation to grow in water and gel. First, we have modeled a gel like structure with a preexisting bubble of 5 nm radius. A control model containing a 5 nm bubble in pure water is also created. Then, we have applied hydrostatic tensile pressure at two different expansion rates in the gel and water models. The results show that a gel-like structure requires higher pressure for the cavitation to grow, and both gel and water models exhibit strain rate effect on the cavitation threshold pressure. We have also found that the cavitation collapse time is dominated by the viscosity of the medium.

Sequential ultrasonication and deep eutectic solvent pretreatment to remove lignin and recover xylose from oil palm fronds

This study demonstrated the effect of two-pot sequential pretreatment, comprising of ultrasound assisted deep eutectic solvent (DES) with the aim to investigate the effects of ultrasound amplitude and duration in enhancing delignification. Oil palm fronds (OPF) were ultrasonicated in a water medium, followed by a pretreatment using DES (choline chloride:urea). Fourier transform infra-red spectroscopy, X-ray diffraction, field emission scanning electron microscope, Brunauer-Emmet-Teller and solubilised lignin concentration were conducted to confirm the effectiveness of ultrasound assisted DES on the pretreatment of OPF. The recommended ultrasound conditions were determined to be 70% amplitude and duration of 30 min, where the sequential DES pretreatment was able to reduce lignin content of OPF to 14.01%, while improving xylose recovery by 58%.

Diverse Structural Conversion and Aggregation Pathways of Alzheimer's Amyloid-β (1-40)

Complex amyloid aggregation of amyloid-β (1-40) (Aβ_1-40) in terms of monomer structures has not been fully understood. Herein, we report the microscopic mechanism and pathways of Aβ_1-40 aggregation with macroscopic viewpoints through tuning its initial structure and solubility. Partial helical structures of Aβ_1-40 induced by low solvent polarity accelerated cytotoxic Aβ_1-40 amyloid fibrillation, while predominantly helical folds did not aggregate. Changes in the solvent polarity caused a rapid formation of β-structure-rich protofibrils or oligomers via aggregation-prone helical structures. Modulation of the pH and salt concentration transformed oligomers to protofibrils, which proceeded to amyloid formation. We reveal diverse molecular mechanisms underlying Aβ_1-40 aggregation with conceptual energy diagrams and propose that aggregation-prone partial helical structures are key to inducing amyloidogenesis. We demonstrate that context-dependent protein aggregation is comprehensively understood using the macroscopic phase diagram, which provides general insights into differentiation of amyloid formation and phase separation from unfolded and folded structures.

Acceleration-induced pressure gradients and cavitation in soft biomaterials

The transient, dynamic response of soft materials to mechanical impact has become increasingly relevant due to the emergence of numerous biomedical applications, e.g., accurate assessment of blunt injuries to the human body. Despite these important implications, acceleration-induced pressure gradients in soft materials during impact and the corresponding material response, from small deformations to sudden bubble bursts, are not fully understood. Both through experiments and theoretical analyses, we empirically show, using collagen and agarose model systems, that the local pressure in a soft sample is proportional to the square of the sample depth in the impact direction. The critical acceleration that corresponds to bubble bursts increases with increasing gel stiffness. Bubble bursts are also highly sensitive to the initial bubble size, e.g., bubble bursts can occur only when the initial bubble diameter is smaller than a critical size (≈10 μm). Our study gives fundamental insight into the physics of injury mechanisms, from blunt trauma to cavitation-induced brain injury.

Damage and Failure of Axonal Microtubule under Extreme High Strain Rate: An In-Silico Molecular Dynamics Study

As a major cytoskeleton element of the axon, the breaking of microtubules (MTs) has been considered as a major cause of the axon degeneration. High strain rate loading is considered as one of the key factors in microtubule breaking. Due to the small size of microtubule, the real-time behavior of microtubule breaking is hard to capture. This study employs fully-atomistic molecular dynamics (MD) simulation to determine the failure modes of microtubule under different loadings conditions such as, unidirectional stretching, bending and hydrostatic expansion. For each loading conditions, MT is subjected to extreme high strain rate (108-109 s-1) loading. We argue that such level of high strain rate may be realized during cavitation bubble implosion. For each loading type, we have determined the critical energy for MT rupture. The associated rupture mechanisms are also discussed. We observed that the stretching has the lowest energy barrier to break the MT at the nanosecond time scale. Moreover, the breakage between the dimers starts at ~16% of total strain when stretched, which is much smaller compared to the reported strain-at-failure (50%) for lower strain rate loading. It suggests that MT fails at a significantly smaller strain states when loaded at higher strain rates.

Cavitation nucleation in gelatin: Experiment and mechanism

Dynamic cavitation in soft materials is becoming increasingly relevant due to emerging medical implications such as the potential of cavitation-induced brain injury or cavitation created by therapeutic medical devices. However, the current understanding of dynamic cavitation in soft materials is still very limited, mainly due to lack of robust experimental techniques. To experimentally characterize cavitation nucleation under dynamic loading, we utilize a recently developed experimental instrument, the integrated drop tower system. This technique allows quantitative measurements of the critical acceleration (a_cr) that corresponds to cavitation nucleation while concurrently visualizing time evolution of cavitation. Our experimental results reveal that a_cr increases with increasing concentration of gelatin in pure water. Interestingly, we have observed the distinctive transition from a sharp increase (pure water to 1% gelatin) to a much slower rate of increase (∼10× slower) between 1% and 7.5% gelatin. Theoretical cavitation criterion predicts the general trend of increasing a_cr, but fails to explain the transition rates. As a likely mechanism, we consider concentration-dependent material properties and non-spherical cavitation nucleation sites, represented by pre-existing bubbles in gels, due to possible interplay between gelatin molecules and nucleation sites. This analysis shows that cavitation nucleation is very sensitive to the initial configuration of a bubble, i.e., a non-spherical bubble can significantly increase a_cr. This conclusion matches well with the experimentally observed liquid-to-gel transition in the critical acceleration for cavitation nucleation.

STATEMENT OF SIGNIFICANCE

From a medical standpoint, understanding dynamic cavitation within soft materials, i.e., tissues, is important as there are both potential injury implications (blast-induced cavitation within the brain) as well as treatments utilizing the phenomena (lithotripsy). In this regard, the main results of the present work are (1) quantitative characterization of cavitation nucleation in gelatin samples as a function of gel concentration utilizing well-controlled mechanical impacts and (2) mechanistic understanding of complex coupling between cavitation and liquid-/solid-like material properties of gel. The new capabilities of testing soft gels, which can be tuned to mimic material properties of target organs, at high loading rate conditions and accurately predicting their cavitation behavior are an important step towards developing reliable cavitation criteria in the scope of their biomedical applications.