DeepConf: Machine Learning Conformer Reconstruction of Biomolecules from Scanning Tunneling Microscopy Images

Kavli Affiliate: Stephan Rauschenbach | Summary:Improving the detailed understanding of the underlying properties and functions of biomolecules has recently attracted growing interest, enabled by the possibility of real-space imaging of single, intact macromolecules using Scanning Tunneling Microscopy (STM) in combination with electrospray ion beam deposition and soft landing. This combination provides key insights into biomolecular […]


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Temporal Entanglement and Witnesses of Non-Classicality

Kavli Affiliate: Andrew Baldwin | Summary:The universality of quantum theory has been questioned ever since it was proposed. Key to this long-unsolved question is to test whether a given physical system has non-classical features. Here we connect recently proposed witnesses of non-classicality, based on information-theoretic ideas, with the theory of temporal entanglement. We provide a […]


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Measurements of molecular size and shape on a chip

Kavli Affiliate: Justin Benesch | Summary:Size and shape are critical discriminators between molecular species and states. We describe a micro-chip based high-throughput imaging approach offering rapid and precise determination of molecular properties under native solution conditions. Our method detects differences in molecular weight across at least three orders of magnitude, and down to two carbon […]


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High-resolution cryoEM structure determination of soluble proteins after soft-landing electrospray ion beam deposition

Kavli Affiliate: Carol Robinson | Summary:Electrospray ion beam deposition (ESIBD) is the intact, chemically selective deposition of molecular ions on surfaces in vacuum. Here, we present a general method and dedicated instrumentation for ESIBD-based cryoEM sample preparation of soluble proteins. Precise control over deposition energy, sample environment, and reproducible growth of thin, homogeneous, vitreous ice […]


Continue.. High-resolution cryoEM structure determination of soluble proteins after soft-landing electrospray ion beam deposition

High-resolution cryoEM structure determination of soluble proteins after soft-landing ESIBD

Kavli Affiliate: Lindsay Baker | Summary:Soft-landing electrospray ion beam deposition (ESIBD), i.e. the chemically selective, intact deposition of large and complex molecules on surfaces in vacuum, is a well-established sample preparation method for scanning probe microscopy (SPM), where it facilitates the high-resolution imaging of large and complex molecules. Inherited from mass spectrometry, the advantageous properties […]


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Mesoscopic heterogeneity in biomolecular condensates from sequence patterning

Kavli Affiliate: Andrew Baldwin | Summary:Biomolecular condensates composed of intrinsically disordered proteins (IDPs) are vital for proper cellular function, and their dysfunction is associated with diseases including neurodegeneration and cancer. Despite their biological importance, the precise physical mechanisms underlying condensate (dys)function are unclear, in part owing to the difficulties in understanding how biomolecular sequence patterns […]


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Hyperspectral unmixing for Raman spectroscopy via physics-constrained autoencoders

Kavli Affiliate: Molly Stevens | Summary:Raman spectroscopy is widely used across scientific domains to characterize the chemical composition of samples in a non-destructive, label-free manner. Many applications entail the unmixing of signals from mixtures of molecular species to identify the individual components present and their proportions, yet conventional methods for chemometrics often struggle with complex […]


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Transfer Learning Bayesian Optimization to Design Competitor DNA Molecules for Use in Diagnostic Assays

Kavli Affiliate: Molly Stevens | Summary:With the rise in engineered biomolecular devices, there is an increased need for tailor-made biological sequences. Often, many similar biological sequences need to be made for a specific application meaning numerous, sometimes prohibitively expensive, lab experiments are necessary for their optimization. This paper presents a transfer learning design of experiments […]


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RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis

Kavli Affiliate: Molly Stevens | Summary:Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still impeded by the lack of software, methodological and data standardisation, and the ensuing fragmentation and lack […]


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A new twist on PIFE: photoisomerisation-related fluorescence enhancement

Kavli Affiliate: Achillefs Kapanidis | Summary:PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate of cis/trans photoisomerisation. It is clear now that […]


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