High speed volumetric optical microscopy is an important tool for observing rapid processes in living cells or for real-time tracking of sub-cellular components. However, the 3D imaging capability often comes at the price of a high technical complexity of the imaging system and/or the requirement of demanding image analysis. Here, we propose a combination of conventional phase-contrast imaging with a customized multi-plane beam-splitter for enabling simultaneous acquisition of images in eight different focal planes. Our method is technically straightforward and does not require complex post-processing image analysis. We apply our multi-plane phase-contrast microscope to the real-time observation of the fast motion of reactivated Chlamydomonas axonemes with sub-µm spatial and 4 ms temporal resolution. Our system allows us to observe not only bending but also the three-dimensional torsional dynamics of these micro-swimmers.

The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino acids, the biochemical environment and the temporal sequence of distinct interactions yield a complex folding process that cannot yet be easily tracked for all proteins. To gain qualitative insights into the fundamental mechanisms behind the folding dynamics and generic features of the folded structure, we propose a simple model of structure formation that takes into account only fundamental geometric constraints and otherwise assumes randomly paired connections. We find that despite its simplicity, the model results in a network ensemble consistent with key overall features of the ensemble of Protein Residue Networks we obtained from more than 1000 biological protein geometries as available through the Protein Data Base. Specifically, the distribution of the number of interaction neighbors a unit (amino acid) has, the scaling of the structure's spatial extent with chain length, the eigenvalue spectrum and the scaling of the smallest relaxation time with chain length are all consistent between model and real proteins. These results indicate that geometric constraints alone may already account for a number of generic features of protein tertiary structures.

No abstract

We study intrachain dynamics of intrinsically disordered proteins, as manifested by the time scales of loop formation, using atomistic simulations, experiment-parametrized coarse-grained models, and one-dimensional theories assuming Markov or non-Markov dynamics along the reaction coordinate. Despite the generally non-Markov character of monomer dynamics in polymers, we find that the simplest model of one-dimensional diffusion along the reaction coordinate (equated to the distance between the loop-forming monomers) well captures the mean first passage times to loop closure measured in coarse-grained and atomistic simulations, which, in turn, agree with the experimental values. This justifies use of the one-dimensional diffusion model in interpretation of experimental data. At the same time, the transition path times for loop closure in longer polypeptide chains show significant non-Markov effects; at intermediate times, these effects are better captured by the generalized Langevin equation model. At long times, however, atomistic simulations predict long tails in the distributions of transition path times, which are at odds with both the one-dimensional diffusion model and the generalized Langevin equation model.

Generation of electromagnetic fields by moving charges is a fascinating topic where the tight connection between classical electrodynamics and special relativity becomes particularly apparent. One can gain direct insight into the fascinating structure of such fields by visualizing the electric field lines. However, the calculation of electric field lines for arbitrarily moving charges is far from trivial. Here, we derive an equation for the director that points from the retarded position of a moving charge towards a specific field line position, which allows for a simple construction of these lines. We analytically solve this equation for several special but important cases: for an arbitrary rectilinear motion, for the motion within the wiggler magnetic field of a free electron laser, and for the motion in a synchrotron. arXiv:1809.05868v2 [physics.class-ph]