arXiv subjects

Dhaneesh Kumar

Publications and source records attributed to Dhaneesh Kumar.

8 recordsLinked to original sources

arXiv2026

DeepConf: Machine Learning Conformer Reconstruction of Biomolecules from Scanning Tunneling Microscopy Images

Improving the detailed understanding of the underlying properties and functions of biomolecules has recently attracted growing interest, enabled by the possibility of real-space imaging of single, intact macromolecules using Scanning Tunneling Microscopy (STM) in combination with electrospray ion beam deposition and soft landing. This combination provides key insights into biomolecular behavior, but it also imposes stringent requirements on rapid and reliable data analysis. A major limiting factor for applying machine learning to STM images is often the scarcity of training data, caused by the long acquisition times required for both experimental imaging and high-accuracy simulations. Here, we propose a framework for the rapid generation of three-dimensional structures of glycans, peptides, and glycopeptides and their corresponding STM-like image simulations, based on state-of-the-art, machine-learning-accelerated Density Functional Theory (DFT). We generate datasets for the polypeptide bradykinin and for a representative glycan molecule, and we train a conformer estimation model to predict a molecule's three-dimensional structure from an STM image. On synthetic data, our approach achieves high accuracy, with median atomic deviations below $2\,\AA{}$ for peptides and below $4\,\AA{}$ for glycans. Application to experimental data predominantly yields a precise, reliable, and visually convincing determination of the local positions of molecular subunits. The application to experimental data represents an important milestone towards a fully automated structural search pipeline for complex, biologically relevant systems imaged with STM.

cond-mat.mes-hall↗

arXiv2025

Atomic-scale control of substrate-spin coupling via vertical manipulation of a 2D metal-organic framework

Two-dimensional (2D) materials with frustrated crystal geometries can host strongly correlated electrons, potentially leading to a range of exotic many-body quantum phases such as Mott insulators, quantum spin-liquids, and Kondo lattices. The ability to control exchange-coupling within these systems is therefore highly desirable. Here, we use an atomically sharp scanning tunneling microscope probe to vertically manipulate a 2D Mott insulating kagome metal-organic framework (MOF) featuring Kondo-screened local magnetic moments on Ag(111). We show that by controlling the adsorption height of the MOF, we can also controllably and reversibly change the strength of Kondo coupling between the MOF's local spins and the substrate's conduction electrons. This mechanical control of Kondo coupling could be extended to other forms of interlayer exchange coupling, potentially allowing for atomic-scale design or control of spintronics technologies.

cond-mat.str-el↗

arXiv2024

Upper Bound Estimate of the Electronic Scattering Potential of a Weakly Interacting Molecular Film on a Metal

Thin organic films and two-dimensional (2D) molecular assemblies on solid surfaces yield the potential for applications in molecular electronics, optoelectronics, catalysis, and sensing. These applications rely on the intrinsic electronic properties of the hybrid organic/inorganic interface. Here, we investigate the energy dispersion of 2D electronic states at the interface between an atomically thin self-assembled molecular film, comprised of flat, noncovalently bonded 9,10-dicyanoanthracene (DCA) molecules, and a Ag(111) surface. Using Fourier-transformed scanning tunnelling spectroscopy (FT-STS), we determined that the 2D electronic wave functions with wavevectors within ~80% of the first Brillouin zone (BZ) area close to the Gamma-point are free-electron-like, suggesting a weak electronic interaction between the 2D molecular film and the metal surface. Via a perturbative second-order correction to the free electron energy dispersion, we further established an upper bound for the amplitude of the scattering potential resulting from the self-assembled molecular film that the interface electrons are subject to, on the order of 1.5 eV. Our approach allows for quantifying electronic interactions at hybrid 2D interfaces and heterostructures.

cond-mat.mtrl-sci↗

arXiv2024

Electric Field Control of Molecular Charge State in a Single-Component 2D Organic Nanoarray

Quantum dots (QD) with electric-field-controlled charge state are promising for electronics applications, e.g., digital information storage, single-electron transistors and quantum computing. Inorganic QDs consisting of semiconductor nanostructures or heterostructures often offer limited control on size and composition distribution, as well as low potential for scalability and/or nanoscale miniaturization. Owing to their tunability and self-assembly capability, using organic molecules as building nano-units can allow for bottom-up synthesis of two-dimensional (2D) nanoarrays of QDs. However, 2D molecular self-assembly protocols are often applicable on metals surfaces, where electronic hybridization and Fermi level pinning can hinder electric-field control of the QD charge state. Here, we demonstrate the synthesis of a single-component self-assembled 2D array of molecules [9, 10-dicyanoanthracene (DCA)] that exhibit electric-field-controlled spatially periodic charging on a noble metal surface, Ag(111). The charge state of DCA can be altered (between neutral and negative), depending on its adsorption site, by the local electric field induced by a scanning tunneling microscope tip. Limited metal-molecule interactions result in an effective tunneling barrier between DCA and Ag(111) that enables electric-field-induced electron population of the lowest unoccupied molecular orbital (LUMO) and hence charging of the molecule. Subtle site-dependent variation of the molecular adsorption height translates into a significant spatial modulation of the molecular polarizability, dielectric constant and LUMO energy level alignment, giving rise to a spatially dependent effective molecule-surface tunneling barrier and likelihood of charging. This work offers potential for high-density 2D self-assembled nanoarrays of identical QDs whose charge states can be addressed individually with an electric field.

cond-mat.mtrl-sci↗

arXiv2023

Selective Activation of Aromatic C-H Bonds Catalyzed by Single Gold Atoms at Room Temperature

Selective activation and controlled functionalization of C-H bonds in organic molecules is one of the most desirable processes in synthetic chemistry. Despite progress in heterogeneous catalysis using metal surfaces, this goal remains challenging due to the stability of C-H bonds and their ubiquity in precursor molecules, hampering regioselectivity. Here, we examine the interaction between 9,10-dicyanoanthracene (DCA) molecules and Au adatoms on a Ag(111) surface at room temperature (RT). Characterization via low-temperature scanning tunneling microscopy, spectroscopy, and noncontact atomic force microscopy, supported by theoretical calculations, revealed the formation of organometallic DCA-Au-DCA dimers, where C atoms at the ends of the anthracene moieties are bonded covalently to single Au atoms. The formation of this organometallic compound is initiated by a regioselective cleaving of C-H bonds at RT. Hybrid quantum mechanics/molecular mechanics calculations show that this regioselective C-H bond cleaving is enabled by an intermediate metal-organic complex which significantly reduces the dissociation barrier of a specific C-H bond. Harnessing the catalytic activity of single metal atoms, this regioselective on-surface C-H activation reaction at RT offers promising routes for future synthesis of functional organic and organometallic materials.

physics.chem-ph↗

arXiv2021

Manifestation of strongly correlated electrons in a 2D kagome metal-organic framework

The kagome lattice, whose electronic valence band (VB) structure includes two Dirac bands and one flat band, offers a rich space to realise tuneable topological and strongly correlated electronic phases in two-dimensional (2D) and layered materials. While strong electron correlations have been observed in inorganic kagome crystals, they remain elusive in organic systems. The latter offer versatile synthesis protocols via molecular self-assembly and metal-ligand coordination. Here, we report the synthesis of a 2D metal-organic framework (MOF) where di-cyano-anthracene (DCA) molecules form a kagome arrangement via coordination with copper (Cu) atoms on a silver surface [Ag(111)]. Low-temperature scanning tunnelling spectroscopy revealed Kondo screening--by the Ag(111) conduction electrons--of magnetic moments localised at Cu and DCA sites of the MOF. Density functional theory and mean-field Hubbard modelling show that these local moments emerge from strong interactions between kagome MOF electrons, enabling organic 2D materials as viable platforms for strongly correlated nanoelectronics and spintronics.

cond-mat.str-el↗

arXiv2018

Iron-based trinuclear metal-organic nanostructures on a surface with local charge accumulation

Coordination chemistry relies on harnessing active metal sites within organic matrices. Polynuclear complexes - consisting of organic ligands binding to clusters of several metal atoms are of particular interest, owing to their electronic/magnetic properties and potential for functional reactivity pathways. However, their synthesis remains challenging; only a limited number of geometries and configurations have been achieved. Here, we synthesise - via supramolecular chemistry on a noble metal surface - one-dimensional metal-organic nanostructures composed of terpyridine (tpy)-based molecules coordinated with well-defined polynuclear iron clusters. By a combination of low-temperature scanning probe microscopy techniques and density functional theory, we demonstrate that the coordination motif consists of coplanar tpy's linked via a linear tri-iron node in a mixed (positive) valence, metal-metal bond configuration. This unusual linkage is stabilized by a local accumulation of electrons at the interface between cations, ligand and surface. The latter, enabled by the bottom-up on-surface synthesis, hints at a chemically active metal centre, and opens the door to the engineering of nanomaterials with novel catalytic and magnetic functionalities.

cond-mat.mes-hall↗

arXiv2017

Toolboxes and handing students a hammer: The effects of cueing and instruction on getting students to think critically

Developing critical thinking skills is a common goal of an undergraduate physics curriculum. How do students make sense of evidence and what do they do with it? In this study, we evaluated students' critical thinking behaviors through their written notebooks in an introductory physics laboratory course. We compared student behaviors in the Structured Quantitative Inquiry Labs (SQILabs) curriculum to a control group and evaluated the fragility of these behaviors through procedural cueing. We found that the SQILabs were generally effective at improving the quality of students' reasoning about data and making decisions from data. These improvements in reasoning and sensemaking were thwarted, however, by a procedural cue. We describe these changes in behavior through the lens of epistemological frames and task orientation, invoked by the instructional moves.

physics.ed-ph↗