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Filtered Finite State Projection Method for the Analysis and Estimation of Stochastic Biochemical Reaction Networks
Item type: Journal Article
D'Ambrosio, Elena; Fang, Zhou; Gupta, Ankit; et al. (2026)
Time-lapse microscopy has become increasingly prevalent in biological experimentation, as it provides single-cell trajectories that unveil valuable insights into underlying networks and their stochastic dynamics. However, the limited availability of fluorescent reporters typically constrains tracking to only a few network species. Addressing this challenge, the dynamic estimation of hidden state components becomes crucial, for which stochastic filtering presents a robust mathematical framework. Yet, the complexity of biological networks often renders direct solutions to the filtering equation intractable due to high dimensionality and nonlinear interactions. In this study, we establish and rigorously prove the well-posedness of the filtering equation for the time evolution of the conditional distribution of hidden species. Focusing on continuous-time, noise-free observations within a continuous-time discrete state-space Markov chain model, we develop the filtered finite state projection (FFSP) method. This computational approach offers an approximated solution by truncating the hidden species' state space, accompanied by computable error bounds. We illustrate the effectiveness of FFSP through diverse numerical examples, comparing it with established filtering techniques such as the Kalman filter, extended Kalman filter, and particle filter. Finally, we show an application of our methodology with real time-lapse microscopy data. This work not only advances the application of stochastic filtering to biological systems but also contributes towards more accurate implementation of biomolecular feedback controllers.
Investigating trends in actinide covalency and magnetism with 35/37Cl SSNMR spectroscopy and first-principles calculations
Item type: Journal Article
Altenhof, Adam R.; Erickson, Karla A.; Rehn, Daniel A.; et al. (2026)
Solid-state NMR (SSNMR) spectroscopy is a powerful technique for studying actinide chemistry but has been significantly limited due to the complex paramagnetism, and radiological hazards presented by these materials. Lanthanide and actinide salts often feature magnetic ordering and can be paramagnetic, ferromagnetic, or antiferromagnetic depending on temperature and electronic structure. Paramagnetic interactions can manifest in SSNMR both as secular spectral shifts and/or couplings as well as contributions from non-secular relaxation. Both effects can be directly measured with NMR and used to extrapolate rich chemical information such as coordination environments, bonding characteristics, local molecular dynamics, and correlation times. Typically, these studies are carried out on high-gamma and highly abundant NMR-active isotopes (e.g., 1H, 6/7Li, 19F, 23Na, etc.) or on enriched rare isotopes (e.g., 2H and 17O), which can be expensive. Herein, we present a facile methodology to measure the 35/37Cl electric-field gradient (EFG) and paramagnetic shift anisotropy (SA) tensor components using static wideline SSNMR measurements of LaCl3, NdCl3, UCl3, and UCl4. The static powder spectra were measured with both 35Cl and 37Cl SSNMR to increase the fidelity of the extracted tensor parameters. Variable temperature NMR of a select case confirms the Curie-Weiss paramagnetism. Relaxation measurements of both nuclei further corroborate observations owing to the paramagnetic relaxation enhancement and reveal simultaneous quadrupolar relaxation mechanisms. Density functional theory (DFT) calculations using Hubbard U corrections to the uranium valence orbitals show excellent agreement with experimental EFG tensor parameters and help describe the bonding characteristics in these lanthanide and actinide systems.
The environmental stress response regulates biophysics of the cytoplasm and survival in quiescence
Item type: Journal Article
Kronig, Lorena; Weber, Carmen A.; Gomez-Garcia, Pablo Aurelio; et al. (2026)
All organisms employ strategies to cope with changing environmental conditions. In budding yeast, nutrient deprivation induces a reversible non-proliferative state known as quiescence, characterized by extensive remodeling of gene expression, metabolism, and cellular biophysical properties. Yeast cells survive prolonged periods of starvation-induced quiescence, provided they can respire in the early stages of glucose withdrawal, and blocking respiration causes premature aging and markedly reduced survival and cytoplasmic diffusion. We find that respiration is required to initiate a quiescence-specific adaptive program. Induction of such a program prior to glucose withdrawal bypasses the need for respiration, rescuing survival and biophysical properties to the levels of respiration-competent cells. This rescue relies on proteomic adaptation and is mediated by Ras/PKA inactivation and Msn2/4-dependent activation of the environmental stress response, leading to modulation of cytoplasmic diffusion. Together, this enables long-term survival in quiescence even in the absence of respiration, underscoring the role of the stress response and the modulation of cytoplasmic properties in quiescence and aging.
Mechanistic Insights into PFAS Rejection in Nanofiltration and Reverse Osmosis from Data-Driven Analysis
Item type: Journal Article
Tomsovic, Yukai; Gu, Siwei; Doudrick, Kyle; et al. (2026)
The structural diversity and complex transport behavior of per- and polyfluoroalkyl substances (PFAS) complicate a universal characterization of their removal in membrane systems. This study compiles 2353 data points from the literature on PFAS rejection by nanofiltration and reverse osmosis membranes, spanning a broad range of PFAS, membranes, feedwater compositions, and operating conditions. Using machine learning, this data set is modeled to evaluate how solute, membrane, and solution properties jointly influence PFAS removal. Of the 13 experimental system descriptors analyzed, membrane water permeance and PFAS molecular volume demonstrated the strongest main effect on rejection, emphasizing the significance of steric exclusion. The effects of background ions and dissolved organic matter were highly condition-dependent, exhibiting nonmonotonic behavior governed by competing mechanisms. Low concentrations of organic matter and ions enhanced PFAS rejection, consistent with complexation that increases apparent solute size, while higher concentrations reduced PFAS rejection, indicating that charge shielding and concentration polarization increasingly drive transport behavior. Overall, this analysis provides a unified, data-driven framework for interpreting previously inconsistent findings across studies, identifies critical gaps in existing experimental data, and highlights opportunities to guide targeted membrane design and treatment strategies.
Exact Stoichiometry Far-Off Neutrality Catanionic Nanotubes: Unconventional Self-Assembly of Oppositely Charged Surfactants
Item type: Journal Article
La Gambina, Valerio; Rocchi, Lorenzo A.; Sennato, Simona; et al. (2026)
Electrostatic energy plays a pivotal role in the minimization of the free energy of self-assembling oppositely charged ions. This is a fundamental principle that guides the formation of aggregates and the separation of phases characterized by a stoichiometric balance between the opposite charges. However, this study unveils the self-assembly of catanionic nanotubes from a mixture of oppositely charged surfactants in aqueous buffer, comprising an anionic bile salt derivative and the cationic cetyltrimethylammonium bromide (CTAB) at an exact strongly unbalanced charge ratio of 9 anions to 1 cation. This anomalous aggregation leads to the formation of highly stable and ordered supramolecular nanotubes with a uniform cross-section of about 20 nm. The key to this behavior lies in the unique, rigid, and facial amphiphilic structure of the bile salt derivative, allocating hydrogen bond donors/acceptors and an aromatic residue, which promotes geometrically constrained derivative-derivative interactions. This facilitates the assembly of the anionic derivative into parallel, helically wrapped, negatively charged ribbons with interspersed CTAB cations, acting to promote their adhesion. Supramolecular nanotubes are highly valued in nanotechnology for applications such as catalysis and tissue engineering due to their rigidity, intrinsic directionality, and capability for dual compartmentalization (inner cavity and outer surface). The catanionic structures reported here are ordered architectures that allow for a high charge and a minimal interference from free monomers, which are essential for optimizing functions such as material loading. A loading ability was demonstrated here by the nanotube interaction with positively charged carbon dots and gold nanorods.