At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge de novo with relative ease. At early times of molecular evolution, random polymers could have sufficed for the appearance of incipient chemical activity, while the cellular environment harbours a myriad of proto-functional molecules. The emergence of function is facilitated by several mechanisms intrinsic to molecular organization, such as redundant mapping of sequences into structures, phenotypic plasticity, modularity or cooperative associations between genomic sequences. It is the availability of niches in the molecular ecology that filters new potentially functional proposals. New phenotypes and subsequent levels of molecular complexity could be attained through combinatorial explorations of currently available molecular variants. Natural selection does the rest. This article is part of the theme issue ‘Emergent phenomena in complex physical and socio-technical systems: from cells to societies’.
{"title":"The simple emergence of complex molecular function","authors":"S. Manrubia","doi":"10.1098/rsta.2020.0422","DOIUrl":"https://doi.org/10.1098/rsta.2020.0422","url":null,"abstract":"At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge de novo with relative ease. At early times of molecular evolution, random polymers could have sufficed for the appearance of incipient chemical activity, while the cellular environment harbours a myriad of proto-functional molecules. The emergence of function is facilitated by several mechanisms intrinsic to molecular organization, such as redundant mapping of sequences into structures, phenotypic plasticity, modularity or cooperative associations between genomic sequences. It is the availability of niches in the molecular ecology that filters new potentially functional proposals. New phenotypes and subsequent levels of molecular complexity could be attained through combinatorial explorations of currently available molecular variants. Natural selection does the rest. This article is part of the theme issue ‘Emergent phenomena in complex physical and socio-technical systems: from cells to societies’.","PeriodicalId":20020,"journal":{"name":"Philosophical Transactions of the Royal Society A","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87162341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This paper presents a geometric microcanonical ensemble perspective on two-dimensional truncated Euler flows, which contain a finite number of (Fourier) modes and conserve energy and enstrophy. We explicitly perform phase space volume integrals over shells of constant energy and enstrophy. Two applications are considered. In the first part, we determine the average energy spectrum for highly condensed flow configurations and show that the result is consistent with Kraichnan’s canonical ensemble description, despite the fact that no thermodynamic limit is invoked. In the second part, we compute the probability density for the largest-scale mode of a free-slip flow in a square, which displays reversals. We test the results against numerical simulations of a minimal model and find excellent agreement with the microcanonical theory, unlike the canonical theory, which fails to describe the bimodal statistics. This article is part of the theme issue ‘Mathematical problems in physical fluid dynamics (part 2)’.
{"title":"Geometric microcanonical theory of two-dimensional truncated Euler flows","authors":"A. V. Kan, A. Alexakis, M. Brachet","doi":"10.1098/rsta.2021.0049","DOIUrl":"https://doi.org/10.1098/rsta.2021.0049","url":null,"abstract":"This paper presents a geometric microcanonical ensemble perspective on two-dimensional truncated Euler flows, which contain a finite number of (Fourier) modes and conserve energy and enstrophy. We explicitly perform phase space volume integrals over shells of constant energy and enstrophy. Two applications are considered. In the first part, we determine the average energy spectrum for highly condensed flow configurations and show that the result is consistent with Kraichnan’s canonical ensemble description, despite the fact that no thermodynamic limit is invoked. In the second part, we compute the probability density for the largest-scale mode of a free-slip flow in a square, which displays reversals. We test the results against numerical simulations of a minimal model and find excellent agreement with the microcanonical theory, unlike the canonical theory, which fails to describe the bimodal statistics. This article is part of the theme issue ‘Mathematical problems in physical fluid dynamics (part 2)’.","PeriodicalId":20020,"journal":{"name":"Philosophical Transactions of the Royal Society A","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85472476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-02-08DOI: 10.1098/RSTA.2020.0185RSTA20200185
H. Eklund, S. Wedemeyer, B. Snow, D. Jess, S. Jafarzadeh, S. D. Grant, M. Carlsson, M. Szydlarski
{"title":"Characterization of shock wave signatures at millimetre wavelengths from Bifrost simulations: Shock wave signatures at mm-wavelengths","authors":"H. Eklund, S. Wedemeyer, B. Snow, D. Jess, S. Jafarzadeh, S. D. Grant, M. Carlsson, M. Szydlarski","doi":"10.1098/RSTA.2020.0185RSTA20200185","DOIUrl":"https://doi.org/10.1098/RSTA.2020.0185RSTA20200185","url":null,"abstract":"","PeriodicalId":20020,"journal":{"name":"Philosophical Transactions of the Royal Society A","volume":"58 1","pages":"20200185"},"PeriodicalIF":0.0,"publicationDate":"2021-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74673928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-01-11DOI: 10.1098/RSTA.2020.0141RSTA20200141
Eads Ryker, J. Angel
{"title":"A 20 m wide-field diffraction-limited telescope: 20 m, wide field UVOIR telescope","authors":"Eads Ryker, J. Angel","doi":"10.1098/RSTA.2020.0141RSTA20200141","DOIUrl":"https://doi.org/10.1098/RSTA.2020.0141RSTA20200141","url":null,"abstract":"","PeriodicalId":20020,"journal":{"name":"Philosophical Transactions of the Royal Society A","volume":"22 1","pages":"20200141"},"PeriodicalIF":0.0,"publicationDate":"2021-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87414963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-01-11DOI: 10.1098/RSTA.2020.0142RSTA20200142
N. Woolf, R. Angel
{"title":"Pantheon habitat made from regolith, with a focusing solar reflector: Pantheon Habitat","authors":"N. Woolf, R. Angel","doi":"10.1098/RSTA.2020.0142RSTA20200142","DOIUrl":"https://doi.org/10.1098/RSTA.2020.0142RSTA20200142","url":null,"abstract":"","PeriodicalId":20020,"journal":{"name":"Philosophical Transactions of the Royal Society A","volume":"42 1","pages":"20200142"},"PeriodicalIF":0.0,"publicationDate":"2021-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84559143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Javier G'omez-Serrano, Jaemin Park, Jia Shi, Yao Yao
In this paper, we construct new, uniformly rotating solutions of the vortex sheet equation bifurcating from circles with constant vorticity amplitude. The proof is accomplished via a Lyapunov–Schmidt reduction and a second-order expansion of the reduced system. This article is part of the theme issue ‘Mathematical problems in physical fluid dynamics (part 2)’.
{"title":"Remarks on stationary and uniformly rotating vortex sheets: flexibility results","authors":"Javier G'omez-Serrano, Jaemin Park, Jia Shi, Yao Yao","doi":"10.1098/rsta.2021.0045","DOIUrl":"https://doi.org/10.1098/rsta.2021.0045","url":null,"abstract":"In this paper, we construct new, uniformly rotating solutions of the vortex sheet equation bifurcating from circles with constant vorticity amplitude. The proof is accomplished via a Lyapunov–Schmidt reduction and a second-order expansion of the reduced system. This article is part of the theme issue ‘Mathematical problems in physical fluid dynamics (part 2)’.","PeriodicalId":20020,"journal":{"name":"Philosophical Transactions of the Royal Society A","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78686915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-12-11DOI: 10.1098/RSTA.2019.0598RSTA20190598
Elisah J. VandenBussche, D. Flannigan
{"title":"High-resolution analogue of time-domain phonon spectroscopy in the transmission electron microscope: UEM Imaging of GaAs Phonon Dynamics","authors":"Elisah J. VandenBussche, D. Flannigan","doi":"10.1098/RSTA.2019.0598RSTA20190598","DOIUrl":"https://doi.org/10.1098/RSTA.2019.0598RSTA20190598","url":null,"abstract":"","PeriodicalId":20020,"journal":{"name":"Philosophical Transactions of the Royal Society A","volume":"51 1","pages":"20190598"},"PeriodicalIF":0.0,"publicationDate":"2020-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76903656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We consider the problem of asymptotic synchronization of different spatial points coupled to each other in inhomogeneous space–time and undergoing chaotic Mixmaster oscillations towards the singularity. We demonstrate that for couplings larger than some threshold value, two Mixmaster spatial points A,B, with A in the past of B, synchronize and thereby proceed in perfect unison towards the initial singularity. We further show that there is a Lyapunov function for the synchronization dynamics that makes different spatial points able to synchronize exponentially fast in the past direction. We provide an elementary proof of how an arbitrary spatial point responds to the mean field created by the oscillators, leading to their direct interaction through spontaneous synchronization. These results ascribe a clear physical meaning of early-time synchronization leading to a resetting effect for the two BKL maps corresponding to two distinct oscillating spatial points, as the two maps converge to each other to become indistinguishable at the end of synchronization. Our results imply that the universe generically organizes itself through simpler, synchronized, states as it approaches the initial singularity. A discussion of further implications of early-time inhomogeneous Mixmaster synchronization is also provided. This article is part of the theme issue ‘The future of mathematical cosmology, Volume 1’.
{"title":"Onset of synchronization in coupled Mixmaster oscillators","authors":"S. Cotsakis","doi":"10.1098/rsta.2021.0189","DOIUrl":"https://doi.org/10.1098/rsta.2021.0189","url":null,"abstract":"We consider the problem of asymptotic synchronization of different spatial points coupled to each other in inhomogeneous space–time and undergoing chaotic Mixmaster oscillations towards the singularity. We demonstrate that for couplings larger than some threshold value, two Mixmaster spatial points A,B, with A in the past of B, synchronize and thereby proceed in perfect unison towards the initial singularity. We further show that there is a Lyapunov function for the synchronization dynamics that makes different spatial points able to synchronize exponentially fast in the past direction. We provide an elementary proof of how an arbitrary spatial point responds to the mean field created by the oscillators, leading to their direct interaction through spontaneous synchronization. These results ascribe a clear physical meaning of early-time synchronization leading to a resetting effect for the two BKL maps corresponding to two distinct oscillating spatial points, as the two maps converge to each other to become indistinguishable at the end of synchronization. Our results imply that the universe generically organizes itself through simpler, synchronized, states as it approaches the initial singularity. A discussion of further implications of early-time inhomogeneous Mixmaster synchronization is also provided. This article is part of the theme issue ‘The future of mathematical cosmology, Volume 1’.","PeriodicalId":20020,"journal":{"name":"Philosophical Transactions of the Royal Society A","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73099816","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Roy Johnston received his BA (1983) and D.Phil. (1986) from the University of Oxford, where he was a member of St. Catherine’s College. His D.Phil., on theoretical aspects of cluster molecules, was carried out under the supervision of Prof. Mike Mingos, FRS. From 1987 to 1989, he was a SERC/NATO postdoctoral fellow in the USA, spending a year each at Cornell University, working with one of us (Roald Hoffmann) on theoretical solid state chemistry and the University of Arizona, working with Prof. Dennis Lichtenberger on gas phase and surface photoelectron spectroscopy.
罗伊·约翰斯顿获得文学学士学位(1983年)和哲学博士学位。1986年毕业于牛津大学圣凯瑟琳学院(St. Catherine’s College)。他的哲学博士。1987年至1989年，他作为美国SERC/NATO博士后，分别在康奈尔大学(Cornell University)和亚利桑那大学(University of Arizona)分别花了一年时间，与我们中的一位(Roald Hoffmann)一起研究固体化学理论，与Dennis Lichtenberger教授一起研究气相和表面光电子能谱。
{"title":"Dedication: Professor Roy Luigi Johnston","authors":"Roy Johnston","doi":"10.1098/rsta.2020.0247","DOIUrl":"https://doi.org/10.1098/rsta.2020.0247","url":null,"abstract":"Roy Johnston received his BA (1983) and D.Phil. (1986) from the University of Oxford, where he was a member of St. Catherine’s College. His D.Phil., on theoretical aspects of cluster molecules, was carried out under the supervision of Prof. Mike Mingos, FRS. From 1987 to 1989, he was a SERC/NATO postdoctoral fellow in the USA, spending a year each at Cornell University, working with one of us (Roald Hoffmann) on theoretical solid state chemistry and the University of Arizona, working with Prof. Dennis Lichtenberger on gas phase and surface photoelectron spectroscopy.","PeriodicalId":20020,"journal":{"name":"Philosophical Transactions of the Royal Society A","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74968118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Boris Sokolov, M. Rossi, Guillermo Garc'ia-P'erez, S. Maniscalco
We introduce an experimentally accessible network representation for many-body quantum states based on entanglement between all pairs of its constituents. We illustrate the power of this representation by applying it to a paradigmatic spin chain model, the XX model, and showing that it brings to light new phenomena. The analysis of these entanglement networks reveals that the gradual establishment of quasi-long range order is accompanied by a symmetry regarding single-spin concurrence distributions, as well as by instabilities in the network topology. Moreover, we identify the existence of emergent entanglement structures, spatially localized communities enforced by the global symmetry of the system that can be revealed by model-agnostic community detection algorithms. The network representation further unveils the existence of structural classes and a cyclic self-similarity in the state, which we conjecture to be intimately linked to the community structure. Our results demonstrate that the use of tools and concepts from complex network theory enables the discovery, understanding and description of new physical phenomena even in models studied for decades. This article is part of the theme issue ‘Emergent phenomena in complex physical and socio-technical systems: from cells to societies’.
{"title":"Emergent entanglement structures and self-similarity in quantum spin chains","authors":"Boris Sokolov, M. Rossi, Guillermo Garc'ia-P'erez, S. Maniscalco","doi":"10.1098/rsta.2020.0421","DOIUrl":"https://doi.org/10.1098/rsta.2020.0421","url":null,"abstract":"We introduce an experimentally accessible network representation for many-body quantum states based on entanglement between all pairs of its constituents. We illustrate the power of this representation by applying it to a paradigmatic spin chain model, the XX model, and showing that it brings to light new phenomena. The analysis of these entanglement networks reveals that the gradual establishment of quasi-long range order is accompanied by a symmetry regarding single-spin concurrence distributions, as well as by instabilities in the network topology. Moreover, we identify the existence of emergent entanglement structures, spatially localized communities enforced by the global symmetry of the system that can be revealed by model-agnostic community detection algorithms. The network representation further unveils the existence of structural classes and a cyclic self-similarity in the state, which we conjecture to be intimately linked to the community structure. Our results demonstrate that the use of tools and concepts from complex network theory enables the discovery, understanding and description of new physical phenomena even in models studied for decades. This article is part of the theme issue ‘Emergent phenomena in complex physical and socio-technical systems: from cells to societies’.","PeriodicalId":20020,"journal":{"name":"Philosophical Transactions of the Royal Society A","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78716260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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