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

Abstract

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.diffraction ͉ imaging ͉ structural dynamics ͉ ultrafast electron microscopy T he transformation of amorphous structures, such as liquids or random-coiled proteins, into ordered structures involves complex dynamical processes that ultimately lead to the final native state. The mechanism is determined by the scales of time, length, and energy as they define the nature of the elementary steps involved. For example, an amorphous bulk liquid crystallizes depending on the degree of initial (nanoscale) nucleation, the time scale of heat diffusion, and the latent energy acquired. Similarly, for a protein, the funneling toward the native structure requires the balance of the entropic and enthalpic free energy contributions, as well as the ''diffusion'' through many energy barriers, possibly with nucleation on the path to the final state.To observe such processes on the time-length scale of the phenomena, our method of choice has been 4D space-time visualization (ref. 1 and references therein, and ref. 2) developed in ultrafast electron microscopy (UEM) and diffraction for imaging with a wide scope (3) of applications (1-10). For microscopy, the concept of femtosecond single (or few) electron packets was introduced to allow for the study of structural dynamics in the temporal, space-charge-free regime and to obtain the atomic-scale spatial resolution. In this mode of UEM operation, a train of electron packets coherently ''builds up'' and coheres into the final image. However, for nonequilibrium irreversible processes, such as crystallization, the transformation must be visualized through single-pulse imaging.In this contribution, we augment the UEM apparatus to include this single-pulse capability, thus covering domains of femtoseconds (fs) to seconds. Using this mode of imaging, here reported is the ...

Biological imaging with 4D ultrafast electron microscopy

“…All experiments were done by using the second generation ultrafast electron microscope (UEM-2) within the Physical Biology Center at Caltech (36). The UEM methodology can be adjusted to suit a wide range of experimental requirements, and the interested reader is referred to previous works for additional details (14,37,38). The specific configuration used for the work reported here is now described.…”

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

“…All experiments reported here were performed using Caltech's second-generation ultrafast electron microscope (UEM-2) (28, 29), the operation of which in the single-pulse mode has been described elsewhere (30,31). Briefly, two synchronized pulses are utilized, an optical one for inducing a T-jump and a probing electron pulse for recording an image or diffraction pattern at a well-defined time (t) with respect to the initiation of the structural change at t 0 .…”

“…Because of the thickness involved (≤100 nm total), heat transfer in that dimension is ultrafast within the used T-jump pulse as evidenced in the rise time (≤20 ns) of the diffraction peak separations. The dissipation of heat in the specimen occurs laterally and for this 2D diffusion one can estimate the time constant (30 (36)], and the density (1.12 g∕cm 3 ), the time for the axial temperature to drop to one half of its initial value, t 1∕2 is 2.1 to 3.2 ms, depending on the value of specific heat; the radius at half-height of the initial pulsed-heat distribution is 30 μm. For the amorphous carbon layer and the Formvar substrate, similar time constants were obtained (3-4 ms).…”

Compression of single-electron pulses with a microwave cavity

“…Structural dynamics can either be imaged directly by ultrafast 4D electron microscopy [1] or studied by diffraction in reciprocal space [2][3][4]. Many recent results demonstrate the ability of these laser-pump/electron-probe techniques to provide a largely complete, dynamical picture of atomic motion [5][6][7][8] or processes on nanometer/picoseconds scales [9][10][11][12].…”