Article
Physics, Multidisciplinary
Manish Trivedi, Dhruv Saxena, Wai Kit Ng, Riccardo Sapienza, Giorgio Volpe
Summary: Experiments show that external optical stimulus can reconfigure colloidal random lasers spatially and continuously adjust their lasing threshold. These dynamic random lasers can self-organize and respond to external stimuli, presenting a tunable lasing threshold.
Review
Chemistry, Multidisciplinary
Xinyu Wang, Shengnan Zhang, Jicong Zhang, Yaomin Wang, Xiaoyu Jiang, Youqi Tao, Dan Li, Chao Zhong, Cong Liu
Summary: This review provides a comprehensive overview of the design principles for functional amyloid fibrillar assemblies from an engineering perspective and through the lens of structural insights. The article introduces the fundamental structural configurations and functions of amyloid assemblies, and then focuses on two prevalent strategies for the design of functional amyloid fibrillar assemblies. Characterization techniques contribute to unveiling the structural polymorphism of amyloid fibrils and clarifying the regulation mechanisms of assembly and disassembly. The integration of structural tunability, synthetic biology, and artificial intelligence may lead to a new trend in functional amyloid design.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Chemistry, Multidisciplinary
Yike Huang, Minh-Kha Nguyen, Vu Hoang Nguyen, Jacky Loo, Arttu J. Lehtonen, Anton Kuzyk
Summary: This study presents a strategy to characterize aptamers using DNA origami-based chiral plasmonic assemblies as reporters and establishing a competitive hybridization reaction-based thermodynamic model. The characterization scheme demonstrated reliable and reproducible characterization of various aptamers, facilitating the development of aptamer-based applications.
Article
Engineering, Electrical & Electronic
Zhaohui Yang, Wei Xu, Chongwen Huang, Jianfeng Shi, Mohammad Shikh-Bahaei
Summary: This article investigates the problem of resource allocation for multiuser communication networks with an RIS-assisted wireless transmitter. A joint optimization problem is proposed, and a dual method is used to solve the problem to minimize the total transmit power under SINR constraints of the users.
IEEE TRANSACTIONS ON COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Yun Chang Choi, Shengsong Yang, Christopher B. Murray, Cherie R. Kagan
Summary: Researchers have reported a thermally reconfigurable chiroptical metamaterial composed of phase change material VO2 and metallic Au nanoparticles. This all-solid-state metamaterial shows dynamic switching in the mid-infrared range and has potential applications in various fields.
Article
Biochemical Research Methods
Harry F. Thompson, Joseph L. Beesley, Hannah D. Langlands, Caitlin L. Edgell, Nigel J. Savery, Derek N. Woolfson
Summary: This study reports two designed systems that can disassemble and reassemble upon site-specific phosphorylation and dephosphorylation. By utilizing hyperthermostable de novo antiparallel and parallel coiled-coil heterotetramers as starting points, control in downstream applications can be achieved. The switches are incorporated by adding protein kinase A phosphorylation sites, R-R-X-S, which can assemble as designed and unfold reversibly when heated. Phosphorylation can be reversed resulting in tetramer reassembly.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Optics
Giovanna Calo, Gaetano Bellanca, Marina Barbiroli, Franco Fuschini, Giovanni Serafino, Davide Bertozzi, Velio Tralli, Vincenzo Petruzzelli
Summary: This paper reports the design of a device for on-chip optical wireless interconnections using Optical Phased Arrays (OPA), aiming to provide high-bandwidth, power-efficient reconfigurable connections between nodes. The communication through an optical wireless switch offers a novel approach to overcome wired communication bottlenecks and network flexibility, with consideration for multipath propagation effects in on-chip multi-layered media.
Review
Chemistry, Multidisciplinary
Jinqiao Dong, Yan Liu, Yong Cui
Summary: The exploration of chiral crystalline porous materials, such as metal-organic complexes (MOCs) or metal-organic frameworks (MOFs), has been one of the most exciting recent developments in materials science. New developments in artificial metal-peptide assemblies (MPAs) are addressing the current bottlenecks of chiral porous materials by providing unprecedented control over chiral recognition sites, conformational flexibility, cavity sizes, and hydrophilic segments. Exemplary MPAs, including structurally well-defined metal-peptide complexes and highly crystalline metal-peptide frameworks, are discussed, showcasing the potential for enhanced enantioselective recognition and enabling key biochemical processes in next-generation biomimetic materials.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Fabian C. Herbert, Sameera S. Abeyrathna, Nisansala S. Abeyrathna, Yalini H. Wijesundara, Olivia R. Brohlin, Francesco Carraro, Heinz Amenitsch, Paolo Falcaro, Michael A. Luzuriaga, Alejandra Durand-Silva, Shashini D. Diwakara, Ronald A. Smaldone, Gabriele Meloni, Jeremiah J. Gassensmith
Summary: This study demonstrates the successful generation and immobilization of metastable lipid, protein-detergent, and protein-lipid supramolecular complexes within a zeolitic-imidazole framework (ZIF) to enhance stability against various stressors. The immobilized complexes exhibit resistance to elevated temperatures, chemical denaturants, aging, and mechanical stresses, maintaining their native morphology, structure, and activity. Immobilizing lipid nanoparticles and lipid-protein assemblies remains challenging due to lipid dynamics and protein instability, but this work shows promise for long-term storage at room temperature.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Rekha G. Nair, S. Natarajamani
Summary: This article presents a novel composite transmission line based reconfigurable power divider with high power division ratio and variable negative group delay. The power divider achieves a wide range of power division ratios, sufficient isolation, and negative group delay without using additional group delay circuits. The design contributes to the wide reconfigurable power division, negative group delay, and reduced size.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Multidisciplinary
Xinkai Qiu, Sylvia Rousseva, Gang Ye, Jan C. Hummelen, Ryan C. Chiechi
Summary: The reconfiguration of molecular tunneling junctions through self-assembly of bilayers of glycol ethers allows for modulation of rectification magnitude and direction. Memory bits are fabricated from crossbar junctions prepared by injecting eutectic Ga-In (EGaIn) into microfluidic channels, enabling logical operations and memristor-like properties.
ADVANCED MATERIALS
(2021)
Article
Engineering, Biomedical
Bojiao Tang, Xiaoling Xie, Ruhui Yang, Sijie Zhou, Ronggui Hu, Jiayao Feng, Qinxiang Zheng, Xingjie Zan
Summary: The hydrophobicity of nanoparticles plays a significant role in their ability to penetrate biological barriers. This study successfully encapsulated the protein drug Ava by decorating hydrophobic amino acid tyrosine (Y) onto a peptide chain, resulting in improved bioavailability and therapeutic outcomes.
ACTA BIOMATERIALIA
(2022)
Article
Materials Science, Multidisciplinary
Jianming Huang, Kaixiang Shu, Nabuqi Bu, Yong Yan, Tao Zheng, Mengmeng Yang, Zhaoqiang Zheng, Nengjie Huo, Jingbo Li, Wei Gao
Summary: In this study, a PtSe2/WSe2/Au asymmetric Schottky photodiode was successfully fabricated, demonstrating gate-tunable rectifying behavior and high photoresponsivity. Furthermore, the scanning photocurrent mapping revealed that the photocurrent was primarily distributed at the edge of the interface, confirming the asymmetric Schottky structure.
SCIENCE CHINA-MATERIALS
(2023)
Review
Biochemistry & Molecular Biology
Noelia Ferruz, Michael Heinzinger, Mehmet Akdel, Alexander Goncearenco, Luca Naef, Christian Dallago
Summary: The process of designing biomolecules, particularly proteins, is undergoing rapid changes fueled by advancements in artificial intelligence and computational methods. By leveraging natural language processing and computer vision techniques, researchers are able to learn patterns from biological databases and use them to gain insights into mechanistic biology and design biomolecules. However, understanding and applying the latest protein design tools can be complex. To address this, recent advances in deep learning-assisted protein design are documented, and a practical pipeline is presented. Challenges and opportunities in the protein design field are also discussed.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Materials Science, Multidisciplinary
Tian Chen, Kristina Shea
Summary: The paper introduces a method for generating fabrication surfaces that can be reconfigured into multiple statically stable target shapes. By discretizing target shapes, mapping them to fabrication surfaces, and using bistable actuators to accommodate defects, a planar structure can be fabricated to reconfigure into distinct and stable shapes.
MATERIALS & DESIGN
(2021)
Article
Surgery
Natasha I. Edman, Sara L. Zettervall, Maianna N. Dematteis, Amir Ghaffarian, Sherene Shalhub, Matthew P. Sweet
Summary: This study assessed the gender-related differences in clinical comorbidities, anatomic suitability, and frailty among an unselected cohort of patients with TAAA5. The study found that women with TAAA5 had higher metrics of frailty and anatomic risk that were not captured by comorbidity-based risk assessments, which could explain the lower intervention rates for women with TAAA5.
JOURNAL OF VASCULAR SURGERY
(2022)
Article
Multidisciplinary Sciences
A. Courbet, J. Hansen, Y. Hsia, N. Bethel, Y-J Park, C. Xu, A. Moyer, S. E. Boyken, G. Ueda, U. Nattermann, D. Nagarajan, D-A Silva, W. Sheffler, J. Quispe, A. Nord, N. King, P. Bradley, D. Veesler, J. Kollman, D. Baker
Summary: This study explores the construction of protein machinery by designing axle and rotor components, achieving successful assembly in vitro and in vivo, and demonstrating a new approach to protein structure construction.
Article
Cell Biology
Andrew C. Hunt, James Brett Case, Young-Jun Park, Longxing Cao, Kejia Wu, Alexandra C. Walls, Zhuoming Liu, John E. Bowen, Hsien-Wei Yeh, Shally Saini, Louisa Helms, Yan Ting Zhao, Tien-Ying Hsiang, Tyler N. Starr, Inna Goreshnik, Lisa Kozodoy, Lauren Carter, Rashmi Ravichandran, Lydia B. Green, Wadim L. Matochko, Christy A. Thomson, Bastian Vogeli, Antje Kruger, Laura A. VanBlargan, Rita E. Chen, Baoling Ying, Adam L. Bailey, Natasha M. Kafai, Scott E. Boyken, Ajasja Ljubetic, Natasha Edman, George Ueda, Cameron M. Chow, Max Johnson, Amin Addetia, Mary-Jane Navarro, Nuttada Panpradist, Michael Gale, Benjamin S. Freedman, Jesse D. Bloom, Hannele Ruohola-Baker, Sean P. J. Whelan, Lance Stewart, Michael S. Diamond, David Veesler, Michael C. Jewett, David Baker
Summary: Researchers used a cell-free expression workflow to screen and optimize constructs containing computationally designed miniprotein inhibitors of SARS-CoV-2. They found that a homotrimeric version of the ACE2 mimic AHB2 (TRI2-2) achieved the broadest efficacy. The TRI2-2 miniprotein neutralized Omicron, Delta, and other variants with greater potency than clinically used monoclonal antibodies. It also provided prophylactic and therapeutic protection against SARS-CoV-2 in mice when administered intranasally. The designed miniprotein receptor mimics offer a widely applicable antiviral therapeutic strategy with advantages over antibodies and native receptor traps.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Oncology
DeLayna Goulding, Lauren Arguinchona, Amy Anderson-Mellies, Margit Mikkelsen, Megan Eguchi, Hannah Marinoff, Shadi Zahedi, Karina Braga Ribeiro, Myles Cockburn, Carlos Rodriguez Galindo, Adam L. Green
Summary: Osteosarcoma (OST) and Ewing sarcoma (ES) are the most common pediatric bone cancers. Demographic and socioeconomic disparities are associated with a higher likelihood of metastatic disease at diagnosis and poor survival outcomes in both OST and ES. Factors such as race, ethnicity, insurance status, and education levels contribute to these disparities. Improving access to care and addressing treatment inequities are needed to reduce these disparities and improve outcomes in pediatric bone cancers.
JOURNAL OF PEDIATRIC HEMATOLOGY ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
B. I. M. Wicky, L. F. Milles, A. Courbet, R. J. Ragotte, J. Dauparas, E. Kinfu, S. Tipps, R. D. Kibler, M. Baek, F. DiMaio, X. Li, L. Carter, A. Kang, H. Nguyen, A. K. Bera, D. Baker
Summary: Deep learning generative approaches can generate diverse and novel protein structures beyond natural protein sequences and structures. These structures differ considerably from previously solved structures and have potential applications in designing complex components for nanomachines and biomaterials.
Review
Radiology, Nuclear Medicine & Medical Imaging
Bastiaan M. M. Prive, Mohamed A. A. Boussihmad, Bart Timmermans, Willemijn A. A. van Gemert, Steffie M. B. Peters, Yvonne H. W. Derks, Sanne A. M. van Lith, Niven Mehra, James Nagarajah, Sandra Heskamp, Harm Westdorp
Summary: This study reviews the current (pre)clinical data on FAP targeted radionuclide therapy (TRT) and discusses its perspective towards broader clinical implementation. The reported data shows that FAP targeted radionuclide therapy has resulted in objective responses in difficult to treat end stage cancer patients with manageable adverse events. Although no prospective data is yet available, these early data encourages further research.
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2023)
Article
Multidisciplinary Sciences
Isaac D. Lutz, Shunzhi Wang, Christoffer Norn, Alexis Courbet, Andrew J. Borst, Yan Ting Zhao, Annie Dosey, Longxing Cao, Jinwei Xu, Elizabeth M. Leaf, Catherine Treichel, Patrisia Litvicov, Zhe Li, Alexander D. Goodson, Paula Rivera-Sanchez, Ana -Maria Bratovianu, Minkyung Baek, Neil P. King, Hannele Ruohola-Baker, David Baker
Summary: Due to evolutionary selection, naturally occurring protein assemblies have subunits that fit together with substantial shape complementarity to create optimal architectures for function. We present a top-down reinforcement learning-based design approach that utilizes Monte Carlo tree search to sample protein conformers while considering overall architecture and specific functional constraints. Cryo-electron microscopy structures of designed disk-shaped nanopores and ultracompact icosahedra closely resemble computational models. The icosahedra facilitate high-density display of immunogens and signaling molecules, enhancing vaccine response and angiogenesis induction. Our approach allows for top-down design of complex protein nanomaterials with desired properties and exemplifies the power of reinforcement learning in protein design.
Article
Biochemistry & Molecular Biology
Linna An, Derrick R. Hicks, Dmitri Zorine, Justas Dauparas, Basile I. M. Wicky, Lukas F. Milles, Alexis Courbet, Asim K. Bera, Hannah Nguyen, Alex Kang, Lauren Carter, David Baker
Summary: This study developed a deep-learning approach to design closed repeat proteins with central binding pockets, which can be used for specific binding of small molecules. By constructing 38 structurally diverse pseudocyclic designs and validating them with biophysical data, the authors found that the designed structures closely resembled the actual structures. Docking studies suggested that the diversity of folds and central pockets in these proteins provide effective starting points for designing small-molecule binders and enzymes.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Florian Praetorius, Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman, Cullen Demakis, Acacia F. Dishman, Arvind Pillai, Abbas Idris, David Juergens, Justas Dauparas, Xinting Li, Paul M. Levine, Mila Lamb, Ryanne K. Ballard, Stacey R. Gerben, Hannah Nguyen, Alex Kang, Banumathi Sankaran, Asim K. Bera, Brian F. Volkman, Jeff Nivala, Stefan Stoll, David Baker
Summary: The design of hinge proteins that can switch between two distinct structural states in response to ligand binding has been achieved with atomic level accuracy. This finding demonstrates the close coupling between conformational and binding equilibria in these designed proteins.
Article
Biotechnology & Applied Microbiology
Jason Z. Zhang, Hsien-Wei Yeh, Alexandra C. Walls, Basile I. M. Wicky, Kaitlin R. Sprouse, Laura A. VanBlargan, Rebecca Treger, Alfredo Quijano-Rubio, Minh N. Pham, John C. Kraft, Ian C. Haydon, Wei Yang, Michelle DeWitt, John E. Bowen, Cameron M. Chow, Lauren Carter, Rashmi Ravichandran, Mark H. Wener, Lance Stewart, David Veesler, Michael S. Diamond, Alexander L. Greninger, David M. Koelle, David Baker
Summary: The protein biosensor designed in this study utilizes thermodynamic coupling to detect neutralizing antibodies against SARS-CoV-2 variants, without the need for target modification, and can better distinguish differences between samples compared to traditional methods.
NATURE BIOTECHNOLOGY
(2022)