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Feng Ding

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preprint2026arXiv

ML-CLIPSim: Multi-Layer CLIP Similarity for Machine-Oriented Image Quality

We study full-reference image quality assessment from a machine-centric perspective, where images are evaluated by how well they preserve information for downstream models. We formulate machine-oriented quality as a latent machine utility and approximate it through pairwise predictive-consistency comparisons. To this end, we construct PCMP, a dataset of PSNR-matched distortion pairs labeled by consistency votes from multiple pretrained models. We further propose ML-CLIPSim, a differentiable quality metric built on a frozen CLIP visual encoder, which aggregates intermediate patch-token similarities and global image embeddings. Experiments on machine-preference benchmarks, human-IQA datasets, and learned image compression show that ML-CLIPSim better aligns with machine-oriented preferences than conventional fidelity and perceptual metrics, while remaining competitive for human quality prediction. Used as a compression distortion term, it improves rate--task trade-offs across multiple downstream tasks.

preprint2025arXiv

Non-Euclidean interfaces decode the continuous landscape of graphene-induced surface reconstructions

Interfacial reconstruction between two-dimensional (2D) materials and metal substrates fundamentally governs heterostructure properties, yet conventional flat substrates fail to capture the continuous crystallographic landscape. Here, we overcome this topological limitation using non-Euclidean interfaces-curved 2D graphene-copper surfaces as a model system-to traverse the infinite spectrum of lattice orientations. By integrating multimodal microscopy with a deep-learning-enhanced dimensional upscaling framework, we translate 2D scanning electron microscopy (SEM) contrast into quantitative three-dimensional (3D) morphologies with accurate facet identification. Coupling these observations with machine-learning-assisted density functional theory, we demonstrate that reconstruction is governed by a unified thermodynamic mechanism where high-index facets correspond to specific local minima in the surface energy landscape. This work resolves the long-standing complexity of graphene-copper faceting and establishes non-Euclidean surface topologies as a generalizable paradigm for decoding and controlling interfacial reconstruction in diverse metal-2D material systems.

preprint2022arXiv

Atomically Sharp, Closed Bilayer Phosphorene Edges by Self-Passivation

Two-dimensional (2D) crystals' edge structures not only influence their overall properties but also dictate their formation due to edge-mediated synthesis and etching processes. Edges must be carefully examined because they often display complex, unexpected features at the atomic scale, such as reconstruction, functionalization, and uncontrolled contamination. Here, we examine atomic-scale edge structures and uncover reconstruction behavior in bilayer phosphorene. We use in situ transmission electron microscopy (TEM) of phosphorene/graphene specimens at elevated temperatures to minimize surface contamination and reduce e-beam damage, allowing us to observe intrinsic edge configurations. Bilayer zigzag (ZZ) edge was found the most stable edge configuration under e-beam irradiation. Through first-principles calculations and TEM image analysis under various tilting and defocus conditions, we find that bilayer ZZ edges undergo edge reconstruction and so acquire closed, self-passivated edge configurations. The extremely low formation energy of the closed bilayer ZZ edge and its high stability against e-beam irradiation are confirmed by first-principles calculations. Moreover, we fabricate bilayer phosphorene nanoribbons with atomically-sharp closed ZZ edges. The identified bilayer ZZ edges will aid in the fundamental understanding of the synthesis, degradation, reconstruction, and applications of phosphorene and related structures.

preprint2022arXiv

Bottom-up Growth of Graphene Nanospears and Nanoribbons

Graphene nanoribbons (GNRs) are considered one of the most promising materials for next generation electronics, however a reliable and controllable synthesis method is still lacking. Here, we report the CVD growth of GNRs on a copper surface and the corresponding mechanisms of growth. One-dimensional GNR growth is enabled by a vapor-liquid-solid (VLS) graphene growth guided by on-surface propagation of a liquid catalyst particle. Controlling the suppression of vapor-solid-solid (VSS) graphene growth along the width direction of the GNR by tuning the flow of H2 during growth gives rise to a spear head-shaped graphene that we term graphene nanospears (GNSs). The real-time visual and spatially resolved observations confirm the VSS growth of graphene can be fully suppressed and lead to GNR formation on Cu surface. These findings reveal key insight into the growth mechanism of graphene and open a door for achieving a facile and scalable method of synthesizing free standing GNRs.

preprint2022arXiv

Catalytic growth of ultralong graphene nanoribbons on insulating substrates

Graphene nanoribbons (GNRs) with widths of a few nanometres are promising candidates for future nano-electronic applications due to their structurally tunable bandgaps, ultrahigh carrier mobilities, and exceptional stability. However, the direct growth of micrometre-long GNRs on insulating substrates, which is essential for the fabrication of nano-electronic devices, remains an immense challenge. Here, we report the epitaxial growth of GNRs on an insulating hexagonal boron nitride (h-BN) substrate through nanoparticle-catalysed chemical vapor deposition (CVD). Ultra-narrow GNRs with lengths of up to 10 μm are synthesized. Remarkably, the as-grown GNRs are crystallographically aligned with the h-BN substrate, forming one-dimensional (1D) moiré superlattices. Scanning tunnelling microscopy reveals an average width of 2 nm and a typical bandgap of ~1 eV for similar GNRs grown on conducting graphite substrates. Fully atomistic computational simulations support the experimental results and reveal a competition between the formation of GNRs and carbon nanotubes (CNTs) during the nucleation stage, and van der Waals sliding of the GNRs on the h-BN substrate throughout the growth stage. Our study provides a scalable, single-step method for growing micrometre-long narrow GNRs on insulating substrates, thus opening a route to explore the performance of high-quality GNR devices and the fundamental physics of 1D moiré superlattices.

preprint2022arXiv

Distributed simultaneous state and parameter estimation of nonlinear systems

In this paper, we consider distributed simultaneous state and parameter estimation for a class of nonlinear systems, for which the augmented model comprising both the states and the parameters is only partially observable. Specifically, we first illustrate how the sensitivity analysis (SA) can select variables for simultaneous state and parameter estimation. Then, a community structure detection (CSD) based process decomposition method is proposed for dividing the entire system into interconnected subsystems as the basis of distributed estimation. Next, we develop local moving horizon estimators based on the configured subsystem models, and the local estimators communicate with each other to exchange their estimates. Finally, an SA and CSD based distributed moving horizon estimation (DMHE) mechanism is proposed. The effectiveness of the proposed approach is illustrated using a chemical process consisting of four connected reactors.

preprint2022arXiv

Prospects for water vapor detection in the atmospheres of temperate and arid rocky exoplanets around M-dwarf stars

Detection of water vapor in the atmosphere of temperate rocky exoplanets would be a major milestone on the path towards characterization of exoplanet habitability. Past modeling work has shown that cloud formation may prevent the detection of water vapor on Earth-like planets with surface oceans using the James Webb Space Telescope (JWST). Here we analyze the potential for atmospheric detection of H2O on a different class of targets: arid planets. Using transit spectrum simulations, we show that atmospheric H2O may be easier to be detected on arid planets with cold-trapped ice deposits on the surface, because such planets will not possess thick H2O cloud decks that limit the transit depth of spectral features. However, additional factors such as band overlap with CO2 and other gases, extinction by mineral dust, overlap of stellar and planetary H2O lines, and the ultimate noise floor obtainable by JWST still pose important challenges. For this reason, combination of space- and ground-based spectroscopic observations will be essential for reliable detection of H2O on rocky exoplanets in the future.

preprint2021arXiv

Amplifying asymmetry with correlated catalysts

We investigate the basic constraint on amplifying the asymmetry in quantum states with correlated catalysts. Here a correlated catalyst is a finite-dimensional auxiliary, which exactly preserves its reduced state while allowed to become correlated to the quantum system. Interestingly, we prove that under translationally invariant operations, catalysts in pure states are useless in any state transformation, while with a correlated catalyst in a mixed state, one can enlarge the set of accessible states from an initially asymmetric state. Moreover, we show that the power of a catalyst increases with its dimension, and further, with a large enough catalyst, a qubit state with arbitrarily small amount of asymmetry can be converted to any mixed qubit state. In doing so, we build a bridge between two important results concerning the restrictions on coherence conversion, the no-broadcasting theorem and the catalytic coherence. Our results may also apply to the constraints on coherence evolution in quantum thermodynamics, and to the distribution of timing information between quantum clocks.

preprint2020arXiv

Comet-like tails of disintegrating exoplanets explained by escaping outflows emanated from the permanent nightside: day-side versus night-side escape

Ultra-hot disintegrating exoplanets have been detected with tails trailing behind and/or shooting ahead of them. These tails are believed to be made of dusts that are carried upward by the supersonic flow escaping the planet's gravity field from the fiercely heated permanent day-side. Conserving angular momentum, this day-side escape flux would lead the planet in orbit. In order to explain the trailing tails in observation, radiation pressure, a repulsive force pushing the escape flow away from the host star is considered to be necessary. We here investigate whether escape could occur on the night-side as the escape flow is deflected by the pressure gradient force. We demonstrate in an idealized framework that escape flux from the night-side could dominate that from the day-side; and the former may naturally explain the commonly-observed trailing tails based on angular momentum conservation, without the need to invoke radiation pressure, which has previously been thought to be the key. We also find analytical approximations for both dayside and nightside escape fluxes, which may be applied to study planetary evolution of disintegrating planets and to infer planetary sizes from observations of the properties of their dusty tails.

preprint2020arXiv

Stabilization of dayside surface liquid water via tropopause cold trapping on arid slowly rotating tidally locked planets

Terrestrial-type exoplanets orbiting nearby red dwarf stars (M-dwarfs) are among the best targets for atmospheric characterization and biosignature searches in the near future. Recent evolutionary studies have suggested that terrestrial planets in the habitable zone of M-dwarfs are probably tidally locked and have limited surface water inventories as a result of their host stars' high early luminosities. Several previous climate simulations of such planets have indicated that their remaining water would be transported to the planet's permanent nightside and become trapped as surface ice, leaving the dayside devoid of water. Here we use a three-dimensional general circulation model with a water cycle and accurate radiative transfer scheme to investigate the surface water evolution on slowly rotating tidally locked terrestrial planets with limited surface water inventories. We show that there is a competition for water trapping between the nightside surface and the substellar tropopause in this type of climate system. Although under some conditions the surface water remains trapped on the nightside as an ice sheet, in other cases liquid water stabilizes in a circular area in the substellar region as a wetland. Planets with 1 bar N$_2$ and atmospheric CO$_2$ levels greater than 0.1 bar retain stable dayside liquid water, even with very small surface water inventories. Our results reveal the diversity of possible climate states on terrestrial-type exoplanets and highlight the importance of surface liquid water detection techniques for future characterization efforts.

preprint2019arXiv

Chemically Induced Transformation of CVD-Grown Bilayer Graphene into Single Layer Diamond

Notwithstanding numerous density functional studies on the chemically induced transformation of multilayer graphene into a diamond-like film, a comprehensive convincing experimental proof of such a conversion is still lacking. We show that the fluorination of graphene sheets in Bernal (AB)-stacked bilayer graphene (AB-BLG) grown by chemical vapor deposition on a single crystal CuNi(111) surface triggers the formation of interlayer carbon-carbon bonds, resulting in a fluorinated diamond monolayer (F-diamane). Induced by fluorine chemisorption, the phase transition from AB-BLG to single layer diamond was studied and verified by X-ray photoelectron, ultraviolet photoelectron, Raman, UV-Vis, electron energy loss spectroscopies, transmission electron microscopy, and DFT calculations.

preprint2016arXiv

Convection in Condensible-rich Atmospheres

Condensible substances are nearly ubiquitous in planetary atmospheres. For the most familiar case-water vapor in Earth's present climate-the condensible gas is dilute, in the sense that its concentration is everywhere small relative to the noncondensible background gases. A wide variety of important planetary climate problems involve nondilute condensible substances. These include planets near or undergoing a water vapor runaway and planets near the outer edge of the conventional habitable zone, for which CO2 is the condensible. Standard representations of convection in climate models rely on several approximations appropriate only to the dilute limit, while nondilute convection differs in fundamental ways from dilute convection. In this paper, a simple parameterization of convection valid in the nondilute as well as dilute limits is derived and used to discuss the basic character of nondilute convection. The energy conservation properties of the scheme are discussed in detail and are verified in radiative-convective simulations. As a further illustration of the behavior of the scheme, results for a runaway greenhouse atmosphere for both steady instellation and seasonally varying instellation corresponding to a highly eccentric orbit are presented. The latter case illustrates that the high thermal inertia associated with latent heat in nondilute atmospheres can damp out the effects of even extreme seasonal forcing.

preprint2016arXiv

Dynamic Modulation of the Transport Properties of the LaAlO3/SrTiO3 Interface Using Uniaxial Strain

Among the interfacial transport modulations to the LaAlO3/SrTiO3 (LAO/STO) heterostructure, mechanical strain has been proven to be an effective approach by growing the LAO/STO films on different substrates with varying lattice mismatches to STO. However, this lattice-mismatch-induced strain effect is static and biaxial, hindering the study of the strain effect in a dynamic way. In this work we realize dynamic and uniaxial strain to the LAO/STO oxide heterostructure at low temperature, through mechanical coupling from a magnetostrictive template. This anisotropic strain results in symmetry breaking at the interface and induces further splitting of the electronic band structure and therefore produces different conductivities along the x and y in-plane directions. In particular, we observe that along the strained direction the interface conductivity decreases by up to 70% under a tensile strain, while it increases by 6.8% under a compressive strain at 2 K. Also, it is revealed that the modulation on the interfacial transport property can be anisotropic, i.e., the resistance changes differently when an excitation current is parallel or perpendicular to the strain direction. This approach of strain engineering provides another degree of freedom for control of transport properties of oxide heterostructures and opens an additional way to investigate strain effects in materials science.

preprint2016arXiv

Dynamics of atmospheres with a non-dilute condensible component

The diversity of characteristics for the host of recently discovered exoplanets opens up a great deal of fertile new territory for geophysical fluid dynamics, particularly when the fluid flow is coupled to novel thermodynamics, radiative transfer or chemistry. In this paper, we survey one of these new areas-the climate dynamics of atmospheres with a non-dilute condensible component, defined as the situation in which a condensible component of the atmosphere makes up a substantial fraction of the atmospheric mass within some layer. Non-dilute dynamics can occur for a wide range of condensibles, generically applying near both the inner and the outer edges of the conventional habitable zone and in connection with runaway greenhouse phenomena. It also applies in a wide variety of other planetary circumstances. We first present a number of analytical results developing some key features of non-dilute atmospheres, and then show how some of these features are manifest in simulations with a general circulation model adapted to handle non-dilute atmospheres. We find that non-dilute atmospheres have weak horizontal temperature gradients even for rapidly rotating planets, and that their circulations are largely barotropic. The relative humidity of the condensible component tends towards 100% as the atmosphere becomes more non-dilute, which has important implications for runaway greenhouse thresholds. Non-dilute atmospheres exhibit a number of interesting organized convection features, for which there is not yet any adequate theoretical understanding.

preprint2015arXiv

Silane-Catalyzed Fast Growth of Large Single-Crystalline Graphene on Hexagonal Boron Nitride

The direct growth of high-quality, large single-crystalline domains of graphene on a dielectric substrate is of vital importance for applications in electronics and optoelectronics. Traditionally, graphene domains grown on dielectrics are typically only ~1 nm with a growth rate of ~1 nm/min or less, the main reason is the lack of a catalyst. Here we show that silane, serving as a gaseous catalyst, is able to boost the graphene growth rate to ~1 um/min, thereby promoting graphene domains up to 20 um in size to be synthesized via chemical vapor deposition on hexagonal boron nitride. Hall measurements show that the mobility of the sample reaches 20,000 cm2/Vs at room temperature, which is among the best for CVD-grown graphene. Combining the advantages of both catalytic CVD and the ultra-flat dielectric substrate, gaseous catalyst-assisted CVD paves the way for synthesizing high-quality graphene for device applications while avoiding the transfer process.

preprint2015arXiv

Synthesis of large single-crystal hexagonal boron nitride grains on Cu-Ni alloy

Hexagonal boron nitride (h-BN) has attracted significant attention due to its superior properties as well as its potential as an ideal dielectric layer for graphene-based devices. The h-BN films obtained via chemical vapor deposition in earlier reports are always polycrystalline with small grains due to high nucleation density on substrates. Here we report the successful synthesis of large single-crystal h-BN grains on rational designed Cu-Ni alloy foils. It is found that the nucleation density can be greatly reduced to 60 per mm2 by optimizing Ni ratio in substrates. The strategy enables the growth of single-crystal h-BN grains up to 7,500 um2, about 2 orders larger than that in previous reports. This work not only provides valuable information for understanding h-BN nucleation and growth mechanisms, but also gives an effective alternative to exfoliated h-BN as a high-quality dielectric layer for large-scale nano-electronic applications.

preprint2015arXiv

Wafer-scale CVD Growth of Monolayer Hexagonal Boron Nitride with Large Domain Size by Cu Foil Enclosure Approach

Chemical vapor deposition synthesis of large domain hexagonal boron nitride (h-BN) with uniform thickness on Cu foils is of great challenge, originating from the extremely high nucleation densities and the reverse hydrogen etching competition reaction. We report herein the successful growth of wafer-scale high-quality h-BN monolayer film with the largest single crystalline domain sizes up to 72 micrometer in edge length using a folded Cu enclosure approach. The highly-confined growth space with this facile and unique approach enables the drastic decrease of nucleation centers together with the effective suppression of hydrogen etching reaction. It is revealed, for the first time, that the orientations of as-grown h-BN monolayers are strongly correlated with the crystalline facets of growth substrates, with the Cu (111) being the best substrate for growing high-quality single crystalline h-BN monolayer, consistent with the density functional theory calculations. The present study offers a practical pathway for growing high-quality h-BN films and deepens the fundamental understanding of h-BN growth process.

preprint2014arXiv

The Kinetics of Chirality Assignment in Catalytic Single Walled Carbon Nanotube Growth

Chirality-selected single-walled carbon nanotubes (SWCNTs) ensure a great potential of building ~1 nm sized electronics. However, the reliable method for chirality-selected SWCNT is still pending. Here we present a theoretical study on the SWCNT's chirality assignment and control during the catalytic growth. This study reveals that the chirality of a SWCNT is determined by the kinetic incorporation of the pentagon formation during SWCNT nucleation. Therefore, chirality is randomly assigned on a liquid catalyst surface. Furthermore, based on the understanding, two potential methods of synthesizing chirality-selected SWCNTs are proposed: i) by using Ta, W, Re, Os, or their alloys as solid catalysts, and ii) by changing the SWCNT's chirality frequently during the growth.

preprint2012arXiv

Direct observation of silver nanoparticle-ubiquitin corona formation

Upon entering physiological environments, nanoparticles readily assume the form of a nanoparticle-protein corona that dictates their biological identity. Understanding the structure and dynamics of nanoparticle-protein corona is essential for predicting the fate, transport, and toxicity of nanomaterials in living systems and for enabling the vast applications of nanomedicine. We combined multiscale molecular dynamics simulations and complementary experiments to characterize the silver nanoparticle-ubiquitin corona formation. Specifically, ubiquitins competed with citrates for the nanoparticle surface and bound to the particle in a specific manner. Under a high protein/nanoparticle stoichiometry, ubiquitions formed a multi-layer corona on the particle surface. The binding exhibited an unusual stretched-exponential behavior, suggesting a rich kinetics originated from protein-protein, protein-citrate, and protein-nanoparticle interactions. Furthermore, the binding destabilized the α-helices while increasing the β-sheets of the proteins. Our results revealed the structural and dynamic complexities of nanoparticle-protein corona formation and shed light on the origin of nanotoxicity.

preprint2011arXiv

Graphene Nucleation on Transition Metal Surface: Structure Transformation and Role of the Metal Step Edge

The nucleation of graphene on a transition metal (TM) surface, either on a terrace or near a step edge, is systematically explored using density functional theory (DFT) calculations and applying the two-dimensional (2D) crystal nucleation theory. Careful optimization of the supported carbon clusters, CN (with size N ranging from 1 to 24), on the Ni(111) surface indicates a ground state structure transformation from a one-dimensional (1D) C chain to a two-dimensional (2D) sp2 C network at N ~ 10-12. Furthermore, the crucial parameters controlling graphene growth on the metal surface, nucleation barrier, nucleus size, and the nucleation rate on a terrace or near a step edge, are calculated. In agreement with numerous experimental observations, our analysis shows that graphene nucleation near a metal step edge is superior to that on a terrace. Based on our analysis, we propose the use of seeded graphene to synthesize high-quality graphene in large area.

preprint2006arXiv

The role of the catalytic particle temperature gradient for SWNT growth from small particles

The Vapour-Liquid-Solid (VLS) model, which often includes a temperature gradient (TG) across the catalytic metal particle, is often used to describe the nucleation and growth of carbon nanostructures. Although the TG may be important for the growth of carbon species from large metal particles, molecular dynamics simulations show that it is not required for single-walled carbon nanotube growth from small catalytic particles.

preprint2004arXiv

Folding Trp-cage to NMR resolution native structure using a coarse-grained model

We develop a coarse-grained protein model with a simplified amino acid interaction potential. We perform discrete molecular dynamics folding simulations of a small 20 residue protein - Trp-cage - from a fully extended conformation. We demonstrate the ability of the Trp-cage model to consistently reach conformations within 2angstrom backbone root-mean-square distance (RMSD) from the corresponding NMR structures. The minimum RMSD of Trp-cage conformations in the simulation can be smaller than 1.00angstrom. Our findings suggest that, at least for the case of Trp-cage, a detailed all-atom protein model with a physical molecular mechanics force field is not necessary to reach the native state of a protein. Our results also suggest that the success folding Trp-cage in our simulations and in the reported all-atom molecular mechanics simulations studies may be mainly due to the special stabilizing features specific to this miniprotein.

Feng Ding

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22 published item(s)

ML-CLIPSim: Multi-Layer CLIP Similarity for Machine-Oriented Image Quality

Non-Euclidean interfaces decode the continuous landscape of graphene-induced surface reconstructions

Atomically Sharp, Closed Bilayer Phosphorene Edges by Self-Passivation

Bottom-up Growth of Graphene Nanospears and Nanoribbons

Catalytic growth of ultralong graphene nanoribbons on insulating substrates

Distributed simultaneous state and parameter estimation of nonlinear systems

Prospects for water vapor detection in the atmospheres of temperate and arid rocky exoplanets around M-dwarf stars

Amplifying asymmetry with correlated catalysts

Comet-like tails of disintegrating exoplanets explained by escaping outflows emanated from the permanent nightside: day-side versus night-side escape

Stabilization of dayside surface liquid water via tropopause cold trapping on arid slowly rotating tidally locked planets

Chemically Induced Transformation of CVD-Grown Bilayer Graphene into Single Layer Diamond

Convection in Condensible-rich Atmospheres

Dynamic Modulation of the Transport Properties of the LaAlO3/SrTiO3 Interface Using Uniaxial Strain

Dynamics of atmospheres with a non-dilute condensible component

Silane-Catalyzed Fast Growth of Large Single-Crystalline Graphene on Hexagonal Boron Nitride

Synthesis of large single-crystal hexagonal boron nitride grains on Cu-Ni alloy

Wafer-scale CVD Growth of Monolayer Hexagonal Boron Nitride with Large Domain Size by Cu Foil Enclosure Approach

The Kinetics of Chirality Assignment in Catalytic Single Walled Carbon Nanotube Growth

Direct observation of silver nanoparticle-ubiquitin corona formation

Graphene Nucleation on Transition Metal Surface: Structure Transformation and Role of the Metal Step Edge

The role of the catalytic particle temperature gradient for SWNT growth from small particles

Folding Trp-cage to NMR resolution native structure using a coarse-grained model