No abstract

Pulsed electron beams allow for the direct atomic-scale observation of structures with femtosecond to picosecond temporal resolution in a variety of fields ranging from materials science to chemistry and biology, and from the condensed phase to the gas phase. Motivated by recent developments in ultrafast electron diffraction and imaging techniques, we present here a comprehensive account of the fundamental processes involved in electron pulse propagation, and make comparisons with experimental results. The electron pulse, as an ensemble of charged particles, travels under the influence of the space-charge effect and the spread of the momenta among its electrons. The shape and size, as well as the trajectories of the individual electrons, may be altered. The resulting implications on the spatiotemporal resolution capabilities are discussed both for the N-electron pulse and for single-electron coherent packets introduced for microscopy without space-charge.

We elucidate the keto-enol tautomeric equilibrium in acetylacetone, the structure of both keto and enol forms, and the nature of the intramolecular O-H...O HB in enolic acetylacetone using our ultrafast electron diffraction apparatus, thereby shedding new light on the nature of the hydrogen bond in resonant tautomeric structures. The enolic structure exhibits some pi-resonance delocalization; however, this delocalization is not strong enough to give a symmetric skeletal geometry. The long O...O distance in the refined structure renders the homonuclear O-H...O hydrogen bond in acetylacetone localized and asymmetric.

Supporting Online Material S1. Refined ground-state structures of pyridine, picoline and lutidine. Distances are in angstroms and angles are in degrees. S2. Refined transient structures of hot ground-state lutidine and ring-opened picoline. Distances are in angstroms and angles are in degrees.

Nitro compounds release NO, NO2, and other species, but neither the structures during the reactions nor the time scales are known. Ultrafast electron diffraction (UED) allowed the study of the NO release from nitrobenzene, and the molecular pathways and the structures of the transient species were identified. It was observed, in contrast to previous inferences, that nitric oxide and phenoxyl radicals are formed dominantly and that the time scale of formation is 8.8+/-2.2 ps. The structure of the phenoxyl radical was determined for the first time, and found to be quinoid-like. The mechanism proposed involves a repulsive triplet state, following intramolecular rearrangement. This efficient generation of NO may have important implications for the control of by-products in drug delivery and other applications.

The photophysics and photochemistry of molecules with complex electronic structures, such as aromatic carbonyls, involve dark structures of radiationless processes. With ultrafast electron diffraction ͑UED͒ of isolated molecular beams it is possible to determine these transient structures, and in this contribution we examine the nature of structural dynamics in two systems, benzaldehyde and acetophenone. Both molecules are seen to undergo a bifurcation upon excitation ͑S 2 ͒. Following femtosecond conversion to S 1 , the bifurcation leads to the formation of molecular dissociation products, benzene and carbon monoxide for benzaldehyde, and benzoyl and methyl radicals for acetophenone, as well as intersystem crossing to the triplet state in both cases. The structure of the triplet state was determined to be "quinoidlike" of * character with the excitation being localized in the phenyl ring. For the chemical channels, the product structures were also determined. The difference in photochemistry between the two species is discussed with respect to the change in large amplitude motion caused by the added methyl group in acetophenone. This discussion is also expanded to compare these results with the prototypical aliphatic carbonyl compounds, acetaldehyde and acetone. From these studies of structural dynamics, experimental and theoretical, we provide a landscape picture for, and the structures involved in, the radiationless pathways which determine the fate of molecules following excitation. For completeness, the UED methodology and the theoretical framework for structure determination are described in this full account of an earlier communication ͓J. S. Feenstra et al., J. Chem. Phys. 123, 221104 ͑2005͔͒.

This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields. De novo genome assembly and large scale DNA resequencing to understand genomic variations are popular genomic research tools for processing a tremendous amount of data at low cost. Studies on transcriptomes are now available, from previous-hybridization based microarray methods. Epigenetic studies are also available with NGS applications such as whole genome methylation sequencing and chromatin immunoprecipitation followed by sequencing. Human genetics has faced a new paradigm of research and medical genomics by sequencing technologies since the Human Genome Project. The trend of NGS technologies in human genomics has brought a new era of WGS by enabling the building of human genomes databases and providing appropriate human reference genomes, which is a necessary component of personalized medicine and precision medicine.

Amyloid is an important class of proteinaceous material because of its close association with protein misfolding disorders such as Alzheimer's disease and type II diabetes. Although the degree of stiffness of amyloid is critical to the understanding of its pathological and biological functions, current estimates of the rigidity of these β-sheet-rich protein aggregates range from soft (10 8 Pa) to hard (10 10 Pa) depending on the method used. Here, we use timeresolved 4D EM to directly and noninvasively measure the oscillatory dynamics of freestanding, self-supporting amyloid beams and their rigidity. The dynamics of a single structure, not an ensemble, were visualized in space and time by imaging in the microscope an amyloid-dye cocrystal that, upon excitation, converts light into mechanical work. From the oscillatory motion, together with tomographic reconstructions of three studied amyloid beams, we determined the Young modulus of these highly ordered, hydrogenbonded β-sheet structures. We find that amyloid materials are very stiff (10 9 Pa). The potential biological relevance of the deposition of such a highly rigid biomaterial in vivo are discussed.cross-β structure | nanomechanics | microcantilever A myloid fibrils are filamentous polypeptide aggregates whose intra-and extracellular deposition is associated with more than 50 human disorders ranging from Alzheimer's disease to type II diabetes (1, 2). Normally soluble peptides or proteins with a wide range of amino acid sequences can aggregate into amyloid fibrils with a characteristic "cross-β" core structure composed of arrays of β-sheets running parallel to the long axis of the fibrils (3, 4). It is thought that this universal cross-β structure is responsible for the persistence and stability of these obdurate aggregates as a result of the long-range order of its hydrogenbonded β-sheets (5-7). However, indirect ensemble measurements of the stiffness, or Young modulus (Y), of amyloid by statistical analysis of fluctuations in fibril shape have resulted in conflicting results, ranging from highly flexible [Y range of 90-320 MPa (8)] to extremely stiff [Y range of 2-14 GPa (6)]. More direct methods such as atomic force microscopy (AFM) nanoindentation, in which an AFM tip directly presses on an individual fibril to measure the contact stiffness, display an equally large Y range; results vary, e.g., for insulin fibrils, from 5 to 50 MPa (9) in one study and from 3 to 4 GPa (10) in another study.The difference in Y of more than three orders of magnitude presents a serious question: is amyloid highly flexible like elastin [Y = 1.1 MPa (11)] or is it rigid like spider dragline silk [Y range of 1-10 GPa (12)]? To answer this important question, we measured Y values of amyloid "single particles" directly by visualizing in space and time the oscillations of three individual "amyloid beams" composed of the universal cross-β structure by using time-resolved 4D EM (13,14). Results and DiscussionTime-Resolved Dynamics of the Cross-β Steric Zipper. The concept is as fol...