Hongkun Park

Generation of single optical plasmons in metallic nanowires coupled to quantum dots

Control over the interaction between single photons and individual optical emitters is an outstanding problem in quantum science and engineering. It is of interest for ultimate control over light quanta, as well as for potential applications such as efficient photon collection, single-photon switching and transistors, and long-range optical coupling of quantum bits. Recently, substantial advances have been made towards these goals, based on modifying photon fields around an emitter using high-finesse optical cavities. Here we demonstrate a cavity-free, broadband approach for engineering photon–emitter interactions via subwavelength confinement of optical fields near metallic nanostructures. When a single CdSe quantum dot is optically excited in close proximity to a silver nanowire, emission from the quantum dot couples directly to guided surface plasmons in the nanowire, causing the wire’s ends to light up. Non-classical photon correlations between the emission from the quantum dot and the ends of the nanowire demonstrate that the latter stems from the generation of single, quantized plasmons. Results from a large number of devices show that efficient coupling is accompanied by more than 2.5-fold enhancement of the quantum dot spontaneous emission, in good agreement with theoretical predictions.

Kondo resonance in a single-molecule transistor

When an individual molecule, nanocrystal, nanotube or lithographically defined quantum dot is attached to metallic electrodes via tunnel barriers, electron transport is dominated by single-electron charging and energy-level quantization. As the coupling to the electrodes increases, higher-order tunnelling and correlated electron motion give rise to new phenomena, including the Kondo resonance. To date, all of the studies of Kondo phenomena in quantum dots have been performed on systems where precise control over the spin degrees of freedom is difficult. Molecules incorporating transition-metal atoms provide powerful new systems in this regard, because the spin and orbital degrees of freedom can be controlled through well-defined chemistry. Here we report the observation of the Kondo effect in single-molecule transistors, where an individual divanadium molecule serves as a spin impurity. We find that the Kondo resonance can be tuned reversibly using the gate voltage to alter the charge and spin state of the molecule. The resonance persists at temperatures up to 30 K and when the energy separation between the molecular state and the Fermi level of the metal exceeds 100 meV.

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Recent molecular studies have shown that, even when derived from a seemingly homogenous population, individual cells can exhibit substantial differences in gene expression, protein levels and phenotypic output, with important functional consequences. Existing studies of cellular heterogeneity, however, have typically measured only a few pre-selected RNAs or proteins simultaneously, because genomic profiling methods could not be applied to single cells until very recently. Here we use single-cell RNA sequencing to investigate heterogeneity in the response of mouse bone-marrow-derived dendritic cells (BMDCs) to lipopolysaccharide. We find extensive, and previously unobserved, bimodal variation in messenger RNA abundance and splicing patterns, which we validate by RNA-fluorescence in situ hybridization for select transcripts. In particular, hundreds of key immune genes are bimodally expressed across cells, surprisingly even for genes that are very highly expressed at the population average. Moreover, splicing patterns demonstrate previously unobserved levels of heterogeneity between cells. Some of the observed bimodality can be attributed to closely related, yet distinct, known maturity states of BMDCs; other portions reflect differences in the usage of key regulatory circuits. For example, we identify a module of 137 highly variable, yet co-regulated, antiviral response genes. Using cells from knockout mice, we show that variability in this module may be propagated through an interferon feedback circuit, involving the transcriptional regulators Stat2 and Irf7. Our study demonstrates the power and promise of single-cell genomics in uncovering functional diversity between cells and in deciphering cell states and circuits.

Fabry-Perot interference in a nanotube electron waveguide

The behaviour of traditional electronic devices can be understood in terms of the classical diffusive motion of electrons. As the size of a device becomes comparable to the electron coherence length, however, quantum interference between electron waves becomes increasingly important, leading to dramatic changes in device properties. This classical-to-quantum transition in device behaviour suggests the possibility for nanometer-sized electronic elements that make use of quantum coherence. Molecular electronic devices are promising candidates for realizing such device elements because the electronic motion in molecules is inherently quantum mechanical and it can be modified by well defined chemistry. Here we describe an example of a coherent molecular electronic device whose behaviour is explicitly dependent on quantum interference between propagating electron waves—a Fabry–Perot electron resonator based on individual single-walled carbon nanotubes with near-perfect ohmic contacts to electrodes. In these devices, the nanotubes act as coherent electron waveguides, with the resonant cavity formed between the two nanotube–electrode interfaces. We use a theoretical model based on the multichannel Landauer–Büttiker formalism to analyse the device characteristics and find that coupling between the two propagating modes of the nanotubes caused by electron scattering at the nanotube–electrode interfaces is important.

Nanometre-scale thermometry in a living cell

Sensitive probing of temperature variations on nanometre scales is an outstanding challenge in many areas of modern science and technology. In particular, a thermometer capable of subdegree temperature resolution over a large range of temperatures as well as integration within a living system could provide a powerful new tool in many areas of biological, physical and chemical research. Possibilities range from the temperature-induced control of gene expression and tumour metabolism to the cell-selective treatment of disease and the study of heat dissipation in integrated circuits. By combining local light-induced heat sources with sensitive nanoscale thermometry, it may also be possible to engineer biological processes at the subcellular level. Here we demonstrate a new approach to nanoscale thermometry that uses coherent manipulation of the electronic spin associated with nitrogen–vacancy colour centres in diamond. Our technique makes it possible to detect temperature variations as small as 1.8 mK (a sensitivity of 9 mK Hz−1/2) in an ultrapure bulk diamond sample. Using nitrogen–vacancy centres in diamond nanocrystals (nanodiamonds), we directly measure the local thermal environment on length scales as short as 200 nanometres. Finally, by introducing both nanodiamonds and gold nanoparticles into a single human embryonic fibroblast, we demonstrate temperature-gradient control and mapping at the subcellular level, enabling unique potential applications in life sciences.

Single cell RNA Seq reveals dynamic paracrine control of cellular variation

High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation between identically stimulated dendritic cells, in both the fraction of cells detectably expressing a given messenger RNA and the transcript’s level within expressing cells. Distinct gene modules are characterized by different temporal heterogeneity profiles. In particular, a ‘core’ module of antiviral genes is expressed very early by a few ‘precocious’ cells in response to uniform stimulation with a pathogenic component, but is later activated in all cells. By stimulating cells individually in sealed microfluidic chambers, analysing dendritic cells from knockout mice, and modulating secretion and extracellular signalling, we show that this response is coordinated by interferon-mediated paracrine signalling from these precocious cells. Notably, preventing cell-to-cell communication also substantially reduces variability between cells in the expression of an early-induced ‘peaked’ inflammatory module, suggesting that paracrine signalling additionally represses part of the inflammatory program. Our study highlights the importance of cell-to-cell communication in controlling cellular heterogeneity and reveals general strategies that multicellular populations can use to establish complex dynamic responses.

Dynamic regulatory network controlling Th17 cell differentiation

Despite their importance, the molecular circuits that control the differentiation of naive T cells remain largely unknown. Recent studies that reconstructed regulatory networks in mammalian cells have focused on short-term responses and relied on perturbation-based approaches that cannot be readily applied to primary T cells. Here we combine transcriptional profiling at high temporal resolution, novel computational algorithms, and innovative nanowire-based perturbation tools to systematically derive and experimentally validate a model of the dynamic regulatory network that controls the differentiation of mouse TH17 cells, a proinflammatory T-cell subset that has been implicated in the pathogenesis of multiple autoimmune diseases. The TH17 transcriptional network consists of two self-reinforcing, but mutually antagonistic, modules, with 12 novel regulators, the coupled action of which may be essential for maintaining the balance between TH17 and other CD4+ T-cell subsets. Our study identifies and validates 39 regulatory factors, embeds them within a comprehensive temporal network and reveals its organizational principles; it also highlights novel drug targets for controlling TH17 cell differentiation.

Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells

A generalized platform for introducing a diverse range of biomolecules into living cells in high-throughput could transform how complex cellular processes are probed and analyzed. Here, we demonstrate spatially localized, efficient, and universal delivery of biomolecules into immortalized and primary mammalian cells using surface-modified vertical silicon nanowires. The method relies on the ability of the silicon nanowires to penetrate a cell’s membrane and subsequently release surface-bound molecules directly into the cell’s cytosol, thus allowing highly efficient delivery of biomolecules without chemical modification or viral packaging. This modality enables one to assess the phenotypic consequences of introducing a broad range of biological effectors (DNAs, RNAs, peptides, proteins, and small molecules) into almost any cell type. We show that this platform can be used to guide neuronal progenitor growth with small molecules, knock down transcript levels by delivering siRNAs, inhibit apoptosis using peptides, and introduce targeted proteins to specific organelles. We further demonstrate codelivery of siRNAs and proteins on a single substrate in a microarray format, highlighting this technology’s potential as a robust, monolithic platform for high-throughput, miniaturized bioassays.

Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits

Deciphering the neuronal code--the rules by which neuronal circuits store and process information--is a major scientific challenge. Currently, these efforts are impeded by a lack of experimental tools that are sensitive enough to quantify the strength of individual synaptic connections and also scalable enough to simultaneously measure and control a large number of mammalian neurons with single-cell resolution. Here, we report a scalable intracellular electrode platform based on vertical nanowires that allows parallel electrical interfacing to multiple mammalian neurons. Specifically, we show that our vertical nanowire electrode arrays can intracellularly record and stimulate neuronal activity in dissociated cultures of rat cortical neurons and can also be used to map multiple individual synaptic connections. The scalability of this platform, combined with its compatibility with silicon nanofabrication techniques, provides a clear path towards simultaneous, high-fidelity interfacing with hundreds of individual neurons.

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.

Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the regulatory mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive transcriptional and epigenetic profiling of populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers. Integration of whole-genome bisulfite sequencing, chromatin immunoprecipitation sequencing, and RNA sequencing reveals unique events associated with specification toward each lineage. Lineage-specific dynamic alterations in DNA methylation and H3K4me1 are evident at putative distal regulatory elements that are frequently bound by pluripotency factors in the undifferentiated hESCs. In addition, we identified germ-layer-specific H3K27me3 enrichment at sites exhibiting high DNA methylation in the undifferentiated state. A better understanding of these initial specification events will facilitate identification of deficiencies in current approaches, leading to more faithful differentiation strategies as well as providing insights into the rewiring of human regulatory programs during cellular transitions.