Self-heating tilted fiber Bragg grating device for melt curve analysis of solid-phase DNA hybridization and thermal cycling.

We demonstrate a DNA-based optical fiber device that uses an in-fiber grating, a light absorbing coating with surface anchored DNA, and a built-in optical thermometer. This device is used for precisely thermal cycling surface DNA spots bound by a simple UV cross-linking technique. Near-infrared light of wavelengths near 1550 nm and guided power near 300 mW is coupled out of the fiber core by a tilted fiber Bragg grating inscribed in the fiber and absorbed by the coating to increase its temperature to more than 95 °C. A co-propagating broadband light signal (also in the near-infrared region) is used to measure the reflection spectrum of the grating and thus the temperature from the wavelength shifts of the reflection peaks. The device is capable of sensitive DNA melt analysis and can be used for DNA amplification. Graphical abstract.

Mapping molecular motions leading to charge delocalization with ultrabright electrons.

Ultrafast processes can now be studied with the combined atomic spatial resolution of diffraction methods and the temporal resolution of femtosecond optical spectroscopy by using femtosecond pulses of electrons or hard X-rays as structural probes. However, it is challenging to apply these methods to organic materials, which have weak scattering centres, thermal lability, and poor heat conduction. These characteristics mean that the source needs to be extremely bright to enable us to obtain high-quality diffraction data before cumulative heating effects from the laser excitation either degrade the sample or mask the structural dynamics. Here we show that a recently developed, ultrabright femtosecond electron source makes it possible to monitor the molecular motions in the organic salt (EDO-TTF)2PF6 as it undergoes its photo-induced insulator-to-metal phase transition. After the ultrafast laser excitation, we record time-delayed diffraction patterns that allow us to identify hundreds of Bragg reflections with which to map the structural evolution of the system. The data and supporting model calculations indicate the formation of a transient intermediate structure in the early stage of charge delocalization (less than five picoseconds), and reveal that the molecular motions driving its formation are distinct from those that, assisted by thermal relaxation, convert the system into a metallic state on the hundred-picosecond timescale. These findings establish the potential of ultrabright femtosecond electron sources for probing the primary processes governing structural dynamics with atomic resolution in labile systems relevant to chemistry and biology.

Full characterization of RF compressed femtosecond electron pulses using ponderomotive scattering.

High bunch charge, femtosecond, electron pulses were generated using a 95 kV electron gun with an S-band RF rebunching cavity. Laser ponderomotive scattering in a counter-propagating beam geometry is shown to provide high sensitivity with the prerequisite spatial and temporal resolution to fully characterize, in situ, both the temporal profile of the electron pulses and RF time timing jitter. With the current beam parameters, we determined a temporal Instrument Response Function (IRF) of 430 fs FWHM. The overall performance of our system is illustrated through the high-quality diffraction data obtained for the measurement of the electron-phonon relaxation dynamics for Si (001).

Femtosecond dynamics of the ring closing process of diarylethene: a case study of electrocyclic reactions in photochromic single crystals.

The cyclization reaction of the photochromic diarylethene derivative 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)perfluorocyclopentene was studied in its single crystal phase with femtosecond transient absorption spectroscopy. The transient absorption measurements were performed with a robust acquisition scheme that explicitly exploits the photoreversibility of the molecular system and monitors the reversibility conditions. The crystalline system demonstrated 3 × 10(4) repeatable cycles before significant degradation was observed. Immediately following photoexcitation, the excited state absorption associated with the open-ring conformation undergoes a large spectral shift with a time constant of approximately 200 fs. Following this evolution on the excited state potential energy surface, the ring closure occurs with a time constant of 5.3 ps, which is significantly slower than previously reported measurements for similar derivatives in the solution phase. Time resolved electron diffraction studies were used to further demonstrate the assignment of the transient absorption dynamics to the ring closing reaction. The mechanistic details of the ring closing are discussed in the context of prior computational work along with a vibrational mode analysis using density functional theory to give some insight into the primary motions involved in the ring closing reaction.

Cellular orientation is guided by strain gradients.

The strain-induced reorientation response of cyclically stretched cells has been well characterized in uniform strain fields. In the present study, we comprehensively analyse the behaviour of human fibroblasts subjected to a highly non-uniform strain field within a polymethylsiloxane microdevice. Our results indicate that the strain gradient amplitude and direction regulate cell reorientation through a coordinated gradient avoidance response. We provide critical evidence that strain gradient is a key physical cue that can guide cell organization. Specifically, our work suggests that cells are able to pinpoint the location under the cell of multiple physical cues and integrate this information (strain and strain gradient amplitudes and directions), resulting in a coordinated response. To gain insight into the underlying mechanosensing processes, we studied focal adhesion reorganization and the effect of modulating myosin-II contractility. The extracted focal adhesion orientation distributions are similar to those obtained for the cell bodies, and their density is increased by the presence of stretching forces. Moreover, it was found that the myosin-II activity promoter calyculin-A has little effect on the cellular response, while the inhibitor blebbistatin suppresses cell and focal adhesion alignment and reduces focal adhesion density. These results confirm that similar internal structures involved in sensing and responding to strain direction and amplitude are also key players in strain gradient mechanosensing and avoidance.

A magnetic liquid deformable mirror for high stroke and low order axially symmetrical aberrations.

We present a new class of magnetically shaped deformable liquid mirrors made of a magnetic liquid (ferrofluid). Deformable liquid mirrors offer advantages with respect to deformable solid mirrors: large deformations, low costs and the possibility of very large mirrors with added aberration control. They have some disadvantages (e.g. slower response time). We made and tested a deformable mirror, producing axially symmetrical wavefront aberrations by applying electric currents to 5 concentric coils made of copper wire wound on aluminum cylinders. Each of these coils generates a magnetic field which combines to deform the surface of a ferrofluid to the desired shape. We have carried out laboratory tests on a 5 cm diameter prototype mirror and demonstrated defocus as well as Seidel and Zernike spherical aberrations having amplitudes up to 20 microm, which was the limiting measurable amplitude of our equipment.

Ring-closing reaction in diarylethene captured by femtosecond electron crystallography.

The photoinduced ring-closing reaction in diarylethene, which serves as a model system for understanding reactive crossings through conical intersections, was directly observed with atomic resolution using femtosecond electron diffraction. Complementary ab initio calculations were also performed. Immediately following photoexcitation, subpicosecond structural changes associated with the formation of an open-ring excited-state intermediate were resolved. The key motion is the rotation of the thiophene rings, which significantly decreases the distance between the reactive carbon atoms prior to ring closing. Subsequently, on the few picosecond time scale, localized torsional motions of the carbon atoms lead to the formation of the closed-ring photoproduct. These direct observations of the molecular motions driving an organic chemical reaction were only made possible through the development of an ultrabright electron source to capture the atomic motions within the limited number of sampling frames and the low data acquisition rate dictated by the intrinsically poor thermal conductivity and limited photoreversibility of organic materials.

'Making the molecular movie': first frames.

Recent advances in high-intensity electron and X-ray pulsed sources now make it possible to directly observe atomic motions as they occur in barrier-crossing processes. These rare events require the structural dynamics to be triggered by femtosecond excitation pulses that prepare the system above the barrier or access new potential energy surfaces that drive the structural changes. In general, the sampling process modifies the system such that the structural probes should ideally have sufficient intensity to fully resolve structures near the single-shot limit for a given time point. New developments in both source intensity and temporal characterization of the pulsed sampling mode have made it possible to make so-called 'molecular movies', i.e. measure relative atomic motions faster than collisions can blur information on correlations. Strongly driven phase transitions from thermally propagated melting to optically modified potential energy surfaces leading to ballistic phase transitions and bond stiffening are given as examples of the new insights that can be gained from an atomic level perspective of structural dynamics. The most important impact will likely be made in the fields of chemistry and biology where the central unifying concept of the transition state will come under direct observation and enable a reduction of high-dimensional complex reaction surfaces to the key reactive modes, as long mastered by Mother Nature.