Resolving the ethical concerns regarding animal-based experiments, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) represent a virtually limitless pool of human <i>in vitro</i> models in cardiology. They open up new opportunities for patient-specific safety cardiac pharmacology as they share the same genotype with patients and exhibit the same pathological traits as their real-life counterparts. Computational models of hiPSC-CMs assist us in bridging important vital gaps. Namely, i) Enhancing our quantitative understanding of intracellular interactions in preclinical drug trials and exploring genotype-phenotype relationships; ii) High-throughput risk stratification and prediction of vulnerability to arrhythmia; iii) addressing electrophysiological, contractile, and biochemical differences between in vitro hiPSC-CMs and <i>in silico</i> human adult ventricular CMs, since the combination of <i>in vitro</i> hiPSC-CMs and <i>in silico</i> human adult ventricular cardiomyocytes (hV-CMs) has been proposed as a promising new paradigm in drug screening by the FDA (the comprehensive proarrhythmia assay).

The first aim of this thesis was to develop a robust whole-cell model of hiPSC- CMs electromechanics capturing the mechano-electric feedback by integrating a reparametrized contractile element (CE) into the ionic model of hiPSC-CMs. The second aim was proposing a computational approach toward deep-phenotyping mutation-specific hypertrophic cardiomyopathy (HCM), specifically MYH7^R403Q/+ and exploring the effects and action mechanisms of Mavacamten (MAVA), Blebbistatin (BLEB), and Omecamtive mecarbil (OM). The final aim was refining the hiPSC-CMs model of electro-mechano-energetic coupling to explore the interorganellar crosstalks in ischemia/reperfusion (I/R). A novel oxygen dynamic formulation was introduced to link the capillary level to extracellular oxygen concentrations affected by Na⁺/K⁺ exchanger, sarcolemmal Ca²⁺ pump current, and the contractile ATPase rate. The common methodology in Studies I-IV of the thesis is use of a set of <i>in vitro</i> data for model calibrations and another set of <i>in vitro</i> data for quantitative/qualitative results validations prioritizing hiPSC-CMs <i>in vitro</i> findings.

Meeting the accurate fractional cell shortening (FCS), time from peak contraction to 50% of relaxation (CRT50), and active tension (AT) amplitude were introduced as the optimization goals of the cell electromechanical calibrations. The sensitivity analysis on the CE machinery in Studies I & II offer a robust reparameterization roadmap from animal-based computational models to hiPSC-CMs phenotype. A correct categorization of inotropic effects of non-cardiomyocytes was recapitulated in accord with hiPSC-CMs experimental reports. In Study III, the metabolite- sensitivity in the CE played a key role in capturing the contractile dysfunction, in terms of hypercontractility and irregular CRT50, in MYH7^R403Q/+ HCM and the cardioprotective effect of MAVA, through affecting myofilament crossbridge (XB) state transitions and Pi, MgATP, and MgADP. The therapeutic compounds in Study III were sarcomere targeting molecules; MAVA, BLEB, and OM. Therefore, their mechanism of action was modeled by CE optimizations accordingly, and the XB parameter governing the dose-dependence of OM and BLEB inotropic effect was identified. In Study IV, in accord with Levosimendan (Levo) inotropic data, the dose-dependent effect of Levo as an IKATP agonist was included in the drug-induced calibration besides the channel-blockings for INa, ICaL, and IKr. Explicitly, introducing the novel oxygen dynamic formulation with a contractile ATPase rate was a first step toward linking the cellular energetics to oxygen consumption rate (OCR). Based on the sarco/endoplasmic reticulum Ca²⁺-ATPase pump (SERCA) calibration in Study IV, increased affinity of proton binding for luminal-oriented Ca²⁺ docking sites was suggested as a mechanism of SERCA response to I/R condition leading to increased Ca²⁺ concentration in SR. Study IV predicted the upper hand of Ca²⁺ flux to the myofilament in comparison with SERCA Ca²⁺ uptake, also recapitulating the fact that Levo does not increase the inotropy at the expense of elevated oxygen demand. Study IV findings suggest that, mechanistically, SERCA contributes similarly in I/R and sepsis-induced heart failure conditions. Furthermore, Study IV suggested that the increase in proton leak in I/R, which results in elevated oxidative stress, may also contribute to the ischemic Ca²⁺ overload through disrupted competitive proton binding in SERCA, as a step toward establishing the connection between the elevation of oxidative stress and Ca2+ overload as the two main mechanisms of I/R injuries. Finally, Study IV linked the ameliorative effect of Levo on the contractile relaxation dysfunction to the drug's specific Ca²⁺ sensitizing mechanism, which involves Ca²⁺-bound troponin C and Ca²⁺ flux to the myofilament rather than SERCA phosphorylation inhibition.

To summarize, this thesis offers novel and robust computational frameworks of electro-mechano-energetic coupling in hiPSC-CMs, leveraging recent advances in human-based <i>in vitro</i> data acquisition. Ultimately, the presented models can serve as a platform to test advanced treatment ideas according to the temporal evolution of metabolites and molecular mechanisms in cardiomyocytes.