28 papers · ranked by Valyu relevance
Vasu Chetty, Sean Warnick
Dynamics and structure are two of the most important properties of a system. A system's dynamics describe its behavior, that is, how it constrains allowed combinations of manifest variables and defines what is possible and impossible [1]. So, for example, a deterministic signal-processing system restricts the allowed…
Michele Stasi, Alba Monferrer i Sureda, Leon Babl, Sreekar Wunnava + 5 more
Molecular machines, such as ATPases or motor proteins, couple the catalysis of a chemical reaction, most commonly hydrolysis of nucleotide triphosphates, to their conformational change. In essence, they continuously convert a chemical fuel to drive their motion. An outstanding goal of nanotechnology remains to…
Authors not listed
Active assembly of matter is a defining trait of living systems, enabling the creation of far-from-equilibrium materials essential for the functionality of life. This is achieved through energy-dissipative, multi-step processes facilitated by various biomolecular agents for chemical and mechanical assembly of matter.…
Zhenwei Luo, Yiqiu Zhang, Gang Xu, Qinghua Wang + 1 more
Cryo-electron microscopy (cryo-EM) datasets preserves a wide range of structural heterogeneities in macromolecules, arising from both large-scale dynamics and compositional changes. The deep learning framework OPUS-DSD has been developed to characterize the structural heterogeneities in cryo-EM data. However, different…
Zeyu Yang, Steve Marston, ian gould
Phosphorylation of cardiac muscle troponin I by protein kinase A enhances troponin regulatory dynamics and is an essential part of the’ flight or fight’ response to adrenaline. Elucidating how phosphorylation at serines 22 and 23 modulates structural dynamics has been difficult as key regulatory segments of troponin…
Abigael J. Kosgei, Mitchell D. Miller, Minakshi Bhardwaj, Weijun Xu + 3 more
The crystal structure of DynF was determined to a resolution of 1.50 Å, revealing a dimeric eight-stranded β-barrel structure with palmitic acid bound in the interior.
Viktoras Veitas, David Weinbaum
We propose a conceptual framework for thinking about a dynamically changing social system: the Living Cognitive Society. Importantly, we show how it follows from a much broader philosophical framework, guided by the theory of individuation, which emphasizes the importance of relationships and interactive processes in…
Casey Grun, Justin Werfel, David Yu Zhang, Peng Yin
Dynamic DNA nanotechnology provides a promising avenue for implementing sophisticated assembly processes, mechanical behaviours, sensing and computation at the nanoscale. However, design of these systems is complex and error-prone, because the need to control the kinetic pathway of a system greatly increases the number…
Kristy Rochon, Brianna L. Bauer, Nathaniel A. Roethler, Yuli Buckley + 7 more
Mitochondrial fission is crucial for distributing cellular energy throughout cells and for isolating damaged regions of the organelle that are targeted for degradation. This multistep process is initiated by the enhanced recruitment and oligomerization of dynamin-related protein 1 (Drp1) at the surface of mitochondria.…
Wibke Schumann, Birgit Strodel
Dynamin superfamily proteins are mechanochemical GTPases that operate in highly oligomeric and highly cooperative superstructures to deform lipid membranes. It is known from the structures of a bacterial dynamin-like protein (BDLP) that binding of GTP and association of BDLP with lipids causes a transition from closed…
Fabian Späth, Michele Stasi, Héctor Soria-Carrera, Judit Sastre + 2 more
Dynamic combinatorial chemistry (DCC) creates libraries of molecules that are constantly interchanging in a dynamic combinatorial library. When a library member self-assembles, it can displace the equilibria, leading to emergent phenomena like its selection or even its replication. However, such dynamic combinatorial…
Anelise N. Hutson, Kristy Rochon, Jason A. Mears
Dynamin superfamily proteins (DSPs) are large GTPases that play crucial roles in membrane remodeling processes, including vesicle uptake, mitochondrial fission, and opposing fusion events. Among them, dynamin and dynamin-related protein 1 (Drp1) share a conserved domain architecture, yet exhibit unique structural and…
Haoyu Zhang, Wentao Zhang, Hao Miao, Xinke Jiang + 2 more
'Yifan Zhang'] Spatio-Temporal Graph Neural Networks (STGNNs) have emerged as a powerful tool for modeling dynamic graph-structured data across diverse domains. However, they often fail to generalize in Spatio-Temporal Out-of-Distribution (STOOD) scenarios, where both temporal dynamics and spatial structures evolve…
Xiaohua Lu, Leshanshui Yang
In this paper, we explore different approaches to anomaly detection on dynamic knowledge graphs, specifically in a microservices environment for Kubernetes applications. Our approach explores three dynamic knowledge graph representations: sequential data, one-hop graph structure, and two-hop graph structure, with each…
Hao Wu, Haomin Wen, Guibin Zhang, Yutong Xia + 4 more
Deep learning has revolutionized spatio-temporal (ST) forecasting, demonstrating remarkable proficiency in distilling valuable insights from extensive ST datasets (e.g., human mobility [29, 51], precipitation [5, 60], frame dynamics [23, 50], and meteorology [30, 52]). In recent years, the widespread deployment of…
Arslan Hameed
Human epidermal growth factor receptor 2 (HER2) is a transmembrane tyrosine kinase receptor that is overexpressed in many types of cancer, including breast cancer. HER2 overexpression is associated with poor prognosis and resistance to therapy. Therefore, HER2 is a promising target for cancer therapy. In this study, we…
Pablo Sartori, Stanislas Leibler
One of the tenets of molecular biology is that dynamical transitions between three dimensional structures largely determine the function of individual proteins, as well as multi-protein assemblies. Therefore, it seems only natural that evolutionary analysis of proteins, presently based mainly on their primary sequence…
Martina Crippa, Claudio Perego, Anna de Marco, Giovanni M. Pavan
Supramolecular polymers are composed of monomers that self-assemble non-covalently, generating distributions of monodimensional fibres in continuous communication with each other and with the surrounding solution. Fibres, exchanging molecular species, and external environment constitute a sole complex system, which…
Keerti Singh, Thomas J. Pucadyil
Membranes are fundamental to biological systems as they serve as barriers to compartmentalize the cell and its cytoplasm. They are constantly remodeled in shape and composition during the formation and maintenance of organelles. The large GTPase dynamins are well characterized for membrane shape remodeling in…
Kenta Ishibashi, Hitoshi Sakakibara, Kazuhiro Oiwa
In eukaryotic cilia and flagella, various types of axonemal dyneins orchestrate their distinct functions to generate oscillatory bending of axonemes. The force-generating mechanism of dyneins has recently been well elucidated, mainly in cytoplasmic dyneins, thanks to progress in single-molecule measurements, X-ray…
Wibke Schumann, Jennifer Loschwitz, Jens Reiners, Daniel Degrandi + 5 more
Guanylate binding proteins (GBPs) are interferon-γ-activated large GTPases, effective against intracellular pathogens like Toxoplasma gondii. Their host-protective functions require oligomerization, however, the oligomer structures have not been completely resolved yet. Here, we provide dimer models for hGBP1 and the…
Babak Heydari, Mohsen Mosleh, Kia Dalili
This paper introduces a conceptual, yet quantifiable, architecture framework by extending the notion of system modularity in its broadest sense. Acknowledging that modularity is not a binary feature and comes in various types and levels, the proposed framework introduces higher levels of modularity that naturally…
Marcin Konopka, Lau Halgreen, Anca-Elena Dascalu, Matúš Chvojka + 1 more
Stimuli-responsive transmembrane ion transport has become a prominent area of research due to its fundamental importance in cellular processes and potential therapeutic applications. Commonly used stimuli include pH, light, and reduction or oxidation agents. This paper presents the use of dynamic covalent chemistry…
Jiguang Jia, Xuan Sun, Ting Liu, Jiazhi Tang + 3 more
'Xianxuan Hu' 'Srikanth Saripalli'] The main aim of this paper is to explore new approaches to structural design and to solve the problem of lightweight design of structures involving multivariable and multi-objectives. An integrated optimization design methodology is proposed by combining intelligent optimization…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
Alireza Tabrizikahou, Mieczysław Kuczma, Piotr Nowotarski, Małgorzata Kwiatek + 2 more
'Małgorzata Kwiatek' 'Ahad Javanmardi' 'Edyta Pawluczuk'] Every year, structural flaws or breakdowns cause thousands of people to be harmed and cost billions of dollars owing to the limitations of design methods and materials to withstand extreme earthquakes. Since earthquakes have a significant effect on…
Alireza Farzampour, Marco Corradi
To resist the imposed lateral forces on the structures, hysteric dampers are developed from steel plates and strategically implemented within various structural applications. Structural shear dampers have recently been used to alleviate damage, while remaining members remain intact and undamaged. The practical use of…
Marcos Reyes-Martinez, Alain Kadar, Steven Dunne, Sharon C. Glotzer + 2 more
Propagation Through Complex Strut Lattices Authors: ['Marcos Reyes-Martinez' 'Alain Kadar' 'Steven Dunne' 'Sharon C. Glotzer' 'Christopher L. Soles' 'Nicholas A. Kotov'] Interconnected networks of rigid struts are critical for application in lightweight, loadbearing structures. However, accurately modeling stress…