Integrated intracellular organization and its variations in human iPS cells.

Understanding how a subset of expressed genes dictates cellular phenotype is a considerable challenge owing to the large numbers of molecules involved, their combinatorics and the plethora of cellular behaviours that they determine1,2. Here we reduced this complexity by focusing on cellular organization-a key readout and driver of cell behaviour3,4-at the level of major cellular structures that represent distinct organelles and functional machines, and generated the WTC-11 hiPSC Single-Cell Image Dataset v1, which contains more than 200,000 live cells in 3D, spanning 25 key cellular structures. The scale and quality of this dataset permitted the creation of a generalizable analysis framework to convert raw image data of cells and their structures into dimensionally reduced, quantitative measurements that can be interpreted by humans, and to facilitate data exploration. This framework embraces the vast cell-to-cell variability that is observed within a normal population, facilitates the integration of cell-by-cell structural data and allows quantitative analyses of distinct, separable aspects of organization within and across different cell populations. We found that the integrated intracellular organization of interphase cells was robust to the wide range of variation in cell shape in the population; that the average locations of some structures became polarized in cells at the edges of colonies while maintaining the 'wiring' of their interactions with other structures; and that, by contrast, changes in the location of structures during early mitotic reorganization were accompanied by changes in their wiring.

Native Frames: Disentangling Sequential from Concerted Three-Body Fragmentation.

A key question concerning the three-body fragmentation of polyatomic molecules is the distinction of sequential and concerted mechanisms, i.e., the stepwise or simultaneous cleavage of bonds. Using laser-driven fragmentation of OCS into O^{+}+C^{+}+S^{+} and employing coincidence momentum imaging, we demonstrate a novel method that enables the clear separation of sequential and concerted breakup. The separation is accomplished by analyzing the three-body fragmentation in the native frame associated with each step and taking advantage of the rotation of the intermediate molecular fragment, CO^{2+} or CS^{2+}, before its unimolecular dissociation. This native-frame method works for any projectile (electrons, ions, or photons), provides details on each step of the sequential breakup, and enables the retrieval of the relevant spectra for sequential and concerted breakup separately. Specifically, this allows the determination of the branching ratio of all these processes in OCS^{3+} breakup. Moreover, we find that the first step of sequential breakup is tightly aligned along the laser polarization and identify the likely electronic states of the intermediate dication that undergo unimolecular dissociation in the second step. Finally, the separated concerted breakup spectra show clearly that the central carbon atom is preferentially ejected perpendicular to the laser field.

Dependence on the Initial Configuration of Strong Field-Driven Isomerization of C2H2 Cations and Anions.

We have investigated the femtosecond laser-induced fragmentation of C2H2 q ion beam targets in various initial configurations, including acetylene (linear HCCH), vinylidene (H2CC), and cis/ trans. The initial configuration is shown to have a tremendous impact on the branching ratio of acetylene-like (CH q1 + CH q2) and vinylidene-like (C q1' + CH2 q2') dissociation of a specific C2H2 q molecular ion. In particular, whereas C2H2+ generated from C2H2, a linear HCCH target, exhibits comparable levels of acetylene-like and vinylidene-like fragmentation, vinylidene or cis/ trans configuration ion beams preferably undergo vinylidene-like fragmentation, with an acetylene branching ratio ranging from 13.9% to zero.

The importance of Rydberg orbitals in dissociative ionization of small hydrocarbon molecules in intense laser fields.

Much of our intuition about strong-field processes is built upon studies of diatomic molecules, which typically have electronic states that are relatively well separated in energy. In polyatomic molecules, however, the electronic states are closer together, leading to more complex interactions. A combined experimental and theoretical investigation of strong-field ionization followed by hydrogen elimination in the hydrocarbon series C2D2, C2D4 and C2D6 reveals that the photofragment angular distributions can only be understood when the field-dressed orbitals rather than the field-free orbitals are considered. Our measured angular distributions and intensity dependence show that these field-dressed orbitals can have strong Rydberg character for certain orientations of the molecule relative to the laser polarization and that they may contribute significantly to the hydrogen elimination dissociative ionization yield. These findings suggest that Rydberg contributions to field-dressed orbitals should be routinely considered when studying polyatomic molecules in intense laser fields.

Mechanisms and time-resolved dynamics for trihydrogen cation (H3+) formation from organic molecules in strong laser fields.

Strong-field laser-matter interactions often lead to exotic chemical reactions. Trihydrogen cation formation from organic molecules is one such case that requires multiple bonds to break and form. We present evidence for the existence of two different reaction pathways for H3+ formation from organic molecules irradiated by a strong-field laser. Assignment of the two pathways was accomplished through analysis of femtosecond time-resolved strong-field ionization and photoion-photoion coincidence measurements carried out on methanol isotopomers, ethylene glycol, and acetone. Ab initio molecular dynamics simulations suggest the formation occurs via two steps: the initial formation of a neutral hydrogen molecule, followed by the abstraction of a proton from the remaining CHOH2+ fragment by the roaming H2 molecule. This reaction has similarities to the H2 + H2+ mechanism leading to formation of H3+ in the universe. These exotic chemical reaction mechanisms, involving roaming H2 molecules, are found to occur in the ~100 fs timescale. Roaming molecule reactions may help to explain unlikely chemical processes, involving dissociation and formation of multiple chemical bonds, occurring under strong laser fields.

Note: Determining the detection efficiency of excited neutral atoms by a microchannel plate detector.

We present a method for determining the detection efficiency of neutral atoms relative to keV ions. Excited D* atoms are produced by D2 fragmentation in a strong laser field. The fragments are detected by a micro-channel plate detector either directly as neutrals or as keV ions following field ionization and acceleration by a static electric field. Moreover, we propose a new mechanism by which neutrals are detected. We show that the ratio of the yield of neutrals and ions can be related to the relative detection efficiency of these species.