Explanipedia

DoE-It-Yourself (DoEIY): An Open-Access Web Platform for Democratizing Experimental Design in Chemical and Materials Research Open

Niamh Mac Fhionnlaoich, Yang Ye, Runzhang Qi, Federico Galvanin, Stefan Guldin · 2025

Achieving predictable and reproducible outcomes is a central challenge across synthetic workflows. Design of Experiments (DoE) offers a structured, multivariate framework for exploring complex parameter spaces, yet its wider adoption has b…

Predicting Colloidal Interaction Parameters from Small-Angle X-ray Scattering Curves Using Artificial Neural Networks and Markov Chain Monte Carlo Sampling Open

Kelvin Wong, Runzhang Qi, Ye Yang, Zhi Luo, Stefan Guldin , et al. · 2024

Small-angle X-ray scattering (SAXS) is a characterization technique that allows for the study of colloidal interactions by fitting the structure factor of the SAXS profile with a selected model and closure relation. However, the applicabil…

Multidimensional Protein Solubility Optimization with an Ultrahigh-Throughput Microfluidic Platform Open

Nadia A. Erkamp, Marc Oeller, Tomas Šneideris, Hannes Ausserwӧger, Aviad Levin , et al. · 2023

Protein-based biologics are highly suitable for drug development as they exhibit low toxicity and high specificity for their targets. However, for therapeutic applications, biologics must often be formulated to elevated concentrations, mak…

Biomolecular condensate phase diagrams with a combinatorial microdroplet platform Open

William E. Arter, Runzhang Qi, Nadia A. Erkamp, Georg Krainer, Kieran Didi , et al. · 2022

DoE-It-Yourself: A Case Study for Implementing Design of Experiments into Nanoparticle Synthesis Open

Niamh Mac Fhionnlaoich, Yang Ye, Runzhang Qi, Federico Galvanin, Stefan Guldin · 2022

Predictable and repeatable outcome is a major issue in nanoparticle synthesis. Traditionally, a one-factor-at-a-time (OFAT) method is relied upon to investigate and optimise synthetic processes; however, this method is inefficient and ofte…

The Chromatin Regulator HMGA1a Undergoes Phase Separation in the Nucleus** Open

Hongjia Zhu, Masako Narita, Jerelle A. Joseph, Georg Krainer, William E. Arter , et al. · 2022

The protein high mobility group A1 (HMGA1) is an important regulator of chromatin organization and function. However, the mechanisms by which it exerts its biological function are not fully understood. Here, we report that the HMGA isoform…

Multi-dimensional protein solubility optimization with an ultra-high-throughput microfluidic platform Open

Nadia A. Erkamp, Marc Oeller, Tomas Šneideris, Hannes Ausserwӧger, Aviad Levin , et al. · 2022

Protein-based biologics are highly suitable for drug development, as they exhibit low toxicity and high specificity for their targets. However, for therapeutic applications, biologics must often be formulated to very high concentrations, m…

Microfluidics for multiscale studies of biomolecular condensates Open

Nadia A. Erkamp, Runzhang Qi, Timothy J. Welsh, Tuomas P. J. Knowles · 2022

Combining microfluidics with existing techniques allows for novel and more high-throughput measurements of the thermodynamics, kinetics and characteristics of biomolecular condensates.

Recent Advances in Microgels: From Biomolecules to Functionality Open

Yufan Xu, Hongjia Zhu, Akhila Denduluri, Yangteng Ou, Nadia A. Erkamp , et al. · 2022

The emerging applications of hydrogel materials at different length scales, in areas ranging from sustainability to health, have driven the progress in the design and manufacturing of microgels. Microgels can provide miniaturized, monodisp…

Source data for 'High Resolution Biomolecular Condensate Phase Diagrams with a Combinatorial Microdroplet Platform' Open

Will Arter, Runzhang Qi, Nadia A. Erkamp, Georg Krainer, Timothy J. Welsh , et al. · 2022

Data for figures in manuscript and supporting information for ' High Resolution Biomolecular Condensate Phase Diagrams with a Combinatorial Microdroplet Platform'. Data for protein phase diagrams generation and related supporting informati…

The chromatin regulator HMGA1a undergoes phase separation in the nucleus Open

Hongjia Zhu, Masako Narita, Jerelle A. Joseph, Georg Krainer, William E. Arter , et al. · 2021

The protein high mobility group A1 (HMGA1) is an important regulator of chromatin organization and function. However, the mechanisms by which it exerts its biological function are not fully understood. Here, we report that the HMGA isoform…

Liquid–liquid phase separation underpins the formation of replication factories in rotaviruses Open

Florian Geiger, Julia Acker, Guido Papa, Xinyu Wang, William E. Arter , et al. · 2021

Liquid–Liquid Phase‐Separated Systems from Reversible Gel–Sol Transition of Protein Microgels Open

Yufan Xu, Runzhang Qi, Hongjia Zhu, Bing Li, Yi Shen , et al. · 2021

Liquid–liquid phase‐separated biomolecular systems are increasingly recognized as key components in the intracellular milieu where they provide spatial organization to the cytoplasm and the nucleoplasm. The widespread use of phase‐separate…

Learning the molecular grammar of protein condensates from sequence determinants and embeddings Open

Kadi L. Saar, Alexey S. Morgunov, Runzhang Qi, William E. Arter, Georg Krainer , et al. · 2021

Significance The tendency of many cellular proteins to form protein-rich biomolecular condensates underlies the formation of subcellular compartments and has been linked to various physiological functions. Understanding the molecular basis…

Rotavirus Replication Factories Are Complex Ribonucleoprotein Condensates Open

Florian Geiger, Guido Papa, William E. Arter, Julia Acker, Kadi L. Saar , et al. · 2020

RNA viruses induce formation of subcellular organelles that provide microenvironments conducive to their replication. Here we show that replication factories of rotaviruses represent protein-RNA condensates that are formed via liquid-liqui…

Construction of a liquid-liquid phase separation system from the gel-sol transition of elongated protein microgels in a crowding agent Open

Yufan Xu, Runzhang Qi, Hongjia Zhu, Bing Li, Yi Shen , et al. · 2020

Liquid proteinaceous materials have been frequently found in cells or tissues and are crucial for various biological processes. Unlike their solid-state counterparts, liquid-state protein compartments are challenging to engineer and contro…

Machine learning models for predicting protein condensate formation from sequence determinants and embeddings Open

Kadi L. Saar, Alexey S. Morgunov, Runzhang Qi, William E. Arter, Georg Krainer , et al. · 2020

Intracellular phase separation of proteins into biomolecular condensates is increasingly recognised as an important phenomenon for cellular compartmentalisation and regulation of biological function. Different hypotheses about the paramete…

High Resolution Biomolecular Condensate Phase Diagrams with a Combinatorial Microdroplet Platform Open

William E. Arter, Runzhang Qi, Nadia A. Erkamp, Georg Krainer, Kieran Didi , et al. · 2020

The assembly of intracellular proteins into biomolecular condensates is a fundamental process underlying the organisation of intracellular space and the regulation of many cellular processes. Mapping and characterising phase behaviour of b…

Comparative characterisation of non-monodisperse gold nanoparticle populations by X-ray scattering and electron microscopy Open

Ye Yang, Suiyang Liao, Zhi Luo, Runzhang Qi, Niamh Mac Fhionnlaoich , et al. · 2020

A cross-method comparison for quasi-monodisperse, polydisperse and bimodal gold nanoparticles of 2–7 nm in diameter between conventional image analysis of transmission electron micrographs and small-angle X-ray scattering with form-free Mo…

A Cross-Method Comparison of Sub-10 nm Nanoparticle Size Distribution Open

Ye Yang, Suiyang Liao, Zhi Luo, Runzhang Qi, Niamh Mac Fhionnlaoich , et al. · 2019

Accurate nanoparticle (NP) size determination is essential across research domains, with many functions in nanoscience and biomedical research being size-dependent. Although transmission electron microscopy (TEM) is capable of resolving a …

A Cross-Method Comparison of Sub-10 nm Nanoparticle Size Distribution Open

Ye Yang, Suiyang Liao, Zhi Luo, Runzhang Qi, Niamh Mac Fhionnlaoich , et al. · 2019

Accurate nanoparticle (NP) size determination is essential across research domains, with many functions in nanoscience and biomedical research being size-dependent. Although transmission electron microscopy (TEM) is capable of resolving a …

Application of the Spatial Distribution Function to Colloidal Ordering Open

Niamh Mac Fhionnlaoich, Runzhang Qi, Stefan Guldin · 2019

2D colloidal assembly is a vital process in the fabrication of nanostructured devices and remains of widespread interest in fundamental research. Characterising the ordering is crucial to develop an understanding of the driving forces behi…

Application of the Spatial Distribution Function to Colloidal Ordering Open

Niamh Mac Fhionnlaoich, Runzhang Qi, Stefan Guldin · 2019

2D colloidal assembly is a vital process in the fabrication of nanostructured devices and remains of widespread interest in fundamental research. Characterising the ordering is crucial to develop an understanding of the driving forces behi…

DoE-It-Yourself: A Case Study for Implementing Design of Experiments into Nanoparticle Synthesis Open

Niamh Mac Fhionnlaoich, Ye Yang, Runzhang Qi, Federico Galvanin, Stefan Guldin · 2019

Predictable and repeatable outcome is a major issue in nanoparticle synthesis. Traditionally, chemists rely on the one-factor-at-a-time method to investigate and optimise synthetic processes; however, this method is inefficient and often m…

DoE-It-Yourself: A Case Study for Implementing Design of Experiments into Nanoparticle Synthesis Open

Niamh Mac Fhionnlaoich, Ye Yang, Runzhang Qi, Federico Galvanin, Stefan Guldin · 2019

Predictable and repeatable outcome is a major issue in nanoparticle synthesis. Traditionally, chemists rely on the one-factor-at-a-time method to investigate and optimise synthetic processes; however, this method is inefficient and often m…

Probing the interaction of nanoparticles with small molecules in real time<i>via</i>quartz crystal microbalance monitoring Open

Ye Yang, Guillaume Poss, Yini Weng, Runzhang Qi, Hanrui Zheng , et al. · 2019

We report on a novel screening route to obtain quantitative measures for nanoparticle binding affinities to target analytes.

A Toolkit to Quantify Target Compounds in Thin-Layer-Chromatography Experiments Open

Niamh Mac Fhionnlaoich, Stuart Ibsen, Luis A. Serrano, Alaric Taylor, Runzhang Qi , et al. · 2018

Thin-layer chromatography (TLC) is one of the basic analytical procedures in chemistry and allows the demonstration of various chemical principles in an educational setting. An often-overlooked aspect of TLC is the capability to quantify i…

A Toolkit to Quantify Target Compounds in Thin Layer Chromatography Experiments Open

Stuart Ibsen, Niamh Mac Fhionnlaoich, Luís Serrano, Alaric Taylor, Runzhang Qi , et al. · 2018

Thin layer chromatography (TLC) is one of the basic experimental procedures in chemistry and allows the demonstration of various chemical principles in an educational setting. An often-overlooked aspect of TLC is the capability to quantify…

A Toolkit to Quantify Target Compounds in Thin Layer Chromatography Experiments Open

Stuart Ibsen, Niamh Mac Fhionnlaoich, Luís Serrano, Alaric Taylor, Runzhang Qi , et al. · 2018

Thin layer chromatography (TLC) is one of the basic experimental procedures in chemistry and allows the demonstration of various chemical principles in an educational setting. An often-overlooked aspect of TLC is the capability to quantify…

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