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computational modeling of the Prefrontal-Cingulate Cortex to Investigate the Role of Coupling Relationships for Balancing Emotion and Cognition

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Neuroscience Bulletin 2025年第1期41卷 33-45页

作者： Jinzhao Wei Licong Li Jiayi Zhang Erdong Shi Jianli Yang Xiuling Liu Key Laboratory of Digital Medical Engineering of Hebei Province Hebei UniversityBaoding071000China College of Electronic Information Engineering Hebei UniversityBaoding071000China

Within the prefrontal-cingulate cortex,abnormalities in coupling between neuronal networks can disturb the emotion-cognition interactions,contributing to the development of mental disorders such as *** this understanding,the neural circuit mechanisms underlying this phenomenon remain *** this study,we present a biophysical computational model encompassing three crucial regions,including the dorsolateral prefrontal cortex,subgenual anterior cingulate cortex,and ventromedial prefrontal *** objective is to investigate the role of coupling relationships within the prefrontal-cingulate cortex networks in balancing emotions and cognitive *** numerical results confirm that coupled weights play a crucial role in the balance of emotional cognitive ***,our model predicts the pathogenic mechanism of depression resulting from abnormalities in the subgenual cortex,and network functionality was restored through intervention in the dorsolateral prefrontal *** study utilizes computational modeling techniques to provide an insight explanation for the diagnosis and treatment of depression.

关键词： Prefrontal-cingulate cortex computational modeling Coupling relationships Depression Emotion and cognition

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computational modeling of Bone Fracture Healing Under Different Initial Conditions and Mechanical Load

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IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING 2024年第7期71卷 2105-2118页

作者： Yang, Yuanyuan Zhao, Zeyu Qi, Xiaozhi Hu, Ying Li, Bing Zhang, Lihai Chinese Acad Sci Shenzhen Inst Adv Technol Shenzhen Key Lab Minimally Invas Surg Robot & Syst Beijing Peoples R China Chinese Acad Sci Shenzhen Inst Adv Technol Shenzhen Key Lab Minimally Invas Surg Robot & Syst Shenzhen 518055 Peoples R China Harbin Inst Technol Harbin Peoples R China Chinese Peoples Liberat Army Gen Hosp Dept Orthopaed Beijing Peoples R China

Objective: computational model of bone healing can replace animal experiments to study the parameters affecting the bone healing process, thus reducing the damage to experimental animals and saving a lot of time. We propose a computational model for continuous simulation of four phases of bone healing to study the effects of mechanical environmental and biological factors, including initial conditions at the fracture site, mechanical stimulus loading, and vascular growth rate. Methods: A finite element model of mechanobiological fracture healing containing several pre-determined variables was developed for bone healing after fracture in sheep, which included many relevant parameters and biological effects during fracture healing, such as the effects of mechanical environment, blood supply level in the local fracture area, cell migration and diffusion, and resorption effects of fracture healing. The effects of several parameters on indices such as Young's modulus of the callus during bone healing were obtained by simulation. Results: The initial geometry of the healing tissue and mechanical loading had the greatest effect on fracture healing, and different preset values were likely to cause delayed or non-healing fractures. Changed initial tissue properties of the healing tissue showed a nonlinear effect on fracture healing rather than a linear delay or advancement. Parameters related to angiogenesis had a greater effect on fracture healing compared to those related to cell migration. Conclusion: This paper quantified the effect of fracture healing pre-determined variables on fracture healing to better understand the application of mechanobiology in fracture healing simulation models and optimization of treatment strategies. Significance: The importance of initial conditions and loads on fracture healing has been shown to help physicians treat bone nonunion or delayed bone healing after a fracture.

关键词： Bones computational modeling Load modeling Strain Biological system modeling Finite element analysis Mathematical models Fracture healing mechanobiological modeling angiogenesis finite element numerical simulation

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computational modeling to study the impact of changes in Nav1.8 sodium channel on neuropathic pain

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FRONTIERS IN computational NEUROSCIENCE 2024年 18卷 1327986页

作者： Kan, Peter Zhu, Yong Fang Ma, Junling Singh, Gurmit McMaster Univ Dept Hlth Sci Hamilton ON Canada Redeemer Univ Dept Hlth Sci Hamilton ON Canada Univ Victoria Dept Math & Stat Victoria BC Canada McMaster Univ Dept Pathol & Mol Med Hamilton ON Canada McMaster Univ Michael G DeGroote Inst Pain Res & Care Hamilton ON Canada

Objective Nav1.8 expression is restricted to sensory neurons;it was hypothesized that aberrant expression and function of this channel at the site of injury contributed to pathological pain. However, the specific contributions of Nav1.8 to neuropathic pain are not as clear as its role in inflammatory pain. The aim of this study is to understand how Nav1.8 present in peripheral sensory neurons regulate neuronal excitability and induce various electrophysiological features on neuropathic *** To study the effect of changes in sodium channel Nav1.8 kinetics, Hodgkin-Huxley type conductance-based models of spiking neurons were constructed using the NEURON v8.2 simulation software. We constructed a single-compartment model of neuronal soma that contained Nav1.8 channels with the ionic mechanisms adapted from some existing small DRG neuron models. We then validated and compared the model with our experimental data from in vivo recordings on soma of small dorsal root ganglion (DRG) sensory neurons in animal models of neuropathic pain (NEP).Results We show that Nav1.8 is an important parameter for the generation and maintenance of abnormal neuronal electrogenesis and hyperexcitability. The typical increased excitability seen is dominated by a left shift in the steady state of activation of this channel and is further modulated by this channel's maximum conductance and steady state of inactivation. Therefore, modified action potential shape, decreased threshold, and increased repetitive firing of sensory neurons in our neuropathic animal models may be orchestrated by these modulations on *** computational modeling is a novel strategy to understand the generation of chronic pain. In this study, we highlight that changes to the channel functions of Nav1.8 within the small DRG neuron may contribute to neuropathic pain.

关键词： computational modeling DRG Nav1.8 electrophysiology neuropathy

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computational modeling of the Laser-Initiated, Gas-Embedded Z-Pinch

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IEEE TRANSACTIONS ON PLASMA SCIENCE 2024年第10期52卷 4782-4785页

作者： Lindemuth, Irvin R. Tucson Tucson AZ USA

From 1977 to 1981, a high-density, laser- initiated, gas-embedded z-pinch experimental and theoretical program was conducted at the Los Alamos National Laboratory. The experimental measurements and the computations indicated for the usual mode of operation the production experimentally of a hydrogen plasma characterized by n(e) = 10(20)/cm(3), T = 200 eV, and n(e)tau > 2 x 10(13) s/cm(3). The computations modeled all aspects of the experiment from t = 0: the Marx-bank transmission line energy source, the initiating laser and optical system, the electrical breakdown process, and the dynamic behavior of the pinch column. The computations reproduced the experimental diagnostics reasonably well and demonstrated that traditional interpretations of data based upon the Bennet relation, visible light emission, and x-ray emission gave conflicting results that could only be reconciled through detailed computation.

关键词： Plasmas computational modeling Laser modes Plasma temperature Gas lasers Plasma measurements Mathematical models Fusion magnetohydrodynamics plasma simulations z-pinch

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computational modeling Reveals a Catch-and-Guide Interaction Between Kinesin-1 and Tubulin C-Terminal Tails

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TRAFFIC 2025年第1-3期26卷 e70002页

作者： Nguyen, Trini Gross, Steven P. Miles, Christopher E. Univ Calif Irvine Ctr Complex Biol Syst Irvine CA 92697 USA Univ Calif Irvine Dept Dev & Cell Biol Irvine CA USA Univ Calif Irvine Dept Phys Irvine CA USA Univ Calif Irvine Dept Math Irvine CA 92697 USA

The delivery of intracellular cargoes by kinesins is modulated at scales ranging from the geometry of the microtubule networks down to interactions with individual tubulins and their code. The complexity of the tubulin code and the difficulty in directly observing motor-tubulin interactions have hindered progress in pinpointing the precise mechanisms by which kinesin's function is modulated. As one such example, past experiments show that cleaving tubulin C-terminal tails (CTTs) lowers kinesin-1's processivity and velocity on microtubules, but how these CTTs intertwine with kinesin's processive cycle remains unclear. In this work, we formulate and interrogate several plausible mechanisms by which CTTs contribute to and modulate kinesin motion. computational modeling bridges the gap between effective transport observations (processivity, velocities) and microscopic mechanisms. Ultimately, we find that a guiding mechanism can best explain the observed differences in processivity and velocity. Altogether, our work adds a new understanding of how the CTTs and their modulation via the tubulin code may steer intracellular traffic in both health and disease.

关键词： computational modeling cytoskeleton kinesin microtubules tubulin

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computational modeling of cardiac electrophysiology and arrhythmogenesis: toward clinical translation

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PHYSIOLOGICAL REVIEWS 2024年第3期104卷 1265页

作者： Trayanova, Natalia A. Lyon, Aurore Shade, Julie Heijman, Jordi Johns Hopkins Univ Dept Biomed Engn Baltimore MD 21218 USA Johns Hopkins Univ Alliance Cardiovasc Diag & Treatment Innovat Baltimore MD 21218 USA Maastricht Univ CARIM Sch Cardiovasc Dis Dept Biomed Engn Maastricht Netherlands Univ Med Ctr Utrecht Dept Med Physiol Div Heart & Lungs Utrecht Netherlands Maastricht Univ CARIM Sch Cardiovasc Dis Dept Cardiol Maastricht Netherlands

The complexity of cardiac electrophysiology, involving dynamic changes in numerous components across multiple spatial (from ion channel to organ) and temporal (from milliseconds to days) scales, makes an intuitive or empirical analysis of cardiac arrhythmogenesis challenging. Multiscale mechanistic computational models of cardiac electrophysiology provide precise control over individual parameters, and their reproducibility enables a thorough assessment of arrhythmia mechanisms. This review provides a comprehensive analysis of models of cardiac electrophysiology and arrhythmias, from the single cell to the organ level, and how they can be leveraged to better understand rhythm disorders in cardiac disease and to improve heart patient care. Key issues related to model development based on experimental data are discussed, and major families of human cardiomyocyte models and their applications are highlighted. An overview of organ-level computational modeling of cardiac electrophysiology and its clinical applications in personalized arrhythmia risk assessment and patient-specific therapy of atrial and ventricular arrhythmias is provided. The advancements presented here highlight how patient-specific computational models of the heart reconstructed from patient data have achieved success in predicting risk of sudden cardiac death and guiding optimal treatments of heart rhythm disorders. Finally, an outlook toward potential future advances, including the combination of mechanistic modeling and machine learning/artificial intelligence, is provided. As the field of cardiology is embarking on a journey toward precision medicine, personalized modeling of the heart is expected to become a key technology to guide pharmaceutical therapy, deployment of devices, and surgical interventions.

关键词： arrhythmias atrial fibrillation cardiac electrophysiology computational modeling sudden cardiac death

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computational modeling of the Subject-Specific Effects of Annuloplasty Ring Sizing on the Mitral Valve to Repair Functional Mitral Regurgitation

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ANNALS OF BIOMEDICAL ENGINEERING 2023年第9期51卷 1984-2000页

作者： Gaidulis, Gediminas Padala, Muralidhar Emory Univ Struct Heart Res & Innovat Lab Carlyle Fraser Heart Ctr Hosp Midtown Atlanta GA 30322 USA Emory Univ Div Cardiothorac Surg Sch Med Atlanta GA 30322 USA

Surgical repair of functional mitral regurgitation (FMR) that occurs in nearly 60% of heart failure (HF) patients is currently performed with undersizing mitral annuloplasty (UMA), which lacks short- and long-term durability. Heterogeneity in valve geometry makes tailoring this repair to each patient challenging, and predictive models that can help with planning this surgery are lacking. In this study, we present a 3D echo-derived computational model, to enable subject-specific, pre-surgical planning of the repair. Three computational models of the mitral valve were created from 3D echo data obtained in three pigs with HF and FMR. An annuloplasty ring model in seven sizes was created, each ring was deployed, and post-repair valve closure was simulated. The results indicate that large annuloplasty rings (> 32 mm) were not effective in eliminating regurgitant gaps nor in restoring leaflet coaptation or reducing leaflet stresses and chordal tension. Smaller rings (& LE;32 mm) restored better systolic valve closure in all investigated cases,but excessive valve tethering and restricted motion of the leaflets were still present. This computational study demonstrates that for effective correction of FMR, the extent of annular reduction differs between subjects, and overly reducing the annulus has deleterious effects on the valve.

关键词： Cardiac mechanics Mitral valve Mitral regurgitation Mitral annuloplasty computational modeling Finite element method

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computational modeling predicts regulation of central pattern generator oscillations by size and density of the underlying heterogenous network

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JOURNAL OF computational NEUROSCIENCE 2023年第1期51卷 87-105页

作者： Ilies, Iulian Zupanc, Gunther K. H. Northeastern Univ Dept Biol Lab Neurobiol Boston MA 02115 USA

Central pattern generators are characterized by a heterogeneous cellular composition, with different cell types playing distinct roles in the production and transmission of rhythmic signals. However, little is known about the functional implications of individual variation in the relative distributions of cells and their connectivity patterns. Here, we addressed this question through a combination of morphological data analysis and computational modeling, using the pacemaker nucleus of the weakly electric fish Apteronotus leptorhynchus as case study. A neural network comprised of 60-110 interconnected pacemaker cells and 15-30 relay cells conveying its output to electromotoneurons in the spinal cord, this nucleus continuously generates neural signals at frequencies of up to 1 kHz with high temporal precision. We systematically explored the impact of network size and density on oscillation frequencies and their variation within and across cells. To accurately determine effect sizes, we minimized the likelihood of complex dynamics using a simplified setup precluding differential delays. To identify natural constraints, parameter ranges were extended beyond experimentally recorded numbers of cells and connections. Simulations revealed that pacemaker cells have higher frequencies and lower within-population variability than relay cells. Within-cell precision and between-cells frequency synchronization increased with the number of pacemaker cells and of connections of either type, and decreased with relay cell count in both populations. Network-level frequency-synchronized oscillations occurred in roughly half of simulations, with maximized likelihood and firing precision within biologically observed parameter ranges. These findings suggest the structure of the biological pacemaker nucleus is optimized for generating synchronized sustained oscillations.

关键词： Apteronotus leptorhynchus Central pattern generator computational modeling Neural network Pacemaker nucleus Weakly electric fish

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computational modeling of Ice Sheets and Glaciers

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COMPUTING IN SCIENCE & ENGINEERING 2023年第3期25卷 4-6页

作者： Tezaur, Irina Ahlkrona, Josefin Hoffman, Matthew Perego, Mauro Sandia Natl Labs Quantitat Modeling & Software Engn Dept Livermore CA 94587 USA Stockholm Univ Dept Math Sci Comp Applicat Climate Sci SE-10691 Stockholm Sweden Los Alamos Natl Lab Fluid Dynam & Solid Mech Grp Los Alamos NM 87545 USA Sandia Natl Labs Ctr Comp Res Albuquerque NM 87185 USA

The four articles in this special section focus on the development and efficient implementation of numerical, computational, and data driven methods for reliable, next-generation ISMs, toward addressing some of these challenges. These articles span a variety of topics, ranging from mechanics based modeling of hydrofracture and ice calving, to novel, compatible finite-element discretizations, to data-driven methods that can enable UQ within the field of ice-sheet modeling.

关键词： Special issues and sections Ice thickness Ice surface computational modeling Antarctica Numerical models Solid modeling Data models Surface treatment Sea level Three-dimensional displays

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computational modeling as a Tool to Drive the Development of a Novel, Chemical Device for Monitoring the Injured Brain and Body

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ACS CHEMICAL NEUROSCIENCE 2023年第19期14卷 3599-3608页

作者： Murray, De-Shaine Stickel, Laure Boutelle, Martyn Imperial Coll London Dept Bioengn London SW7 2AZ England Yale Univ Sch Engn & Appl Sci New Haven CT 06520 USA Inst Curie Lab Phys Chim Curie F-75005 Paris France

Real-time measurement of dynamic changes, occurring in the brain and other parts of the body, is useful for the detection and tracked progression of disease and injury. Chemical monitoring of such phenomena exists but is not commonplace, due to the penetrative nature of devices, the lack of continuous measurement, and the inflammatory responses that require pharmacological treatment to alleviate. Soft, flexible devices that more closely match the moduli and shape of monitored tissue and allow for surface microdialysis provide a viable alternative. Here, we show that computational modeling can be used to aid the development of such devices and highlight the considerations when developing a chemical monitoring probe in this way. These models pave the way for the development of a new class of chemical monitoring devices for monitoring neurotrauma, organs, and skin.

关键词： neuromonitoring computational modeling microdialysis neurotrauma chemical analytical

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