A synthetic mimic of phosphodiesterase type 5 based on corona phase molecular recognition of single-walled carbon nanotubes by Dong, Juyao, Lee, Michael A, Rajan, Ananth Govind, Rahaman, Imon, Sun, Jessica H, Park, Minkyung, Salem, Daniel P, Strano, Michael S

“…Molecular recognition binding sites that specifically identify a target molecule are essential for life science research, clinical diagnoses, and therapeutic development. …”
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Tetra-gel enables superior accuracy in combined super-resolution imaging and expansion microscopy by Lee, Hsuan, Yu, Chih-Chieh, Boyden, Edward S, Zhuang, Xiaowei, Kosuri, Pallav

“…Our study thus provides direct measurements of the single-molecule distortions resulting from hydrogel embedding, and presents a way to improve super-resolution microscopy through combination with tetra-gel ExM.…”
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Chromosome organization by one-sided and two-sided loop extrusion by Banigan, Edward J, van den Berg, Aafke A, Brandão, Hugo B, Marko, John F, Mirny, Leonid A

“…Modeling assuming two-sided loop extrusion reproduces key features of chromatin organization across different organisms. In vitro single-molecule experiments confirmed that yeast condensins extrude loops, however, they remain anchored to their loading sites and extrude loops in a “one-sided” manner. …”
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Rapid screening of nanopore candidates in nanoporous single-layer graphene for selective separations using molecular visualization and interatomic potentials by Bondaz, Luc, Chow, Chun-Man, Karnik, Rohit

“…Through the 3D representation and visualization of the pores' and molecules' atoms with their van der Waals radii using open-source software, we could identify suitable C-passivated nanopores for both gas- and liquid-phase separation while accounting for the pore and molecule shapes. …”
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Designing Next Generation Nucleic Acid Diagnostics Using Synthetic Biology and Artificial Intelligence by Angenent-Mari, Nicolaas Manuel

“…Second, I describe the prototyping of a platform for the deployment of freeze-dried synthetic biology-based diagnostic assays in wearable formats, including examples of NAT assays and also assays for small molecule analytes. Third, I describe the synthesis and subsequent analysis using deep learning of a toehold switch library, demonstrating the potential for high-throughput AI-guided design of diagnostic tools. …”
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The design and synthesis of organic chromophores for Faraday rotation and photoluminescence by Nelson, Zachary

“…This thesis summarizes the design, synthesis, and application of novel small-molecule and polymeric materials, with emphasis on understanding and tuning the chromophore electronic structure to maximize properties including Faraday rotation and delayed fluorescence. …”
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Detailed Reaction Mechanism for 350–400 °C Pyrolysis of an Alkane, Aromatic, and Long-Chain Alkylaromatic Mixture by Payne, A. Mark, Spiekermann, Kevin A., Green, William H.

“…Many technologically important systems involve mixtures of fairly large molecules and relatively unselective chemistry, leading to complex product mixtures. …”
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Heparin‐Coated Albumin Nanoparticles for Drug Combination in Targeting Inflamed Intestine by Zhang, Sufeng, Cho, Won Joon, Jin, Amy T, Kok, Lie Yun, Shi, Yunhua, Heller, David E, Lee, Young-Ah Lucy, Zhou, Yixuan, Xie, Xi, Korzenik, Joshua R, Lennerz, Jochen K, Traverso, Giovanni

“…Here an inflammation-targeting (IT) approach based on heparin-coated human serum albumin nanoparticles (HEP-HSA NPs) that utilize the increased intestinal permeability and changes in electrostatic interaction at the site of intestinal inflammation is described. Using small-molecule and biologic drugs as a model for drug combination, the HEP-HSA NPs demonstrate the capacity to load both drugs simultaneously; the dual-drug loaded HEP-HSA NPs exhibit a higher anti-inflammatory effect than both of the single-drug loaded NPs in vitro and selectively bind to inflamed intestine after enema administration in vivo in a murine model of colitis. …”
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Phosphorylation-Dependent Conformations of the Disordered Carboxyl-Terminus Domain in the Epidermal Growth Factor Receptor by Regmi, Raju, Srinivasan, Shwetha, Latham, Andrew P, Kukshal, Vandna, Cui, Weidong, Zhang, Bin, Bose, Ron, Schlau-Cohen, Gabriela S

“…We investigated the overall conformational states of the isolated EGFR carboxyl-terminus domain using single-molecule Förster resonance energy transfer and coarse-grained simulations. …”
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Rational Fabrication of Nano-to-Microsphere Polycrystalline Opals Using Slope Self-Assembly by Díaz-Marín, Carlos D, Shetty, Rishabh M, Cheung, Samantha, Vaartstra, Geoffrey, Gopinath, Ashwin, Wang, Evelyn N

“…These insights provide a guide for the simple and fast fabrication of opals that can be used as optical coatings, templates for high power density electrodes, molecule templates, and high-performance thermo-fluidic devices.…”
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Exploring Structure Function Relationship using Bio-Inspired DNA-Chromophore Complexes by Chen, Wei Jia

“…However, novel protein molecules are difficult to systematically manipulate. …”
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On Applications of Resonances, from One to Infinity by Benzaouia, Mohammed

“…These bounds are shape independent and only function of the material constants and the separation distance from the Raman molecule. They can be evaluated analytically or by simple numerical integration. …”
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Highly sensitive Curcumin-conjugated nanotheranostic platform for detecting amyloid-beta plaques by magnetic resonance imaging and reversing cognitive deficits of Alzheimer's disea... by Ruan, Yuting, Xiong, Ying, Fang, Wenli, Yu, Qun, Mai, Yingren, Cao, Zhiyu, Wang, Kexi, Lei, Ming, Xu, Jiaxin, Liu, Yan, Zhang, Xingcai, Liao, Wang, Liu, Jun

“…Results Herein, we developed a nanotheranostics platform consisting of Curcumin (Cur), an anti-inflammatory molecule, and superparamagnetic iron oxide (SPIO) nanoparticles encapsulated by diblock 1,2-dio-leoyl-sn-glycero-3-phosphoethanolamine-n-[poly(ethylene glycol)] (DSPE-PEG) that are modified with CRT and QSH peptides on its surface. …”
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Reconstitution of Phase-Separated Signaling Clusters and Actin Polymerization on Supported Lipid Bilayers by Cheng, Xiaohang, Ullo, Maria F, Case, Lindsay B

“…<jats:p>Liquid–liquid phase separation driven by weak interactions between multivalent molecules contributes to the cellular organization by promoting the formation of biomolecular condensates. …”
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Applications of Engineered Proteins in Redox Biology and Biomarker Detection Assay Development by Hao, Yining

“…Then, a genetically encoded FRET sensor was used to design a high-throughput screening assay that identified three small-molecule drugs from over 600 compounds that can mediate toxicity through H₂O₂. …”
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Continuous Directed Evolution in Mammalian Cells by Hendel, Samuel Joseph

“…We demonstrated the platform’s efficacy in proof-of-principle evolution experiments by evolving a transcription factor to be insensitive to a small molecule inhibitor. We then engineered selection circuits for evolving endogenous human G-protein coupled receptors, wherein viral replication is coupled to an endogenous signaling pathway. …”
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Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles by Jones, Ross D, Qian, Yili, Ilia, Katherine, Wang, Benjamin, Laub, Michael T, Del Vecchio, Domitilla, Weiss, Ron

“…Finally, we implement a tunable negative feedback controller via a small molecule-stabilized phosphatase, reducing output expression variance and mitigating the context-dependent effects of off-target regulation and resource competition. …”
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Structure and specificity of an anti-chloramphenicol single domain antibody for detection of amphenicol residues by Swofford, Charles A, Nordeen, Sarah A, Chen, Lu, Desai, Mahaam M, Chen, Joanna, Springs, Stacy L, Schwartz, Thomas U, Sinskey, Anthony J

“…To combat this, we set out to discover and engineer single-domain antibodies (VHHs) that bind to small molecule antibiotics, and that can be used in rapid test kits. …”
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Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation by Mead, Benjamin E, Hattori, Kazuki, Levy, Lauren, Imada, Shinya, Goto, Norihiro, Vukovic, Marko, Sze, Daphne, Kummerlowe, Conner, Matute, Juan D, Duan, Jinzhi, Langer, Robert, Blumberg, Richard S, Ordovas-Montanes, Jose, Yilmaz, Ömer H, Karp, Jeffrey M, Shalek, Alex K

“…Yet, methods for the identification of biological targets regulating epithelial composition and function, and of small molecules modulating them, are lacking. Here we show that druggable biological targets and small-molecule regulators of intestinal stem cell differentiation can be identified via multiplexed phenotypic screening using thousands of miniaturized organoid models of intestinal stem cell differentiation into Paneth cells, and validated via longitudinal single-cell RNA-sequencing. …”
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Thermal Proteome Profiling to Identify Protein-ligand Interactions in the Apicomplexan Parasite Toxoplasma gondii by Herneisen, Alice, Lourido, Sebastian

“…As a proteomic alternative that directly probes the physical interaction between compound and protein, thermal proteome profiling (TPP), also known as the cellular thermal shift assay (CETSA), recently emerged as a method to identify small molecule-target interactions in living cells and cell extracts in a variety of organisms, including unicellular eukaryotic pathogens. …”
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