Direct observation of the external force mediated conformational dynamics of an IHF bound Holliday junction

Subhas C. Bera, Tapas Paul, A. N. Sekar Iyengar and Padmaja P. Mishra

We have investigated the isomerization dynamics and plausible energy landscape of 4-way Holliday junctions (4WHJs) bound to integration host factor (IHF, a DNA binding protein), considering the effect of applied external force, by single-molecule FRET methods. A slowing down of the forward as well as the backward rates of the isomerization process of the protein bound 4WHJ has been observed under the influence of an external force, which indicates an imposed restriction on the conformational switching. This has also been reflected by an increase in rigidity, as observed from the increase in the single-molecule FRET (smFRET)-anisotropy values (0.270 ± 0.012 to 0.360 ± 0.008). The application of an external force has assisted the conformational transitions to share the unstacked open structure intermediate, with different rate-limiting steps and a huge induced variation in the energy landscape. Furthermore, the associated landscape of the 4WHJ is visualized in terms of rarely interconverting states embedded into the two isoforms by using nonlinear dynamics analysis, which shows that the chaoticity of the system increases at intermediate force (0.4 to 1.6 pN). The identification of chaos in our investigation provides useful information for a comprehensive explanation of the origin of the complex behavior of the system, which effectively helps us to perceive the dynamics of IHF bound 4WHJs under the influence of external force, and also demonstrates the applicability of nonlinear dynamics analysis in the field of biology.

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Accurate Representations of the Physicochemical Properties of Atmospheric Aerosols: When are Laboratory Measurements of Value?

Aleksandra Marsh, Grazia Rovelli, Young-Chul Song, Kelly L. Pereira, Rose E. Willoughby, Bryan R. Bzdek, Jacqueline Hamilton, Andrew Orr-Ewing, David Owen Topping and Jonathan P Reid

Laboratory studies can provide important insights into the processes that occur at the mesoscale in ambient aerosol. We examine the accuracies of measurements of core physicochemical properties of aerosols that can be made in single particle studies and explore the impact of these properties on the microscopic processes that occur in ambient aerosol. Presenting new measurements, we examine here the refinements in our understanding of aerosol hygroscopicity, surface tension, viscosity and optical properties that can be gained from detailed laboratory measurements for complex mixtures through to surrogates for secondary organic atmospheric aerosols.

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Large-scale dynamic assembly of metal nanostructures in plasmofluidic field

Partha Pratim Patra, Rohit Chikkaraddy, Sreeja Thampi, Ravi P. N. Tripathi and G. V. Pavan Kumar

We discuss two aspects of the plasmofluidic assembly of plasmonic nanostructures at the metal–fluid interface. First, we experimentally show how three and four spot evanescent-wave excitation can lead to unconventional assembly of plasmonic nanoparticles at the metal–fluid interface. We observed that the pattern of assembly was mainly governed by the plasmon interference pattern at the metal–fluid interface, and further led to interesting dynamic effects within the assembly. The interference patterns were corroborated by 3D finite-difference time-domain simulations. Secondly, we show how anisotropic geometry, such as Ag nanowires, can be assembled and aligned in unstructured and structured plasmofluidic fields. We found that by structuring the metal-film, Ag nanowires can be aligned at the metal–fluid interface with a single evanescent-wave excitation, thus highlighting the prospect of assembling plasmonic circuits in a fluid. An interesting aspect of our method is that we obtain the assembly at locations away from the excitation points, thus leading to remote assembly of nanostructures. The results discussed herein may have implications in realizing a platform for reconfigurable plasmonic metamaterials, and a test-bed to understand the effect of plasmon interference on assembly of nanostructures in fluids.

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Optical forces in nanoplasmonic systems: How do they work, what can they be useful for?

Olivier Martin, T.V. Raziman and R.I. Wolke

In this article, we share our vision for a future nanofactory, where plasmonic trapping is used to control the different manufacturing steps associated with the transformation of initial nanostructures to produce complex compounds. All the different functions existing in a traditional factory can be translated at the nanoscale using the optical forces produced by plasmonic nanostructures. A detailed knowledge of optical forces in plasmonic nanostructures is however essential to design such a nanofactory. To this end, we review the numerical techniques for computing optical forces on nanostructures immersed in a strong optical field and show under which conditions approximate solutions, like the dipole approximation, can be used in a satisfactory manner. Internal optical forces on realistic plasmonic antennas are investigated and the reconfiguration of a Fano-resonant plasmonic system using such internal forces is also studied in detail.

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Real-space studies of the structure and dynamics of self-assembled colloidal clusters

Rebecca W. Perry , Guangnan Meng , Thomas G. Dimiduk , Jerome Fung and Vinothan N. Manoharan

The energetics and assembly pathways of small clusters may yield insights into processes occurring at the earliest stages of nucleation. We use a model system consisting of micrometer-sized, spherical colloidal particles to study the structure and dynamics of small clusters, where the number of particles is small (N ≤ 10). The particles interact through a short-range depletion attraction with a depth of a few kBT. We describe two methods to form colloidal clusters, one based on isolating the particles in microwells and another based on directly assembling clusters in the gas phase using optical tweezers. We use the first technique to obtain ensemble-averaged probabilities of cluster structures as a function of N. These experiments show that clusters with symmetries compatible with crystalline order are rarely formed under equilibrium conditions. We use the second technique to study the dynamics of the clusters, and in particular how they transition between free-energy minima. To monitor the clusters we use a fast three-dimensional imaging technique, digital holographic microscopy, that can resolve the positions of each particle in the cluster with 30–45 nm precision on millisecond timescales. The real-space measurements allow us to obtain estimates for the lifetimes of the energy minima and the transition states. It is not yet clear whether the observed dynamics are relevant for small nuclei, which may not have sufficient time to transition between states before other particles or clusters attach to them. However, the measurements do provide some glimpses into how systems containing a small number of particles traverse their free-energy landscape.
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