1
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Donkor ED, Offei-Danso A, Rodriguez A, Sciortino F, Hassanali A. Beyond Local Structures in Critical Supercooled Water through Unsupervised Learning. J Phys Chem Lett 2024; 15:3996-4005. [PMID: 38574274 DOI: 10.1021/acs.jpclett.4c00383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
The presence of a second critical point in water has been a topic of intense investigation for the last few decades. The molecular origins underlying this phenomenon are typically rationalized in terms of the competition between local high-density (HD) and low-density (LD) structures. Their identification often requires designing parameters that are subject to human intervention. Herein, we use unsupervised learning to discover structures in atomistic simulations of water close to the liquid-liquid critical point (LLCP). Encoding the information on the environment using local descriptors, we do not find evidence for two distinct thermodynamic structures. In contrast, when we deploy nonlocal descriptors that probe instead heterogeneities on the nanometer length scale, this leads to the emergence of LD and HD domains rationalizing the microscopic origins of the density fluctuations close to criticality.
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Affiliation(s)
- Edward Danquah Donkor
- The Abdus Salam International Center for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Adu Offei-Danso
- The Abdus Salam International Center for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Alex Rodriguez
- The Abdus Salam International Center for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy
- Dipartimento di Matematica, Informatica e Geoscienze, Università degli studi di Trieste, via Valerio 12/1, 34127 Trieste, Italy
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Ali Hassanali
- The Abdus Salam International Center for Theoretical Physics (ICTP), Strada Costiera 11, 34151 Trieste, Italy
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2
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Liu XY, Yan XY, Liu Y, Qu H, Wang Y, Wang J, Guo QY, Lei H, Li XH, Bian F, Cao XY, Zhang R, Wang Y, Huang M, Lin Z, Meijer EW, Aida T, Kong X, Cheng SZD. Self-assembled soft alloy with Frank-Kasper phases beyond metals. NATURE MATERIALS 2024; 23:570-576. [PMID: 38297141 DOI: 10.1038/s41563-023-01796-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/22/2023] [Indexed: 02/02/2024]
Abstract
Soft building blocks, such as micelles, cells or soap bubbles, tend to adopt near-spherical geometry when densely packed together. As a result, their packing structures do not extend beyond those discovered in metallic glasses, quasicrystals and crystals. Here we report the emergence of two Frank-Kasper phases from the self-assembly of five-fold symmetric molecular pentagons. The μ phase, an important intermediate in superalloys, is indexed in soft matter, whereas the ϕ phase exhibits a structure distinct from known Frank-Kasper phases in metallic systems. We find a broad size and shape distribution of self-assembled mesoatoms formed by molecular pentagons while approaching equilibrium that contribute to the unique packing structures. This work provides insight into the manipulation of soft building blocks that deviate from the typical spherical geometry and opens avenues for the fabrication of 'soft alloy' structures that were previously unattainable in metal alloys.
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Affiliation(s)
- Xian-You Liu
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China
| | - Xiao-Yun Yan
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China.
- Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH, USA.
- Department of Mechanical Engineering, MIT, Cambridge, MA, USA.
| | - Yuchu Liu
- Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH, USA
| | - Hang Qu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Yicong Wang
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China
| | - Jing Wang
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China
| | - Qing-Yun Guo
- Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH, USA
| | - Huanyu Lei
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China
| | - Xing-Han Li
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China
| | - Fenggang Bian
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Yu Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Rui Zhang
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou, China
| | - Yu Wang
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou, China
| | - Mingjun Huang
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou, China
| | - Zhiwei Lin
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou, China
| | - E W Meijer
- Laboratory of Macromolecular and Organic Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Takuzo Aida
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
- Riken Center for Emergent Matter Science, Wako, Japan
| | - Xian Kong
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou, China.
| | - Stephen Z D Cheng
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, China.
- Department of Polymer Science, School of Polymer Science and Polymer Engineering, University of Akron, Akron, OH, USA.
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Zhang X, Adapa S, Feng T, Zeng J, Chung KM, Ho C, Albrecht K, Chen R. Micromechanical origin of heat transfer to granular flow. Phys Rev E 2024; 109:L042902. [PMID: 38755816 DOI: 10.1103/physreve.109.l042902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/18/2024] [Indexed: 05/18/2024]
Abstract
Heat transfer across a granular flow is comprised of two resistances in series : near the wall and within the bulk particle bed, neither of which is well understood due to the lack of experimental probes to separate their respective contribution. Here, we use a frequency modulated photothermal technique to separately quantify the thermal resistances in the near-wall and the bulk bed regions of particles in flowing states. Compared to the stationary state, the flowing leads to a higher near-wall resistance and a lower thermal conductivity of bulk beds. Coupled with discrete element method simulation, we show that the near-wall resistance can be explained by particle diffusion in granular flows.
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Affiliation(s)
- Xintong Zhang
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Sarath Adapa
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Tianshi Feng
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Jian Zeng
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Ka Man Chung
- Program in Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Clifford Ho
- Concentrating Solar Technologies Department, Sandia National Laboratories, 1515 Eubank Boulevard SE, Albuquerque, New Mexico 87123, USA
| | - Kevin Albrecht
- Concentrating Solar Technologies Department, Sandia National Laboratories, 1515 Eubank Boulevard SE, Albuquerque, New Mexico 87123, USA
| | - Renkun Chen
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California 92093, USA
- Program in Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
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4
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Robert Y, Siaraferas T, Fratoni M. Proof of concept for hyper-fidelity depletion of full-scale pebble bed reactors. ANN NUCL ENERGY 2023. [DOI: 10.1016/j.anucene.2022.109648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Farain K, Bonn D. Quantitative Understanding of the Onset of Dense Granular Flows. PHYSICAL REVIEW LETTERS 2023; 130:108201. [PMID: 36962056 DOI: 10.1103/physrevlett.130.108201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/23/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The question of when and how dense granular materials start to flow under stress, despite many industrial and geophysical applications, remains largely unresolved. We develop and test a simple equation for the onset of quasistatic flows of granular materials which is based on the frictional aging of the granular packing. The result is a nonmonotonic stress-strain relation which-akin to classical friction-is independent of the shear rate. This relation suffices to understand the quasistatic deformations of aging granular media, and its solid-to-liquid transition. Our results also elucidate the (flow) history dependence of the mechanical properties, and the sensitivity to the initial preparation of granular media.
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Affiliation(s)
- Kasra Farain
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Science Park 904, 1098XH Amsterdam, Netherlands
| | - Daniel Bonn
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Science Park 904, 1098XH Amsterdam, Netherlands
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6
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Zhang X, Tang L, Yang B, Hu H, Tan S. Study on the effect of the size irregularity gradient of metal foams on macroscopic compressive properties. Heliyon 2022; 8:e12531. [PMID: 36593857 PMCID: PMC9803721 DOI: 10.1016/j.heliyon.2022.e12531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/22/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Size irregularity gradient and cell wall gradient, combined as the density gradient in previous studies, affect the macroscopic mechanical properties of the gradient metal foam. More and more complex mesostructures are designed and applied in metal foams, and the density gradient becomes insufficient to describe the difference in mesostructures. To explore the effect of mesostructures carefully, this study focuses on the effect of the size irregularity gradient on the macroscopic compressive properties of metal foams. A series of metal foam models were developed using the 3D Voronoi technique. These models have the same average relative densities, the same average diameters and different size irregularity gradients. Simulation results indicated that the macroscopic mechanical properties of cell wall gradient metal foams are significantly different from those of size irregularity gradient metal foams, though these models have the same relative density gradient. To explore the effect of size irregularity gradient, a theoretical model was developed to characterize the compression process from the first cell-collapse to full condensation. Theoretical results showed a linear relationship between the nominal stress and the current relative density. These findings can provide efficient guidance for the design and applications of gradient metal foams.
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Affiliation(s)
- Xiaoyang Zhang
- School of Mathematics and Physics, University of South China, 421001, Hengyang, Hunan, China
| | - Liqun Tang
- Department of Engineering Mechanics, School of Civil Engineering and Transportation; State Key Laboratory of Subtropical Building Science, South China University of Technology, 510641, Guangzhou, Guangdong, China,Corresponding author.
| | - Bao Yang
- Department of Engineering Mechanics, School of Civil Engineering and Transportation; State Key Laboratory of Subtropical Building Science, South China University of Technology, 510641, Guangzhou, Guangdong, China
| | - Heping Hu
- School of Mathematics and Physics, University of South China, 421001, Hengyang, Hunan, China
| | - Shifeng Tan
- School of Mathematics and Physics, University of South China, 421001, Hengyang, Hunan, China
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7
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Geometry-controlled phase transition in vibrated granular media. Sci Rep 2022; 12:14989. [PMID: 36056168 PMCID: PMC9440227 DOI: 10.1038/s41598-022-18965-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/23/2022] [Indexed: 11/08/2022] Open
Abstract
We report experiments on the dynamics of vibrated particles constrained in a two-dimensional vertical container, motivated by the following question: how to get the most out of a given external vibration to maximize internal disorder (e.g. to blend particles) and agitation (e.g. to absorb vibrations)? Granular media are analogs to classical thermodynamic systems, where the injection of energy can be achieved by shaking them: fluidization arises by tuning either the amplitude or the frequency of the oscillations. Alternatively, we explore what happens when another feature, the container geometry, is modified while keeping constant the energy injection. Our method consists in modifying the container base into a V-shape to break the symmetries of the inner particulate arrangement. The lattice contains a compact hexagonal solid-like crystalline phase coexisting with a loose amorphous fluid-like phase, at any thermal agitation. We show that both the solid-to-fluid volume fraction and the granular temperature depend not only on the external vibration but also on the number of topological defects triggered by the asymmetry of the container. The former relies on the statistics of the energy fluctuations and the latter is consistent with a two-dimensional melting transition described by the KTHNY theory.
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8
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Wu M, Gui N, Yang X, Tu J, Jiang S. Numerical investigation of flow characteristics and packing structure of binary-sized pebble flow in a circulating pebble bed. PROGRESS IN NUCLEAR ENERGY 2022. [DOI: 10.1016/j.pnucene.2022.104312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Chen Z, Yang L, Hu X, Wirth BD, Ye M. MD simulation of the He bubble effect on H retention in BCC iron. FUSION ENGINEERING AND DESIGN 2022. [DOI: 10.1016/j.fusengdes.2022.113184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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10
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Solute Diffusivity and Local Free Volume in Cross-Linked Polymer Network: Implication of Optimizing the Conductivity of Polymer Electrolyte. Polymers (Basel) 2022; 14:polym14102061. [PMID: 35631943 PMCID: PMC9145971 DOI: 10.3390/polym14102061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 02/02/2023] Open
Abstract
The diffusion of small molecules or ions within polymeric materials is critical for their applications, such as polymer electrolytes. Cross-linking has been one of the common strategies to modulate solute diffusivity and a polymer’s mechanical properties. However, various studies have shown different effects of cross-linking on altering the solute transports. Here, we utilized coarse-grained molecular dynamics simulation to systematically analyze the effects of cross-linking and polymer rigidity of solute diffusive behaviors. Above the glass transition temperature Tg, the solute diffusion followed the Vogel–Tammann–Fulcher (VTF) equation, D = D0 e−Ea/R(T−T0). Other than the conventional compensation relation between the activation energy Ea and the pre-exponential factor D0, we also identified a correlation between Ea and Vogel temperature T0. We further characterized an empirical relation between T0 and cross-linking density. Integrating the newly identified correlations among the VTF parameters, we formulated a relation between solute diffusion and the cross-linking density. The combined results proposed the criteria for the optimal solute diffusivity in cross-linked polymers, providing generic guidance for novel polymer electrolyte design.
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11
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Park JS, Yun J, Chun B, Jung HW. Mild stratification in drying films of colloidal mixtures. SOFT MATTER 2022; 18:3487-3497. [PMID: 35438125 DOI: 10.1039/d2sm00205a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Size stratification of bidisperse colloidal mixtures during vertical drying was investigated using the implicit solvent Langevin dynamics (LD) simulation and the explicit solvent lattice Boltzmann (LB) method. Simulations were performed for the Péclet number (Pe) over a wide range of 1-1000. In the case of a low size ratio of 2, mild stratification was observed in both simulation methods, in contrast to distinct stratification with thick "small-on-top" or "large-on-top" layers. The LD simulations exhibited a "small-on-top" stratification or mixed state. In contrast, the LB simulations exhibited a "large-on-top" or mixed state, according to the variation in Pe. The results demonstrated that the explicit solvent reduced the collective diffusion under moderate Pe conditions. This suppressed the steep concentration gradient of small particles in the packed region of particles near the air-solvent interface. Thus, distinguishable stratification patterns were obtained for the implicit and explicit solvent models.
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Affiliation(s)
- Jin Seok Park
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Jinseong Yun
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Byoungjin Chun
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
| | - Hyun Wook Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
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12
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Molecular Dynamics Simulations of Xe Behaviors at the Grain Boundary in UO2. METALS 2022. [DOI: 10.3390/met12050763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, we investigated the behavior of xenon (Xe) bubbles in uranium dioxide (UO2) grain boundaries using molecular dynamics simulations and compared it to that in the UO2 bulk. The results show that the formation energy of Xe clusters at the Σ5 grain boundaries (GBs) is much lower than in the bulk. The diffusion activation energy of a single interstitial Xe atom at the GBs was approximately 1 eV lower than that in the bulk. Furthermore, the nucleation and growth of Xe bubbles in the Σ5 GBs at 1000 and 2000 K were simulated. The volume and pressure of bubbles with different numbers of Xe atoms were simulated. The bubble pressure dropped with increasing temperature at low Xe concentrations, whereas the volume increased. The radial distribution function was computed to explore the configuration evolution of Xe bubbles. The bubble structures in the GB and bulk material at the same temperature were also compared. Xe atoms were more regular in the bulk, whereas multiple Xe atoms formed a planar structure at the GBs.
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13
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14
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Li B, Gui N, Wu H, Yang X, Tu J, Jiang S. Effects of the 3-D wall structures on the flow and mixing characteristics of pebbles in pebble beds in HTR-10. ANN NUCL ENERGY 2021. [DOI: 10.1016/j.anucene.2021.108607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Bester P, Du Toit C, Potgieter M. A numerical analysis of the porosity of the HTR-10 packed pebble bed. NUCLEAR ENGINEERING AND DESIGN 2021. [DOI: 10.1016/j.nucengdes.2021.111438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Chrono::GPU: An Open-Source Simulation Package for Granular Dynamics Using the Discrete Element Method. Processes (Basel) 2021. [DOI: 10.3390/pr9101813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We report on an open-source, publicly available C++ software module called Chrono::GPU, which uses the Discrete Element Method (DEM) to simulate large granular systems on Graphics Processing Unit (GPU) cards. The solver supports the integration of granular material with geometries defined by triangle meshes, as well as co-simulation with the multi-physics simulation engine Chrono. Chrono::GPU adopts a smooth contact formulation and implements various common contact force models, such as the Hertzian model for normal force and the Mindlin friction force model, which takes into account the history of tangential displacement, rolling frictional torques, and cohesion. We report on the code structure and highlight its use of mixed data types for reducing the memory footprint and increasing simulation speed. We discuss several validation tests (wave propagation, rotating drum, direct shear test, crater test) that compare the simulation results against experimental data or results reported in the literature. In another benchmark test, we demonstrate linear scaling with a problem size up to the GPU memory capacity; specifically, for systems with 130 million DEM elements. The simulation infrastructure is demonstrated in conjunction with simulations of the NASA Curiosity rover, which is currently active on Mars.
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17
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Feng Y, Gong B, Cheng H, Wang L, Wang X. Effects of fixed wall and pebble size ratio on packing properties and contact force distribution in binary-sized pebble mixed beds at the maximum packing efficiency state. POWDER TECHNOL 2021. [DOI: 10.1016/j.powtec.2021.05.099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Klatt MA, Ziff RM, Torquato S. Critical pore radius and transport properties of disordered hard- and overlapping-sphere models. Phys Rev E 2021; 104:014127. [PMID: 34412300 DOI: 10.1103/physreve.104.014127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/29/2021] [Indexed: 02/01/2023]
Abstract
Transport properties of porous media are intimately linked to their pore-space microstructures. We quantify geometrical and topological descriptors of the pore space of certain disordered and ordered distributions of spheres, including pore-size functions and the critical pore radius δ_{c}. We focus on models of porous media derived from maximally random jammed sphere packings, overlapping spheres, equilibrium hard spheres, quantizer sphere packings, and crystalline sphere packings. For precise estimates of the percolation thresholds, we use a strict relation of the void percolation around sphere configurations to weighted bond percolation on the corresponding Voronoi networks. We use the Newman-Ziff algorithm to determine the percolation threshold using universal properties of the cluster size distribution. The critical pore radius δ_{c} is often used as the key characteristic length scale that determines the fluid permeability k. A recent study [Torquato, Adv. Wat. Resour. 140, 103565 (2020)10.1016/j.advwatres.2020.103565] suggested for porous media with a well-connected pore space an alternative estimate of k based on the second moment of the pore size 〈δ^{2}〉, which is easier to determine than δ_{c}. Here, we compare δ_{c} to the second moment of the pore size 〈δ^{2}〉, and indeed confirm that, for all porosities and all models considered, δ_{c}^{2} is to a good approximation proportional to 〈δ^{2}〉. However, unlike 〈δ^{2}〉, the permeability estimate based on δ_{c}^{2} does not predict the correct ranking of k for our models. Thus, we confirm 〈δ^{2}〉 to be a promising candidate for convenient and reliable estimates of the fluid permeability for porous media with a well-connected pore space. Moreover, we compare the fluid permeability of our models with varying degrees of order, as measured by the τ order metric. We find that (effectively) hyperuniform models tend to have lower values of k than their nonhyperuniform counterparts. Our findings could facilitate the design of porous media with desirable transport properties via targeted pore statistics.
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Affiliation(s)
- Michael A Klatt
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA.,Institut für Theoretische Physik, FAU Erlangen-Nürnberg, Staudtstr. 7, 91058 Erlangen, Germany
| | - Robert M Ziff
- Center for the Study of Complex Systems and Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Salvatore Torquato
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA.,Department of Chemistry, Princeton Institute for the Science and Technology of Materials, and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
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19
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Twisting of a Pristine α-Fe Nanowire: From Wild Dislocation Avalanches to Mild Local Amorphization. NANOMATERIALS 2021; 11:nano11061602. [PMID: 34207172 PMCID: PMC8234800 DOI: 10.3390/nano11061602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022]
Abstract
The torsion of pristine α-Fe nanowires was studied by molecular dynamics simulations. Torsion-induced plastic deformation in pristine nanowires is divided into two regimes. Under weak torsion, plastic deformation leads to dislocation nucleation and propagation. Twisting-induced dislocations are mainly 12<111> screw dislocations in a <112>-oriented nanowire. The nucleation and propagation of these dislocations were found to form avalanches which generate the emission of energy jerks. Their probability distribution function (PDF) showed power laws with mixing between different energy exponents. The mixing stemmed from simultaneous axial and radial dislocation movements. The power-law distribution indicated strongly correlated 'wild' dislocation dynamics. At the end of this regime, the dislocation pattern was frozen, and further twisting of the nanowire did not change the dislocation pattern. Instead, it induced local amorphization at the grip points at the ends of the sample. This "melting" generated highly dampened, mild avalanches. We compared the deformation mechanisms of twinned and pristine α-Fe nanowires under torsion.
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20
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Effects of 3D contraction on pebble flow uniformity and stagnation in pebble beds. NUCLEAR ENGINEERING AND TECHNOLOGY 2021. [DOI: 10.1016/j.net.2020.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Brehm M, Thomas M. Optimized Atomic Partial Charges and Radii Defined by Radical Voronoi Tessellation of Bulk Phase Simulations. Molecules 2021; 26:1875. [PMID: 33810337 PMCID: PMC8036805 DOI: 10.3390/molecules26071875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/05/2022] Open
Abstract
We present a novel method for the computation of well-defined optimized atomic partial charges and radii from the total electron density. Our method is based on a two-step radical Voronoi tessellation of the (possibly periodic) system and subsequent integration of the total electron density within each Voronoi cell. First, the total electron density is partitioned into the contributions of each molecule, and subsequently the electron density within each molecule is assigned to the individual atoms using a second set of atomic radii for the radical Voronoi tessellation. The radii are optimized on-the-fly to minimize the fluctuation (variance) of molecular and atomic charges. Therefore, our method is completely free of empirical parameters. As a by-product, two sets of optimized atomic radii are produced in each run, which take into account many specific properties of the system investigated. The application of an on-the-fly interpolation scheme reduces discretization noise in the Voronoi integration. The approach is particularly well suited for the calculation of partial charges in periodic bulk phase systems. We apply the method to five exemplary liquid phase simulations and show how the optimized charges can help to understand the interactions in the systems. Well-known effects such as reduced ion charges below unity in ionic liquid systems are correctly predicted without any tuning, empiricism, or rescaling. We show that the basis set dependence of our method is very small. Only the total electron density is evaluated, and thus, the approach can be combined with any electronic structure method that provides volumetric total electron densities-it is not limited to Hartree-Fock or density functional theory (DFT). We have implemented the method into our open-source software tool TRAVIS.
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Affiliation(s)
- Martin Brehm
- Institut für Chemie, Martin-Luther-Universität Halle–Wittenberg, von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany;
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Rahman M, Carter BMGD, Saw S, Douglass IM, Costigliola L, Ingebrigtsen TS, Schrøder TB, Pedersen UR, Dyre JC. Isomorph Invariance of Higher-Order Structural Measures in Four Lennard-Jones Systems. Molecules 2021; 26:molecules26061746. [PMID: 33804670 PMCID: PMC8003765 DOI: 10.3390/molecules26061746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
In the condensed liquid phase, both single- and multicomponent Lennard-Jones (LJ) systems obey the "hidden-scale-invariance" symmetry to a good approximation. Defining an isomorph as a line of constant excess entropy in the thermodynamic phase diagram, the consequent approximate isomorph invariance of structure and dynamics in appropriate units is well documented. However, although all measures of the structure are predicted to be isomorph invariant, with few exceptions only the radial distribution function (RDF) has been investigated. This paper studies the variation along isomorphs of the nearest-neighbor geometry quantified by the occurrence of Voronoi structures, Frank-Kasper bonds, icosahedral local order, and bond-orientational order. Data are presented for the standard LJ system and for three binary LJ mixtures (Kob-Andersen, Wahnström, NiY2). We find that, while the nearest-neighbor geometry generally varies significantly throughout the phase diagram, good invariance is observed along the isomorphs. We conclude that higher-order structural correlations are no less isomorph invariant than is the RDF.
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Affiliation(s)
- Mahajabin Rahman
- Department of Physics, Emory University, Atlanta, GA 30322, USA;
| | | | - Shibu Saw
- “Glass and Time”, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark; (S.S.); (I.M.D.); (L.C.); (T.S.I.); (T.B.S.); (U.R.P.)
| | - Ian M. Douglass
- “Glass and Time”, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark; (S.S.); (I.M.D.); (L.C.); (T.S.I.); (T.B.S.); (U.R.P.)
| | - Lorenzo Costigliola
- “Glass and Time”, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark; (S.S.); (I.M.D.); (L.C.); (T.S.I.); (T.B.S.); (U.R.P.)
| | - Trond S. Ingebrigtsen
- “Glass and Time”, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark; (S.S.); (I.M.D.); (L.C.); (T.S.I.); (T.B.S.); (U.R.P.)
| | - Thomas B. Schrøder
- “Glass and Time”, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark; (S.S.); (I.M.D.); (L.C.); (T.S.I.); (T.B.S.); (U.R.P.)
| | - Ulf R. Pedersen
- “Glass and Time”, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark; (S.S.); (I.M.D.); (L.C.); (T.S.I.); (T.B.S.); (U.R.P.)
| | - Jeppe C. Dyre
- “Glass and Time”, IMFUFA, Department of Science and Environment, Roskilde University, P.O. Box 260, DK-4000 Roskilde, Denmark; (S.S.); (I.M.D.); (L.C.); (T.S.I.); (T.B.S.); (U.R.P.)
- Correspondence:
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23
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Experimental study on the discharge flow rate of binary mixture in a two-dimensional silo. ADV POWDER TECHNOL 2021. [DOI: 10.1016/j.apt.2021.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Analysis of particle shape effect on the discharging of non-spherical particles in HTR-10 reactor core. NUCLEAR ENGINEERING AND DESIGN 2021. [DOI: 10.1016/j.nucengdes.2020.110934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Scagliarini A, Pagonabarraga I. Unravelling the role of phoretic and hydrodynamic interactions in active colloidal suspensions. SOFT MATTER 2020; 16:8893-8903. [PMID: 32895692 DOI: 10.1039/c8sm01831f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Active fluids comprise a variety of systems composed of elements immersed in a fluid environment which can convert some form of energy into directed motion; as such they are intrinsically out-of-equilibrium in the absence of any external force. A fundamental problem in the physics of active matter concerns the understanding of how the characteristics of autonomous propulsion and agent-agent interactions determine the collective dynamics of the system. We study numerically the suspensions of self-propelled diffusiophoretic colloids, in (quasi)-2d configurations, accounting for both dynamically resolved solute-mediated phoretic interactions and solvent-mediated hydrodynamic interactions. Our results show that the system displays different scenarios at changing the colloid-solute affinity and it develops a cluster phase in the chemoattractive case. We study the statistics of cluster sizes and cluster morphologies for different magnitudes of colloidal activity. Finally, we provide evidences that hydrodynamics plays a relevant role in the aggregation kinetics and cluster morphology, significantly hindering cluster growth.
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Affiliation(s)
- Andrea Scagliarini
- IAC-CNR, Isituto per le Applicazioni del Calcolo "Mauro Picone", Via dei Taurini 19, 00185 Rome, Italy.
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26
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Effects of restitution coefficient on pebble motion in a thin pebble bed – Lagrangian analysis. ANN NUCL ENERGY 2020. [DOI: 10.1016/j.anucene.2020.107549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Lee S, Shin SJ, Baek H, Choi Y, Hyun K, Seo M, Kim K, Koh DY, Kim H, Choi M. Dynamic metal-polymer interaction for the design of chemoselective and long-lived hydrogenation catalysts. SCIENCE ADVANCES 2020; 6:eabb7369. [PMID: 32923599 PMCID: PMC7455483 DOI: 10.1126/sciadv.abb7369] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/27/2020] [Indexed: 06/02/2023]
Abstract
Metal catalysts are generally supported on hard inorganic materials because of their high thermochemical stabilities. Here, we support Pd catalysts on a thermochemically stable but "soft" engineering plastic, polyphenylene sulfide (PPS), for acetylene partial hydrogenation. Near the glass transition temperature (~353 K), the mobile PPS chains cover the entire surface of Pd particles via strong metal-polymer interactions. The Pd-PPS interface enables H2 activation only in the presence of acetylene that has a strong binding affinity to Pd and thus can disturb the Pd-PPS interface. Once acetylene is hydrogenated to weakly binding ethylene, re-adsorption of PPS on the Pd surface repels ethylene before it is further hydrogenated to ethane. The Pd-PPS interaction enables selective partial hydrogenation of acetylene to ethylene even in an ethylene-rich stream and suppresses catalyst deactivation due to coke formation. The results manifest the unique possibility of harnessing dynamic metal-polymer interaction for designing chemoselective and long-lived catalysts.
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Affiliation(s)
- Songhyun Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seung-Jae Shin
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hoyong Baek
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Yeonwoo Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kyunglim Hyun
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Myungeun Seo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kyunam Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Dong-Yeun Koh
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyungjun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Minkee Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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28
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Affiliation(s)
- Sara Capponi
- Department of Industrial and Applied Genomics, IBM AI and Cognitive Software Organization, IBM Almaden Research Center, San Jose, California 95120-6099, United States
- NSF Center for Cellular Construction, University of California, San Francisco, San Francisco, California 94115, United States
| | - Fernando Alvarez
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU) - Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
- Departamento de Física de Materiales, UPV/EHU, Apartado 1072, 20080 San Sebastián, Spain
| | - Dušan Račko
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 3, 841 45 Bratislava, Slovak Republic
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Brehm M, Thomas M, Gehrke S, Kirchner B. TRAVIS—A free analyzer for trajectories from molecular simulation. J Chem Phys 2020; 152:164105. [DOI: 10.1063/5.0005078] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- M. Brehm
- Institut für Chemie, Martin-Luther-Universität Halle–Wittenberg, von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany
| | - M. Thomas
- Institut für Chemie, Martin-Luther-Universität Halle–Wittenberg, von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany
| | - S. Gehrke
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4+6, D-53115 Bonn, Germany
| | - B. Kirchner
- Mulliken Center for Theoretical Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4+6, D-53115 Bonn, Germany
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30
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Li T, Zhang H, Kuang S, Yan H, Diao X, Huang Z, Bo H, Dong Y. Experimental and numerical study of coarse particle conveying in the small absorber sphere system: Overview and some recent CFD-DEM simulations. NUCLEAR ENGINEERING AND DESIGN 2020. [DOI: 10.1016/j.nucengdes.2019.110420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Dave A, Sun K, Hu L. Numerical assessment of packed-bed heat transfer correlations for molten salt. ANN NUCL ENERGY 2020. [DOI: 10.1016/j.anucene.2019.107002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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32
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Effects of density difference and loading ratio on pebble flow in a three-dimensional two-region-designed pebble bed. ANN NUCL ENERGY 2019. [DOI: 10.1016/j.anucene.2019.07.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Hagita K. Particle-mesh two-dimensional pattern reverse Monte Carlo analysis on filled-gels during uniaxial expansion. SOFT MATTER 2019; 15:7237-7249. [PMID: 31478543 DOI: 10.1039/c9sm01060b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A particle-mesh-based two-dimensional pattern reverse Monte Carlo (RMC) analysis method (PM-2DpRMC) is proposed for analyzing two-dimensional small-angle-scattering (2D-SAS) patterns. The results of analyzing such patterns in expanded gel networks filled with spherical nano-particles during uniaxial elongation are provided. Previously, characteristic 2D-SAS patterns, such as the two-point bar plate and figure-8 patterns, were observed to possess high stretching ratios in a coarse-grained molecular dynamics (CGMD) simulation, and the patterns were found to depend on the properties of the networks, such as whether they were topologically percolated or not. To establish real-space visualizations of the changes in the particle-configurations corresponding to the 2D-SAS patterns, the on-the-fly PM-2DpRMC method was employed to model the morphology changes of the filler particles during stretching in a series of 2D-SAS patterns. The use of quasi-dynamics to express deformation was validated by evaluating the accuracy of the elongation speed and the number of RMC trials predicted from the behavior of the converged χ2. The results confirm that the obtained sequences of 3D configurations were similar to the original configurations obtained in the CGMD simulations. Further, a demonstrative test using actual experimental data was conducted to verify the completeness of the confirmation.
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Affiliation(s)
- Katsumi Hagita
- Department of Applied Physics, National Defense Academy, 1-10-20 Hashirimizu, Yokosuka 239-8686, Japan.
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34
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Wu M, Gui N, Wu H, Yang X, Tu J, Jiang S. Numerical study of mixing pebble flow with different density in circulating packed bed. ANN NUCL ENERGY 2019. [DOI: 10.1016/j.anucene.2019.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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35
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Tang Y, Zhang L, Guo Q, Xia B, Yin Z, Cao J, Tong J, Rycroft CH. Analysis of the pebble burnup profile in a pebble-bed nuclear reactor. NUCLEAR ENGINEERING AND DESIGN 2019. [DOI: 10.1016/j.nucengdes.2019.01.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Bililign ES, Kollmer JE, Daniels KE. Protocol Dependence and State Variables in the Force-Moment Ensemble. PHYSICAL REVIEW LETTERS 2019; 122:038001. [PMID: 30735414 DOI: 10.1103/physrevlett.122.038001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Stress-based ensembles incorporating temperaturelike variables have been proposed as a route to an equation of state for granular materials. To test the efficacy of this approach, we perform experiments on a two-dimensional photoelastic granular system under three loading conditions: uniaxial compression, biaxial compression, and simple shear. From the interparticle forces, we find that the distributions of the normal component of the coarse-grained force-moment tensor are exponential tailed, while the deviatoric component is Gaussian distributed. This implies that the correct stress-based statistical mechanics conserves both the force-moment tensor and the Maxwell-Cremona force-tiling area. As such, two variables of state arise: the tensorial angoricity (α[over ^]) and a new temperaturelike quantity associated with the force-tile area which we name keramicity (κ). Each quantity is observed to be inversely proportional to the global confining pressure; however, only κ exhibits the protocol independence expected of a state variable, while α[over ^] behaves as a variable of process.
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Affiliation(s)
- Ephraim S Bililign
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jonathan E Kollmer
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Karen E Daniels
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
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Abstract
The formation mechanism of < 100 > interstitial dislocation loops in ferritic steels stemming from irradiation remains elusive, as their formations are either too short for experiments, or too long for molecular dynamics simulations. Here, we report on the formation of both interstitial and vacancy dislocation loops in high energy displacement cascades using large-scale molecular dynamics simulations with up to 220 million atoms. Riding the supersonic shockwave generated in the cascade, self-interstitial atoms are punched out to form < 100 > dislocation loops in only a few picoseconds during one single cascade event, which is several orders of magnitude faster than any existing mechanisms. The energy analysis suggests that the formation of the interstitial loops depends on kinetic energy redistribution, where higher incidence energy or larger atom mass could improve the probability of the direct nucleation of interstitial dislocation loops. Irradiating iron introduces defects such as interstitial dislocation loops, whose exact formation mechanism remains unclear. Here, the authors use large scale molecular dynamics simulations to reveal a punch out mechanism that can directly create < 100 > interstitial dislocation loops.
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38
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Brehm M, Sebastiani D. Simulating structure and dynamics in small droplets of 1-ethyl-3-methylimidazolium acetate. J Chem Phys 2018; 148:193802. [PMID: 30307180 DOI: 10.1063/1.5010342] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To investigate the structure and dynamics of small ionic liquid droplets in gas phase, we performed a DFT-based ab initio molecular dynamics study of several 1-ethyl-3-methylimidazolium acetate clusters in vacuum as well as a bulk phase simulation. We introduce an unbiased criterion for average droplet diameter and density. By extrapolation of the droplet densities, we predict the experimental bulk phase density with a deviation of only a few percent. The hydrogen bond geometry between cations and anions is very similar in droplets and bulk, but the hydrogen bond dynamics is significantly slower in the droplets, becoming slower with increasing system size, with hydrogen bond lifetimes up to 2000 ps. From a normal mode analysis of the trajectories, we identify the modes of the ring proton C-H stretching, which are strongly affected by hydrogen bonding. From analyzing these, we find that the hydrogen bond becomes weaker with increasing system size. The cations possess an increased concentration inside the clusters, whereas the anions show an excess concentration on the outside. Almost all anions point towards the droplet center with their carboxylic groups. Ring stacking is found to be a very important structural motif in the droplets (as in the bulk), but side chain interactions are only of minor importance. By using Voronoi tessellation, we define the exposed droplet surface and find that it consists mainly of hydrogen atoms from the cation's and anion's methyl and ethyl groups. Polar atoms are rarely found on the surface, such that the droplets appear completely hydrophobic on the outside.
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Affiliation(s)
- Martin Brehm
- Institut für Chemie-Theoretische Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Daniel Sebastiani
- Institut für Chemie-Theoretische Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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39
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Racko D, Benedetti F, Goundaroulis D, Stasiak A. Chromatin Loop Extrusion and Chromatin Unknotting. Polymers (Basel) 2018; 10:E1126. [PMID: 30961051 PMCID: PMC6403842 DOI: 10.3390/polym10101126] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 12/31/2022] Open
Abstract
It has been a puzzle how decondensed interphase chromosomes remain essentially unknotted. The natural expectation is that in the presence of type II DNA topoisomerases that permit passages of double-stranded DNA regions through each other, all chromosomes should reach the state of topological equilibrium. The topological equilibrium in highly crowded interphase chromosomes forming chromosome territories would result in formation of highly knotted chromatin fibres. However, Chromosome Conformation Capture (3C) methods revealed that the decay of contact probabilities with the genomic distance in interphase chromosomes is practically the same as in the crumpled globule state that is formed when long polymers condense without formation of any knots. To remove knots from highly crowded chromatin, one would need an active process that should not only provide the energy to move the system from the state of topological equilibrium but also guide topoisomerase-mediated passages in such a way that knots would be efficiently unknotted instead of making the knots even more complex. We perform coarse-grained molecular dynamics simulations of the process of chromatin loop extrusion involving knotted and catenated chromatin fibres to check whether chromatin loop extrusion may be involved in active unknotting of chromatin fibres. Our simulations show that the process of chromatin loop extrusion is ideally suited to actively unknot, decatenate and demix chromatin fibres in interphase chromosomes.
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Affiliation(s)
- Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
- Polymer Institute of the Slovak Academy of Sciences, 842 36 Bratislava, Slovakia.
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Dimos Goundaroulis
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
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Huang P, Shen L, Gan Y, Nguyen GD, El-Zein A, Maggi F. Coarse-grained modeling of multiphase interactions at microscale. J Chem Phys 2018; 149:124505. [PMID: 30278659 DOI: 10.1063/1.5038903] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The objective of this study is to develop and test a coarse-grained molecular dynamics framework to model microscale multiphase systems with different inter-particle interactions and recover emerging thermodynamic and mechanical properties at the microscale. A water-vapor model and a fused silica model are developed to demonstrate the capability of our framework. The former can reproduce the water density and surface tension over a wide range of temperatures; the latter can reproduce experimental density, tensile strength, and Young's modulus of fused silica. Therefore, the deformable solid model is implemented in the proposed framework. Validations of spatial scaling methods for solid, liquid, and multiphase systems suggest that the proposed framework can be calibrated at an arbitrary microscale and used at a different length scale without recalibration. Different values of wettability for a solid-liquid-vapor system that is characterized by the contact angle can be achieved by changing the solid-liquid inter-particle potential. Thanks to these features, the proposed coarse-grained molecular dynamics framework can potentially find applications in modeling systems in which multiple phases coexist and have substantial interactions.
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Affiliation(s)
- Pengyu Huang
- School of Civil Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Luming Shen
- School of Civil Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yixiang Gan
- School of Civil Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Giang D Nguyen
- School of Civil, Environmental and Mining Engineering, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Abbas El-Zein
- School of Civil Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Federico Maggi
- School of Civil Engineering, The University of Sydney, Sydney, NSW 2006, Australia
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41
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Liang X, Guo C, Liu S, Dang Z, Wei Y, Yi X, Abel S. Cosolubilization of phenanthrene and pyrene in surfactant micelles: Experimental and atomistic simulations studies. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.04.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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42
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Configuration correlation governs slow dynamics of supercooled metallic liquids. Proc Natl Acad Sci U S A 2018; 115:6375-6380. [PMID: 29866833 DOI: 10.1073/pnas.1802300115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The origin of dramatic slowing down of dynamics in metallic glass-forming liquids toward their glass transition temperatures is a fundamental but unresolved issue. Through extensive molecular dynamics simulations, here we show that, contrary to the previous beliefs, it is not local geometrical orderings extracted from instantaneous configurations but the intrinsic correlation between configurations that captures the structural origin governing slow dynamics. More significantly, it is demonstrated by scaling analyses that it is the correlation length extracted from configuration correlation rather than dynamic correlation lengths that is the key to determine the drastic slowdown of supercooled metallic liquids. The key role of the configuration correlation established here sheds important light on the structural origin of the mysterious glass transition and provides an essential piece of the puzzle for the development of a universal theoretical understanding of glass transition in glasses.
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Study of Pressure Drop in Fixed Bed Reactor Using a Computational Fluid Dynamics (CFD) Code. CHEMENGINEERING 2018. [DOI: 10.3390/chemengineering2020014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pressure drops of water and critical steam flowing in the fixed bed of mono-sized spheres are studied using SolidWorks 2017 Flow Simulation CFD code. The effects of the type of bed formation, flow velocity, density, and pebble size are evaluated. A new equation is concluded from the data, which is able to estimate pressure drop of a packed bed for high particle Reynolds number, from 15,000 to 1,000,000.
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Qin C, Tang J, Qiu X, Xi Z, Zhao L. Improving particle flow in liquid-solid countercurrent extraction tower by insert structure optimization: A combined study on experiments and DEM simulations. POWDER TECHNOL 2018. [DOI: 10.1016/j.powtec.2018.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hagita K, Tominaga T, Sone T. Large-scale reverse Monte Carlo analysis for the morphologies of silica nanoparticles in end-modified rubbers based on ultra-small-angle X-ray scattering data. POLYMER 2018. [DOI: 10.1016/j.polymer.2017.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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47
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Tang YS, Zhang LG, Guo QJ, Cao JZ, Tong JJ. Numerical solutions for the kinematic model of pebble flow velocity profiles and its applications in pebble-bed nuclear reactor. J NUCL SCI TECHNOL 2017. [DOI: 10.1080/00223131.2017.1331763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yu-shi Tang
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing, P. R. China
| | - Li-guo Zhang
- Institute of Nuclear and New Energy Technology, Collaborative Innovation Center of Advanced Nuclear Energy Technology, Key Laboratory of Advanced Reactor Engineering and Safety of Ministry of Education, Tsinghua University, Beijing, P. R. China
| | - Qiu-ju Guo
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing, P. R. China
| | - Jian-zhu Cao
- Institute of Nuclear and New Energy Technology, Collaborative Innovation Center of Advanced Nuclear Energy Technology, Key Laboratory of Advanced Reactor Engineering and Safety of Ministry of Education, Tsinghua University, Beijing, P. R. China
| | - Jie-juan Tong
- Institute of Nuclear and New Energy Technology, Collaborative Innovation Center of Advanced Nuclear Energy Technology, Key Laboratory of Advanced Reactor Engineering and Safety of Ministry of Education, Tsinghua University, Beijing, P. R. China
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Auwerda GJ, Kloosterman JL, Lathouwers D, Van Der Hagen THJJ. Macroscopic and Microscopic Packing Properties of Experimental and Computational Pebble Beds. NUCL TECHNOL 2017. [DOI: 10.13182/nt13-a19417] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gert Jan Auwerda
- Delft University of Technology, Department of Radiation, Radionuclides and Reactors Mekelweg 15, Delft, Netherlands
| | - Jan-Leen Kloosterman
- Delft University of Technology, Department of Radiation, Radionuclides and Reactors Mekelweg 15, Delft, Netherlands
| | - Danny Lathouwers
- Delft University of Technology, Department of Radiation, Radionuclides and Reactors Mekelweg 15, Delft, Netherlands
| | - Tim H. J. J. Van Der Hagen
- Delft University of Technology, Department of Radiation, Radionuclides and Reactors Mekelweg 15, Delft, Netherlands
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Guan Y, Wang E, Liu X, Wang S, Luan H. The Quantified Characterization Method of the Micro-Macro Contacts of Three-Dimensional Granular Materials on the Basis of Graph Theory. MATERIALS 2017; 10:ma10080898. [PMID: 28771208 PMCID: PMC5578264 DOI: 10.3390/ma10080898] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 12/02/2022]
Abstract
We have attempted a multiscale and quantified characterization method of the contact in three-dimensional granular material made of spherical particles, particularly in cemented granular material. Particle contact is defined as a type of surface contact with voids in its surroundings, rather than a point contact. Macro contact is a particle contact set satisfying the restrictive condition of a two-dimensional manifold with a boundary. On the basis of graph theory, two dual geometrical systems are abstracted from the granular pack. The face and the face set, which satisfies the two-dimensional manifold with a boundary in the solid cell system, are extracted to characterize the particle contact and the macro contact, respectively. This characterization method is utilized to improve the post-processing in DEM (Discrete Element Method) from a micro perspective to describe the macro effect of the cemented granular material made of spherical particles. Since the crack has the same shape as its corresponding contact, this method is adopted to characterize the crack and realize its visualization. The integral failure route of the sample can be determined by a graph theory algorithm. The contact force is assigned to the weight value of the face characterizing the particle contact. Since the force vectors can be added, the macro contact force can be solved by adding the weight of its corresponding faces.
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Affiliation(s)
- Yanpeng Guan
- The State Key Laboratory of Hydro-Science and Engineering, Tsinghua University, Beijing 100084, China.
- Sanjiangyuan Collaborative Innovation Center, Tsinghua University, Beijing 100084, China.
| | - Enzhi Wang
- The State Key Laboratory of Hydro-Science and Engineering, Tsinghua University, Beijing 100084, China.
- Sanjiangyuan Collaborative Innovation Center, Tsinghua University, Beijing 100084, China.
| | - Xiaoli Liu
- The State Key Laboratory of Hydro-Science and Engineering, Tsinghua University, Beijing 100084, China.
- Sanjiangyuan Collaborative Innovation Center, Tsinghua University, Beijing 100084, China.
| | - Sijing Wang
- The State Key Laboratory of Hydro-Science and Engineering, Tsinghua University, Beijing 100084, China.
- Sanjiangyuan Collaborative Innovation Center, Tsinghua University, Beijing 100084, China.
| | - Hebing Luan
- The State Key Laboratory of Hydro-Science and Engineering, Tsinghua University, Beijing 100084, China.
- Sanjiangyuan Collaborative Innovation Center, Tsinghua University, Beijing 100084, China.
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50
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Khara GS, Murphy ST, Duffy DM. Dislocation loop formation by swift heavy ion irradiation of metals. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:285303. [PMID: 28541249 DOI: 10.1088/1361-648x/aa74f8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A coupled two-temperature, molecular dynamics methodology is used to simulate the structural evolution of bcc metals (Fe and W) and fcc metals (Cu and Ni) following irradiation by swift heavy ions. Electronic temperature dependent electronic specific heat capacities and electron-phonon coupling strengths are used to capture the full effects of the variation in the electronic density of states. Tungsten is found to be significantly more resistant to damage than iron, due both to the higher melting temperature and the higher thermal conductivity. Very interesting defect structures, quite different from defects formed in cascades, are found to be created by swift heavy ion irradiation in the bcc metals. Isolated vacancies form a halo around elongated interstitial dislocation loops that are oriented along the ion path. Such configurations are formed by rapid recrystallization of the molten cylindrical region that is created by the energetic ion. Vacancies are created at the recrystallization front, resulting in excess atoms at the core which form interstitial dislocation loops on completion of crystallization. These unique defect structures could, potentially, be used to create metal films with superior mechanical properties and interesting nanostructures.
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Affiliation(s)
- Galvin S Khara
- Department of Physics and Astronomy and The London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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