Article
Chemistry, Multidisciplinary
Teng Wang, Jiaojiao Hu, Yanan Li, Lulu Bi, Lijuan Guo, Xinshuo Jia, Xia Zhang, Dan Li, Xi-Miao Hou, Mauro Modesti, Xu-Guang Xi, Cong Liu, Bo Sun
Summary: The study reveals that Bloom syndrome protein (BLM) possesses the intrinsic ability for phase separation and can co-phase separate with single-stranded DNA (ssDNA) to form co-condensates. ATP enhances BLM's condensation capability on ssDNA and promotes ssDNA compression against a resistive force. BLM can also condense replication protein A (RPA)- or RAD51-coated ssDNA by dismantling these ssDNA-binding proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Biochemistry & Molecular Biology
Zheng Wang, Jizhong Lou, Hong Zhang
Summary: Intracellular biological condensates play crucial roles in cellular functions and their material properties are key for their physiological functions. This review summarizes recent studies and methods for characterizing and measuring the material properties of biological condensates.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Chun-Wei Lin, Laura M. Nocka, Brittany L. Stinger, Joseph B. DeGrandchamp, L. J. Nugent Lew, Steven Alvarez, Henry T. Phan, Yasushi Kondo, John Kuriyan, Jay T. Groves
Summary: This study demonstrates that the protein condensation phase transition of EGFR:Grb2 acts as a regulator of signal propagation from EGFR to the MAPK pathway.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Chun-Wei Lin, Laura M. Nocka, Brittany L. Stinger, Joseph B. DeGrandchamp, L. J. Nugent Lew, Steven Alvarez, Henry T. Phan, Yasushi Kondo, John Kuriyan, Jay T. Groves
Summary: This study demonstrates the importance of a protein condensation phase transition between EGFR and Grb2 in regulating signal propagation from EGFR to the MAPK pathway. The condensation state of the EGFR tail controls the ability of SOS to activate Ras.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Optics
Koichiro Furutani, Luca Salasnich
Summary: This theoretical study investigates the superfluid properties of a one-dimensional annular superfluid with a boost. It reveals that the emergence of solitons affects the superfluid fraction, with different conditions leading to a decrease in superfluid fraction.
Article
Chemistry, Physical
Hao Wu, Zhenjie Feng, Arnab Pal, Hongliang Dong, Chao Jing, Ke Wang, Shihui Zhang, Wen Deng, Shujia Li, Jiajia Feng, Jiafeng Chen, Yanhong Chen, Jingying Si, Jun-Yi Ge, Shixun Cao, Bin Chen, Jincang Zhang
Summary: A pure and large-size l-FeTe2 single crystal was successfully synthesized, exhibiting metastable behavior and undergoing a first-order isostructural phase transition from an insulating to metallic state at 120-150 K. Additionally, Shubnikov-de Haas oscillations were observed under a high magnetic field at 4 K.
CHEMISTRY OF MATERIALS
(2021)
Article
Physics, Multidisciplinary
Jim Skulte, Phatthamon Kongkhambut, Sahana Rao, Ludwig Mathey, Hans Kessler, Andreas Hemmerich, Jayson G. Cosme
Summary: We form a condensate in a dark state of momentum states in a pumped and shaken cavity-BEC system. The system consists of an ultracold quantum gas in a high-finesse cavity, pumped transversely by a phase-modulated laser. The dark state concept provides a general approach to efficiently prepare complex many-body states in an open quantum system, as demonstrated through time-of-flight and photon emission measurements.
PHYSICAL REVIEW LETTERS
(2023)
Article
Multidisciplinary Sciences
Wenbo Zhang, Ruonan Wang, Mingwei Liu, Shucong Li, Asher E. Vokoun, Weichen Deng, Robert L. Dupont, Feiyi Zhang, Shuyuan Li, Yang Wang, Zhenyu Liu, Yongfang Zheng, Shuli Liu, Yanlian Yang, Chen Wang, Lanlan Yu, Yuxing Yao, Xiaoguang Wang, Chenxuan Wang
Summary: This study utilizes scanning tunneling microscopy (STM) to analyze conformational substate ensembles of beta sheet peptides. It shows that STM can capture a thorough picture of the conformational substates and can complement conventional characterization techniques.
Article
Physics, Applied
Yazhen Wang, Daixuan Wu, Meilin Yang, Shuhuai Bai, Sitong Huang, Mingjing Wang, Ruinan Liu, Zhaohui Li, Dan Li, Yuecheng Shen
Summary: Single-pixel imaging (SPI) is a computational imaging modality that reconstructs images with a single-pixel detector. In this work, SPI is extended to microscopic Mueller-matrix polarimetry, allowing for polarization-sensitive measurements of biological tissue with high resolution. The technique was applied to esophagus tissues from patients to examine polarization effects, and the Mueller matrices were reconstructed. This technique holds promise for advancing both SPI and Mueller-matrix polarimetry.
APPLIED PHYSICS LETTERS
(2023)
Article
Materials Science, Ceramics
Volker Kahlenberg, Jonathan Vinke, Hannes Krueger, Sho Ito, Christian J. Schuermann
Summary: In this study, the phase assemblages of mixtures containing Na2CO3, CaCO3, and SiO2 in the molar ratio 1:3:2 at elevated temperatures have been investigated. A new high-temperature polymorph of Na2Ca6Si4O15, called gamma-phase, has been discovered and structurally characterized. It was found that the previously described Na2Ca3Si2O8 is likely the misinterpreted gamma-Na2Ca6Si4O15, and a sodium calcium silicate with a molar ratio of Na2O:CaO:SiO2 = 1:3:2 may not exist.
JOURNAL OF THE AMERICAN CERAMIC SOCIETY
(2022)
Review
Chemistry, Physical
Jelena Dinic, B. Amanda Marciel, V. Matthew Tirrell
Summary: This review examines the current understanding of molecular interactions governing liquid-liquid phase separation of biological condensates, focusing on how charge patterns influence the conformation and phase behavior of IDPs, and theoretical treatments of polyampholytes showing that increased charge segregation leads to a higher tendency for phase separation.
CURRENT OPINION IN COLLOID & INTERFACE SCIENCE
(2021)
Review
Immunology
Shelley Bhattacharya, Chayan Munshi
Summary: C-reactive protein (CRP) is an important member of the acute phase protein family and has its origin in the animal kingdom. CRP plays a key role in inflammation and immune diseases, with functions including complement activation, phagocytosis, and regulation of cytokine production. The structure of CRP shows some relatedness among different species, while invertebrates rely on the multifunctionality of CRP for evolutionary success.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biology
Anton A. Polyansky, Laura D. Gallego, Roman G. Efremov, Alwin Koehler, Bojan Zagrovic
Summary: Non-membrane-bound biomolecular condensates are an important mode of subcellular organization, but their spatial organization and dynamics at the atomic level are not well understood. This study combines molecular dynamics simulations with in vitro behavior to analyze the Lge1(1-80) protein condensates. Analysis of protein-protein interactions reveals the key factors in condensate formation and the relationship between configurational entropy, valency, and compactness of proteins inside the condensates. The derived analytical formalism describes condensate architecture across length scales, providing an atomistically resolved model of Lge1(1-80) condensates and their agreement with in vitro morphologies.
Article
Geochemistry & Geophysics
Benjamin L. Hess, Jay J. Ague
Summary: This study examines the effects of non-hydrostatic stress on the stability of polymorph pairs and finds that normal stress controls polymorph stability to a large extent, with stress variations normal to an interface having a greater impact than those parallel to an interface. Non-hydrostatic stress is likely to play a significant role in the evolution of metamorphic systems and fundamental rock properties.
JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH
(2021)
Article
Chemistry, Physical
Kevin S. Silmore, Rajeev Kumar
Summary: This study focuses on the dynamic structure of polyampholyte chains in weak coupling or under weak external electric fields, with deviations in scaling from the classic theory and predictions for scattering experiments. The research shows that dynamics are highly dependent on charge distribution under weak coupling, but largely independent of charge distribution under weak fields.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Adnan Choudhary, Christopher Maffeo, Aleksei Aksimentiev
Summary: Modeling and simulation play a crucial role in the development of nanopore sensing systems. The inability of the current signal to provide direct information about the chemical structure of biomolecules is a limitation of nanopore sensing. To overcome this, coarse-grained and all-atom molecular dynamics simulations are used to characterize the nanopore translocation process. However, traditional simulations have limitations in predicting ionic current blockades with atomic resolution. This study describes a multi-resolution framework for modeling the passage of DNA molecules and nanostructures through synthetic nanopore systems, providing accurate modeling capability to research laboratories without access to supercomputers.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
S. Kasra Tabatabaei, Bach Pham, Chao Pan, Jingqian Liu, Shubham Chandak, Spencer A. Shorkey, Alvaro G. Hernandez, Aleksei Aksimentiev, Min Chen, Charles M. Schroeder, Olgica Milenkovic
Summary: Researchers have developed a prototype DNA data storage system that uses an extended molecular alphabet to differentiate between natural and chemically modified nucleotides. They also demonstrated the capability of single-molecule sequencing using a neural network architecture, achieving an accuracy exceeding 60%.
Article
Chemistry, Multidisciplinary
Jie Shen, Arundhati Roy, Himanshu Joshi, Laxmicharan Samineni, Ruijuan Ye, Yu-Ming Tu, Woochul Song, Matthew Skiles, Manish Kumar, Aleksei Aksimentiev, Huaqiang Zeng
Summary: In this study, we report a novel class of fluorofoldamer-based artificial water channels that have excellent water transport rate and selectivity, as well as structural simplicity and robustness. The best-performing channel is a decorated foldamer nanotube, which exhibits an ultrafast water conduction rate and can exclude salts and protons. The inwardly facing C(sp2)-F atoms in the channel are proposed to be critical for enabling the ultrafast and superselective water transport properties.
Article
Chemistry, Multidisciplinary
Tobias Ensslen, Kumar Sarthak, Aleksei Aksimentiev, Jan C. Behrends
Summary: The use of a protein nanopore is demonstrated to differentiate posttranslational modifications (PTMs) in proteins or peptides based on the positions of acetylated and methylated lysine residues. This method detects PTMs and their positions by sensing the shape of a fully entrapped peptide, eliminating the need for controlled translocation. This molecular shape-sensing principle offers a versatile, label-free, and high-throughput characterization of protein isoforms.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Kaikai Chen, Adnan Choudhary, Sarah E. Sandler, Christopher Maffeo, Caterina Ducati, Aleksei Aksimentiev, Ulrich F. Keyser
Summary: High-resolution analysis of biomolecules has greatly advanced biosensing, but there are limited methods available for high-resolution analysis of unlabeled single molecules in their native states. In this work, label-free electrical sensing of single molecules with nanometer resolution is demonstrated using a narrow solid-state nanopore. The super-resolution ability is attributed to the enhancement of the electric field at the tip of the nanopore induced by nanostructures. This work presents a general approach to improve the resolution of single-molecule nanopore sensing and has implications for label-free high-resolution DNA sequence mapping and digital information storage.
ADVANCED MATERIALS
(2023)
Article
Biotechnology & Applied Microbiology
Luning Yu, Xinqi Kang, Fanjun Li, Behzad Mehrafrooz, Amr Makhamreh, Ali Fallahi, Joshua C. Foster, Aleksei Aksimentiev, Min Chen, Meni Wanunu
Summary: The electrical current blockade caused by a peptide or protein passing through a nanopore can be used as a fingerprint for molecule identification in biosensor applications. This study presents an enzyme-free method for slow, unidirectional transport of full-length proteins through nanopores. By using a chemically resistant biological nanopore, alpha-hemolysin, and a high concentration guanidinium chloride buffer, protein transport can be propelled by electroosmotic effect. The translocation dynamics of proteins resemble that of single-stranded DNA, and single-translocation events contain enough information for orientation and identity determination with over 90% accuracy using a supervised machine-learning classifier.
NATURE BIOTECHNOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Christopher Maffeo, Lauren Quednau, James Wilson, Aleksei Aksimentiev
Summary: Flowing fluid past chiral objects has been used to power rotary motion in man-made machines for centuries. In nanoscale biological or chemical systems, rotary motion is generated by biasing Brownian motion through cyclic chemical reactions. In this study, we demonstrate that a chiral biological molecule (DNA or RNA duplex) rotates unidirectionally at billions of revolutions per minute when an electric field is applied along the duplex, with the rotation direction determined by the duplex's chirality. The rotation is powered by the drag force of the electro-osmotic flow, mimicking the operating principle of a macroscopic turbine at the nanoscale.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Physical
Kumar Sarthak, David Winogradoff, Yingda Ge, Sua Myong, Aleksei Aksimentiev
Summary: Proteins with disordered regions are important for cellular signaling and biological condensates, but mutations can lead to neurodegenerative diseases. Molecular dynamics simulations were used to study the effects of different force fields on the structure and dynamics of a protein called FUS. The simulations showed that certain force fields produced conformations within the experimental range and also influenced the stability of RNA-protein complexes. The findings suggest that a combination of protein and RNA force fields can provide an optimal description of proteins with both structured and disordered regions and their interactions with RNA.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Siddharth Krishnan, Aleksei Aksimentiev, Stuart Lindsay, Dmitry Matyushov
Summary: Single-molecule measurements reveal that proteins without redox cofactors can still exhibit electrical conductance over nanometer scale distances. This is surprising considering the expected time scale for electron transport based on hopping rates and energy barriers. However, molecular dynamics simulations combined with an electron transfer theory show that the unique molecular configurations of non-redox-active proteins allow for long-range conductivity with low reorganization energies. These findings are supported by experimental current decay calculations.
ACS PHYSICAL CHEMISTRY AU
(2023)
Review
Chemistry, Multidisciplinary
Xiaojun Wei, Tadas Penkauskas, Joseph E. Reiner, Celeste Kennard, Mark J. Uline, Qian Wang, Sheng Li, Aleksei Aksimentiev, Joseph W. F. Robertson, Chang Liu
Summary: Biotechnological innovations have advanced large-scale protein studies, but current methods for identifying and quantifying individual proteins are insufficient for single-molecule protein sequencing. Nanopore-inspired systems have been developed for genome sequencing, and are now emerging as tools for protein identification and analysis, with potential for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors for protein sequencing, including amino acid identification, controlled translocation of peptides and proteins, and device and algorithm development supported by simulations. The review highlights the need for collaborative efforts across multiple disciplines to enable practical implementation of nanopore-based protein sequencing.
Correction
Biotechnology & Applied Microbiology
Luning Yu, Xinqi Kang, Fanjun Li, Behzad Mehrafrooz, Amr Makhamreh, Ali Fallahi, Joshua C. Foster, Aleksei Aksimentiev, Min Chen, Meni Wanunu
NATURE BIOTECHNOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Xin Shi, Anna-Katharina Pumm, Christopher Maffeo, Fabian Kohler, Elija Feigl, Wenxuan Zhao, Daniel Verschueren, Ramin Golestanian, Aleksei Aksimentiev, Hendrik Dietz, Cees Dekker
Summary: In this study, we experimentally demonstrate the feasibility of developing functional synthetic turbines at the nanoscale by rationally designing nanoscale DNA origami turbines. These turbines can utilize transmembrane electrochemical potentials to rotate autonomously and operate in physiological conditions. This research opens new possibilities for engineering active robotics at the nanoscale.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Physical
Prabhat Tripathi, Behzad Mehrafrooz, Aleksei Aksimentiev, Sophie E. Jackson, Martin Gruebele, Meni Wanunu
Summary: This study investigates the behavior of knotted protein structures during translocation through a pore. Using single molecule nanopore experiments and all-atom MD simulations, the researchers observed an unusual behavior in which the rate of translocation plateaus or slows down as the electric potential driving the reaction increases. This study sheds light on the influence of topology on the forced translocation of knotted proteins.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Merle Scherf, Florian Scheffler, Christopher Maffeo, Ulrich Kemper, Jingjing Ye, Aleksei Aksimentiev, Ralf Seidel, Uta Reibetanz
Summary: The development of DNA origami technique has inspired the use of three-dimensional DNA cages for targeted drug delivery. This study presents a method using DNA origami nanotubes for efficient loading and retention of cargo molecules within the DNA cages.
Article
Chemistry, Multidisciplinary
Prabhat Tripathi, Morgan Chandler, Christopher Michael Maffeo, Ali Fallahi, Amr Makhamreh, Justin Halman, Aleksei Aksimentiev, Kirill A. Afonin, Meni Wanunu
Summary: This study characterizes and distinguishes RNA fiber structures with different degrees of branching using solid-state nanopore experiments and simulations. It is found that fibers with more branches produce longer and deeper ionic current blockades. Additionally, the study shows that the kissing loop interactions in the fibers are resistant to heating.