Article
Chemistry, Multidisciplinary
Reece W. Lewis, Benjamin Klemm, Mariano Macchione, Rienk Eelkema
Summary: This study demonstrates the use of a chemical reaction network to drive the coacervation of macromolecular species, resulting in the assembly and disassembly of chemical triggered complex coacervates. Unlike other systems, this chemical reaction network operates at constant physiological pH without the need for complex biomolecules.
Article
Nanoscience & Nanotechnology
Quirin Prasser, Thomas Fuhs, Bernhard Torger, Richard Neubert, Erica Brendler, Carla Vogt, Florian Mertens, Felix A. Plamper
Summary: Climate change necessitates improved temperature monitoring in logistics/transportation, which can be achieved using temperature-sensitive copolymers that undergo irreversible coagulation upon temperature change. This study presents the synthesis and characterization of pentablock copolymers (PBCP) and demonstrates their ability to self-assemble into flower-like micelles in cold water, offering colloidal stability over months. The temperature dependence of the oil-water interfacial tension makes PBCP a promising candidate for simple temperature monitoring during transport and storage.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Multidisciplinary Sciences
Mario Mastriani
Summary: This study shows that entanglement can be exclusively formed by quantum Fourier transform (QFT) blocks and establishes a connection between entanglement and QFT. Incorporating spectral analysis into the traditional temporal approach of entanglement can lead to the development of more efficient and fault-tolerant protocols for use in quantum computing and communication, particularly in the future quantum Internet.
SCIENTIFIC REPORTS
(2021)
Article
Computer Science, Interdisciplinary Applications
Navjot Kaur, Cheng-Chun Lee, Ali Mostafavi, Ali Mahdavi-Amiri
Summary: This paper presents a novel deep-learning model, DAHiTrA, with hierarchical transformers to classify building damages based on satellite images. The proposed network leverages hierarchical spatial features and captures temporal differences in the feature domain. It achieves state-of-the-art performance on building localization, damage classification, and change detection tasks. Additionally, a new high-resolution satellite imagery data set, Ida-BD, is introduced for domain adaptation.
COMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING
(2023)
Article
Computer Science, Interdisciplinary Applications
Kyeong-Beom Park, Jae Yeol Lee
Summary: This study proposes a novel deep learning model, SwinE-Net, for accurate colorectal polyp segmentation. The model effectively combines a CNN-based EfficientNet and Vision Transformer-based Swin Transformer. The proposed approach is evaluated and compared on multiple datasets, demonstrating its superior performance in polyp segmentation.
JOURNAL OF COMPUTATIONAL DESIGN AND ENGINEERING
(2022)
Article
Materials Science, Multidisciplinary
Tuokai Peng, Hui-Qing Peng
Summary: Piperazine is reported as a promising building block for the construction of aggregation-induced emission (AIE) materials, utilizing its electron-donating ability and chair conformation.
JOURNAL OF MATERIALS CHEMISTRY C
(2023)
Article
Computer Science, Artificial Intelligence
Zhanhao Peng, Qing Zhou
Summary: This work proposes a hierarchical model and develops a novel empirical Bayes estimate for the connectivity matrix of a stochastic block model to approximate the graphon function, introducing a new model selection criterion for choosing the number of communities. Numerical results on extensive simulations and two well-annotated social networks demonstrate the superiority of the approach in terms of parameter estimation and model selection.
PEERJ COMPUTER SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Shamila Firdaus, Susanne Boye, Andreas Janke, Peter Friedel, Anna Janaszewska, Dietmar Appelhans, Martin Mueller, Barbara Klajnert-Maculewicz, Brigitte Voit, Albena Lederer
Summary: This study evaluates the effect of dendritic topology on the antiamyloidogenic activity of macromolecules. The compactness, position of surface units, and size of glyco-architectures are found to influence their activity against amyloid plaques. The study introduces asymmetric flow field flow fractionation as a suitable method for quantification of complex aggregates. The second-generation glyco-pseudodendrimer shows the best antiamyloidogenic properties, confirming the importance of macromolecular conformation and optimal functional group distribution.
Article
Construction & Building Technology
Yunyang Ye, Matthew Strong, Yingli Lou, Cary A. Faulkner, Wangda Zuo, Satish Upadhyaya
Summary: This paper investigates the feasibility of using Generative Adversarial Networks (GANs) for large-scale building power demand prediction and identifies suitable GAN models. Physics-based energy models are developed to generate training and reference data, and a new evaluation indicator is proposed to assess the performance of different GAN models. The results show that the Original GAN and cGAN are recommended models under different training sample sizes and building type numbers.
ENERGY AND BUILDINGS
(2022)
Review
Chemistry, Multidisciplinary
Nethmi De Alwis Watuthanthrige, Progyateg Chakma, Dominik Konkolewicz
Summary: Introducing dynamic and exchangeable bonds can enhance polymers by providing self-healing, enhanced toughness, or adaptability, with the synergy between the exchangeable bonds and polymer architecture tuning the material properties and facilitating dynamic exchange pathways.
TRENDS IN CHEMISTRY
(2021)
Review
Chemistry, Multidisciplinary
Li Shao, Jinrong Ma, Jesse L. Prelesnik, Yicheng Zhou, Mary Nguyen, Mingfei Zhao, Samson A. Jenekhe, Sergei V. Kalinin, Andrew L. Ferguson, Jim Pfaendtner, Christopher J. Mundy, James J. De Yoreo, Franccommaois Baneyx, Chun-Long Chen
Summary: This article discusses the characteristics and applications of hierarchical materials that exhibit order over multiple length scales. It highlights the advantages of using proteins, peptides, and peptidomimetics as building blocks for hierarchical structures. The article reviews recent progress in the rational design and characterization of hierarchical materials, with a focus on stimuli-responsive and smart architectures. It also explores the use of computational simulations and data-driven predictions to understand the assembly process of hierarchical materials. The article suggests that further research in these areas will enable predictive materials synthesis based on designed interactions, surface effects, and solution conditions.
Review
Chemistry, Multidisciplinary
Xingyu Wu, Christopher Barner-Kowollik
Summary: The development of synthetic macromolecular chemistry has made significant progress in controlling the properties of soft matter materials with molecular precision. Fluorescence-based techniques have emerged as a powerful tool for macromolecular characterization, providing detailed information and deeper insights beyond commonly used analytical methods. This article critically examines the applications of fluorescence phenomena, principles, and techniques in characterizing macromolecules and soft matter materials, highlighting recent advances and discussing future opportunities and challenges.
Article
Quantum Science & Technology
Cristhian Roman-Vicharra, James J. Cai
Summary: In this study, a quantum circuit model was proposed to infer gene regulatory networks (GRNs) from single-cell transcriptomic data. The model utilized qubit entanglement to simulate interactions between genes, showing competitive performance and potential for further exploration. The application of the quantum GRN modeling approach to human lymphoblastoid cells successfully predicted regulatory interactions between genes and estimated the strength of these interactions. This work highlights the potential of quantum computing in biology for a better understanding of single-cell GRNs.
NPJ QUANTUM INFORMATION
(2023)
Article
Geochemistry & Geophysics
Hani Alzahrani, Jeffrey Shragge
Summary: Data-driven artificial neural networks have advantages over conventional methods in geophysical problems. A new approach using LSTM-RNN for velocity model building shows high accuracy in recovering models compared to true ones. Challenges remain in effective and efficient network training.
IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING
(2022)
Article
Construction & Building Technology
Guangchen Li, Wei Tian, Hu Zhang, Xing Fu
Summary: This paper proposes a new method for creating time series models for building energy analysis based on machine learning techniques. The method includes two steps of model preselection and data folding to take advantage of the sequential nature during the process of constructing meta-models. The results of a case study show that the time-series meta-models constructed using this new method have very high accuracy with a moderate computational cost.
ENERGY AND BUILDINGS
(2023)
Article
Biochemical Research Methods
Minghan Chen, Brandon D. Amos, Layne T. Watson, John J. Tyson, Young Cao, Clifford A. Shaffer, Michael W. Trosset, Cihan Oguz, Gisella Kakoti
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2019)
Article
Computer Science, Information Systems
Austin Cory Bart, Javier Tibau, Dennis Kafura, Clifford A. Shaffer, Eli Tilevich
IEEE TRANSACTIONS ON EMERGING TOPICS IN COMPUTING
(2020)
Article
Biology
John J. Tyson, Teeraphan Laomettachit, Pavel Kraikivski
JOURNAL OF THEORETICAL BIOLOGY
(2019)
Article
Mathematical & Computational Biology
Jenna E. Gallegos, Neil R. Adames, Mark F. Rogers, Pavel Kraikivski, Aubrey Ibele, Kevin Nurzynski-Loth, Eric Kudlow, T. M. Murali, John J. Tyson, Jean Peccoud
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2020)
Review
Biochemical Research Methods
Jae Kyoung Kim, John J. Tyson
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Computer Science, Software Engineering
Ayaan M. Kazerouni, James C. Davis, Arinjoy Basak, Clifford A. Shaffer, Francisco Servant, Stephen H. Edwards
Summary: Educators are now evaluating the adequacy of students' software tests by incorporating mutation analysis, which provides a stronger measure compared to code coverage. Research shows that in large programming courses, costs can be reduced while maintaining accuracy by selecting a subset of mutation operators.
JOURNAL OF SYSTEMS AND SOFTWARE
(2021)
Review
Cell Biology
Bela Novak, John J. Tyson
Summary: Cells must delay progression in the replication-division cycle if threats to genome integrity are detected; once they decide to continue, cells enter a qualitatively different biochemical state, making transitions between cell cycle phases irreversible and switch-like; different cell cycle phases are controlled by unique signalling networks, yet they exhibit bistable behavior as a hallmark of molecular memory devices.
CURRENT OPINION IN CELL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Bronson R. Weston, John J. Tyson, Yang Cao
Summary: The phosphorylated CtrA can displace the CtrA similar to P on Cori to inhibit DNA replication. Model analysis reveals that this mechanism allows for a faster transition into S phase, stabilizes the timing of chromosome replication, and improves the viability of various mutant strains.
Article
Biochemical Research Methods
Xiangyu Yao, Benjamin L. Heidebrecht, Jing Chen, John J. Tyson
Summary: This paper explores mathematical models of genetic oscillators based on transcription-translation feedback and investigates modifications to improve the accuracy of the models. The study relaxes constraints by introducing multistep reaction chains and replacing rate laws, resulting in more realistic parameter values. Additionally, the addition of a supplementary positive feedback loop enhances the robustness of the oscillations. The results provide testable predictions for future experimental studies.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Mathematics, Applied
Dorjsuren Battogtokh, John J. Tyson
Summary: Shoot apical meristems (SAMs) are responsible for the development of above-ground tissues in plants. The growth and expansion of SAMs rely on the division of stem cells in a central zone, which is regulated by a transcription factor called WUSCHEL. WUSCHEL is self-activating and downregulated by a signaling pathway involving CLAVATA proteins. While most mathematical models of stem cell confinement in the SAM rely on Turing's mechanism, this study proposes a bistable-switch model based on interactions between WUSCHEL and CLAVATA. Comparisons between the two mechanisms demonstrate that the bistable-switch provides a better explanation for the nucleation and confinement of stem cells.
Article
Biology
Rajat Singhania, John J. Tyson
Summary: When a perfume is released in a room, the initial occupants will smell it but become desensitized after a few minutes, while newcomers can still smell it. This adaptation behavior is studied in this paper, which focuses on the molecular basis behind it using an evolutionary search approach.
Review
Biology
John J. Tyson, Bela Novak
Summary: Cell growth, DNA replication, mitosis, and division are fundamental processes for passing on life. The eukaryotic cell cycle is a periodic process that plays a crucial role in maintaining the integrity of the genome. Key factors in cell cycle control include mitosis promoting factor and cyclin-dependent kinases.
Article
Mathematical & Computational Biology
Mansooreh Ahmadian, John J. Tyson, Jean Peccoud, Yang Cao
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2020)
Article
Computer Science, Interdisciplinary Applications
Ehsan Elgendi, Clifford A. Shaffer
FRONTIERS IN COMPUTER SCIENCE
(2020)
Article
Education & Educational Research
Sally Hamouda, Stephen H. Edwards, Hicham G. Elmongui, Jeremy V. Ernst, Clifford A. Shaffer
COMPUTER SCIENCE EDUCATION
(2020)
