1
|
Abstract
Earth's core is less dense than iron, and therefore it must contain "light elements," such as S, Si, O, or C. We use ab initio molecular dynamics to calculate the density and bulk sound velocity in liquid metal alloys at the pressure and temperature conditions of Earth's outer core. We compare the velocity and density for any composition in the (Fe-Ni, C, O, Si, S) system to radial seismological models and find a range of compositional models that fit the seismological data. We find no oxygen-free composition that fits the seismological data, and therefore our results indicate that oxygen is always required in the outer core. An oxygen-rich core is a strong indication of high-pressure and high-temperature conditions of core differentiation in a deep magma ocean with an FeO concentration (oxygen fugacity) higher than that of the present-day mantle.
Collapse
|
Research Support, Non-U.S. Gov't |
11 |
230 |
2
|
Komsa HP, Krasheninnikov AV. Two-Dimensional Transition Metal Dichalcogenide Alloys: Stability and Electronic Properties. J Phys Chem Lett 2012; 3:3652-6. [PMID: 26291001 DOI: 10.1021/jz301673x] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Using density-functional theory calculations, we study the stability and electronic properties of single layers of mixed transition metal dichalcogenides (TMDs), such as MoS2xSe2(1-x), which can be referred to as two-dimensional (2D) random alloys. We demonstrate that mixed MoS2/MoSe2/MoTe2 compounds are thermodynamically stable at room temperature, so that such materials can be manufactured using chemical-vapor deposition technique or exfoliated from the bulk mixed materials. By applying the effective band structure approach, we further study the electronic structure of the mixed 2D compounds and show that general features of the band structures are similar to those of their binary constituents. The direct gap in these materials can continuously be tuned, pointing toward possible applications of 2D TMD alloys in photonics.
Collapse
|
|
13 |
140 |
3
|
Guo GC, Wang D, Wei XL, Zhang Q, Liu H, Lau WM, Liu LM. First-Principles Study of Phosphorene and Graphene Heterostructure as Anode Materials for Rechargeable Li Batteries. J Phys Chem Lett 2015; 6:5002-8. [PMID: 26623923 DOI: 10.1021/acs.jpclett.5b02513] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
There is a great desire to develop the high-efficient anodes materials for Li batteries, which require not only large capacity but also high stability and mobility. In this work, the phosphorene/graphene heterostructure (P/G) was carefully explored based on first-principles calculations. The binding energy of Li on the pristine phosphorene is relatively weak (within 1.9 eV), whereas the phosphorene/graphene heterostructure (P/G) can greatly improve the binding energy (2.6 eV) without affecting the high mobility of Li within the layers. The electronic structures show that the large Li adsorption energy and fast diffusion ability of the P/G origin from the interfacial synergy effect. Interestingly, the P/G also displays ultrahigh stiffness (Cac = 350 N/m, Czz = 464 N/m), which can effectively avoid the distortion of the pristine phosphorene after the insertion of lithium. Thus, P/G can greatly enhance the cycle life of the battery. Owing to the high capacity, good conductivity, excellent Li mobility, and ultrahigh stiffness, P/G is a very promising anode material in Li-ion batteries (LIBs).
Collapse
|
|
10 |
103 |
4
|
Part-crystalline part-liquid state and rattling-like thermal damping in materials with chemical-bond hierarchy. Proc Natl Acad Sci U S A 2014; 111:15031-5. [PMID: 25288751 DOI: 10.1073/pnas.1410349111] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding thermal and phonon transport in solids has been of great importance in many disciplines such as thermoelectric materials, which usually requires an extremely low lattice thermal conductivity (LTC). By analyzing the finite-temperature structural and vibrational characteristics of typical thermoelectric compounds such as filled skutterudites and Cu3SbSe3, we demonstrate a concept of part-crystalline part-liquid state in the compounds with chemical-bond hierarchy, in which certain constituent species weakly bond to other part of the crystal. Such a material could intrinsically manifest the coexistence of rigid crystalline sublattices and other fluctuating noncrystalline sublattices with thermally induced large-amplitude vibrations and even flow of the group of species atoms, leading to atomic-level heterogeneity, mixed part-crystalline part-liquid structure, and thus rattling-like thermal damping due to the collective soft-mode vibrations similar to the Boson peak in amorphous materials. The observed abnormal LTC close to the amorphous limit in these materials can only be described by an effective approach that approximately treats the rattling-like damping as a "resonant" phonon scattering.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
11 |
94 |
5
|
Chen W, Hao J, Hu W, Zang Z, Tang X, Fang L, Niu T, Zhou M. Enhanced Stability and Tunable Photoluminescence in Perovskite CsPbX 3 /ZnS Quantum Dot Heterostructure. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1604085. [PMID: 28407459 DOI: 10.1002/smll.201604085] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/20/2017] [Indexed: 05/25/2023]
Abstract
All-inorganic perovskite CsPbX3 (X = Cl, Br, I) and related materials are promising candidates for potential solar cells, light emitting diodes, and photodetectors. Here, a novel architecture made of CsPbX3 /ZnS quantum dot heterodimers synthesized via a facile solution-phase process is reported. Microscopic measurements show that CsPbX3 /ZnS heterodimer has high crystalline quality with enhanced chemical stability, as also evidenced by systematic density functional theory based first-principles calculations. Remarkably, depending on the interface structure, ZnS induces either n-type or p-type doping in CsPbX3 and both type-I and type-II heterojunctions can be achieved, leading to rich electronic properties. Photoluminescence measurement results show a strong blue-shift and decrease of recombination lifetime with increasing sulfurization, which is beneficial for charge diffusion in solar cells and photovoltaic applications. These findings are expected to shed light on further understanding and design of novel perovskite heterostructures for stable, tunable optoelectronic devices.
Collapse
|
|
8 |
93 |
6
|
Oba F, Choi M, Togo A, Tanaka I. Point defects in ZnO: an approach from first principles. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2011; 12:034302. [PMID: 27877390 PMCID: PMC5090462 DOI: 10.1088/1468-6996/12/3/034302] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 05/27/2011] [Accepted: 03/16/2011] [Indexed: 05/03/2023]
Abstract
Recent first-principles studies of point defects in ZnO are reviewed with a focus on native defects. Key properties of defects, such as formation energies, donor and acceptor levels, optical transition energies, migration energies and atomic and electronic structure, have been evaluated using various approaches including the local density approximation (LDA) and generalized gradient approximation (GGA) to DFT, LDA+U/GGA+U, hybrid Hartree-Fock density functionals, sX and GW approximation. Results significantly depend on the approximation to exchange correlation, the simulation models for defects and the post-processes to correct shortcomings of the approximation and models. The choice of a proper approach is, therefore, crucial for reliable theoretical predictions. First-principles studies have provided an insight into the energetics and atomic and electronic structures of native point defects and impurities and defect-induced properties of ZnO. Native defects that are relevant to the n-type conductivity and the non-stoichiometry toward the O-deficient side in reduced ZnO have been debated. It is suggested that the O vacancy is responsible for the non-stoichiometry because of its low formation energy under O-poor chemical potential conditions. However, the O vacancy is a very deep donor and cannot be a major source of carrier electrons. The Zn interstitial and anti-site are shallow donors, but these defects are unlikely to form at a high concentration in n-type ZnO under thermal equilibrium. Therefore, the n-type conductivity is attributed to other sources such as residual impurities including H impurities with several atomic configurations, a metastable shallow donor state of the O vacancy, and defect complexes involving the Zn interstitial. Among the native acceptor-type defects, the Zn vacancy is dominant. It is a deep acceptor and cannot produce a high concentration of holes. The O interstitial and anti-site are high in formation energy and/or are electrically inactive and, hence, are unlikely to play essential roles in electrical properties. Overall defect energetics suggests a preference for the native donor-type defects over acceptor-type defects in ZnO. The O vacancy, Zn interstitial and Zn anti-site have very low formation energies when the Fermi level is low. Therefore, these defects are expected to be sources of a strong hole compensation in p-type ZnO. For the n-type doping, the compensation of carrier electrons by the native acceptor-type defects can be mostly suppressed when O-poor chemical potential conditions, i.e. low O partial pressure conditions, are chosen during crystal growth and/or doping.
Collapse
|
Review |
14 |
77 |
7
|
Wang Y, Zhang R, Li J, Li L, Lin S. First-principles study on transition metal-doped anatase TiO2. NANOSCALE RESEARCH LETTERS 2014; 9:46. [PMID: 24472374 PMCID: PMC3914371 DOI: 10.1186/1556-276x-9-46] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/05/2013] [Indexed: 05/21/2023]
Abstract
The electronic structures, formation energies, and band edge positions of anatase TiO2 doped with transition metals have been analyzed by ab initio band calculations based on the density functional theory with the planewave ultrasoft pseudopotential method. The model structures of transition metal-doped TiO2 were constructed by using the 24-atom 2 × 1 × 1 supercell of anatase TiO2 with one Ti atom replaced by a transition metal atom. The results indicate that most transition metal doping can narrow the band gap of TiO2, lead to the improvement in the photoreactivity of TiO2, and simultaneously maintain strong redox potential. Under O-rich growth condition, the preparation of Co-, Cr-, and Ni-doped TiO2 becomes relatively easy in the experiment due to their negative impurity formation energies, which suggests that these doping systems are easy to obtain and with good stability. The theoretical calculations could provide meaningful guides to develop more active photocatalysts with visible light response.
Collapse
|
research-article |
11 |
75 |
8
|
Zaborenko N, Shi Z, Corredor CC, Smith-Goettler BM, Zhang L, Hermans A, Neu CM, Alam MA, Cohen MJ, Lu X, Xiong L, Zacour BM. First-Principles and Empirical Approaches to Predicting In Vitro Dissolution for Pharmaceutical Formulation and Process Development and for Product Release Testing. AAPS J 2019; 21:32. [PMID: 30790200 PMCID: PMC6394641 DOI: 10.1208/s12248-019-0297-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/02/2018] [Indexed: 11/30/2022] Open
Abstract
This manuscript represents the perspective of the Dissolution Working Group of the International Consortium for Innovation and Quality in Pharmaceutical Development (IQ) and of two focus groups of the American Association of Pharmaceutical Scientists (AAPS): Process Analytical Technology (PAT) and In Vitro Release and Dissolution Testing (IVRDT). The intent of this manuscript is to show recent progress in the field of in vitro predictive dissolution modeling and to provide recommended general approaches to developing in vitro predictive dissolution models for both early- and late-stage formulation/process development and batch release. Different modeling approaches should be used at different stages of drug development based on product and process understanding available at those stages. Two industry case studies of current approaches used for modeling tablet dissolution are presented. These include examples of predictive model use for product development within the space explored during formulation and process optimization, as well as of dissolution models as surrogate tests in a regulatory filing. A review of an industry example of developing a dissolution model for real-time release testing (RTRt) and of academic case studies of enabling dissolution RTRt by near-infrared spectroscopy (NIRS) is also provided. These demonstrate multiple approaches for developing data-rich empirical models in the context of science- and risk-based process development to predict in vitro dissolution. Recommendations of modeling best practices are made, focused primarily on immediate-release (IR) oral delivery products for new drug applications. A general roadmap is presented for implementation of dissolution modeling for enhanced product understanding, robust control strategy, batch release testing, and flexibility toward post-approval changes.
Collapse
|
Review |
6 |
57 |
9
|
Performance of Intrinsic and Modified Graphene for the Adsorption of H 2S and CH 4: A DFT Study. NANOMATERIALS 2020; 10:nano10020299. [PMID: 32050612 PMCID: PMC7075213 DOI: 10.3390/nano10020299] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/01/2020] [Accepted: 02/01/2020] [Indexed: 11/16/2022]
Abstract
In this study, the adsorption performances of graphene before and after modification to H2S and CH4 molecules were studied using first principles with the density functional theory (DFT) method. The most stable adsorption configuration, the adsorption energy, the density of states, and the charge transfer are discussed to research the adsorption properties of intrinsic graphene (IG), Ni-doped graphene (Ni–G), vacancy defect graphene (DG), and graphene oxide (G–OH) for H2S and CH4. The weak adsorption and charge transfer of IG achieved different degrees of promotion by doping the Ni atom, setting a single vacancy defect, and adding oxygen-containing functional groups. It can be found that a single vacancy defect significantly enhances the strength of interaction between graphene and adsorbed molecules. DG peculiarly shows excellent adsorption performance for H2S, which is of great significance for the study of a promising sensor for H2S gas.
Collapse
|
Journal Article |
5 |
50 |
10
|
Wu P, Zhang W, Li Z, Yang J. Mechanisms of graphene growth on metal surfaces: theoretical perspectives. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:2136-2150. [PMID: 24687872 DOI: 10.1002/smll.201303680] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 02/26/2014] [Indexed: 06/03/2023]
Abstract
Graphene is an important material with unique electronic properties. Aiming to obtain high quality samples at a large scale, graphene growth on metal surfaces has been widely studied. An important topic in these studies is the atomic scale growth mechanism, which is the precondition for a rational optimization of growth conditions. Theoretical studies have provided useful insights for understanding graphene growth mechanisms, which are reviewed in this article. On the mostly used Cu substrate, graphene growth is found to be more complicated than a simple adsorption-dehydrogenation-growth model. Growth on Ni surface is precipitation dominated. On surfaces with a large lattice mismatch to graphene, epitaxial geometry determin a robust nonlinear growth behavior. Further progresses in understanding graphene growth mechanisms is expected with intense theoretical studies using advanced simulation techniques, which will make a guided design of growth protocols practical.
Collapse
|
|
11 |
41 |
11
|
Zhang X, Jin L, Dai X, Chen G, Liu G. Two-Dimensional GaN: An Excellent Electrode Material Providing Fast Ion Diffusion and High Storage Capacity for Li-Ion and Na-Ion Batteries. ACS APPLIED MATERIALS & INTERFACES 2018; 10:38978-38984. [PMID: 30354050 DOI: 10.1021/acsami.8b15139] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Identifying applicable anode materials is a significant task for Li- and Na-ion battery (LIB and NIB) technologies. We propose the GaN monolayer (2D GaN) can be a good anode candidate. The GaN monolayer manifests stable Li/Na adsorption and inherently low theoretical voltages. Most excitingly, both high storage capacity and extremely fast Li/Na diffusion can be simultaneously realized in the GaN monolayer. For Li, the storage capacity and diffusion barrier is 938 mA h g-1 and 79 meV, respectively. And, the values for Na are 625 mA h g-1 and 22 meV. Compared with known two-dimensional (2D) anode materials with similar scale of ion diffusion barriers, the GaN monolayer almost possesses the highest Li/Na storage capacity discovered to date. Our work suggests that the 2D GaN is a prospective anode material offering fast ion diffusion and high storage capacity.
Collapse
|
|
7 |
37 |
12
|
Kopač D, Likozar B, Huš M. How Size Matters: Electronic, Cooperative, and Geometric Effect in Perovskite-Supported Copper Catalysts for CO 2 Reduction. ACS Catal 2020; 10:4092-4102. [PMID: 32953235 PMCID: PMC7493227 DOI: 10.1021/acscatal.9b05303] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/05/2020] [Indexed: 11/28/2022]
Abstract
In heterogeneous catalysis, bifunctional catalysts often outperform one-component catalysts. The activity is also strongly influenced by the morphology, size, and distribution of catalytic particles. For CO2 hydrogenation, the size of the active copper area on top of the SrTiO3 perovskite catalyst support can affect the activity, selectivity, and stability. Here, a detailed theoretical study of the effect of bifunctionality on an important chemical CO2 transformation reaction, the reverse water gas shift (RWGS) reaction, is presented. Using density functional theory computation results for the RWGS pathway on three surfaces, namely, Cu(111), SrTiO3, and the Cu/SrTiO3 interface between both solid phases, we construct the energy landscape of the reaction. The adsorbate-adsorbate lateral interactions are taken into account for catalytic surfaces, which show a sufficient intermediate coverage. The mechanism, combining all three surfaces, is used in mesoscale kinetic Monte Carlo simulations to study the turnover and yield for CO production as a function of particle size. It is shown that the reaction proceeds faster at the interface. However, including copper and the support sites in addition to the interface accelerates the conversion even further, showing that the bifunctionality of the catalyst manifests in a more complex interplay between the phases than just the interface effect, such as the hydrogen spillover. We identify three distinct effects, the electronic, cooperative, and geometric effects, and show that the surrounded smaller Cu features on the set of supporting SrTiO3 show a higher CO formation rate, resulting in a decreasing RWGS model trend with the increasing Cu island size. The findings are in parallel with experiments, showing that they explain the previously observed phenomena and confirming the size sensitivity for the catalytic RWGS reaction.
Collapse
|
research-article |
5 |
25 |
13
|
Zhang Y, Lane C, Furness JW, Barbiellini B, Perdew JP, Markiewicz RS, Bansil A, Sun J. Competing stripe and magnetic phases in the cuprates from first principles. Proc Natl Acad Sci U S A 2020; 117:68-72. [PMID: 31843896 PMCID: PMC6955329 DOI: 10.1073/pnas.1910411116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Realistic description of competing phases in complex quantum materials has proven extremely challenging. For example, much of the existing density-functional-theory-based first-principles framework fails in the cuprate superconductors. Various many-body approaches involve generic model Hamiltonians and do not account for the interplay between the spin, charge, and lattice degrees of freedom. Here, by deploying the recently constructed strongly constrained and appropriately normed (SCAN) density functional, we show how the landscape of competing stripe and magnetic phases can be addressed on a first-principles basis both in the parent insulator YBa2Cu3O6 and the near-optimally doped YBa2Cu3O7 as archetype cuprate compounds. In YBa2Cu3O7, we find many stripe phases that are nearly degenerate with the ground state and may give rise to the pseudogap state from which the high-temperature superconducting state emerges. We invoke no free parameters such as the Hubbard U, which has been the basis of much of the existing cuprate literature. Lattice degrees of freedom are found to be crucially important in stabilizing the various phases.
Collapse
|
|
5 |
25 |
14
|
Abstract
The separation of 1-butene from the other isomers is an industrially important but challenging task because these isomers mainly differ only by the position of C═C double bond with many of their physical properties very similar. In this work, we propose using first-principles calculations that Fe-MOF-74 can be a promising candidate for the separation of 1-butene from all other isomers with high selectivity. We demonstrate that the underlying mechanism of this olefin separation is the steric interactions; that is, 1-butene with terminal double bond has the smallest steric interactions with the framework and therefore can approach the metal binding sites more closely for stronger π-complexation. This combined effect (π-complexation modulated by steric interactions) in MOFs with open metal sites can offer a promising design strategy for difficult separation of even longer olefin isomers by properly engineering the lengths and functional groups of the MOF linkers.
Collapse
|
|
11 |
22 |
15
|
Chan YH, Qiu DY, da Jornada FH, Louie SG. Giant exciton-enhanced shift currents and direct current conduction with subbandgap photo excitations produced by many-electron interactions. Proc Natl Acad Sci U S A 2021; 118:e1906938118. [PMID: 34155136 PMCID: PMC8237677 DOI: 10.1073/pnas.1906938118] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Shift current is a direct current generated from nonlinear light-matter interaction in a noncentrosymmetric crystal and is considered a promising candidate for next-generation photovoltaic devices. The mechanism for shift currents in real materials is, however, still not well understood, especially if electron-hole interactions are included. Here, we employ a first-principles interacting Green's-function approach on the Keldysh contour with real-time propagation to study photocurrents generated by nonlinear optical processes under continuous wave illumination in real materials. We demonstrate a strong direct current shift current at subbandgap excitation frequencies in monolayer GeS due to strongly bound excitons, as well as a giant excitonic enhancement in the shift current coefficients at above bandgap photon frequencies. Our results suggest that atomically thin two-dimensional materials may be promising building blocks for next-generation shift current devices.
Collapse
|
research-article |
4 |
18 |
16
|
Zhang Z, Zhou M, Zhang T, Yang M, Yang Q, Yu J, Zhang Y. Few-Layer Borophene Prepared by Mechanical Resonance and Its Application in Terahertz Shielding. ACS APPLIED MATERIALS & INTERFACES 2020; 12:19746-19754. [PMID: 32186178 DOI: 10.1021/acsami.9b19407] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Once two-dimensional boron-based materials were forecasted, their excellent physical and chemical properties have realized attractive application value in the field of materials science. However, borophene could not exist independently and stably in nature. Molecular beam epitaxy is the only way being used currently for the preparation of borophene, which has low yield and harsh experimental installation conditions. Here, we propose the theory that few-layer borophene supported by silver nanoparticles can exist stably and large-scale preparation of few-layer borophene can be performed by mechanical resonance first. We have revealed that the structure of the prepared borophene is α-sheet and its thickness is less than 4 nm. The oxidation rate of borophene from the experiment is about 0.19, which indicates that the few-layer borophene possesses good structure stability. We have also studied the structure stability of borophene on silver nanoparticles by first principles calculation. The calculation proves that few-layer borophene can exist stably supported with silver nanoparticles. Furthermore, the terahertz shielding and stealth performance of the few-layer borophene have been explored. The maximum terahertz shielding effectiveness value of the prepared material could reach up to 50 and 21.5 dB for the reflection loss value in the broadband range of 0.1-2.7 THz. The large-scale preparation of few-layer borophene through the mechanical method makes it possible to study the properties of borophene and achieve low-cost large-scale applications, such as the study of terahertz shielding and stealth performance in the article, which facilitates the lightweight material design for terahertz shielding and stealth.
Collapse
|
|
5 |
14 |
17
|
Agajanian S, Alshahrani M, Bai F, Tao P, Verkhivker GM. Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. J Chem Inf Model 2023; 63:1413-1428. [PMID: 36827465 PMCID: PMC11162550 DOI: 10.1021/acs.jcim.2c01634] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Allosteric mechanisms are commonly employed regulatory tools used by proteins to orchestrate complex biochemical processes and control communications in cells. The quantitative understanding and characterization of allosteric molecular events are among major challenges in modern biology and require integration of innovative computational experimental approaches to obtain atomistic-level knowledge of the allosteric states, interactions, and dynamic conformational landscapes. The growing body of computational and experimental studies empowered by emerging artificial intelligence (AI) technologies has opened up new paradigms for exploring and learning the universe of protein allostery from first principles. In this review we analyze recent developments in high-throughput deep mutational scanning of allosteric protein functions; applications and latest adaptations of Alpha-fold structural prediction methods for studies of protein dynamics and allostery; new frontiers in integrating machine learning and enhanced sampling techniques for characterization of allostery; and recent advances in structural biology approaches for studies of allosteric systems. We also highlight recent computational and experimental studies of the SARS-CoV-2 spike (S) proteins revealing an important and often hidden role of allosteric regulation driving functional conformational changes, binding interactions with the host receptor, and mutational escape mechanisms of S proteins which are critical for viral infection. We conclude with a summary and outlook of future directions suggesting that AI-augmented biophysical and computer simulation approaches are beginning to transform studies of protein allostery toward systematic characterization of allosteric landscapes, hidden allosteric states, and mechanisms which may bring about a new revolution in molecular biology and drug discovery.
Collapse
|
Review |
2 |
13 |
18
|
Lee D, Kanai Y. Biomimetic Carbon Nanotube for Catalytic CO2 Hydrolysis: First-Principles Investigation on the Role of Oxidation State and Metal Substitution in Porphyrin. J Phys Chem Lett 2012; 3:1369-1373. [PMID: 26286784 DOI: 10.1021/jz300419u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hydrolysis of carbon dioxide is an important reaction for CO2 collection. Using accurate first-principles electronic structure calculations, we predict how the catalytic hydrolysis reaction in carbonic anhydrase (CA) can be mimicked in a metal-porphyrin carbon nanotube. The two-step catalytic process can be improved remarkably by controlling the porphyrin oxidation state via the nanotube charge state and by substituting the porphyrin metal atom. The oxidation state and the metal substitution both have profound effects on the reaction energetics for the initial hydration reaction step. For the subsequent product-release reaction step, two different reaction mechanisms could take place. These mechanisms are distinctively sensitive to either the oxidation state change or the metal substitution, but not to both. For the overall catalytic cycle, a significant dependence on the nanotube charge state at low pH and on the metal substitution at high pH is expected.
Collapse
|
|
13 |
12 |
19
|
Kareva I, Luddy KA, O’Farrelly C, Gatenby RA, Brown JS. Predator-Prey in Tumor-Immune Interactions: A Wrong Model or Just an Incomplete One? Front Immunol 2021; 12:668221. [PMID: 34531851 PMCID: PMC8438324 DOI: 10.3389/fimmu.2021.668221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/05/2021] [Indexed: 01/05/2023] Open
Abstract
Tumor-immune interactions are often framed as predator-prey. This imperfect analogy describes how immune cells (the predators) hunt and kill immunogenic tumor cells (the prey). It allows for evaluation of tumor cell populations that change over time during immunoediting and it also considers how the immune system changes in response to these alterations. However, two aspects of predator-prey type models are not typically observed in immuno-oncology. The first concerns the conversion of prey killed into predator biomass. In standard predator-prey models, the predator relies on the prey for nutrients, while in the tumor microenvironment the predator and prey compete for resources (e.g. glucose). The second concerns oscillatory dynamics. Standard predator-prey models can show a perpetual cycling in both prey and predator population sizes, while in oncology we see increases in tumor volume and decreases in infiltrating immune cell populations. Here we discuss the applicability of predator-prey models in the context of cancer immunology and evaluate possible causes for discrepancies. Key processes include "safety in numbers", resource availability, time delays, interference competition, and immunoediting. Finally, we propose a way forward to reconcile differences between model predictions and empirical observations. The immune system is not just predator-prey. Like natural food webs, the immune-tumor community of cell types forms an immune-web of different and identifiable interactions.
Collapse
|
Research Support, N.I.H., Extramural |
4 |
11 |
20
|
Kasamatsu S, Watanabe S, Hwang CS, Han S. Emergence of Negative Capacitance in Multidomain Ferroelectric-Paraelectric Nanocapacitors at Finite Bias. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:335-340. [PMID: 26568333 DOI: 10.1002/adma.201502916] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/01/2015] [Indexed: 06/05/2023]
Abstract
The emergence of negative capacitance in an ultrathin ferroelectric/paraelectric bilayer capacitor under electrical bias is examined using first-principles simulation. An antiferroelectric-like behavior is predicted, and negative capacitance is shown to emerge when the monodomain state becomes stable after bias application. The polydomain-monodomain transition is also shown to be a source of capacitance enhancement.
Collapse
|
|
9 |
10 |
21
|
Sc-Decorated Porous Graphene for High-Capacity Hydrogen Storage: First-Principles Calculations. MATERIALS 2017; 10:ma10080894. [PMID: 28767084 PMCID: PMC5578260 DOI: 10.3390/ma10080894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 12/04/2022]
Abstract
The generalized gradient approximation (GGA) function based on density functional theory is adopted to investigate the optimized geometrical structure, electron structure and hydrogen storage performance of Sc modified porous graphene (PG). It is found that the carbon ring center is the most stable adsorbed position for a single Sc atom on PG, and the maximum number of adsorbed H2 molecules is four with the average adsorption energy of −0.429 eV/H2. By adding a second Sc atom on the other side of the system, the hydrogen storage capacity of the system can be improved effectively. Two Sc atoms located on opposite sides of the PG carbon ring center hole is the most suitable hydrogen storage structure, and the hydrogen storage capacity reach a maximum 9.09 wt % at the average adsorption energy of −0.296 eV/H2. The adsorption of H2 molecules in the PG system is mainly attributed to orbital hybridization among H, Sc, and C atoms, and Coulomb attraction between negatively charged H2 molecules and positively charged Sc atoms.
Collapse
|
|
8 |
10 |
22
|
Zhang Q, Xin T, Lu X, Wang Y. Optoelectronic Properties of X-Doped (X = O, S, Te) Photovoltaic CSe with Puckered Structure. MATERIALS 2018; 11:ma11030431. [PMID: 29547504 PMCID: PMC5873010 DOI: 10.3390/ma11030431] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 11/05/2022]
Abstract
We exploited novel two-dimensional (2D) carbon selenide (CSe) with a structure analogous to phosphorene, and probed its electronics and optoelectronics. Calculating phonon spectra using the density functional perturbation theory (DFPT) method indicated that 2D CSe possesses dynamic stability, which made it possible to tune and equip CSe with outstanding properties by way of X-doping (X = O, S, Te), i.e., X substituting Se atoms. Then systematic investigation on the structural, electronic, and optical properties of pristine and X-doped monolayer CSe was carried out using the density functional theory (DFT) method. It was found that the bonding feature of C-X is intimately associated with the electronegativity and radius of the doping atoms, which leads to diverse electronic and optical properties for doping different group VI elements. All the systems possess direct gaps, except for O-doping. Substituting O for Se atoms in monolayer CSe brings about a transition from a direct Γ-Γ band gap to an indirect Γ-Y band gap. Moreover, the value of the band gap decreases with increased doping concentration and radius of doping atoms. A red shift in absorption spectra occurs toward the visible range of radiation after doping, and the red-shift phenomenon becomes more obvious with increased radius and concentration of doping atoms. The results can be useful for filtering doping atoms according to their radius or electronegativity in order to tailor optical spectra efficiently.
Collapse
|
Journal Article |
7 |
8 |
23
|
Yang J, Fan Q, Cheng X. Prediction for electronic, vibrational and thermoelectric properties of chalcopyrite AgX(X=In,Ga)Te 2: PBE + U approach. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170750. [PMID: 29134079 PMCID: PMC5666262 DOI: 10.1098/rsos.170750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/06/2017] [Indexed: 06/07/2023]
Abstract
The electronic, vibrational and thermoelectric transport characteristics of AgInTe2 and AgGaTe2 with chalcopyrite structure have been investigated. The electronic structures are calculated using the density-functional theory within the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof functional considering the Hubbard-U exchange correlation. The band-gaps of AgInTe2 and AgGaTe2 are much larger than previous standard GGA functional results and agree well with the existing experimental data. The effective mass of the hole and the shape of density of states near the edge of the valence band indicate AgInTe2 and AgGaTe2 are considerable p-type thermoelectric materials. An analysis of lattice dynamics shows the low thermal conductivities of AgInTe2 and AgGaTe2. The thermoelectric transport properties' dependence on carrier concentration for p-type AgInTe2 and AgGaTe2 in a wide range of temperatures has been studied in detail. The results show that p-type AgInTe2 and AgGaTe2 at 800 K can achieve the merit values of 0.91 and 1.38 at about 2.12 × 1020 cm-3 and 1.97 × 1020 cm-3 carrier concentrations, respectively. This indicates p-type AgGaTe2 is a potential thermoelectric material at high temperature.
Collapse
|
research-article |
8 |
7 |
24
|
Abstract
Several theories for the origin of life have gained widespread acceptance, led by primordial soup, chemical evolution, metabolism first, and the RNA world. However, while new and existing theories often address a key step, there is less focus on a comprehensive abiogenic continuum leading to the last universal common ancestor. Herein, I present the "minimotif synthesis" hypothesis unifying select origin of life theories with new and revised steps. The hypothesis is based on first principles, on the concept of selection over long time scales, and on a stepwise progression toward complexity. The major steps are the thermodynamically-driven origination of extant molecular specificity emerging from primordial soup leading to the rise of peptide catalysts, and a cyclic feed-forward catalytic diversification of compound and peptides in the primordial soup. This is followed by degenerate, semi-partially conservative peptide replication to pass on catalytic knowledge to progeny protocells. At some point during this progression, the emergence of RNA and selection could drive the separation of catalytic and genetic functions, allowing peptides and proteins to permeate the catalytic space, and RNA to encode higher fidelity information transfer. Translation may have emerged from RNA template driven organization and successive ligation of activated amino acids as a predecessor to translation.
Collapse
|
Journal Article |
9 |
7 |
25
|
Wang J, Chen Y, Yuan L, Zhang M, Zhang C. Scandium Decoration of Boron Doped Porous Graphene for High-Capacity Hydrogen Storage. Molecules 2019; 24:molecules24132382. [PMID: 31252605 PMCID: PMC6651430 DOI: 10.3390/molecules24132382] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 11/16/2022] Open
Abstract
The hydrogen storage properties of the Scandium (Sc) atom modified Boron (B) doped porous graphene (PG) system were studied based on the density functional theory (DFT). For a single Sc atom, the most stable adsorption position on B-PG is the boron-carbon hexagon center after doping with the B atom. The corresponding adsorption energy of Sc atoms was -4.004 eV. Meanwhile, five H2 molecules could be adsorbed around a Sc atom with the average adsorption energy of -0.515 eV/H2. Analyzing the density of states (DOS) and the charge population of the system, the adsorption of H2 molecules in Sc-B/PG system is mainly attributed to an orbital interaction between H and Sc atoms. For the H2 adsorption, the Coulomb attraction between H2 molecules (negatively charged) and Sc atoms (positively charged) also played a critical role. The largest hydrogen storage capacity structure was two Sc atoms located at two sides of the boron-carbon hexagon center in the Sc-B/PG system. Notably, the theoretical hydrogen storage capacity was 9.13 wt.% with an average adsorption energy of -0.225 eV/H2. B doped PG prevents the Sc atom aggregating and improves the hydrogen storage effectively because it can increase the adsorption energy of the Sc atom and H2 molecule.
Collapse
|
|
6 |
7 |