Youbo Zhao | Searcharxiv

arXiv2026

Intracellular Measurement-Informed Multiscale Modeling for Scalable iPSC Manufacturing

Scalable manufacturing of human induced pluripotent stem cells (iPSCs) is essential for industrial-scale production of cell therapies and regenerative medicines. However, the 3D aggregate cultures used in manufacturing exhibit substantial spatial and metabolic heterogeneity compared with the relatively homogeneous monolayer systems used in laboratory studies, complicating mechanistic understanding and predictive metabolic modeling across culture scales. To address this challenge, we developed a modular multiscale mechanistic foundation model that links molecular, cellular, and macroscopic processes while accounting for spatial and metabolic heterogeneity. The framework integrates extracellular culture dynamics, intracellular metabolic fluxes, and cellular redox states by extending a previously established monolayer kinetic network and coupling it with a biological systems-of-systems (Bio-SoS) multiscale model for aggregate cultures, incorporating explicit redox interactions. Systematic monolayer and aggregate experiments (including multiple isotopic tracers, extracellular metabolite profiling, and two-photon optical redox imaging) were used to improve and validate the model. This integrated framework unifies heterogeneous datasets across culture configurations and enables mechanistic interpretation of metabolic and redox responses across heterogeneous culture scales, providing a quantitative foundation for scalable iPSC biomanufacturing.

q-bio.CB↗

arXiv2014

Coherent Phase Control of Internal Conversion in Pyrazine

Shaped ultrafast laser pulses were used to study and control the ionization dynamics of electronically excited pyrazine in a pump and probe experiment. For pump pulses created without feedback from the product signal, the ion growth curve (the parent ion signal as a function of pump/probe delay) was described quantitatively by the classical rate equations for internal conversion of the $S_2$ and $S_1$ states. Very different, non-classical behavior was observed when a genetic algorithm (GA) was used to minimize the ion signal at some pre-determined target time, T. Two qualitatively different control mechanisms were identified for early (T$<1.5$ ps) and late (T$>1.5$ ps) target times. In the former case, the ion signal was largely suppressed for $t 1.5$ ps the ion growth curve followed the classical rate equations for $t<T$, while for $t \gg T$ the quantum yield for the GA-optimized pulse was much smaller than for a TL pulse. We interpret the first type of behavior as an indication that the wave packet produced by the pump laser is localized in a region of the $S_2$ potential energy surface where the vertical ionization energy exceeds the probe photon energy, whereas the second type of behavior may be described by a reduced absorption cross section for $S_0 \rightarrow S_2$ followed by incoherent decay of the excited molecules.

physics.atom-ph↗