arXiv subjects

Rupam Saha

Publications and source records attributed to Rupam Saha.

5 recordsLinked to original sources

arXiv2026

ARTGEL: A temperature-regulated electrophoresis platform for quantitative studies of reversible association in gels

Here we present ARTGEL, an actively regulated-temperature gel electrophoresis platform designed for long-duration experiments under independently controlled thermal and electrical conditions. ARTGEL combines thermoelectric regulation of the gel temperature, a large heated and circulated buffer reservoir, and an automated electrode-wiping mechanism that stabilizes the voltage across the gel during runs exceeding 24 h. The platform was developed to address a limitation of conventional electrophoretic mobility shift assays, which are commonly used to analyze reversible biomolecular association but usually aim to suppress reaction during electrophoresis by dilution, competitors, or reduced temperature so that the gel reports a pre-equilibrated bulk solution. For temperature-sensitive systems, these strategies can alter the chemical state during loading and migration and obscure whether the measured band pattern reflects the original bulk sample or a re-equilibrated state inside the porous gel. Rather than attempting to quench reactions, ARTGEL enables electrophoresis to be performed at the same temperature as complementary bulk measurements, so that reversible association can be quantified directly in the gel and compared with matched measurements in solution. Using DNA origami assemblies, we show that ARTGEL preserves distinct temperature-dependent association states, resolves reaction-dependent distortions of migrating bands, and supports extraction of in-gel kinetic and thermodynamic parameters from reaction-diffusion-advection modeling.

cond-mat.soft↗

arXiv2025

From toroids to helical tubules: Kirigami-inspired programmable assembly of two-periodic curved crystals

Biology is full of intricate molecular structures whose geometries are inextricably linked to their function. Many of these structures exhibit varying curvature, such as the helical structure of the bacterial flagellum, which is critical for their motility. Because synthetic analogues of these shapes could be valuable platforms for nanotechnologies, including drug delivery and plasmonics, controllable synthesis of variable-curvature structures of various material systems, from fullerenes to supramolecular assemblies, has been a long-standing goal. Like two-dimensional crystals, these structures have a two-periodic symmetry, but unlike standard two-dimensional crystals, they are embedded in three dimensions with complex, spatially-varying curvatures that cause the structures to close upon themselves in one or more dimensions. Here, we develop and implement a design strategy to program the self-assembly of a complex spectrum of two-periodic curved crystals with variable periodicity, spatial dimension, and topology, spanning from toroids to achiral serpentine tubules to both left- and right-handed helical tubules. Our design strategy uses a kirigami-based mapping of 2D planar tilings to 3D curved crystals that preserves the periodicity, two-fold rotational symmetries, and subunit dimensions via the arrangement of disclination defects. We survey the modular geometry of these curved crystals and infer the addressable subunit interactions required to assemble them from triangular subunits. To demonstrate this design strategy, we program the self-assembly of toroids, helical- and serpentine-tubules from DNA origami subunits. A simulation model of the assembly pathways reveals physical considerations for programming the geometric specificity of angular folds in the curved crystal required to avoid defect-mediated misassembly.

cond-mat.soft↗

arXiv2025

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

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 completely conserves the scaffold routing across different designs and preserves more than 70% of the DNA staples between designs, dramatically reducing both cost and effort, while enabling precise and independent programming of subunit interactions and binding angles through adjustable overhang lengths and sequences. Using cryogenic electron microscopy, gel electrophoresis, and coarse-grained molecular dynamics simulations, we validate a set of robust design rules. We demonstrate the method's utility by assembling a variety of self-limiting structures, including anisotropic shells with controlled inter-subunit interactions and curvature, and a toroid with globally varying curvature. Our strategy is both cost-effective and versatile, providing a promising and efficient solution for the synthetic fabrication of complex nanostructures.

cond-mat.soft↗

arXiv2024

Economical and versatile subunit design principles for self-assembled DNA origami structures

Self-assembly of nanoscale synthetic subunits is a promising bottom-up strategy for fabrication of functional materials. Here, we introduce a design principle for DNA origami nanoparticles of 50-nm size, exploiting modularity, to make a family of versatile subunits that can target an abundant variety of self-assembled structures. The subunits are based on a core module that remains constant among all the subunits. Variable bond modules and angle modules are added to the exterior of the core to control interaction specificity, strength and structural geometry. A series of subunits with designed bond/angle modules are demonstrated to self-assemble into a rich variety of structures with different Gaussian curvatures, exemplified by sheets, spherical shells, and tubes. The design features flexible joints implemented using single-stranded angle modules between adjacent subunits whose mechanical properties, such as bending elastic moduli, are inferred from cryo-EM. Our findings suggest that incorporating a judicious amount of flexibility in the bond provides error tolerances in design and fabrication while still guaranteeing target fidelity. Lastly, while increasing flexibility could introduce greater variability and potential errors in assembly, these effects can be counterbalanced by increasing the number of distinct bonds, thereby allowing for precise targeting of specific structural binding angles within a broad range of configurations.

cond-mat.soft↗

arXiv2024

Analysis and Detection of Multilingual Hate Speech Using Transformer Based Deep Learning

Hate speech is harmful content that directly attacks or promotes hatred against members of groups or individuals based on actual or perceived aspects of identity, such as racism, religion, or sexual orientation. This can affect social life on social media platforms as hateful content shared through social media can harm both individuals and communities. As the prevalence of hate speech increases online, the demand for automated detection as an NLP task is increasing. In this work, the proposed method is using transformer-based model to detect hate speech in social media, like twitter, Facebook, WhatsApp, Instagram, etc. The proposed model is independent of languages and has been tested on Italian, English, German, Bengali. The Gold standard datasets were collected from renowned researcher Zeerak Talat, Sara Tonelli, Melanie Siegel, and Rezaul Karim. The success rate of the proposed model for hate speech detection is higher than the existing baseline and state-of-the-art models with accuracy in Bengali dataset is 89%, in English: 91%, in German dataset 91% and in Italian dataset it is 77%. The proposed algorithm shows substantial improvement to the benchmark method.

cs.CL↗