Study of Impacts of Two Types of Cellular Aging on the Yeast Bud Morphogenesis

Understanding the mechanisms of cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short lifespan and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. In this study, by analyzing experimental data it was shown that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional chemical-mechanical model was developed and used to suggest and test hypothesized mechanisms of bud morphogenesis during aging. Experimentally calibrated simulations showed that tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip guided by the polarized Cdc42 signal during the early stage of budding. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage, as observed in experiments, through a reduction on the new cell surface material insertion or an expansion of the polarization site. Thus model simulations suggest the maintenance of new cell surface material insertion or chemical signal polarization could be weakened due to cellular aging in yeast and other cell types.

Full-lung simulations of mechanically ventilated lungs incorporating recruitment/derecruitment dynamics

This study developed and investigated a comprehensive multiscale computational model of a mechanically ventilated ARDS lung to elucidate the underlying mechanisms contributing to the development or prevention of VILI. This model is built upon a healthy lung model that incorporates realistic airway and alveolar geometry, tissue distensibility, and surfactant dynamics. Key features of the ARDS model include recruitment and derecruitment (RD) dynamics, alveolar tissue viscoelasticity, and surfactant deficiency. This model successfully reproduces realistic pressure-volume (PV) behavior, dynamic surface tension, and time-dependent descriptions of RD events as a function of the ventilation scenario. Simulations of Time-Controlled Adaptive Ventilation (TCAV) modes, with short and long durations of exhalation (T Low - and T Low +, respectively), reveal a higher incidence of RD for T Low + despite reduced surface tensions due to interfacial compression. This finding aligns with experimental evidence emphasizing the critical role of timing in protective ventilation strategies. Quantitative analysis of energy dissipation indicates that while alveolar recruitment contributes only a small fraction of total energy dissipation, its spatial concentration and brief duration may significantly contribute to VILI progression due to its focal nature and higher intensity. Leveraging the computational framework, the model may be extended to facilitate the development of personalized protective ventilation strategies to enhance patient outcomes. As such, this computational modeling approach offers valuable insights into the complex dynamics of VILI that may guide the optimization of ventilation strategies in ARDS management.

A modular computational framework for medical digital twins

The digital twin paradigm holds great promise for medicine, even though many technical and scientific challenges remain to be overcome, most importantly the efficient integration of many heterogeneous component models. This is an unsolved problem even in industry. It has long been understood that such models need to be built in a modular fashion, connecting together component models of individual biological processes. In conventional implementations, however, the dependency structure of the modules reflects the dependencies among these processes, making it all but impossible to modify or expand the digital twin without breaking it. This paper presents a fundamental reorganization of the internal digital twin architecture into a hub-and-spokes design that completely circumvents this dependency problem.

This paper presents a modular software design for the construction of computational modeling technology that will help implement precision medicine. In analogy to a common industrial strategy used for preventive maintenance of engineered products, medical digital twins are computational models of disease processes calibrated to individual patients using multiple heterogeneous data streams. They have the potential to help improve diagnosis, prognosis, and personalized treatment for a wide range of medical conditions. Their large-scale development relies on both mechanistic and data-driven techniques and requires the integration and ongoing update of multiple component models developed across many different laboratories. Distributed model building and integration requires an open-source modular software platform for the integration and simulation of models that is scalable and supports a decentralized, community-based model building process. This paper presents such a platform, including a case study in an animal model of a respiratory fungal infection.

Stimulus waveform design for decreasing charge and increasing stimulation selectivity in retinal prostheses

Retinal degenerative diseases, such as retinitis pigmentosa, begin with damage to the photoreceptor layer of the retina. In the absence of presynaptic input from photoreceptors, networks of electrically coupled AII amacrine and cone bipolar cells have been observed to exhibit oscillatory behaviour and result in spontaneous firing of ganglion cells. This ganglion cell activity could interfere with external stimuli provided by retinal prosthetic devices and potentially degrade their performance. In this work, the authors computationally investigate stimulus waveform designs, which can improve the performance of retinal prostheses by suppressing undesired spontaneous firing of ganglion cells and generating precise temporal spiking patterns. They utilise a multi-scale computational model for electrical stimulation of degenerated retina based on the admittance method and NEURON simulation environments. They present a class of asymmetric biphasic pulses that can generate precise ganglion cell firing patterns with up to 55% lower current requirements compared to traditional symmetric biphasic pulses. This lower current results in activation of only proximal ganglion cells, provides more focused stimulation and lowers the risk of tissue damage.

Toward a multiscale modeling framework for understanding serotonergic function

Despite its importance in regulating emotion and mental wellbeing, the complex structure and function of the serotonergic system present formidable challenges toward understanding its mechanisms. In this paper, we review studies investigating the interactions between serotonergic and related brain systems and their behavior at multiple scales, with a focus on biologically-based computational modeling. We first discuss serotonergic intracellular signaling and neuronal excitability, followed by neuronal circuit and systems levels. At each level of organization, we will discuss the experimental work accompanied by related computational modeling work. We then suggest that a multiscale modeling approach that integrates the various levels of neurobiological organization could potentially transform the way we understand the complex functions associated with serotonin.

A Multiscale Computational Model Combining a Single Crystal Plasticity Constitutive Model with the Generalized Method of Cells (GMC) for Metallic Polycrystals

A multiscale computational model is developed for determining the elasto-plastic behavior of polycrystal metals by employing a single crystal plasticity constitutive model that can capture the microstructural scale stress field on a finite element analysis (FEA) framework. The generalized method of cells (GMC) micromechanics model is used for homogenizing the local field quantities. At first, the stand-alone GMC is applied for studying simple material microstructures such as a repeating unit cell (RUC) containing single grain or two grains under uniaxial loading conditions. For verification, the results obtained by the stand-alone GMC are compared to those from an analogous FEA model incorporating the same single crystal plasticity constitutive model. This verification is then extended to samples containing tens to hundreds of grains. The results demonstrate that the GMC homogenization combined with the crystal plasticity constitutive framework is a promising approach for failure analysis of structures as it allows for properly predicting the von Mises stress in the entire RUC, in an average sense, as well as in the local microstructural level, i.e., each individual grain. Two–three orders of saving in computational cost, at the expense of some accuracy in prediction, especially in the prediction of the components of local tensor field quantities and the quantities near the grain boundaries, was obtained with GMC. Finally, the capability of the developed multiscale model linking FEA and GMC to solve real-life-sized structures is demonstrated by successfully analyzing an engine disc component and determining the microstructural scale details of the field quantities.

Applications of computational models to better understand microvascular remodelling: a focus on biomechanical integration across scales

Microvascular network remodelling is a common denominator for multiple pathologies and involves both angiogenesis, defined as the sprouting of new capillaries, and network patterning associated with the organization and connectivity of existing vessels. Much of what we know about microvascular remodelling at the network, cellular and molecular scales has been derived from reductionist biological experiments, yet what happens when the experiments provide incomplete (or only qualitative) information? This review will emphasize the value of applying computational approaches to advance our understanding of the underlying mechanisms and effects of microvascular remodelling. Examples of individual computational models applied to each of the scales will highlight the potential of answering specific questions that cannot be answered using typical biological experimentation alone. Looking into the future, we will also identify the needs and challenges associated with integrating computational models across scales.

A computational hypothesis for allostasis: delineation of substance dependence, conventional therapies, and alternative treatments

The allostatic theory of drug abuse describes the brain's reward system alterations as substance misuse progresses. Neural adaptations arising from the reward system itself and from the antireward system provide the subject with functional stability, while affecting the person's mood. We propose a computational hypothesis describing how a virtual subject's drug consumption, cognitive substrate, and mood interface with reward and antireward systems. Reward system adaptations are assumed interrelated with the ongoing neural activity defining behavior toward drug intake, including activity in the nucleus accumbens, ventral tegmental area, and prefrontal cortex (PFC). Antireward system adaptations are assumed to mutually connect with higher-order cognitive processes occurring within PFC, orbitofrontal cortex, and anterior cingulate cortex. The subject's mood estimation is a provisional function of reward components. The presented knowledge repository model incorporates pharmacokinetic, pharmacodynamic, neuropsychological, cognitive, and behavioral components. Patterns of tobacco smoking exemplify the framework's predictive properties: escalation of cigarette consumption, conventional treatments similar to nicotine patches, and alternative medical practices comparable to meditation. The primary outcomes include an estimate of the virtual subject's mood and the daily account of drug intakes. The main limitation of this study resides in the 21 time-dependent processes which partially describe the complex phenomena of drug addiction and involve a large number of parameters which may underconstrain the framework. Our model predicts that reward system adaptations account for mood stabilization, whereas antireward system adaptations delineate mood improvement and reduction in drug consumption. This investigation provides formal arguments encouraging current rehabilitation therapies to include meditation-like practices along with pharmaceutical drugs and behavioral counseling.