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Projects / Programmes source: ARIS

Multiscale modeling and simulation of soft and biological matter in and out of equilibrium

Periods
Research activity

Code Science Field Subfield
1.07.00  Natural sciences and mathematics  Computer intensive methods and applications   
1.02.00  Natural sciences and mathematics  Physics   

Code Science Field
B120  Biomedical sciences  Molecular biophysics 

Code Science Field
1.01  Natural Sciences  Mathematics 
1.03  Natural Sciences  Physical sciences 
Keywords
Multiscale Modeling & Simulation, Molecular Simulations, Open Boundary Molecular Dynamics, Nanofluidics, Grand-Canonical Ensemble, Nonequilibrium Molecular Simulations, Computational Fluid Dynamics, Graph-based Approaches, Machine Learning, Soft and Biological Matter
Evaluation (rules)
source: COBISS
Points
2,668.8
A''
321.38
A'
1,427.02
A1/2
1,975.53
CI10
3,364
CImax
226
h10
29
A1
9.59
A3
1.48
Data for the last 5 years (citations for the last 10 years) on July 12, 2024; A3 for period 2018-2022
Data for ARIS tenders ( 04.04.2019 – Programme tender , archive )
Database Linked records Citations Pure citations Average pure citations
WoS  207  5,109  3,971  19.18 
Scopus  202  5,485  4,267  21.12 
Researchers (12)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  54539  PhD Amaury Coste  Computer intensive methods and applications  Researcher  2020 - 2024 
2.  54675  Aljaž Draškovič-Bračun  Physics  Junior researcher  2020 - 2024 
3.  54982  Luka Golob  Computer intensive methods and applications  Technical associate  2020 - 2021 
4.  25435  PhD Janez Konc  Computer intensive methods and applications  Researcher  2020 - 2024  236 
5.  54623  Nikolaos Ntarakas    Technical associate  2020 - 2024 
6.  52000  PhD Petra Papež  Computer intensive methods and applications  Technical associate  2020 - 2024  11 
7.  54019  PhD Tilen Potisk  Computer intensive methods and applications  Researcher  2020 - 2024  42 
8.  19037  PhD Matej Praprotnik  Computer intensive methods and applications  Head  2020 - 2024  327 
9.  35381  PhD Jurij Sablić  Computer intensive methods and applications  Researcher  2020 - 2024  29 
10.  53609  Ema Slejko  Computer intensive methods and applications  Junior researcher  2020 - 2023 
11.  55057  PhD Jaka Sočan  Computer intensive methods and applications  Researcher  2020 - 2024 
12.  19136  PhD Daniel Svenšek  Physics  Researcher  2020 - 2024  203 
Organisations (1)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  21,237 
Abstract
Soft and biological matter displays properties that span a wide range of spatiotemporal scales. Moreover, their interplay is often crucial for understanding of underlying physical and chemical mechanisms, with the aim to control and design new materials with desired properties. Owing to the limited computational power, however, computational studies of these complex molecular systems are still very challenging. Therefore, computational efficiency for simulating large systems on long time scales has become one of the main targets in constructing modern simulation algorithms. In such molecular simulations, specific chemical details are typically required only in those domains, where a relevant process is unfolding, whereas the remainder of the system can be considered as a macroscopic thermodynamic bath. Hence, an efficient computational strategy is to employ multiscale methods, which concurrently couple models with different resolutions in different domains. Soft and biological matter systems are commonly open, i.e., they exchange mass, momentum, and energy with their surroundings. State-of-the-art molecular simulations are on the other hand predominantly performed using periodic boundary conditions with a constant number of molecules. We aim to develop and apply advanced multiscale computational methods that will allow for open simulations of molecular liquids. The open simulation domain will be resolved atomistically. The multiscale buffers, located at the outer part of the open box, will make the insertion of large coarse-grained molecules into a dense system feasible. This will enable us to perform efficient equilibrium simulations of dense molecular systems in the Grand-Canonical ensemble as well as nonequilibrium fluid flow simulations. We will further extend this open setup to continuum description of fluids, solving the Navier-Stokes equation. Such hybrid approaches are especially useful for simulations of the transport of nanoparticles through fluids, such as in targeted drug delivery. Previous theoretical research has shown that liquid-crystalline polymers exhibit a a general (or generic) geometric coupling between orientational order and density variations. Combining continuum and molecular approaches, we will apply this geometric reasoning to isotropic polymer systems and study to what extent gradients in the density can induce orientational order in a polymer melt. Our focus will be on linear biopolymers, e.g., DNA. We will also combine statistical physics approaches with modern computer techniques to concurrently couple atomistic and supramolecular models, where a coarse-grained bead corresponds to several molecules. We will resort to graph-based and machine learning approaches for systematic supramolecular coarse-graining and seamless coupling to the atomistic resolution. Employing the developed methods, we will study various relevant problems in the field of biophysics, biology and (bio)chemistry, pharmaceutical and materials science.
Significance for science
Molecular simulations have become a well-established and indispensable tool for studies of complex phenomena in soft and biological matter. They provide detailed insight into structural as well as functional properties of biological macromolecules that are sometimes too difficult to obtain experimentally or too complex to be treated theoretically. Biomolecular systems are, however, very challenging to simulate, because they are characterized by physical properties that are determined by the interplay of disparate spatiotemporal scales. This inevitably leads to a trade-off between efficiency and accuracy. Atomistic molecular dynamics (MD) simulations can describe a system in great detail but are computationally expensive. Despite the increasing computational power and ongoing efforts to enhance the efficiency of MD algorithms, they are often incapable of spanning the time and length scales required for solutions of important problems. Multiscale methods are the most efficient way to address the interlinked length and timescales encountered in soft and biological matter, as they overcome the limitations of both atomistic and coarse-grained simulations by providing not only computational advantages but also enhanced insight. We will continue to improve state-of-the-art multiscale models of water and salt solutions, as the most important solvents in biomolecular systems. In particular, we will focus on the coupling atomistic water models with the supramolecular counterparts, e.g., MARTINI and Dissipative Particle Dynamics (DPD). Our multiscale approaches will bridge the hydrodynamics from the atomic to macroscopic scale and enable the study of biophysical problems and processes that are beyond the scope of either atomistic, mesoscopic, or macroscopic simulations. Biomolecular systems are also typically open, i.e., mass, momentum, and energy are exchanged with the surroundings. However, standard molecular simulations are commonly performed using periodic boundary conditions with a constant number of particles. We will further develop and use advanced simulation methods that allow us to go beyond this limitation and make possible molecular simulations of open systems, either in thermodynamic equilibrium in the Grand Canonical ensemble or under arbitrary non-equilibrium conditions. We will simulate fluid flows past and through nano-objects bridging molecular approaches using computational fluid dynamics aiming to reproduce essential features of the fluid flows computed by molecular dynamics. Computational advantages of computational fluid dynamics allow for simulations well beyond the current reach of molecular dynamics. Recent advances in nanotechnology and nanomedicine have triggered much development in theoretical and simulation approaches to study non-equilibrium systems. Simulations can provide insight into such systems when they can access both the atomistic length scales associated with size of the nanoparticles and the micro/macro scales characteristic of the carrier flow field. Simulations using MD can capture the atomistic details of the nanoparticle-liquid interface but due to their computational cost they cannot be extended currently to the macroscale regime of the full flow field. In turn, continuum descriptions, using the Navier-Stokes equations may capture the macro-scale behavior of the fluid flow but they fail to accurately represent the flow field at the nanoparticle surface. The hybrid approaches would combine the powerful features of both descriptions, i.e., the ability to describe the macro-scale behavior of the flow as well as accurate boundary conditions around nanoparticles. We will use and develop state-of-the-art multiscale simulation techniques to study nanoflows in various biologically and technologically important systems. The new hybrid methods will enable us to tackle these systems on microscopic and macroscopic scales concurrently, which was previously not possible without supercomputers. This wil
Significance for the country
The advance of basic science is one of the most important driving forces of the progress and development of the society, as it enables the progress of applied science and thus eventually also facilitates the technological advance. The proposed programme will importantly contribute to top-quality education of young researchers and other young scientists (graduate and postgraduate students). An important part of the programme is close international collaboration with leading scientific institutions and researchers. The programme is, therefore, important in terms of strengthening and enhancing Slovenia’s recognition and reputation within the international scientific community. The results of our research will continue to be published in renowned international scientific journals and presented at international and national scientific conferences. Our programme group transfers the knowledge and experience to other users from the research community and industry. We also participate in the educational process, by mentoring diploma and doctoral students as well as with lectures in fields of physics, biophysics, computer science, pharmacy, and chemistry at different universities in Slovenia and abroad. The novel knowledge, obtained by this project, will contribute to further development of the computational, biophysical, pharmaceutical, biotechnological, and biomedical scientific fields in Slovenia. Indirectly, the programme will influence the national identity as a consequence of publication of scientific achievements in international journals and patents as well as the organization of international scientific conferences in Slovenia.The members of the programme group also collaborate with the users and help them solve their specific problems. In this way gained and developed functional knowledge by the members of the programme team are the fundament, which enables the organization of a high tech spin-off companies. The thus created product can be commercialized and may represent a significant contribution to the economical exploitation of the existing infrastructure at the academic research institutions. The multiscale simulation methods, which couple the atomistic, mesoscopic, and continuum spatial scales, will be developed and employed in this programme, should pave the way for simulation-based studies of pharmaceutical and medical interest, e.g., targeted drug delivery. Since the programme group members collaborate with the Slovenian pharmaceutical industry, i.e., Lek (Sandoz) and Krka, we envisage that our biomolecular simulation results may be of interest for potential applications in the pharmaceutical industry. Furthermore, we organize different scientific meetings, e.g. the CECAM (Centre Européen de Calcul Atomique et Moléculaire) and PRACE (Partnership for Advanced Computing in Europe) conferences, schools, workshops, etc. With the active membership in CECAM and PRACE (programme leader is the Vice-Chair of PRACE Scientific Steering Committee and a council member of CECAM) we contribute to the recognition of Slovenia as well as to the enhancement of the reputation of science in Slovenia.
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