Project acronym CABUM
Project An investigation of the mechanisms at the interaction between cavitation bubbles and contaminants
Researcher (PI) Matevz DULAR
Host Institution (HI) UNIVERZA V LJUBLJANI
Call Details Consolidator Grant (CoG), PE8, ERC-2017-COG
Summary A sudden decrease in pressure triggers the formation of vapour and gas bubbles inside a liquid medium (also called cavitation). This leads to many (key) engineering problems: material loss, noise and vibration of hydraulic machinery. On the other hand, cavitation is a potentially a useful phenomenon: the extreme conditions are increasingly used for a wide variety of applications such as surface cleaning, enhanced chemistry, and waste water treatment (bacteria eradication and virus inactivation).
Despite this significant progress a large gap persists between the understanding of the mechanisms that contribute to the effects of cavitation and its application. Although engineers are already commercializing devices that employ cavitation, we are still not able to answer the fundamental question: What precisely are the mechanisms how bubbles can clean, disinfect, kill bacteria and enhance chemical activity? The overall objective of the project is to understand and determine the fundamental physics of the interaction of cavitation bubbles with different contaminants. To address this issue, the CABUM project will investigate the physical background of cavitation from physical, biological and engineering perspective on three complexity scales: i) on single bubble level, ii) on organised and iii) on random bubble clusters, producing a progressive multidisciplinary synergetic effect.
The proposed synergetic approach builds on the PI's preliminary research and employs novel experimental and numerical methodologies, some of which have been developed by the PI and his research group, to explore the physics of cavitation behaviour in interaction with bacteria and viruses.
Understanding the fundamental physical background of cavitation in interaction with contaminants will have a ground-breaking implications in various scientific fields (engineering, chemistry and biology) and will, in the future, enable the exploitation of cavitation in water and soil treatment processes.
Summary
A sudden decrease in pressure triggers the formation of vapour and gas bubbles inside a liquid medium (also called cavitation). This leads to many (key) engineering problems: material loss, noise and vibration of hydraulic machinery. On the other hand, cavitation is a potentially a useful phenomenon: the extreme conditions are increasingly used for a wide variety of applications such as surface cleaning, enhanced chemistry, and waste water treatment (bacteria eradication and virus inactivation).
Despite this significant progress a large gap persists between the understanding of the mechanisms that contribute to the effects of cavitation and its application. Although engineers are already commercializing devices that employ cavitation, we are still not able to answer the fundamental question: What precisely are the mechanisms how bubbles can clean, disinfect, kill bacteria and enhance chemical activity? The overall objective of the project is to understand and determine the fundamental physics of the interaction of cavitation bubbles with different contaminants. To address this issue, the CABUM project will investigate the physical background of cavitation from physical, biological and engineering perspective on three complexity scales: i) on single bubble level, ii) on organised and iii) on random bubble clusters, producing a progressive multidisciplinary synergetic effect.
The proposed synergetic approach builds on the PI's preliminary research and employs novel experimental and numerical methodologies, some of which have been developed by the PI and his research group, to explore the physics of cavitation behaviour in interaction with bacteria and viruses.
Understanding the fundamental physical background of cavitation in interaction with contaminants will have a ground-breaking implications in various scientific fields (engineering, chemistry and biology) and will, in the future, enable the exploitation of cavitation in water and soil treatment processes.
Max ERC Funding
1 904 565 €
Duration
Start date: 2018-07-01, End date: 2023-06-30
Project acronym DECOR
Project Dynamic assembly and exchange of RNA polymerase II CTD factors
Researcher (PI) Richard Stefl
Host Institution (HI) Masarykova univerzita
Call Details Consolidator Grant (CoG), LS1, ERC-2014-CoG
Summary The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) largest subunit coordinates co-transcriptional processing and it is decorated by many processing factors throughout the transcription cycle. The composition of this supramolecular assembly is diverse and highly dynamic. Many of the factors associate with RNAPII weakly and transiently, and the association is dictated by different post-translational modification patterns and conformational changes of the CTD. To determine how these accessory factors assemble and exchange on the CTD of RNAPII has remained a major challenge. Here, we aim to unravel the structural and mechanistic bases for the dynamic assembly of RNAPII CTD with its processing factors.
Using NMR, we will determine high-resolution structures of several protein factors bound to the CTD carrying specific modifications. This will enable to decode how CTD modification patterns stimulate or prevent binding of a given processing factor. We will also establish the structural and mechanistic bases of proline isomerisation in the CTD that control the timing of isomer-specific protein-protein interactions. Next, we will combine NMR and SAXS approaches to unravel how the overall CTD structure is remodelled by binding of multiple copies of processing factors and how these factors cross-talk with each other. Finally, we will elucidate a mechanistic basis for the exchange of processing factors on the CTD.
Our study will answer the long-standing questions of how the overall CTD structure is modulated on binding to processing factors, and whether these factors cross-talk and compete with each other. The level of detail that we aim to achieve is currently not available for any transient molecular assemblies of such complexity. In this respect, the project will also provide knowledge and methodology for further studies of large and highly flexible molecular assemblies that still remain poorly understood.
Summary
The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) largest subunit coordinates co-transcriptional processing and it is decorated by many processing factors throughout the transcription cycle. The composition of this supramolecular assembly is diverse and highly dynamic. Many of the factors associate with RNAPII weakly and transiently, and the association is dictated by different post-translational modification patterns and conformational changes of the CTD. To determine how these accessory factors assemble and exchange on the CTD of RNAPII has remained a major challenge. Here, we aim to unravel the structural and mechanistic bases for the dynamic assembly of RNAPII CTD with its processing factors.
Using NMR, we will determine high-resolution structures of several protein factors bound to the CTD carrying specific modifications. This will enable to decode how CTD modification patterns stimulate or prevent binding of a given processing factor. We will also establish the structural and mechanistic bases of proline isomerisation in the CTD that control the timing of isomer-specific protein-protein interactions. Next, we will combine NMR and SAXS approaches to unravel how the overall CTD structure is remodelled by binding of multiple copies of processing factors and how these factors cross-talk with each other. Finally, we will elucidate a mechanistic basis for the exchange of processing factors on the CTD.
Our study will answer the long-standing questions of how the overall CTD structure is modulated on binding to processing factors, and whether these factors cross-talk and compete with each other. The level of detail that we aim to achieve is currently not available for any transient molecular assemblies of such complexity. In this respect, the project will also provide knowledge and methodology for further studies of large and highly flexible molecular assemblies that still remain poorly understood.
Max ERC Funding
1 844 604 €
Duration
Start date: 2015-08-01, End date: 2020-07-31
Project acronym LaDIST
Project Large Discrete Structures
Researcher (PI) Daniel Kral
Host Institution (HI) Masarykova univerzita
Call Details Consolidator Grant (CoG), PE1, ERC-2014-CoG
Summary The proposed project seeks to introduce novel methods to analyze and approximate large graphs and other discrete structures and to apply the developed methods to solve specific open problems. A need for such methods comes from computer science where the sizes of input structures are often enormous. Specifically, the project will advance the recently emerged theory of combinatorial limits by developing new insights in the structure of limit objects and by proposing a robust theory bridging the sparse and dense cases. The analytic methods from the theory of combinatorial limits will be used to analyze possible asymptotic behavior of large graphs and they will be applied in conjunction with structural arguments to provide solutions to specific problems in extremal combinatorics. The obtained insights will also be combined with methods from discrete optimization and logic to provide new algorithmic frameworks.
Summary
The proposed project seeks to introduce novel methods to analyze and approximate large graphs and other discrete structures and to apply the developed methods to solve specific open problems. A need for such methods comes from computer science where the sizes of input structures are often enormous. Specifically, the project will advance the recently emerged theory of combinatorial limits by developing new insights in the structure of limit objects and by proposing a robust theory bridging the sparse and dense cases. The analytic methods from the theory of combinatorial limits will be used to analyze possible asymptotic behavior of large graphs and they will be applied in conjunction with structural arguments to provide solutions to specific problems in extremal combinatorics. The obtained insights will also be combined with methods from discrete optimization and logic to provide new algorithmic frameworks.
Max ERC Funding
1 386 859 €
Duration
Start date: 2015-12-01, End date: 2020-11-30
Project acronym MaCChines
Project Molecular machines based on coiled-coil protein origami
Researcher (PI) Roman JERALA
Host Institution (HI) KEMIJSKI INSTITUT
Call Details Advanced Grant (AdG), LS9, ERC-2017-ADG
Summary Proteins are the most versatile and complex smart nanomaterials, forming molecular machines and performing numerous functions from structure building, recognition, catalysis to locomotion. Nature however explored only a tiny fraction of possible protein sequences and structures. Design of proteins with new, in nature unseen shapes and features, offers high rewards for medicine, technology and science. In 2013 my group pioneered the design of a new type of modular coiled-coil protein origami (CCPO) folds. This type of de novo designed proteins are defined by the sequence of coiled-coil (CC) dimer-forming modules that are concatenated by flexible linkers into a single polypeptide chain that self-assembles into a polyhedral cage based on pairwise CC interactions. This is in contrast to naturally evolved proteins where their fold is defined by a compact hydrophobic core. We recently demonstrated the robustness of this strategy by the largest de novo designed single chain protein, construction of tetrahedral, pyramid, trigonal prism and bipyramid cages that self-assemble in vivo.
This proposal builds on unique advantages of CCPOs and represents a new frontier of this branch of protein design science. I propose to introduce functional domains into selected positions of CCPO cages, implement new types of building modules that will enable regulated CCPO assembly and disassembly, test new strategies of caging and release of cargo molecules for targeted delivery, design knotted and crosslinked protein cages and introduce toehold displacement for the regulated structural rearrangement of CCPOs required for designed molecular machines, which will be demonstrated on protein nanotweezers. Technology for the positional combinatorial library-based single pot assembly of CCPO genes will provide high throughput of CCPO variants. Project will result in new methodology, understanding of potentials of CCPOs for designed molecular machines and in demonstration of different applications.
Summary
Proteins are the most versatile and complex smart nanomaterials, forming molecular machines and performing numerous functions from structure building, recognition, catalysis to locomotion. Nature however explored only a tiny fraction of possible protein sequences and structures. Design of proteins with new, in nature unseen shapes and features, offers high rewards for medicine, technology and science. In 2013 my group pioneered the design of a new type of modular coiled-coil protein origami (CCPO) folds. This type of de novo designed proteins are defined by the sequence of coiled-coil (CC) dimer-forming modules that are concatenated by flexible linkers into a single polypeptide chain that self-assembles into a polyhedral cage based on pairwise CC interactions. This is in contrast to naturally evolved proteins where their fold is defined by a compact hydrophobic core. We recently demonstrated the robustness of this strategy by the largest de novo designed single chain protein, construction of tetrahedral, pyramid, trigonal prism and bipyramid cages that self-assemble in vivo.
This proposal builds on unique advantages of CCPOs and represents a new frontier of this branch of protein design science. I propose to introduce functional domains into selected positions of CCPO cages, implement new types of building modules that will enable regulated CCPO assembly and disassembly, test new strategies of caging and release of cargo molecules for targeted delivery, design knotted and crosslinked protein cages and introduce toehold displacement for the regulated structural rearrangement of CCPOs required for designed molecular machines, which will be demonstrated on protein nanotweezers. Technology for the positional combinatorial library-based single pot assembly of CCPO genes will provide high throughput of CCPO variants. Project will result in new methodology, understanding of potentials of CCPOs for designed molecular machines and in demonstration of different applications.
Max ERC Funding
2 497 125 €
Duration
Start date: 2018-09-01, End date: 2023-08-31
Project acronym MATHEF
Project Mathematical Thermodynamics of Fluids
Researcher (PI) Eduard Feireisl
Host Institution (HI) MATEMATICKY USTAV AV CR V.V.I.
Call Details Advanced Grant (AdG), PE1, ERC-2012-ADG_20120216
Summary "The main goal of the present research proposal is to build up a general mathematical theory describing the motion of a compressible, viscous, and heat conductive fluid. Our approach is based on the concept of generalized (weak) solutions satisfying the basic physical principles of balance of mass, momentum, and energy. The energy balance is expressed in terms of a variant of entropy inequality supplemented with an integral identity for the total energy balance.
We propose to identify a class of suitable weak solutions, where admissibility is based on a direct application of the principle of maximal entropy production compatible with Second law of thermodynamics. Stability of the solution family will be investigated by the method of relative entropies constructed on the basis of certain thermodynamics potentials as ballistic free energy.
The new solution framework will be applied to multiscale problems, where several characteristic scales become small or extremely large. We focus on mutual interaction of scales during this process and identify the asymptotic behavior of the quantities that are filtered out in the singular limits. We also propose to study the influence of the geometry of the underlying physical space that may change in the course of the limit process. In particular, problems arising in homogenization and optimal shape design in combination with various singular limits are taken into account.
The abstract approximate scheme used in the existence theory will be adapted in order to develop adequate numerical methods. We study stability and convergence of these methods using the tools developed in the abstract part, in particular, the relative entropies."
Summary
"The main goal of the present research proposal is to build up a general mathematical theory describing the motion of a compressible, viscous, and heat conductive fluid. Our approach is based on the concept of generalized (weak) solutions satisfying the basic physical principles of balance of mass, momentum, and energy. The energy balance is expressed in terms of a variant of entropy inequality supplemented with an integral identity for the total energy balance.
We propose to identify a class of suitable weak solutions, where admissibility is based on a direct application of the principle of maximal entropy production compatible with Second law of thermodynamics. Stability of the solution family will be investigated by the method of relative entropies constructed on the basis of certain thermodynamics potentials as ballistic free energy.
The new solution framework will be applied to multiscale problems, where several characteristic scales become small or extremely large. We focus on mutual interaction of scales during this process and identify the asymptotic behavior of the quantities that are filtered out in the singular limits. We also propose to study the influence of the geometry of the underlying physical space that may change in the course of the limit process. In particular, problems arising in homogenization and optimal shape design in combination with various singular limits are taken into account.
The abstract approximate scheme used in the existence theory will be adapted in order to develop adequate numerical methods. We study stability and convergence of these methods using the tools developed in the abstract part, in particular, the relative entropies."
Max ERC Funding
726 320 €
Duration
Start date: 2013-05-01, End date: 2018-04-30
Project acronym PICOSTRUCTURE
Project Structural studies of human picornaviruses
Researcher (PI) Pavel Plevka
Host Institution (HI) Masarykova univerzita
Call Details Starting Grant (StG), LS1, ERC-2013-StG
Summary Many picornaviruses are human pathogens that cause diseases varying in symptoms from common cold to life-threatening encephalitis. Currently there are no anti-picornavirus drugs approved for human use. We propose to study molecular structures of picornaviruses and their life cycle intermediates in order to identify new targets for anti-viral inhibitors and to lay the foundations for structure-based development of drugs against previously structurally uncharacterized picornaviruses.
We will use X-ray crystallography to determine virion structures of representative viruses from Parechovirus, Kobuvirus, Cardiovirus, and Cosavirus genera and Human Rhinovirus-C species. We will use cryo-electron microscopy to study picornavirus replication complexes in order to explain the mechanism of copy-choice recombination of picornavirus RNA genomes that leads to creation of new picornavirus species. We will determine whether picornavirus virions assemble from capsid protein protomers around the condensed genome or if the genome is packaged into a pre-formed empty capsid. Furthermore, we will investigate how picornaviruses initiate infection by analyzing genome release from virions and its translocation across lipid membrane.
A major innovation in our approach will be the use of focused ion beam micromachining for sample preparation that will allow us to study macromolecular complexes within infected mammalian cells by cryo-electron tomography. Our analysis of virion structure, cell entry, genome replication, and particle assembly will identify molecular details and mechanism of function of critical picornavirus life-cycle intermediates.
Summary
Many picornaviruses are human pathogens that cause diseases varying in symptoms from common cold to life-threatening encephalitis. Currently there are no anti-picornavirus drugs approved for human use. We propose to study molecular structures of picornaviruses and their life cycle intermediates in order to identify new targets for anti-viral inhibitors and to lay the foundations for structure-based development of drugs against previously structurally uncharacterized picornaviruses.
We will use X-ray crystallography to determine virion structures of representative viruses from Parechovirus, Kobuvirus, Cardiovirus, and Cosavirus genera and Human Rhinovirus-C species. We will use cryo-electron microscopy to study picornavirus replication complexes in order to explain the mechanism of copy-choice recombination of picornavirus RNA genomes that leads to creation of new picornavirus species. We will determine whether picornavirus virions assemble from capsid protein protomers around the condensed genome or if the genome is packaged into a pre-formed empty capsid. Furthermore, we will investigate how picornaviruses initiate infection by analyzing genome release from virions and its translocation across lipid membrane.
A major innovation in our approach will be the use of focused ion beam micromachining for sample preparation that will allow us to study macromolecular complexes within infected mammalian cells by cryo-electron tomography. Our analysis of virion structure, cell entry, genome replication, and particle assembly will identify molecular details and mechanism of function of critical picornavirus life-cycle intermediates.
Max ERC Funding
1 997 557 €
Duration
Start date: 2014-03-01, End date: 2019-02-28
Project acronym SUPERCOOL
Project Superelastic Porous Structures for Efficient Elastocaloric Cooling
Researcher (PI) Jaka TUŠEK
Host Institution (HI) UNIVERZA V LJUBLJANI
Call Details Starting Grant (StG), PE8, ERC-2018-STG
Summary Cooling, refrigeration and air-conditioning are crucial for our modern society. In the last decade, the global demands for cooling are growing exponentially. The standard refrigeration technology, based on vapour compression, is old, inefficient and environmentally harmful. In the SUPERCOOL project we will exploit the potential of elastocaloric cooling, probably the most promising solid-state refrigeration technology, which utilizes the latent heat associated with the martensitic transformation in superelastic shape-memory alloys. We have already demonstrated a novel concept of utilizing the elastocaloric effect (eCE) by introducing a superelastic porous structure in an elastocaloric regenerative thermodynamic cycle. Our preliminary results, recently published in Nature Energy, show the tremendous potential of such a system. However, two fundamental challenges remain. First, we need to create a geometry of the superelastic porous structure (elastocaloric regenerator) to ensure sufficient fatigue life, a large eCE and rapid heat transfer. Second, we must have a driver mechanism that can effectively utilize the work released during the unloading of the elastocaloric regenerator. To succeed I am proposing a unique approach to design advanced elastocaloric regenerators with complex structures together with a driver mechanism with the force-recovery principle. We will employ a systematic characterization and bottom-up linking of all three crucial aspects of the elastocaloric regenerator, i.e., the thermo-hydraulic properties, the stability and the structural fatigue, together with a new solution for force recovery in effective drivers. Based on these theoretical, numerical and experimental results we will combine both key elements of our novel elastocaloric concept into a prototype device, which could be the first major breakthrough in cooling technologies for 100 years, providing greater efficiency and reduced levels of pollution, by applying a solid-state refrigerant.
Summary
Cooling, refrigeration and air-conditioning are crucial for our modern society. In the last decade, the global demands for cooling are growing exponentially. The standard refrigeration technology, based on vapour compression, is old, inefficient and environmentally harmful. In the SUPERCOOL project we will exploit the potential of elastocaloric cooling, probably the most promising solid-state refrigeration technology, which utilizes the latent heat associated with the martensitic transformation in superelastic shape-memory alloys. We have already demonstrated a novel concept of utilizing the elastocaloric effect (eCE) by introducing a superelastic porous structure in an elastocaloric regenerative thermodynamic cycle. Our preliminary results, recently published in Nature Energy, show the tremendous potential of such a system. However, two fundamental challenges remain. First, we need to create a geometry of the superelastic porous structure (elastocaloric regenerator) to ensure sufficient fatigue life, a large eCE and rapid heat transfer. Second, we must have a driver mechanism that can effectively utilize the work released during the unloading of the elastocaloric regenerator. To succeed I am proposing a unique approach to design advanced elastocaloric regenerators with complex structures together with a driver mechanism with the force-recovery principle. We will employ a systematic characterization and bottom-up linking of all three crucial aspects of the elastocaloric regenerator, i.e., the thermo-hydraulic properties, the stability and the structural fatigue, together with a new solution for force recovery in effective drivers. Based on these theoretical, numerical and experimental results we will combine both key elements of our novel elastocaloric concept into a prototype device, which could be the first major breakthrough in cooling technologies for 100 years, providing greater efficiency and reduced levels of pollution, by applying a solid-state refrigerant.
Max ERC Funding
1 359 375 €
Duration
Start date: 2019-01-01, End date: 2023-12-31
Project acronym SWEETOOLS
Project Smart Biologics: Developing New Tools in Glycobiology
Researcher (PI) Milan Vrabel
Host Institution (HI) USTAV ORGANICKE CHEMIE A BIOCHEMIE, AV CR, V.V.I.
Call Details Starting Grant (StG), LS9, ERC-2015-STG
Summary Glycans are ubiquitous biomolecules found throughout all kingdoms of life. Early studies contributed considerably to our appreciation of glycan functions by showing that abnormalities in the glycosylation can develop into pathogenesis and severe dysfunctions. Despite the crucial role of sugars in many biological events we still do not have adequate tools to decipher their complexity. To unveil the mysteries in the rapidly emerging field of glycobiology we aim in this proposal to develop new tools that will help us to study and understand these important biomolecules. To realize this, we plan to combine the unique targeting capability of biologics with the inhibitory effect of small molecules into robust constructs with advanced properties. The biological part of the construct will be evolved using synthetic peptide libraries ensuring high selectivity toward particular sugar processing enzymes. The second part of the construct will consist of small molecular inhibitor warhead that will be designed and synthesized based on crystal structure-aided analyses. To merge these two moieties we aim to develop a new target enzyme–templated fluorogenic in situ click chemistry methodology that will enable us to easily monitor and screen whole peptide–small molecule bioconjugate libraries as highly selective inhibitors and manipulators of sugar processing enzymes. In addition, we aim to create new multivalent heteroglycosystems by using bioorthogonal reactions on peptide library scaffold. These structures will enable us to study polyvalent carbohydrate–protein interactions and to generate novel therapeutics such as influenza virus entry blockers. Our goal is to develop a new class of smart bioconjugate probes that will help us to answer fundamental questions in glycobiology. The outcomes of this project will significantly deepen our knowledge of glycoconjugates and in the long term, will allow for the design of efficient vaccines and for the development of selective therapeutics.
Summary
Glycans are ubiquitous biomolecules found throughout all kingdoms of life. Early studies contributed considerably to our appreciation of glycan functions by showing that abnormalities in the glycosylation can develop into pathogenesis and severe dysfunctions. Despite the crucial role of sugars in many biological events we still do not have adequate tools to decipher their complexity. To unveil the mysteries in the rapidly emerging field of glycobiology we aim in this proposal to develop new tools that will help us to study and understand these important biomolecules. To realize this, we plan to combine the unique targeting capability of biologics with the inhibitory effect of small molecules into robust constructs with advanced properties. The biological part of the construct will be evolved using synthetic peptide libraries ensuring high selectivity toward particular sugar processing enzymes. The second part of the construct will consist of small molecular inhibitor warhead that will be designed and synthesized based on crystal structure-aided analyses. To merge these two moieties we aim to develop a new target enzyme–templated fluorogenic in situ click chemistry methodology that will enable us to easily monitor and screen whole peptide–small molecule bioconjugate libraries as highly selective inhibitors and manipulators of sugar processing enzymes. In addition, we aim to create new multivalent heteroglycosystems by using bioorthogonal reactions on peptide library scaffold. These structures will enable us to study polyvalent carbohydrate–protein interactions and to generate novel therapeutics such as influenza virus entry blockers. Our goal is to develop a new class of smart bioconjugate probes that will help us to answer fundamental questions in glycobiology. The outcomes of this project will significantly deepen our knowledge of glycoconjugates and in the long term, will allow for the design of efficient vaccines and for the development of selective therapeutics.
Max ERC Funding
1 405 625 €
Duration
Start date: 2016-02-01, End date: 2021-01-31
