Macromolecular structural dynamics visualized by pulsed dose control in 4D electron microscopy

Macromolecular conformation dynamics, which span a wide range of time scales, are fundamental to the understanding of properties and functions of their structures. Here, we report direct imaging of structural dynamics of helical macromolecules over the time scales of conformational dynamics (ns to subsecond) by means of four-dimensional (4D) electron microscopy in the single-pulse and stroboscopic modes. With temporally controlled electron dosage, both diffraction and real-space images are obtained without irreversible radiation damage. In this way, the order-disorder transition is revealed for the organic chain polymer. Through a series of equilibrium-temperature and temperature-jump dependencies, it is shown that the metastable structures and entropy of conformations can be mapped in the nonequilibrium region of a “funnel-like” free-energy landscape. The T-jump is introduced through a substrate (a “hot plate” type arrangement) because only the substrate is made to absorb the pulsed energy. These results illustrate the promise of ultrafast 4D imaging for other applications in the study of polymer physics as well as in the visualization of biological phenomena

4D visualization of embryonic, structural crystallization by single-pulse microscopy

In many physical and biological systems the transition from an amorphous to ordered native structure involves complex energy landscapes, and understanding such transformations requires not only their thermodynamics but also the structural dynamics during the process. Here, we extend our 4D visualization method with electron imaging to include the study of irreversible processes with a single pulse in the same ultrafast electron microscope (UEM) as used before in the single-electron mode for the study of reversible processes. With this augmentation, we report on the transformation of amorphous to crystalline structure with silicon as an example. A single heating pulse was used to initiate crystallization from the amorphous phase while a single packet of electrons imaged selectively in space the transformation as the structure continuously changes with time. From the evolution of crystallinity in real time and the changes in morphology, for nanosecond and femtosecond pulse heating, we describe two types of processes, one that occurs at early time and involves a nondiffusive motion and another that takes place on a longer time scale. Similar mechanisms of two distinct time scales may perhaps be important in biomolecular folding

Work distribution for the driven harmonic oscillator with time-dependent strength: Exact solution and slow driving

We study the work distribution of a single particle moving in a harmonic oscillator with time-dependent strength. This simple system has a non-Gaussian work distribution with exponential tails. The time evolution of the corresponding moment generating function is given by two coupled ordinary differential equations that are solved numerically. Based on this result we study the behavior of the work distribution in the limit of slow but finite driving and show that it approaches a Gaussian distribution arbitrarily well

SPH Simulations of Galactic Gaseous Disk with Bar: Distribution and Kinematic Structure of Molecular Clouds toward the Galactic Center

We have performed Smoothed Particle Hydrodynamic (SPH) simulations to study the response of molecular clouds in the Galactic disk to a rotating bar and their subsequent evolution in the Galactic Center (GC) region. The Galactic potential in our models is contributed by three axisymmetric components (massive halo, exponential disk, compact bulge) and a non-axisymmetric bar. These components are assumed to be invariant in time in the frame corotating with the bar. Some noticeable features such as an elliptical outer ring, spiral arms, a gas-depletion region, and a central concentration have been developed due to the influence of the bar. The rotating bar induces non-circular motions of the SPH particles, but hydrodynamic collisions tend to suppress the random components of the velocity. The velocity field of the SPH particles is consistent with the kinematics of molecular clouds observed in HCN (1-0) transition; these clouds are thought to be very dense clouds. However, the l-v diagram of the clouds traced by CO is quite different from that of our SPH simulation, being more similar to that obtained from simulations using collisionless particles. The $l-v$ diagram of a mixture of collisional and collisionless particles gives better reproduction of the kinematic structures of the GC clouds observed in the CO line. The fact that the kinematics of HCN clouds can be reproduced by the SPH particles suggests that the dense clouds in the GC are formed via cloud collisions induced by rotating bar.Comment: 31 pages, 10 pigures, accepted for publication in Ap

Interaction between M2-branes and Bulk Form Fields

We construct the interaction terms between the world-volume fields of multiple M2-branes and the 3- and 6-form fields in the context of ABJM theory with U($N$)$\times$U($N$) gauge symmetry. A consistency check is made in the simplest case of a single M2-brane, i.e, our construction matches the known effective action of M2-brane coupled to antisymmetric 3-form field. We show that when dimensionally reduced, our couplings coincide with the effective action of D2-branes coupled to R-R 3- and 5-form fields in type IIA string theory. We also comment on the relation between a coupling with a specific 6-form field configuration and the supersymmetry preserving mass deformation in ABJM theory.Comment: 30 pages, version to appear in JHE

Matrix Inequality Approach to a Novel Stability Criterion for Time-Delay Systems with Nonlinear Uncertainties

Abstract. In this paper, a novel stability criterion is presented for time-delay systems which have nonlinear uncertainties. Based on the Lyapunov method, a stability criterion is derived in terms of matrix inequalities which can be solved easily by efficient convex optimization algorithms. Numerical examples are included to show the effectiveness of the proposed method

Million-atom molecular dynamics simulation by order-N electronic structure theory and parallel computation

Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for silicon nanocrystals of more than millions atoms with the transferable tight-binding Hamiltonian. The efficiency of parallelism is perfect, 98.8 %, and the method is the most suitable to parallel computation. The elapse time for a system of $2\times 10^6$ atoms is 3.0 minutes by a computer system of 64 processors of SGI Origin 3800. The calculated results are in good agreement with the results of the exact diagonalization, with an error of 2 % for the lattice constant and errors less than 10 % for elastic constants.Comment: 5 pages, 3 figure

Nanoscale Mechanical Drumming Visualized by 4D Electron Microscopy

With four-dimensional (4D) electron microscopy, we report in situ imaging of the mechanical drumming of a nanoscale material. The single crystal graphite film is found to exhibit global resonance motion that is fully reversible and follows the same evolution after each initiating stress pulse. At early times, the motion appears “chaotic” showing the different mechanical modes present over the micron scale. At longer time, the motion of the thin film collapses into a well-defined fundamental frequency of 1.08 MHz, a behavior reminiscent of mode locking; the mechanical motion damps out after ∼200 μs and the oscillation has a “cavity” quality factor of 150. The resonance time is determined by the stiffness of the material, and for the 75 nm thick and 40 μm square specimen used here we determined Young’s modulus to be 1.0 TPa for the in-plane stress−strain profile. Because of its real-time dimension, this 4D microscopy should have applications in the study of these and other types of materials structures

Negative modes in the four-dimensional stringy wormholes

We study the Giddings-Strominger wormholes in string theories. We found negative modes among O(4)-symmetric fluctuations about the non-singular wormhole background. Hence the stringy wormhole contribution to the euclidean functional integral is purely imaginary. This means that the stringy wormhole is a bounce (not an instanton) and describes the nucleation and growth of wormholes in the Minkowski spacetime.Comment: 12 pages 2 figures, RevTe