arXiv subjects

Yusong Tu

Publications and source records attributed to Yusong Tu.

18 recordsLinked to original sources

arXiv2025

Unveiling the Oxidation Mechanisms of Octa-Penta Graphene: A Multidimensional Exploration from First-Principles to Machine Learning

Octa-penta graphene (OPG), a novel carbon allotrope characterized by its distinctive arrangement of pentagonal and octagonal rings, has garnered considerable attention due to its exceptional structure and functional properties. This study systematically investigates the oxidation mechanisms of OPG and elucidates the oxygen migration patterns on the OPG monolayer through first-principles calculations and machine-learning-based molecular dynamics (MLMD) simulations. Specifically, the oxidation processes on OPG-L and OPG-Z involve exothermic chemisorption, where oxygen molecules dissociate at the surfaces, forming stable epoxy groups. Furthermore, the integrated-crystal orbital Hamilton population (ICOHP) and Bader charge analyses provide insights into the physical mechanisms of oxygen atom adsorption. Importantly, we found that oxidation also impact the electronic properties of OPG, with OPG-L retaining its metallic characteristics post-oxygen adsorption, whereas OPG-Z undergoes a transformation from a metallic to a semiconducting state due to the introduction of oxygen. Oxygen migration on OPG monolayer involves breaking and reforming of C-O bonds, with varying stability across adsorption sites and limited migration along the basal plane. MLMD simulations corroborate these migration patterns, offering detailed migration trajectories consistent with theoretical predictions. These findings enhance the understanding of oxygen migration dynamics on OPG, facilitate its experimental validations, and highlight its potential as a novel 2D material for applications in batteries, heat-resistant materials, and oxidation-resistant coatings.

cond-mat.mtrl-sci↗

arXiv2025

Exploring Dual-Iron Atomic Catalysts for Efficient Nitrogen Reduction: A Comprehensive Study on Structural and Electronic Optimization

The nitrogen reduction reaction (NRR), as an efficient and green pathway for ammonia synthesis, plays a crucial role in achieving on-demand ammonia production. This study proposes a novel design concept based on dual-iron atomic sites and nitrogen-boron co-doped graphene catalysts, exploring their high efficiency in NRR. By modulating the N and B co-doped ratios, we found that Fe2N3B@G catalyst exhibited significant activity in the adsorption and hydrogenation of N2 molecules, especially with the lowest free energy (0.32 eV) on NRR distal pathway, showing its excellent nitrogen activation capability and NRR performance. The computed electron localization function, crystal orbital Hamiltonian population, electrostatic potential map revealed that the improved NRR kinetics of Fe2N3B@G catalyst derived by N3B co-doping induced optimization of Fe-Fe electronic environment, regulation of Fe-N bond strength, and the continuous electronic support during the N2 breakage and hydrogenation. In particular, machine learning molecular dynamics (MLMD) simulations were employed to verify the high activity of Fe2N3B@G catalyst in NRR, which reveal that Fe2N3B@G effectively regulates the electron density of Fe-N bond, ensuring the smooth generation and desorption of NH3 molecules and avoiding the competition with hydrogen evolution reaction (HER). Furthermore, the determined higher HER overpotential of Fe2N3B@G catalyst can effectively inhibit the HER and enhance the selectivity toward NRR. In addition, Fe2N3B@G catalyst also showed good thermal stability by MD simulations up to 500 K, offering its feasibility in practical applications. This study demonstrates the superior performance of Fe2N3B@G in nitrogen reduction catalysis, and provides theoretical guidance for atomic catalyst design by the co-doping strategy and in-deep electronic environment modulation.

cond-mat.mtrl-sci↗

arXiv2024

Quasiphase transition of a single-file water chain influenced by atomic charges in a water model using orientational-biased replica exchange Monte Carlo simulations

The recently observed temperature-dependent quasiphase transition of the single-file water chain confined within a carbon nanotube in experiments has been validated by the simple lattice theory and molecular dynamics simulations. It has been pointed out that the atomic charges in water models are important, yet how the values will affect the structural details and thermodynamic properties of the quasiphase transition has not been fully revealed. In this work, we perform orientational-biased replica exchange Monte Carlo simulations in the canonical ensemble to explore the effect of atomic charges in the SPC/E water model on the quasiphase transition of a single-file water chain. Based on the atomic charge values reported in literature, three distinct quasiphases are reproduced, comprising a fully hydrogen-bonded water chain at lower temperatures, a more ordered dipolar orientation along the tube axis at intermediate temperatures, and a completely disordered structure at higher temperatures. Then by increasing the atomic charge values, we find that the fragmentation of the entire water chain into shorter water segments, the orientational ordering of water dipoles along the tube axis, and the transition towards complete disorder are all inhibited. Consequently, the transition temperatures between three quasiphases have been shifted to higher temperatures. The thermodynamic analysis demonstrates that the increased atomic charge values enhance the hydrogen bonding between neighbouring water molecules also the electrostatic attraction within the water chain, leading to a longer water dipole correlation length even at higher temperatures. These findings highlight the vital role of atomic charges in water models also the electrostatic interaction in regulating the orientational ordering of water molecules under nanoconfinement.

cond-mat.soft↗

arXiv2024

Factors resisting protein adsorption on hydrophilic/hydrophobic self-assembled monolayers terminated with hydrophilic hydroxyl groups

The hydroxyl-terminated self-assembled monolayer (OH-SAM), as a surface resistant to protein adsorption, exhibits substantial potential in applications such as ship navigation and medical implants, and the appropriate strategies for designing anti-fouling surfaces are crucial. Here, we employ molecular dynamics simulations and alchemical free energy calculations to systematically analyze the factors influencing resistance to protein adsorption on the SAMs terminated with single or double OH groups at three packing densities (Σ = 2.0 nm-2, 4.5 nm-2, and 6.5 nm-2), respectively. For the first time, we observe that the compactness and order of interfacial water enhance its physical barrier effect, subsequently enhancing the resistance of SAM to protein adsorption. Notably, the weak spatial hindrance effect of SAM leads to the embedding of protein into SAM, resulting in a lack of resistance of SAM towards protein. Furthermore, the number of hydroxyl groups per unit area of double OH-terminated SAM at Σ = 6.5 nm-2 is approximately 2 to 3 times that of single OH-terminated SAM at Σ = 6.5 nm-2 and 4.5 nm-2, consequently yielding a weaker resistance of double OH-terminated SAM towards protein. Meanwhile, due to the structure of SAM itself, i.e., the formation of a nearly perfect ice-like hydrogen bond structure, the SAM exhibits the weakest resistance towards protein. This study will complement and improve the mechanism of OH-SAM resistance to protein adsorption, especially the traditional barrier effect of interfacial water.

physics.bio-ph↗

arXiv2023

Unexpectedly Spontaneous Water Dissociation on Graphene Oxide Supported by Copper Substrate

Water dissociation is of fundamental importance in scientific fields and has drawn considerable interest in diverse technological applications. However, the high activation barrier of breaking the O-H bond within the water molecule has been identified as the bottleneck, even for the water adsorbed on the graphene oxide (GO). Herein, using the density functional theory calculations, we demonstrate that the water molecule can be spontaneously dissociated on GO supported by the (111) surface of the copper substrate (Copper-GO). This process involves a proton transferring from water to the interfacial oxygen group, and a hydroxide covalently bonding to GO. Compared to that on GO, the water dissociation barrier on Copper-GO is significantly decreased to be less than or comparable to thermal fluctuations. This is ascribed to the orbital-hybridizing interaction between copper substrate and GO, which enhances the reaction activity of interfacial oxygen groups along the basal plane of GO for water dissociation. Our work provides a novel strategy to access water dissociation via the substrate-enhanced reaction activity of interfacial oxygen groups on GO and indicates that the substrate can serve as an essential key to tuning the catalytic performance of various two-dimensional material devices.

cond-mat.mtrl-sci↗

arXiv2023

Locally Spontaneous Dynamic Oxygen Migration on Biphenylene: A DFT Study

The dynamic oxygen migration at the interface of carbon allotropes dominated by the periodic hexagonal rings, including graphene and carbon nanotube, has opened up a new avenue to realize dynamic covalent materials. However, for the carbon materials with hybrid carbon rings, such as biphenylene, whether the dynamic oxygen migration at its interface can still be found remains unknown. Using both density functional theory calculations and machine-learning-based molecular dynamics (MLMD) simulations, we found that the oxygen migration departing away from the four-membered carbon (C4) ring is hindered, and the oxygen atom prefers to spontaneously migrate toward/around the C4 ring. This locally spontaneous dynamic oxygen migration on the biphenylene is attributed to the high barrier of about 1.5 eV for the former process and relatively low barrier of about 0.3 eV for the latter one, originating from the enhanced activity of C-O bond near/around the C4 ring due to the hybrid carbon rings structure. Moreover, the locally spontaneous dynamic oxygen migration is further confirmed by MLMD simulations. This work sheds light on the potential of biphenylene as a catalyst for spatial-controlled energy conversion and provides the guidance for realizing the dynamic covalent interface at other carbon-based or two-dimensional materials.

cond-mat.mtrl-sci↗

arXiv2022

Unexpectedly resisting protein adsorption on self-assembled monolayers terminated with two hydrophilic hydroxyl groups

The OH-terminated self-assembled monolayers, as protein-resistant surfaces, have significant potential in biocompatible implant devices, which can avoid or reduce adverse reactions caused by protein adhesion to biomaterial surfaces, such as thrombosis, immune response and inflammation. Here, molecular dynamics simulations were performed to evaluate the degree of protein adsorption on the self-assembled monolayer terminated with two hydrophilic OH groups ((OH)2-SAM) at the packing densities (Σ) of 4.5 nm-2 and 6.5 nm-2, respectively. The results show that the (OH)2-SAM itself can significantly improve the performance of its resistance to protein adsorption. This is attributed to the structure of the (OH)2-SAM itself, i.e., the formation of a nearly perfect hexagonal-ice-like hydrogen bond structure in the OH matrix of the (OH)2-SAM at Σ = 4.5 nm-2, which sharply reduces the number of hydrogen bonds (i.e., 0.9) formed between the hydrophobic (OH)2-SAM surface and protein. While for Σ = 6.5 nm-2, the hydrophilic (OH)2-SAM surface can provide more hydrogen bonding sites to form hydrogen bonds (i.e., 7.3) with protein. The number of hydrogen bonds formed between the (OH)2-SAM and protein at Σ = 6.5 nm-2 is ~8 times higher than that at Σ = 4.5 nm-2, reflecting the excellent resistance to protein adsorption exhibited by the structure of (OH)2-SAM itself at Σ = 4.5 nm-2. Compared with traditionally physical barrier effect formed by a large number of hydrogen bonds between the (OH)2-SAM and water above at Σ = 6.5 nm-2, the structure of the (OH)2-SAM itself at Σ = 4.5 nm-2 proposed in this study significantly improves resistance to protein adsorption, which provides new insights into the mechanism of resistance to protein adsorption on the (OH)2-SAM.

physics.app-ph↗

arXiv2022

Oxygen dissociation on the C3N monolayer: A first-principles study

The oxygen dissociation and the oxidized structure on the pristine C3N monolayer in exposure to air are the inevitably critical issues for the C3N engineering and surface functionalization yet have not been revealed in detail. Using the first-principles calculations, we have systematically investigated the possible O2 adsorption sites, various O2 dissociation pathways and the oxidized structures. It is demonstrated that the pristine C3N monolayer shows more O2 physisorption sites and exhibits stronger O2 adsorption than the pristine graphene. Among various dissociation pathways, the most preferable one is a two-step process involving an intermediate state with the chemisorbed O2 and the barrier is lower than that on the pristine graphene, indicating that the pristine C3N monolayer is more susceptible to oxidation than the pristine graphene. Furthermore, we found that the most stable oxidized structure is not produced by the most preferable dissociation pathway but generated from a direct dissociation process. These results can be generalized into a wide range of temperatures and pressures using ab initio atomistic thermodynamics. Our findings deepen the understanding of the chemical stability of 2D crystalline carbon nitrides under ambient conditions, and could provide insights into the tailoring of the surface chemical structures via doping and oxidation.

cond-mat.mtrl-sci↗

arXiv2022

Ultrafast ion sieving in two dimensional graphene oxide membranes

Ultrahigh water permeance, together with a high rejection rate through nanofiltration and separation membranes1,2, is crucial but still challenging for multivalent ion sieving in water treatment processes of desalination, separation, and purification3,4. To date, no theory or equation has ever been quantitatively clarified the mechanism of water permeance in two-dimensional (2D) membranes, despite intensive and prolonged searches. Here, we established a new general equation of permeation through 2D membranes, and experimentally achieved unprecedented advances in water permeance one to two orders of magnitude higher than state-of-the-art membranes while simultaneously maintaining high ion rejection rates for multivalent metal ions, by staking nano-sized reduced graphene oxide (nano-rGO) flakes into nanofiltration membranes. The equation is simply based on a fundamental steady-state flow assumption and provides an essential description of water permeance through 2D membranes, demonstrating that the ultrahigh water permeance is attributed to the high effective channel area and shortened channel length elicited from the nano-sized-flake stacking effects in nano-rGO membranes, consistent with our theoretical simulations and previous experiments. These results pave the way for fabrication of advanced 2D nanofiltration membranes to realize a breakthrough in water permeance with exceptional ion sieving performance.

physics.flu-dyn↗

arXiv2022

Remarkably Enhanced Dynamic Oxygen Migration on Graphene Oxide Supported by Copper Substrate

The dynamic covalent properties of graphene oxide (GO) are of fundamental interest to a broad range of scientific areas and technological applications. It remains a challenge to access the feasible dynamic reactions for reversibly breaking/reforming covalent bonds of oxygen functional groups on GO, although these reactions can be induced by photonic or mechanical routes, or mediated by adsorbed water. Here, using the density functional theory calculations, we demonstrate the remarkably enhanced dynamic oxygen migration along the basal plane of GO supported by copper substrate (GO@copper), with the C-O bond breaking reaction and proton transfer between the neighboring epoxy and hydroxyl groups. Compared to that on GO, the energy barrier of oxygen migration on GO@copper is sharply reduced to be less than or comparable to thermal fluctuations, and meanwhile the crystallographic match between GO and copper substrate induces new oxygen migration paths on GO@copper. This work sheds light on the understanding of metal substrate-enhanced dynamic properties of GO, and evidences the strategy to tune the activity of two-dimension-interfacial oxygen groups for various potential applications.

cond-mat.mtrl-sci↗

arXiv2021

Unexpected Spontaneously Dynamic Oxygen Migration on Carbon Nanotubes

Using the density functional theory calculations, we show that the oxygen functional groups exhibit unexpected spontaneously dynamic behaviors on the interior surface of single-walled carbon nanotubes (SWCNT). Two types of dynamic oxygen migrations - hydroxyl and epoxy migrations - are achieved by the breaking/reforming of C-O bond reaction and the proton transfer reaction. It is demonstrated that the spontaneously dynamic characteristic is attributed to the sharply reduced energy barrier less than or comparable to thermal fluctuations. We also observe a stable intermediate state with a dangling C-O bond, which permits the successive migration of oxygen functional groups. However, on the exterior surface of SWCNT, the oxygen groups are difficult to migrate spontaneously due to the relatively high energy barriers, and the dangling C-O bond prefers to transform into the more stable epoxy configuration. The spontaneous oxygen migration is further confirmed by the long-distance oxygen migration, which comprises three hydroxyl migration reactions and one C-O bond reaction. Our work provides a new understanding of the behavior of oxygen functional groups on interfaces and gives a potential route to design new carbon-based dynamic materials.

cond-mat.mtrl-sci↗

arXiv2021

Unexpected Hydrophobicity on Self-Assembled Monolayers Terminated with Two Hydrophilic Hydroxyl Groups

Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules into surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations show an unexpected hydrophobicity with a contact angle of $82^o$ on a flexible self-assembled monolayer terminated only with two hydrophilic OH groups ($(OH)_2\!-\!SAM$). This hydrophobicity is attributed to the formation of a hexagonal-ice-like H-bonding structure in the OH matrix of $(OH)_2\!-\!SAM$, which sharply reduces the hydrogen bonds between surface and water molecules above. The unique simple interface presented here offers a significant molecular-level platform for examining the bio-interfacial interactions ranging from biomolecules binding to cell adhesion.

physics.app-ph↗

arXiv2020

Remarkable antibacterial activity of reduced graphene oxide functionalized by copper ions

Despite long-term efforts for exploring antibacterial agents or drugs, it remains challenging how to potentiate antibacterial activity and meanwhile minimize toxicity hazards to the environment. Here, we experimentally show that the functionality of reduced graphene oxide (rGO) through copper ions displays selective antibacterial activity significantly stronger than that of rGO itself and no toxicity to mammalian cells. Remarkably, this antibacterial activity is two orders of magnitude greater than the activity of its surrounding copper ions. We demonstrate that the rGO is functionalized through the cation-$π$ interaction to massively adsorb copper ions to form a rGO-copper composite in solution and result in an extremely low concentration level of surrounding copper ions (less than ~0.5 $μM$). These copper ions on rGO are positively charged and strongly interact with negatively charged bacterial cells to selectively achieve antibacterial activity, while rGO exhibits the functionality to not only actuate rapid delivery of copper ions and massive assembly onto bacterial cells but also result in the valence shift in the copper ions from Cu$^{2+}$ into Cu$^{+}$ which greatly enhances the antibacterial activity. Notably, this functionality of rGO through cation-$π$ interaction with copper ions can similarly achieve algaecidal activity but does not exert cytotoxicity against neutrally charged mammalian cells. The remarkable selective antibacterial activity from the rGO functionality as well as the inherent broad-spectrum-antibacterial physical mechanism represents a significant step toward the development of a novel antibacterial material and reagent without environmental hazards for practical application.

physics.app-ph↗

arXiv2018

Water-phospholipid interactions at the interface of lipid membranes: comparison of different force fields

Water-phospholipid interactions at the lipid bilayer/water interfaces are of essential importance for the dynamics, stability and function of biological membrane, and are also strongly associated with numerous biological processes at the interfaces of lipid bilayers. Various force fields, such as the united-atom Berger force field, its two improved versions by Kukol and by Poger, and the all-atom Slipid force field developed recently, can be applied to simulating the structures of lipid bilayer, with their structural predictions in good agreement with experimental data. In this work, we show that despite the similarity in structural predictions of lipid bilayers, there are observable differences in formation of hydrogen bonds and the interaction energy profiles between water and phospholipid groups at the lipid bilayer/water interfaces, when four force fields for dipalmitoylphosphatidylcholine (DPPC) phospholipids are employed in molecular dynamics simulations. In particular, the Slipid force field yields more hydrogen bonds between water and phospholipids and more symmetrical interaction energy distributions for the two carboxylic groups on their respective acyl tails, compared to the Berger and its two improved force fields. These differences are mainly attributed to the different interfacial water distributions and ability to form hydrogen bonds between interfacial water and oxygen atoms of the DPPC lipids using different force fields. These results would be helpful in understanding the behaviors of water as well as its interaction with phospholipids at the lipid bilayer/water interfaces, and provide a guide for making the appropriate choice on the force field in simulations of lipid bilayers.

cond-mat.soft↗

arXiv2013

Inherent fluctuation-mediated equivalent force drives directional motions of nanoscale asymmetric particles -- Surf-riding of asymmetric molecules in thermal fluctuations

Using a simple theoretical model of a nanoscale asymmetric particle/molecule with asymmetric structure or/and asymmetric charge distribution, here using a charge dipole as an example, we show that there is unidirectional transportation mediated by non-white fluctuations if the asymmetric orientation of the particle/molecule is constrained. This indicates the existence of an inherent equivalent force, which drives the particle/molecule itself along the orientation of the asymmetric particle in the environment of fluctuations. In practical systems, equivalent force also exist in the asymmetric molecules, such as water and ethanol, at the ambient condition since thermal fluctuations are not white anymore at nanoscale [Wan, R., J. Hu, and H. Fang, Sci. China Phys. Mech. Astron. 2012, 55, 751]. Molecular dynamic simulations show that there is unidirectional transportation of an ultrathin water layer on solid surface at room temperature when the orientations of water molecules have a preference. The finding will play an essential role in the understanding of the world from a molecular view and the developing of novel technology for various nanoscale and bulk applications, such as chemical separation, water treatment, sensing and drug delivery.

cond-mat.mes-hall↗

arXiv2013

Asymmetrical free diffusion with orientation-dependence of molecules in finite timescales

Using molecular dynamics simulations, we show that free diffusion of a nanoscale particle (molecule) with asymmetric structure critically depends on the orientation in a finite timescale of picoseconds to nanoseconds. In a timescale of ~100 ps, there are ~10% more possibilities for the particle moving along the initial orientation than moving opposite to the orientation; and the diffusion distances of the particle reach ~1 nm. We find that the key to this observation is the orientation-dependence of the damping force to the moving of the nanoscale particle and a finite time is required to regulate the particle orientation. This finding extends the work of Einstein to nano-world beyond random Brownian motion, thus will have a critical role in the understanding of the nanoscale world.

cond-mat.soft↗

arXiv2013

Galilean Invariant Fluid-Solid Interfacial Dynamics in Lattice Boltzmann Simulations

Galilean invariance is a fundamental property; however, although the lattice Boltzmann equation itself is Galilean invariant, this property is usually not taken into account in the treatment of the fluid-solid interface. Here, we show that consideration of Galilean invariance in fluid-solid interfacial dynamics can greatly enhance the computational accuracy and robustness in a numerical simulation. Surprisingly, simulations are so vastly improved that the force fluctuation is very small and a time average becomes unnecessary.

physics.flu-dyn↗

arXiv2012

Evaporation of tiny water aggregation on solid surfaces of different wetting properties

The evaporation of a tiny amount of water on the solid surface with different wettability has been studied by molecular dynamics simulations. We found that, as the surface changed from hydrophobicity to hydrophility, the evaporation speed did not show a monotonically decrease from intuition, but increased first, and then decreased after reached a maximum value. The competition between the number of the water molecules on the water-gas surface from where the water molecules can evaporate and the potential barrier to prevent those water molecules from evaporating results in the unexpected behavior of the evaporation. A theoretical model based on those two factors can fit the simulation data very well. This finding is helpful in understanding the evaporation on the biological surfaces, designing artificial surface of ultra fast water evaporating or preserving water in soil.

cond-mat.soft↗