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Study of adsorption of propane and propylene on CHA zeolite in different Si/Al ratios using molecular dynamics simulation. POWDER TECHNOL 2023. [DOI: 10.1016/j.powtec.2023.118329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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2
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Wang X, Hinkle KR, Jameson CJ, Murad S. Using Molecular Simulations to Facilitate Design and Operation of Membrane-Based and Chiral Separation Processes. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c01470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaoyu Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556
| | - Kevin R. Hinkle
- Department of Chemical and Materials Engineering, University of Dayton, Dayton, Ohio 45469
| | - Cynthia J. Jameson
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sohail Murad
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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Mitra S, Sharma VK, Mukhopadhyay R. Diffusion of confined fluids in microporous zeolites and clay materials. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:066501. [PMID: 33740783 DOI: 10.1088/1361-6633/abf085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Fluids exhibit remarkable variation in their structural and dynamic properties when they are confined at the nanoscopic scale. Various factors, including geometric restriction, the size and shape of the guest molecules, the topology of the host, and guest-host interactions, are responsible for the alterations in these properties. Due to their porous structures, aluminosilicates provide a suitable host system for studying the diffusion of sorbates in confinement. Zeolites and clays are two classes of the aluminosilicate family, comprising very ordered porous or layered structures. Zeolitic materials are important due to their high catalytic activity and molecular sieving properties. Guest molecules adsorbed by zeolites display many interesting features including unidimensional diffusion, non-isotropic rotation, preferred orientation and levitation effects, depending on the guest and host characteristics. These are useful for the separation of hydrocarbons which commonly exist as mixtures in nature. Similarly, clay materials have found application in catalysis, desalination, enhanced oil recovery, and isolation barriers used in radioactive waste disposal. It has been shown that the bonding interactions, level of hydration, interlayer spacing, and number of charge-balancing cations are the important factors that determine the nature of diffusion of water molecules in clays. Here, we present a review of the current status of the diffusion mechanisms of various adsorbed species in different microporous zeolites and clays, as investigated using quasielastic neutron scattering and classical molecular dynamics simulation techniques. It is impossible to write an exhaustive review of the subject matter, as it has been explored over several decades and involves many research topics. However, an effort is made to cover the relevant issues specific to the dynamics of different molecules in microporous zeolites and clay materials and to highlight a variety of interesting features that are important for both practical applications and fundamental aspects.
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Affiliation(s)
- S Mitra
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - R Mukhopadhyay
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
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Cnudde P, Redekop EA, Dai W, Porcaro NG, Waroquier M, Bordiga S, Hunger M, Li L, Olsbye U, Van Speybroeck V. Experimental and Theoretical Evidence for the Promotional Effect of Acid Sites on the Diffusion of Alkenes through Small-Pore Zeolites. Angew Chem Int Ed Engl 2021; 60:10016-10022. [PMID: 33496374 PMCID: PMC8251642 DOI: 10.1002/anie.202017025] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/25/2021] [Indexed: 12/18/2022]
Abstract
The diffusion of saturated and unsaturated hydrocarbons is of fundamental importance for many zeolite‐catalyzed processes. Transport of small alkenes in the confined zeolite pores can become hindered, resulting in a significant impact on the ultimate product selectivity and separation. Herein, intracrystalline light olefin/paraffin diffusion through the 8‐ring windows of zeolite SAPO‐34 is characterized by a complementary set of first‐principle molecular dynamics simulations, PFG‐NMR experiments, and pulse‐response temporal analysis of products measurements, yielding information at different length and time scales. Our results clearly show a promotional effect of the presence of Brønsted acid sites on the diffusion rate of ethene and propene, whereas transport of alkanes is found to be insensitive to the presence of acid sites. The enhanced diffusivity of unsaturated hydrocarbons is ascribed to the formation of favorable π–H interactions with acid protons, as confirmed by IR spectroscopy measurements. The acid site distribution is proven to be an important design parameter for optimizing product distributions and separations.
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Affiliation(s)
- Pieter Cnudde
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark 46, 9052, Zwijnaarde, Belgium
| | - Evgeniy A Redekop
- Center for Materials Science and Nanotechnology (SMN), Department of Chemistry, University of Oslo, P.O. Box 1126 Blindern, 0318, Oslo, Norway
| | - Weili Dai
- School of Materials Science and Engineering & National Institute for Advanced Materials, Nankai University, Tianjin, 300350, P. R. China
| | - Natale G Porcaro
- Department of Chemistry, NIS Centre of Excellence and INSTM Reference Center, University of Turin, Via P. Giuria 7, 10125 10, Torino, Italy
| | - Michel Waroquier
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark 46, 9052, Zwijnaarde, Belgium
| | - Silvia Bordiga
- Department of Chemistry, NIS Centre of Excellence and INSTM Reference Center, University of Turin, Via P. Giuria 7, 10125 10, Torino, Italy
| | - Michael Hunger
- Institute of Chemical Technology, University of Stuttgart, 70550, Stuttgart, Germany
| | - Landong Li
- School of Materials Science and Engineering & National Institute for Advanced Materials, Nankai University, Tianjin, 300350, P. R. China
| | - Unni Olsbye
- Center for Materials Science and Nanotechnology (SMN), Department of Chemistry, University of Oslo, P.O. Box 1126 Blindern, 0318, Oslo, Norway
| | - Veronique Van Speybroeck
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark 46, 9052, Zwijnaarde, Belgium
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Abstract
AbstractNanoporous solids are ubiquitous in chemical, energy, and environmental processes, where controlled transport of molecules through the pores plays a crucial role. They are used as sorbents, chromatographic or membrane materials for separations, and as catalysts and catalyst supports. Defined as materials where confinement effects lead to substantial deviations from bulk diffusion, nanoporous materials include crystalline microporous zeotypes and metal–organic frameworks (MOFs), and a number of semi-crystalline and amorphous mesoporous solids, as well as hierarchically structured materials, containing both nanopores and wider meso- or macropores to facilitate transport over macroscopic distances. The ranges of pore sizes, shapes, and topologies spanned by these materials represent a considerable challenge for predicting molecular diffusivities, but fundamental understanding also provides an opportunity to guide the design of new nanoporous materials to increase the performance of transport limited processes. Remarkable progress in synthesis increasingly allows these designs to be put into practice. Molecular simulation techniques have been used in conjunction with experimental measurements to examine in detail the fundamental diffusion processes within nanoporous solids, to provide insight into the free energy landscape navigated by adsorbates, and to better understand nano-confinement effects. Pore network models, discrete particle models and synthesis-mimicking atomistic models allow to tackle diffusion in mesoporous and hierarchically structured porous materials, where multiscale approaches benefit from ever cheaper parallel computing and higher resolution imaging. Here, we discuss synergistic combinations of simulation and experiment to showcase theoretical progress and computational techniques that have been successful in predicting guest diffusion and providing insights. We also outline where new fundamental developments and experimental techniques are needed to enable more accurate predictions for complex systems.
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Cnudde P, Redekop EA, Dai W, Porcaro NG, Waroquier M, Bordiga S, Hunger M, Li L, Olsbye U, Van Speybroeck V. Experimental and Theoretical Evidence for the Promotional Effect of Acid Sites on the Diffusion of Alkenes through Small‐Pore Zeolites. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Pieter Cnudde
- Center for Molecular Modeling (CMM) Ghent University Technologiepark 46 9052 Zwijnaarde Belgium
| | - Evgeniy A. Redekop
- Center for Materials Science and Nanotechnology (SMN) Department of Chemistry University of Oslo P.O. Box 1126 Blindern 0318 Oslo Norway
| | - Weili Dai
- School of Materials Science and Engineering & National Institute for Advanced Materials Nankai University Tianjin 300350 P. R. China
| | - Natale G. Porcaro
- Department of Chemistry NIS Centre of Excellence and INSTM Reference Center University of Turin Via P. Giuria 7 10125 10 Torino Italy
| | - Michel Waroquier
- Center for Molecular Modeling (CMM) Ghent University Technologiepark 46 9052 Zwijnaarde Belgium
| | - Silvia Bordiga
- Department of Chemistry NIS Centre of Excellence and INSTM Reference Center University of Turin Via P. Giuria 7 10125 10 Torino Italy
| | - Michael Hunger
- Institute of Chemical Technology University of Stuttgart 70550 Stuttgart Germany
| | - Landong Li
- School of Materials Science and Engineering & National Institute for Advanced Materials Nankai University Tianjin 300350 P. R. China
| | - Unni Olsbye
- Center for Materials Science and Nanotechnology (SMN) Department of Chemistry University of Oslo P.O. Box 1126 Blindern 0318 Oslo Norway
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Sun B, Kekenes-Huskey PM. Molecular Basis of S100A1 Activation and Target Regulation Within Physiological Cytosolic Ca 2+ Levels. Front Mol Biosci 2020; 7:77. [PMID: 32656226 PMCID: PMC7324869 DOI: 10.3389/fmolb.2020.00077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
The S100A1 protein regulates cardiomyocyte function through its binding of calcium (Ca2+) and target proteins, including titin, SERCA, and RyR. S100A1 presents two Ca2+ binding domains, a high-affinity canonical EF-hand (cEF) and a low-affinity pseudo EF-hand (pEF), that control S100A1 activation. For wild-type S100A1, both EF hands must be bound by Ca2+ to form the open state necessary for target peptide binding, which requires unphysiological high sub-millimolar Ca2+ levels. However, there is evidence that post-translational modifications at Cys85 may facilitate the formation of the open state at sub-saturating Ca2+ concentrations. Hence, post-translational modifications of S100A1 could potentially increase the Ca2+-sensitivity of binding protein targets, and thereby modulate corresponding signaling pathways. In this study, we examine the mechanism of S100A1 open-closed gating via molecular dynamics simulations to determine the extent to which Cys85 functionalization, namely via redox reactions, controls the relative population of open states at sub-saturating Ca2+ and capacity to bind peptides. We further characterize the protein's ability to bind a representative peptide target, TRKT12 and relate this propensity to published competition assay data. Our simulation results indicate that functionalization of Cys85 may stabilize the S100A1 open state at physiological, micromolar Ca2+ levels. Our conclusions support growing evidence that S100A1 serves as a signaling hub linking Ca2+ and redox signaling pathways.
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Affiliation(s)
- Bin Sun
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, United States
| | - Peter M Kekenes-Huskey
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL, United States
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O'Connor MB, Bennie SJ, Deeks HM, Jamieson-Binnie A, Jones AJ, Shannon RJ, Walters R, Mitchell TJ, Mulholland AJ, Glowacki DR. Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework. J Chem Phys 2019; 150:220901. [PMID: 31202243 DOI: 10.1063/1.5092590] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures.
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Affiliation(s)
- Michael B O'Connor
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Simon J Bennie
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Helen M Deeks
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Alexander Jamieson-Binnie
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Alex J Jones
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Robin J Shannon
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Rebecca Walters
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Thomas J Mitchell
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - David R Glowacki
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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Asl MH, Moosavi F, Sargolzaei J, Sharifi K. Molecular dynamics simulation study: The decryption of bi and tri aromatics behavior with NaX zeolite. J Mol Graph Model 2016; 69:61-71. [DOI: 10.1016/j.jmgm.2016.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/21/2016] [Accepted: 08/08/2016] [Indexed: 11/17/2022]
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Haghighi Asl M, Moosavi F, Sargolzaei J. Molecular dynamics simulation study: The reactivation of NaX zeolite contaminated by bi and tri aromatics using supercritical fluid extraction. J Supercrit Fluids 2016. [DOI: 10.1016/j.supflu.2016.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Haghighi Asl M, Sargolzaei J, Moosavi F. Identification of the coke deposited on 13X industrial zeolite molecular sieves during mercaptan removal process. ASIA-PAC J CHEM ENG 2015. [DOI: 10.1002/apj.1952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- M. Haghighi Asl
- Department of Chemical Engineering; Ferdowsi University of Mashhad; P.O. Box 9177948944 Mashhad Iran
| | - J. Sargolzaei
- Department of Chemical Engineering; Ferdowsi University of Mashhad; P.O. Box 9177948944 Mashhad Iran
| | - F. Moosavi
- Department of Chemistry; Ferdowsi University of Mashhad; P.O. Box 9177948974 Mashhad Iran
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12
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Equilibrium adsorption analysis of microporous adsorbents in propene/propane binary mixture separation. ADSORPTION 2015. [DOI: 10.1007/s10450-015-9695-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Choi SW, Jones CW, Nair S, Sholl DS, Moore JS, Liu Y, Dixit RS, Pendergast JG. Material properties and operating configurations of membrane reactors for propane dehydrogenation. AIChE J 2014. [DOI: 10.1002/aic.14700] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Seung-Won Choi
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology; Atlanta GA 30332
| | - Christopher W. Jones
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology; Atlanta GA 30332
| | - Sankar Nair
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology; Atlanta GA 30332
| | - David S. Sholl
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology; Atlanta GA 30332
| | - Jason S. Moore
- Engineering & Process Sciences, The Dow Chemical Company; Freeport TX 77541
| | - Yujun Liu
- Engineering & Process Sciences, The Dow Chemical Company; Freeport TX 77541
| | - Ravindra S. Dixit
- Engineering & Process Sciences, The Dow Chemical Company; Freeport TX 77541
| | - John G. Pendergast
- Engineering & Process Sciences, The Dow Chemical Company; Freeport TX 77541
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Sun Y, Han S. Diffusion of N2, O2, H2S and SO2in MFI and 4A zeolites by molecular dynamics simulations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.945082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Using temporal analysis of products and flux response technology to determine diffusion coefficients in catalytic monoliths. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2012.10.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Sasegbon A, Hellgardt K. Flux response technology applied in zero length column diffusivity measurements. ADSORPTION 2012. [DOI: 10.1007/s10450-012-9424-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Liu X, Vlugt TJ, Bardow A. Predictive Darken Equation for Maxwell-Stefan Diffusivities in Multicomponent Mixtures. Ind Eng Chem Res 2011. [DOI: 10.1021/ie201008a] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xin Liu
- Lehrstuhl für Technische Thermodynamik, RWTH Aachen University, Schinkelstrasse 8, 52062 Aachen, Germany
- Process & Energy Laboratory, Delft University of Technology, Leeghwaterstraat 44, 2628 CA Delft, The Netherlands
| | - Thijs J.H. Vlugt
- Process & Energy Laboratory, Delft University of Technology, Leeghwaterstraat 44, 2628 CA Delft, The Netherlands
| | - André Bardow
- Lehrstuhl für Technische Thermodynamik, RWTH Aachen University, Schinkelstrasse 8, 52062 Aachen, Germany
- Process & Energy Laboratory, Delft University of Technology, Leeghwaterstraat 44, 2628 CA Delft, The Netherlands
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