Explanipedia

Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures Open

Rupam Saha, Daichi Hayakawa, Thomas E. Videbæk, Mason Price, Wei-Shao Wei , et al. · 2025

Self-assembly of nanoscale building blocks with programmable geometries and interactions offers a powerful route to engineer materials that mimic the complexity of biological structures. DNA origami provides an exceptional platform for thi…

Efficient Monte Carlo Simulation of Faceted Nanoparticles Using Analytical Interaction Potentials Open

Şafak Çallıoğlu, Quanpeng Yang, Yuanchuan Shao, Brian H. Lee, Gaurav Arya · 2025

Understanding how energetic interactions between faceted nanoparticles (NPs) drive their self-assembly into higher-order architectures is a key area of investigation, given the valuable optical, catalytic, and plasmonic properties these as…

Emerging Research on Gene Delivery to the Nucleus via DNA Origami Open

Sierra Sterling, Yin Wei, Gaurav Arya, Carlos E. Castro, Yonggang Ke · 2025

Structural DNA nanotechnology, a research field in which scientists use DNA as the primary material to make designer nanostructures, has experienced rapid growth in the past few decades. The continuous development of the field has produced…

Economical and Versatile Subunit Design Principles for Self-Assembled DNA Origami Structures Open

Wei-Shao Wei, Thomas E. Videbæk, Daichi Hayakawa, Rupam Saha, Juanita Pombo , et al. · 2025

We describe a modular design approach for creating versatile DNA origami subunits that can target diverse self-assembled structures. The subunit consists of a constant "core module" with variable "bond modules" and "angle modules" added to…

Regulation of the ordinal DNA translocation cycle in bacteriophage Φ29 through trans-subunit interactions Open

Rimtas Dargis, Joshua Pajak, Pavan Ariyawansa, Marc C. Morais, Paul J. Jardine , et al. · 2025

Certain viruses such as tailed bacteriophages and herpes simplex virus package double-stranded DNA into empty procapsids via powerful, ring-shaped molecular motors. High-resolution structures and force measurements on the DNA packaging mot…

Comparative Trial of Furosemide-Spironolactone Combination and Furosemide-Metolazone Combination in Treating Refractory Edema in Nephrotic Syndrome Patients Open

Gaurav Arya, Vinod S, Akshay Shukla, Seema Barman, Santosh Kumar Barman , et al. · 2025

Introduction: Nephrotic syndrome is defined as the presence of nephrotic range proteinuria, hypercholesterolemia, and generalized edema. Proteinuria that is more than 85% albumin is selective proteinuria. Albumin has (-ve) charge, and it i…

End‐to‐End Metasurface Design for Temperature Imaging via Broadband Planck‐Radiation Regression Open

Sophie Fisher, Gaurav Arya, Arka Majumdar, Zin Lin, Steven G. Johnson · 2025

A theoretical framework is presented for temperature imaging from long‐wavelength infrared (LWIR) thermal radiation (e.g., 8–12 µm) through the end‐to‐end design of a metasurface‐optics frontend and a computational‐reconstruction backend. …

Impact of Grafting Density on the Assembly and Mechanical Properties of Self-Assembled Metal–Organic Framework Monolayers Open

Min‐Jung Kang, Po-An Lin, Jordan A. Bunch, Darren J. Lipomi, Gaurav Arya , et al. · 2025

Polymer-grafted metal-organic frameworks (MOFs) can be used to form free-standing self-assembled MOF monolayers (SAMMs). Polymer chains can be introduced onto MOF surfaces through either the ligands or metal nodes using both grafting-to an…

Modular programming of interaction and geometric specificity enables assembly of complex DNA origami nanostructures Open

Rupam Saha, Daichi Hayakawa, Thomas E. Videbæk, M.L. PRICE, Wei-Shao Wei , et al. · 2025

We present a modular DNA origami design approach to address the challenges of assembling geometrically complex nanoscale structures, including those with nonuniform Gaussian curvature. This approach features a core structure that completel…

Dynamic DNA superstructures with emergent functions Open

Daniel Linden Duke, Sierra Sterling, Teng Teng, А. V. Altuninа, Irina V. Martynenko , et al. · 2025

This minireview highlights recent breakthroughs and outstanding challenges in the programmable self-assembly of dynamic DNA superstructures with emergent, collective behaviors.

End-to-end metasurface design for temperature imaging via broadband Planck-radiation regression Open

Sophie Fisher, Gaurav Arya, Arka Majumdar, Zin Lin, Steven G. Johnson · 2024

We present a theoretical framework for temperature imaging from long-wavelength infrared thermal radiation (e.g. 8-12 $μ$m) through the end-to-end design of a metasurface-optics frontend and a computational-reconstruction backend. We intro…

Piggybacking functionalized DNA nanostructures into live-cell nuclei Open

Golbarg M. Roozbahani, Patricia Colosi, Attila Oravecz, Elena M. Sorokina, Wolfgang Pfeifer , et al. · 2024

DNA origami nanostructures (DOs) are promising tools for applications including drug delivery, biosensing, detecting biomolecules, and probing chromatin substructures. Targeting these nanodevices to mammalian cell nuclei could provide impa…

Gradient Estimation via Differentiable Metropolis-Hastings Open

Gaurav Arya, Moritz Schauer, Ruben Seyer · 2024

Metropolis-Hastings estimates intractable expectations - can differentiating the algorithm estimate their gradients? The challenge is that Metropolis-Hastings trajectories are not conventionally differentiable due to the discrete accept/re…

Self-assembly of nanocrystal checkerboard patterns via non-specific interactions Open

Yufei Wang, Yilong Zhou, Quanpeng Yang, Rourav Basak, Yu Xie , et al. · 2024

Checkerboard lattices—where the resulting structure is open, porous, and highly symmetric—are difficult to create by self-assembly. Synthetic systems that adopt such structures typically rely on shape complementarity and site-specific chem…

Mechanism of DNA origami folding elucidated by mesoscopic simulations Open

Marcello DeLuca, Daniel Linden Duke, Tao Ye, Michael G. Poirier, Yonggang Ke , et al. · 2024

Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field t…

Piggybacking functionalized DNA nanostructures into live cell nuclei Open

Golbarg M. Roozbahani, Patricia Colosi, Attila Oravecz, Elena M. Sorokina, Wolfgang Pfeifer , et al. · 2024

DNA origami (DO) are promising tools for in vitro or in vivo applications including drug delivery; biosensing, detecting biomolecules; and probing chromatin sub-structures. Targeting these nanodevices to mammalian cell nuclei could provide…

Controlling Silicification on DNA Origami with Polynucleotide Brushes Open

Shuang Wang, Po-An Lin, Marcello DeLuca, Stefan Zauscher, Gaurav Arya , et al. · 2023

DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA…

Many-body potential for simulating the self-assembly of polymer-grafted nanoparticles in a polymer matrix Open

Yilong Zhou, Sigbjørn Løland Bore, Andrea R. Tao, Francesco Paesani, Gaurav Arya · 2023

Many-body interactions between polymer-grafted nanoparticles (NPs) play a key role in promoting their assembly into low-dimensional structures within polymer melts, even when the particles are spherical and isotropically grafted. However, …

Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets Open

Qing Tang, Sebastian Sensale, Charles Bond, Jiazheng Xing, Andy Qiao , et al. · 2023

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures Open

Yunqi Yang, Qinyi Lu, Yu Chen, Marcello DeLuca, Gaurav Arya , et al. · 2023

DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast deg…

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures Open

Yunqi Yang, Qinyi Lu, Yu Chen, Marcello DeLuca, Gaurav Arya , et al. · 2023

DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast deg…

Assessment of clinic-biochemical parameters in severe acute malnutrition children admitted in a tertiary care hospital of Western Uttar Pradesh, India Open

Akshay Shukla, Gaurav Arya, Alok Kumar Gupta, Navin Kumar, Santosh Kumar Barman · 2023

Background: Severe acute malnutrition (SAM) is one of the major causes of mortality and morbidity among children in developing countries and is an important contributing factor to deaths occurring from preventable causes in children <5 yea…

Versatile computer-aided design of free-form DNA nanostructures and assemblies Open

Wolfgang Pfeifer, Chao‐Min Huang, Michael G. Poirier, Gaurav Arya, Carlos E. Castro · 2023

Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDN…

Mechanism of DNA origami folding elucidated by mesoscopic simulations Open

Marcello DeLuca, Tao Ye, Michael G. Poirier, Yonggang Ke, Carlos E. Castro , et al. · 2023

DNA nanotechnology leverages the canonical base-pairing rules and geometry of DNA to create highly precise nanoscale structures with many potential applications. While the design and fabrication of DNA nanostructures is well-established, t…

Differentiating Metropolis-Hastings to Optimize Intractable Densities Open

Gaurav Arya, Ruben Seyer, Frank Schäfer, Alex K. Lew, Mathieu Huot , et al. · 2023

We develop an algorithm for automatic differentiation of Metropolis-Hastings samplers, allowing us to differentiate through probabilistic inference, even if the model has discrete components within it. Our approach fuses recent advances in…

Steric Communication between Dynamic Components on DNA Nanodevices Open

Yuchen Wang, Sebastian Sensale, Miguel Pedrozo, Chao‐Min Huang, Michael G. Poirier , et al. · 2023

Biomolecular nanotechnology has helped emulate basic robotic capabilities such as defined motion, sensing, and actuation in synthetic nanoscale systems. DNA origami is an attractive approach for nanorobotics, as it enables creation of devi…

Many-body Potential for Simulating the Self-Assembly of Polymer-Grafted Nanoparticles in a Polymer Matrix Open

Yilong Zhou, Sigbjorn Bore, Andrea R. Tao, Francesco Paesani, Gaurav Arya · 2023

Many-body interactions between polymer-grafted nanoparticles (NPs) play a key role in promoting their assembly into low-dimensional structures within polymer melts, even when the particles are spherical and isotropically grafted. However, …

Versatile Computer Aided Design of Freeform DNA Nanostructures and Assemblies Open

Wolfgang Pfeifer, Chao‐Min Huang, Michael G. Poirier, Gaurav Arya, Carlos E. Castro · 2023

Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDN…

Transcending shift-invariance in the paraxial regime via end-to-end inverse design of freeform nanophotonics Open

William F. Li, Gaurav Arya, Charles Roques‐Carmes, Zin Lin, Steven G. Johnson , et al. · 2023

Traditional optical elements and conventional metasurfaces obey shift-invariance in the paraxial regime. For imaging systems obeying paraxial shift-invariance, a small shift in input angle causes a corresponding shift in the sensor image. …

Diversity of Insect Pest in Agricultural Crops of Munsiyari, District Pithoragarh (Uttarakhand, India) Open

Mamta Bisht, D. Yogi Goswami, Dhani Arya, Gaurav Arya · 2023

The field investigation of insect pest diversity was done in the year 2019-2020 from agricultural crops of Munsiyari.In this study 15 insect pest were noticed from Agricultural crops which majorily belong to 5 orders of class Insecta.Most …

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