Mathematical and computational methods for polyhedral self-assembly

Code

J1-2481 (C) - included in ARIS records

Head

PhD Nino Bašić

Period

9/1/2020 - 8/31/2023

Range in 2023

0.93 FTE

Science

Natural sciences and mathematics (10)
Engineering sciences and technologies (1)

Reseacher status

Researcher (11)
Junior expert or technical associate (0)

Education

Doctor's degree (10)
Other (1)

Sex

Woman (1)
Man (10)

Status

Employed at RO and RRD (9)
No data on employment in RO (2)

No. of publications

0 (10)
1–9 (1)

Projects / Programmes source: ARIS

source: ARIS

Mathematical and computational methods for polyhedral self-assembly

Research activity

Code	Science	Field	Subfield
1.07.01	Natural sciences and mathematics	Computer intensive methods and applications	Algorithms

Code	Science	Field
1.01	Natural Sciences	Mathematics

Keywords

nanostructure design, self-assembly, polypeptides, polyhedra, symmetry, protein, synthetic biology, coiled-coil, strong trace, topofold, origami, algorithms, modeling, software, topological graph theory, flag graphs, parallel computing, plane tilings

Evaluation (rules)

source: COBISS

Evaluation of bibliographic research performance indicators according to ARIS methodology

Citations Citations for bibliographic records in COBIB.SI that are linked to records in citation databases

source: WoS

source: Scopus

source: COBISS

Researchers (11)

no.	Code	Name and surname	Research area	Role	Period	No. of publicationsNo. of publications
1.	34561	PhD Nino Bašić	Mathematics	Head	2020 - 2023	0
2.	01467	PhD Vladimir Batagelj	Mathematics	Researcher	2020 - 2023	1
3.	04967	PhD Andrej Brodnik	Computer intensive methods and applications	Researcher	2020 - 2023	0
4.	06628	PhD Roman Jerala	Biochemistry and molecular biology	Researcher	2020 - 2023	0
5.	24997	PhD Klavdija Kutnar	Mathematics	Researcher	2020 - 2023	0
6.	37987	PhD Fabio Lapenta	Biochemistry and molecular biology	Researcher	2020	0
7.	53353	Klemen Mezgec	Biochemistry and molecular biology	Researcher	2020 - 2023	0
8.	01941	PhD Tomaž Pisanski	Mathematics	Researcher	2020 - 2023	0
9.	36549	PhD Jernej Rus	Mathematics	Researcher	2020 - 2023	0
10.	38337	PhD Žiga Strmšek	Biochemistry and molecular biology	Researcher	2021 - 2022	0
11.	23555	PhD Jernej Vičič	Computer science and informatics	Researcher	2020 - 2023	0

Organisations (3)

no.	Code	Research organisation	City	Registration number	No. of publicationsNo. of publications
1.	2790	University of Primorska, Faculty of mathematics, Natural Sciences and Information Technologies	Koper	1810014009	1
2.	0104	National Institute of Chemistry	Ljubljana	5051592000	10
3.	2975	ABELIUM d.o.o., research and development	Ljubljana	3557952	0

Abstract

The main goal of this project is to further develop existing mathematical models for self-assembly of nanostructures and also create new ones. In particular, we will make heavy use of flag graphs and results from topological graph theory to produce those models. A stronger link between topological graph theory and synthetic biology will be established. All this will be implemented in the form of a user-friendly well-documented library for Python and/or SageMath, which will enable researchers to do various "in silico" experiments. New data structures and algorithms will be developed and incorporated in this software library. This software library will be used to solve several practical self-assembly problems in synthetic biology to demonstrate its usability. Parallelisable algorithms will be developed to enable (computationally intensive) enumerations of strong traces of large polyhedra on multiprocessor systems and computer clusters, which was not possible so far. We will also consider self-assembly of planar nanostructures from the viewpoint of mathematical theory of tilings. The mathematics and software that will be developed will have direct applications in the area of synthetic biology.