Determination of insulin secretion from stem cell-derived islet organoids with liquid chromatography-tandem mass spectrometry

Organoids are laboratory-grown 3D organ models, mimicking human organs for e.g. drug development and personalized therapy. Islet organoids (typically 100–200 µm), which can be grown from the patient́s own cells, are emerging as prototypes for transplantation-based therapy of diabetes. Selective methods for quantifying insulin production from islet organoids are needed, but sensitivity and carry-over have been major bottlenecks in previous efforts. We have developed a reverse phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) method for studying the insulin secretion of islet organoids. In contrast to our previous attempts using nano-scale LC columns, conventional 2.1 mm inner diameter LC column (combined with triple quadrupole mass spectrometry) was well suited for sensitive and selective measurements of insulin secreted from islet organoids with low microliter-scale samples. Insulin is highly prone to carry-over, so standard tubings and injector parts were replaced with shielded fused silica connectors. As samples were expected to be very limited, an extended Box-Behnken experimental design for the MS settings was conducted to maximize performance. The finale method has excellent sensitivity, accuracy and precision (limit of detection: ≤0.2 pg/µL, relative error: ≤±10%, relative standard deviation: <10%), and was well suited for measuring 20 µL amounts of Krebs buffer containing insulin secreted from islet organoids.publishedVersio

Coupled cluster studies of infinite systems

We investigate how the coupled cluster method at the level of doubles and triples amplitudes contributes to the ground state energy of the homogeneous electron gas. We present and derive the formalism and equations needed, and describe in detail how two independent and conceptually differing computational schemes may be implemented efficiently for the system under study. We finally perform numerous calculations for the infinite electron gas, investigate how the gradual inclusion of more diagrams leading up to the full coupled cluster doubles triples (CCDT) method affects the energy, and we estimate the energy in the thermodynamical limit by extrapolating results from large scale computations. In order to check all equations, we have also developed a software which produces all equations needed at a given level of truncation of coupled cluster theory. This allows for efficient benchmarking of equations as well as codes for implementing various conributions to the theory

Local correlation methods for infinite systems

Quantum Chemistry constitutes an extensive framework for accurately simulating the electronic wavefunction of atoms and molecules. The same framework may in principle be applied to the domain of periodic structures such as crystals, but is in practice severely limited by the infinite nature of these structures in conjunction with the computational complexity of quantum chemical methods. In his thesis, the candidate utilizes a mathematical structure known as bi-infinite block-Toeplitz matrices in order to smoothly transition between the molecular and periodic realm. Furthermore, he extends the divide-expand-consolidate methods originally devised for molecules to the periodic case, and demonstrates that this procedure can reduce the computational scaling of the simulation while retaining systematic control over the error

Smooth potential-energy surfaces in fragmentation-based local correlation methods for periodic systems

Local approximations facilitate the application of post-Hartree–Fock methods in the condensed phase, but simultaneously introduce errors leading to discontinuous potential-energy surfaces. In this work, we explore how these discontinuities arise in periodic systems, their implications, and possible ways of controlling them. In addition, we present a fully periodic Divide-Expand-Consolidate second-order Møller–Plesset approach using an attenuated resolution-of-the-identity approximation for the electron repulsion integrals and a convenient class to handle translation-symmetric tensors in block-Toeplitz format

Divide-Expand-Consolidate Second-Order Møller-Plesset Theory with Periodic Boundary Conditions

We present a generalization of the divide–expand–consolidate (DEC) framework for local coupled-cluster calculations to periodic systems and test it at the second-order Møller–Plesset (MP2) level of theory. For simple model systems with periodicity in one, two, and three dimensions, comparisons with extrapolated molecular calculations and the local MP2 implementation in the Cryscor program show that the correlation energy errors of the extended DEC (X-DEC) algorithm can be controlled through a single parameter, the fragment optimization threshold. Two computational bottlenecks are identified: the size of the virtual orbital spaces and the number of pair fragments required to achieve a given accuracy of the correlation energy. For the latter, we propose an affordable algorithm based on cubic splines interpolation of a limited number of pair-fragment interaction energies to determine a pair cutoff distance in accordance with the specified fragment optimization threshold