266 research outputs found

    Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations

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    The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insight into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that in the last few decades have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state of the art computational methods, by reviewing simulations of e.g. ice nucleation or crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insight into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that in doing so the general applicability of classical nucleation theory has been repeatedly called into question. We have attempted to identify the most pressing open questions in the field. We believe that by improving (i.) existing interatomic potentials; and (ii.) currently available enhanced sampling methods, the community can move towards accurate investigations of realistic systems of practical interest, thus bringing simulations a step closer to experiments

    Structural and Kinetic Studies of Structure I Gas Hydrates via Low Temperature X-Ray Diffraction and High Resolution Neutron Diffraction

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    Gas hydrates are materials of interest as sources for clean energy, carbon sequestration, greenhouse gas mitigation, and gas storage. This body of work presents two projects that each separately explore one aspect of the potential found in gas hydrates. Chapter 1 tackles the structural changes found to occur over the CO2 [carbon dioxide] - CH4 [methane] hydrate solid solution. The application here pertains to the sequestration of CO2 in natural gas hydrates found in permafrost regions and ocean floors. As CO2 is injected into the hydrate reservoir, CH4 is released and recovered for energy use. Samples synthesized from liquid water were studied using high-resolution neutron diffraction. Static images of the nuclear scattering density of the free moving gas molecules were determined. Cage occupants and occupancies, the volume change of the unit cell and the individual cages based on composition were determined. Chapter 2 pertains to the decomposition of methane hydrate and a phenomenon termed anomalous preservation. Three samples were studied using in situ low temperature x-ray diffraction as they decomposed over a temperature range of 140 – 260 K and the kinetics were analyzed using the Avrami model. Activation energies and Avrami constants were determined for two temperature ranges within the overall range

    Autonomous artificial intelligence discovers mechanisms of molecular self-organization in virtual experiments

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    Molecular self-organization driven by concerted many-body interactions produces the ordered structures that define both inanimate and living matter. Understanding the physical mechanisms that govern the formation of molecular complexes and crystals is key to controlling the assembly of nanomachines and new materials. We present an artificial intelligence (AI) agent that uses deep reinforcement learning and transition path theory to discover the mechanism of molecular self-organization phenomena from computer simulations. The agent adaptively learns how to sample complex molecular events and, on the fly, constructs quantitative mechanistic models. By using the mechanistic understanding for AI-driven sampling, the agent closes the learning cycle and overcomes time-scale gaps of many orders of magnitude. Symbolic regression condenses the mechanism into a human-interpretable form. Applied to ion association in solution, gas-hydrate crystal formation, and membrane-protein assembly, the AI agent identifies the many-body solvent motions governing the assembly process, discovers the variables of classical nucleation theory, and reveals competing assembly pathways. The mechanistic descriptions produced by the agent are predictive and transferable to close thermodynamic states and similar systems. Autonomous AI sampling has the power to discover assembly and reaction mechanisms from materials science to biology

    Study and Control of Thermal Transport in Complex Fluids

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    In this thesis, we propose the study of heat transport in liquids as a novel approach to the study of the dynamic structure of liquids. We focus our attention on the thermal conductivity, which is highly sensitive to changes in the dynamic nature of the whole systems. This strategy was used to characterize different fluids, which leads to the discovery of new phenomenology in these systems, with unforeseen applications in areas such important as energy storage or biology. We focus our research in two different projects. First, we study the effect of dissolving different solutes into the tetrahedral structure of liquid water. This shows the sensitivity of the thermal conductivity to changes in the microscopic arrangement, demonstrating the formation of supramolecular structures within the liquid. On the other hand, we perform a systematic study of the thermal transport in ILs, which shows a large thermal conductivity difference between liquid and solid phases. This suggests their use as thermal regulator in different technological aplications. Moreover, we have improved these systems by using azobenzene based compouds, which allow an active control of the thermal conductivity by an external stimulus, in this case the application of UV light

    Simulaciones de sistemas acuosos: de la fase gas a la fase condensada

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    Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Química. Fecha de lectura: 21-11-2017La presente tesis está dedicada a la simulación de sistemas acuosos desde la fase gas hasta la fase condensada. En la misma, se utilizaron enfoques y métodos complementarios para estudiar sistemas acuosos homogéneos y heterogéneos. En particular, se ofrece un análisis detallado de las propiedades estructurales, termodinámicas, espectroscópicas y de transporte en distintas condiciones termodinámicas para estos sistemas. A lo largo de todo el trabajo, las comparaciones entre el experimento y la teoría se establecieron sobre la base de la naturaleza de la interacción entre diferentes sistemas: Agua-Agua, Ion-Agua y hospedador-huésped (agua). Así, el presente trabajo se ha dividido en tres partes principales. En la primera parte, se realizaron simulaciones de dinámica molecular clásica en función de la temperatura para estudiar y determinar las propiedades estructurales y de transporte (tanto individuales como colectivas) del agua líquida. Hasta la fecha, la estimación de viscosidades a partir de simulaciones representa un problema computacional desafiante ya que se requieren tiempos de simulación largos para alcanzar precisión estadística, por lo que aquí se compararon varias estrategias de simulación y también se validan diversos potenciales de interacción disponibles en la literatura. En la segunda parte, se utilizaron cálculos de estructura electrónica de última generación para diseñar, desde un enfoque bottom-up, superficies de energías de potencial analíticas de alta precisión. Dichos modelos de interacción transferibles, son los primeros potenciales de ion-agua polarizables completamente ab-initio para el estudio de electrolitos en diferentes entornos acuosos, por ejemplo, desde la microsolvatación de monohidratos a polihidratos, así como soluciones a dilución infinita, y propiedades interfaciales. En una colaboración con dos grupos experimentales (EEUU y UE), predecimos y validamos la dependencia de la temperatura en el mecanismo de predisociación de un ion en contacto con dos moléculas de agua mediante simulaciones de dinámica molecular mixtas clásico-cuánticas. Finalmente en la tercera parte, estudiamos la encapsulación de átomos y moléculas dentro de las cavidades del clatrato hidrato sI. Estas investigaciones estuvieron motivadas por la disponibilidad de mediciones experimentales a partir de difracción de rayos X y espectros IR, así como de transiciones de fase observadas en el bulk. Para ello, se tomaron como sistemas de referencia el hidrato clatrato de dióxido de carbono, y los hidrato clatrato de gases nobles. En particular se llevaron a cabo cálculos cuánticos con el método de “Multiconfigurational Time Dependent Hartree” para las dos cavidades de clatrato CO2@sI, y por primera vez se presentan resultados sobre los estados traslacionales-rotacionales-vibracionales de dicho sistema. Además, se comprobó el rendimiento de diferentes modelos de interacción analítica, así como cálculos de estructura electrónica para describir la orientación rotacional y la anisotropía angular dentro de ambas cavidades. De igual manera, se llevaron a cabo simulaciones clásicas de “parallel-tempering Monte Carlo” en el ensamble isobárico-isotérmico (NPT) para agregados tipo clatratos con gases nobles de tamaño seleccionado y se presentó un análisis detallado de sus diagramas de fase en temperatura y presión, así como cambios estructurales en un amplio rango de presiones y temperatura.The present thesis is devoted to the simulations of aqueous systems from the gas to the condensed phase. Here we used complementary approaches and methods to study both homogeneous and heterogeneous aqueous systems. In particular, we provided a detailed analysis on their, structural, thermodynamical, spectroscopical and transport properties at different thermodynamic conditions. Along the whole work, comparisons between experiment and theory were established based on the nature of the interactions between different systems. It was divided into three main parts corresponding to: water-water, ion-water and guest-host(water network). In the first part, classical molecular dynamic simulations were performed as a function of temperature, to study and determine the structural and transport properties (both single and collective) of liquid water. Nowadays, the estimation of viscosities from simulations is a challenging computational problem, as long simulation times are required to reach statistical accuracy. So several simulation strategies were compared being able to validate interaction model potentials available in the literature. In the second part, state-of-the-art electronic structure calculations were employed to design, from a bottom-up approach, highly accurate analytical potential energy surfaces. Such transferable interaction models are the first fully ab-initio polarizable ion-water potentials for studying electrolytes at different aqueous environments i.e. from the microsolvation of monohydrates, to polyhydrates, as well as solutions at infinite dilution, and interfacial properties. In a collaboration with two experimental groups (USA and EU) we predict and validate the temperature dependence vibrational predissociation mechanism of an ion in contact with two water molecules by means of mixed quantum-classical molecular dynamic simulations. Finally in the third part, we studied the encapsulation of atoms and molecules within the cavities of sI type clathrate hydrates. These investigations were motivated by available experimental measurements from X-ray diffraction and IR spectra, as well as observed phase transitions in the bulk. For such, we took as reference systems the carbon dioxide clathrate hydrate and the rare gases (Rg) clathrate hydrates. In particular, we performed quantum multi-configuration time-dependent Hartree calculations for the two cages of the sI CO2 clathrate hydrate, and we reported for the first time results on the translational, rotational and vibrational states. Additionally, we tested the performance of different analytical interaction models, as well as electronic structure calculations for describing the rotational orientations and angular anisotropy of the CO2 within both cages. Moreover, classical parallel-tempering Monte Carlo simulations in the isobaric-isothermic (NPT) ensemble were carried out for size-selected Rg clathrate-like clusters and we presented a detailed analysis of their temperature-pressure phase diagrams, as well as structural changes in a wide range of temperatures and pressuresEste trabajo de investigación ha sido posible gracias a la concesión de una beca predoctoral BES2012-054209 enmarcada en el subprograma de ayudas de formación de personal investigador (FPI) del gobierno español, a través del Ministerio de Economía, Industria y Competitividad, y asociada al proyecto de investigación FIS2014-51933-P del CSIC

    Gas hydrates in sustainable chemistry

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    © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hassanpouryouzband, A., Joonaki, E., Farahani, M. V., Takeya, S., Ruppel, C., Yang, J., English, N. J., Schicks, J. M., Edlmann, K., Mehrabian, H., Aman, Z. M., & Tohidi, B. Gas hydrates in sustainable chemistry. Chemical Society Reviews, 49(15), (2020): 5225-5309, doi:10.1039/c8cs00989a.Gas hydrates have received considerable attention due to their important role in flow assurance for the oil and gas industry, their extensive natural occurrence on Earth and extraterrestrial planets, and their significant applications in sustainable technologies including but not limited to gas and energy storage, gas separation, and water desalination. Given not only their inherent structural flexibility depending on the type of guest gas molecules and formation conditions, but also the synthetic effects of a wide range of chemical additives on their properties, these variabilities could be exploited to optimise the role of gas hydrates. This includes increasing their industrial applications, understanding and utilising their role in Nature, identifying potential methods for safely extracting natural gases stored in naturally occurring hydrates within the Earth, and for developing green technologies. This review summarizes the different properties of gas hydrates as well as their formation and dissociation kinetics and then reviews the fast-growing literature reporting their role and applications in the aforementioned fields, mainly concentrating on advances during the last decade. Challenges, limitations, and future perspectives of each field are briefly discussed. The overall objective of this review is to provide readers with an extensive overview of gas hydrates that we hope will stimulate further work on this riveting field.A. H. and K. E. were partially supported by funding from UKRI-EPSRC (grant number EP/S027815/1). C. R. was partially supported by DOE-USGS Interagency agreement DE-FE0023495. C. R. thanks L. Stern and W. Waite for insights that improved her contributions. E. J. is partially supported by Flow Programme project sponsored by Department for Business, Energy and Industrial Strategy (BEIS), UK. Any use of trade, firm or product name is for descriptive purposes only and does not imply endorsement by the U.S. Government

    Computational studies of heterogeneous ice nucleation on non-ideal silver iodide surfaces

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    Pure water can remain in liquid phase in the atmosphere even at -38 ℃. However, ice nucleation can occur at higher temperatures up to -3 ℃ in the presence of atmospheric particles. Numerous studies have been conducted to identify and characterize particles with efficient nucleation enhancing properties. Silver iodide (AgI) is known for excellent ice nucleating capabilities and has long been used in rain seeding applications. In this thesis, we study the influence of various AgI structures on the ice nucleation efficiency using both atomistic and coarse grained molecular dynamics simulations. In particular, we aim to identify which characteristics of the AgI particles contribute to the ice nucleation. Specifically, we investigate ice nucleation in the presence of AgI surfaces with different defects. We also study the effects of confined geometries on ice nucleation using AgI systems with wedge and slit structures. We consider AgI wedges of different angles and AgI slit systems of varying widths. The simulation results show that AgI surfaces with defects lead to ice nucleation at low supercooling, but with a lower intensity than the perfect AgI surface. Moreover, it is observed that confined wedges (systems with angles less than 90°) almost always accelerate the formation of ice. Furthermore, ice nucleation occurs significantly faster when the wedge angle corresponds to that of the ice lattice. The simulation results for the slit structures show that as the slit's gap widens, the nucleation is periodically promoted and hindered: the nucleation process is accelerated when the gap width is an integer multiple of the width of an ice bilayer, and slowed down otherwise. Computer simulations of ice nucleation require efficient algorithms for distinguishing between the liquid and ice phases as well as identifying different types of ice crystals. In this thesis, we develop a novel ice recognition algorithm based on conformation template-matching for the identification of different ice polymorphs and interfacial ice structures. Our algorithm is robust in classifying non-ideal structures or structures with defects making it ideal for studying ice nucleation in the presence of foreign materials. Keywords: heterogeneous ice nucleation, molecular dynamics simulations, silver iodide, ice structure recognition.Puhdas vesi voi pysyä ilmakehässä nestemäisenä jopa -38 asteessa. Jään nukleaatio voi kuitenkin tapahtua korkeammissa lämpötiloissa -3 asteeseen saakka ilmakehässä olevien hiukkasten vaikutuksesta. Nukleaatiota tehostavia ominaisuuksia omaavia hiukkasia on tunnistettu ja karakterisoitu monissa tutkimuksissa. Hopeajodidi (AgI) tunnetaan erinomaisena jäänukleaation aikaansaajana, ja sitä on käytetty jo pitkään keinotekoisen sateen kylvämiseen. Tässä väitöskirjatyössä tutkitaan hopeajodidin eri rakenteiden jäänukleaatioaktiivisuutta atomistisilla ja karkeistetuilla molekyylidynaamisilla simulaatioilla. Erityisesti pyritään tunnistamaan, mitkä hopeajodidihiukkasten ominaisuudet vaikuttavat jäänukleaatioon. Erityisesti tutkimme jäänukleaatiota erilaisia hilavirheitä sisältävien hopeajodidipintojen päällä. Tutkimme jäänukleaatiota myös kiilan ja tasalevyisen raon muotoisissa kahden pinnan geometrioissa, eri kiilan kulmilla ja rakojen leveyksillä. Simulaatiotulokset osoittavat, että hilavirheet eivät estä jäänukleaatiota edes vähäisesti alijäähtyneelle vedelle, mutta ne hidastavat jäänukleaatiota tasaiseen pintaan verrattuna. Havaitaan myös, että kiilat, joiden kulma on alle 90 astetta tehostavat lähes aina jään muodostumista. Erityisesti, jos kiilan kulma vastaa jäähilan rakennetta, jäänukleaatio nopeutuu merkittävästi. Simulaatiotulokset tasalevyisille raoille osoittavat, että kun raon leveys kasvaa, nukleaatio tehostuu ja heikkenee periodisesti: nopeutuen, kun raon leveys vastaa tarkalleen paksuutta, joka on jollain määrällä kokonaisia jääkerroksia, ja hidastuen muussa tapauksessa. Jäänukleaatiota tutkivat tietokonesimulaatiot tarvitsevat tehokkaita algoritmeja veden eri nestemäisten ja jääfaasien erottamiseen, samoin kuin erilaisten jääkristallityyppien tunnistamiseen. Tässä väitöskirjatyössä kehitettiin uudenlainen jääntunnistusalgoritmi, joka perustuu jään eri faasien ja rajapinnoilla olevien rakenteiden tunnistamiseen täsmäytysmallin avulla. Algoritmi tunnistaa luotettavasti epätäydellisiä tai hilavirheitä sisältäviä jäärakenteita, mikä tekee siitä ideaalisen työkalun tutkittaessa jäänukleaatiota muiden materiaalien läsnäollessa. Avainsanat: heterogeeninen jäänukleaatio, molekyylidynaamiset simulaatiot, hopeajodidi, jäärakenteiden tunnistus

    Modelagem molecular de fluidos : colóides, água, álcoois e suas misturas

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    Core-softened fluids comprise a large number of systems whose molecular constituents have competitive interactions. The most prominent example is water whose molecules tend to form hydrogen bonds. The competition between these two conformations leads to a series of anomalous behaviors which can manifest themselves both in colloids and in mixtures of water and short-chain alcohols. The successful description of colloidal systems by two-length-scale potentials is related to the composition of these systems, usually made up of molecular subunits forming a compact central agglomeration and a less dense peripheral area with a prevalence of entropic effects. This core-corona structure can be described by a hard core and a soft corona that well represents the competition between enthalpy and entropic effects. Alcohol molecules bring even more competition to this complex scenario, since the majority do not have spherical symmetry, therefore incorporating anisotropic effects, and because they carry, in addition to the nonpolar carbonic part, hydrophilic hydroxyl groups, capable of forming hydrogen bonds, giving them a high degree of miscibility with water. This thesis focuses on the intricate molecular mechanisms that underlie the behavior of these complex fluids. To this end, we perfom large-scale Molecular Dynamics simulations of distinct systems. First, we analyzed the behavior of a two-dimensional system of polymer-grafted nanoparticles. Effective core-softened potentials were obtained from coarse-grained simulations for two cases: one in which the polymers are free to rotate around the nanoparticle core and a second in which the polymers are fixed, with a 90∘ angle between them. Due to the competition in the system we observe waterlike anomalies, such as the temperature of maximum density (TMD) and the diffusion anomaly. We observe that for the fixed polymers case the waterlike anomalies originate in the competition between the characteristic length scales in the potential, while for the freely rotating case, the anomalies arise due to a smaller region of stability in the phase diagram, with no competition between scales. Subsequently, we propose a two-site model of tert-butanol in which the interactions involving hy- drogen bonding are represented by a Stillinger-Weber potential. The potential model is optimized to yield a reasonable description of experimental excess enthalpies and volumes over the whole composition range of the mixture. This model is able to reproduce the maximum in the change of the temperature of maximum density for very low alcohol mole fractions, followed by a considerable decrease until the density anomaly itself disappears. We have correlated this behavior with changes in the local structure of water and compared it with the results of all-atom simulations of water/tert-butanol mixtures. The third studied system was a core-softened representation of water-alcohol mixtures. This approach allowed us to explore the connection between the spontaneous crystallization observed in the supercooled regime in the vicinity of the liquid-liquid phase transition (LLPT), and the density anomaly by performing extensive Molecular Dynamics simulations of a model mixture of coresoftened water and methanol. Our results illustrate the relation between the vanishing of the density anomaly and an increase in the temperature of spontaneous crystallization. This peculiar feature illustrates how fine-tuning the competitive interactions determines the anomalous behavior of water/alcohol mixtures. Finally, we explored the supercooled regime of pure water and mixtures of water and short-chain alcohols (methanol, ethanol and propanol) using core-softened potential models. Our aim is to understand the influence of chain size on the density anomaly, the liquid-liquid phase Our aim is to understand the influence of chain size on the density anomaly, the liquid-liquid phase transition and on the polymorphism observed in these models.Fluidos modelados por potenciais de caroço amolecido compreendem um grande número de sistemas cujos constituintes moleculares têm interações competitivas. O exemplo mais proeminente é a água, cujas moléculas tendem a formar ligações de hidrogênio ou interagir por ligações covalentes. A competição entre essas duas conformações leva a uma série de comportamentos anômalos os quais podem se manifestar tanto em colóides quanto em misturas de água e álcoois de cadeia curta. A descrição bem sucedida de sistemas coloidas por potenciais de duas escalas está relacionada à composição de tais colóides, geralmente feitos de subunidades moleculares formando uma aglomeração central compactada e uma área periférica, menos densa e mais entrópica. Esta estrutura núcleo-coroa pode ser descrita por um núcleo duro e uma coroa macia que representa bem a competição entre efeitos entálpicos e entrópicos. As moléculas de álcoois trazem ainda mais competição para esse cenário complexo, já que a maioria não possui simetria esférica, incorporando, portanto, efeitos anisotrópicos aos sistemas, e são portadores, além da parte carbônica apolar, de grupos hidroxila hidrofílicos, capazes de formar ligações de hidrogênio, o que lhes confere um alto grau de miscibilidade em água. Esta tese foca nos mecanismos moleculares que descrevem o comportamento destes fluidos complexos. Para tanto, realizamos simulações de Dinâmica Molecular de quatro sistemas distintos. Primeiramente, analisamos o comportamento do sistema bidimensional de nanopartículas enxertadas com polímeros, onde potenciais atenuados de núcleo efetivos foram obtidos a partir de simulações de coarse-grained para dois casos: o primeiro caso onde os polímeros são livres para girar em torno do núcleo da nanopartícula, e um segundo onde os polímeros são fixos, com um ângulo de 90∘ entre eles. Devido à competição no sistema, observamos a presença de anomalias semelhantes às da água, como a temperatura de máxima densidade (TMD) e a anomalia na difusão. Observamos que, para o caso dos polímeros fixos, as anomalias do tipo água são originadas pela competição entre as escalas características potenciais, enquanto para o caso livre para girar as anomalias surgem devido a uma menor região de estabilidade no diagrama de fase sem competição entre as escalas. Depois, foi proposto um modelo de terc-butanol de dois sítios, no qual as interações envolvendo ligações de hidrogênio são representadas por um potencial de três corpos (Stillinger-Weber). O modelo foi otimizado para produzir uma descrição razoável da grandezas de excesso (entalpia e volume) experimentais em toda a faixa de composição da mistura, sendo capaz de reproduzir a presença de um máximo na variação da temperatura de máxima densidade no regime super diluído (frações molares de terbutanol muito baixas), seguido por uma diminuição considerável até o desaparecimento da TMD. Correlacionamos esse comportamento com mudanças na estrutura local da água e comparamos com os resultados de simulações all-atom de misturas de água/terc-butanol. O terceiro sistema estudado foi uma mistura de água e álcool na qual as interações entre ambas as moléculas foram representadas por potenciais de caroço atenuado. A abordagem nos permitiu explorar a conexão entre a cristalização espontânea, observada no regime super-resfriado na vizinhança da transição de fase líquido-líquido (LLPT), e a anomalia na densidade, realizando extensas simulações de Dinâmica Molecular. Nossos resultados ilustram a relação entre o desaparecimento da anomalia de densidade e um aumento na temperatura de cristalização espontânea. Esta característica peculiar ilustra como o ajuste fino das interações competitivas determinam o comportamento anômalo das misturas de água e metanol. Por fim, exploramos o regime super-resfriado de água pura e misturas de água e álcoois de cadeia curta (metanol, etanol e propanol) usando modelos de potenciais de duas escalas. Nosso objetivo foi compreender a influência do tamanho da cadeia carbônica na anomalia de densidade, na transição de fase líquido-líquido e no polimorfismo observado nestes modelos

    Ice structures, patterns, and processes: A view across the ice-fields

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    We look ahead from the frontiers of research on ice dynamics in its broadest sense; on the structures of ice, the patterns or morphologies it may assume, and the physical and chemical processes in which it is involved. We highlight open questions in the various fields of ice research in nature; ranging from terrestrial and oceanic ice on Earth, to ice in the atmosphere, to ice on other solar system bodies and in interstellar space
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