基本信息
Jure Dobnikar  男  博导  中国科学院物理研究所
电子邮件: jd489@cam.ac.uk
通信地址: 北京市海淀区中关村南三街8号
邮政编码:
部门/实验室:软物质实验室

研究领域

胶体,自组织,多体相互作用,磁性胶体, 计算机模拟

招生信息

   
招生专业
070205-凝聚态物理
招生方向
胶体相互作用;自组装动力学;生物系统的多价结合;生物系统的多价结合;细菌运动

教育背景

   
学历

1986 – 1990Gimnazija Maribor中学,马里博尔,斯洛文尼亚;

199610月,卢布亚尔那大学物理学学士学位,斯洛文尼亚;

200103月,卢布亚尔那大学物理学博士学位,斯洛文尼亚;


工作经历

1996-2000,博士研究生,马里博尔大学,约瑟夫斯蒂芬研究院,斯洛文尼亚

2001-2004,博士后,坎斯坦茨大学物理系,德国

2004-2006,玛丽-居里欧洲内部基金,格拉茨大学,奥地利

2006-2007,玛丽-居里重构基金,约瑟夫斯坦芬研究院,斯洛文尼亚

2006-2015,高级研究员,理论物理系,约瑟夫斯蒂芬研究院,斯洛文尼亚

2008-2015,高级研究员,化学系,剑桥大学,英国

2014-2016,主任助理,主要研究员和国际合作主管,国际软物质中心,北京化工大学

2016-2020,(兼职)ITN协调人,化学系,剑桥大学,英国

2016-20××,副教授,物理所,中科院,北京,中国


教授课程

   
课程

2015-20××授课(软物质,统计力学,分子模拟),北京化工大学 

2011.04       客座教授,(研究生软物质课程)巴塞罗那大学,西班牙 

2006-2016 授课(统计力学,计算方法,现代物理学,量子力学,胶体相互作用,物理学)卢布亚尔那大学和马里博尔大学,斯洛文尼亚 

2008-2014 指导(统计力学,软物质)剑桥大学,英国 

1997-2013 助教卢布亚尔那大学,坎斯坦茨大学

出版信息

65 T. Curk, C. A. Brackley, J. D. Farrell, Z. Xing, D. Joshi, S. Direito, U. Bren, S. Angioletti-Uberti, J. Dobnikar*, E. Eiser*, D. Frenkel*, R. J. Allen*, Computational design of probes to detect  bacterial genomes  by multivalent binding, Proc. Nat. Ac. Sci. USA 117 (16) 8719-8726 (2020)

64 Jiachen Wei, Simòn Ramírez-Hinestrosa, Jure Dobnikar*, Daan Frenkel*, Effect of the interaction strength and anisotropy on the diffusio-phoresis of spherical colloids, Soft Matter, 16, 3621-3627 (2020); COVER IMAGE

63 Xipeng Wang, Simòn Ramirez-Hinestrosa, Jure Dobnikar*, Daan Frenkel*, The Lennard-Jones potential: when (not) to use it, in press PCCP, DOI: 10.1039/C9CP05445F (2020); https://doi.org/10.1039/C9CP05445F  arXiv:1910.05746;

62 T. Curk, J.D. Farrell, Jure Dobnikar*, R. Podgornik*, Spontaneous Domain Formation in Spherically-Confined Elastic Filaments, Phys. Rev. Lett. 123 047801 (2019)

61 Yow-Ren Chang, Erick R. Weeks, Daniel Barton, Jure Dobnikar*, William A. Ducker*, Effect of Topographical Steps on the Surface Motility of the Bacterium Pseudomonas aeruginosa, ACS Biomater. Sci. Eng. 5(12) 6436-6445 (2019)

60 J. Dobnikar*, Dynamic Assembly of Magnetic Nanocolloids; in D. Chakrabarti and S. Sacanna (Editors): SELF-ASSEMBLY OF NANO- AND MICRO-STRUCTURED MATERIALS USING COLLOIDAL ENGINEERING; Elsevier Nanoscience Series, in press (2019);

60a J. Dobnikar*, Dynamic Assembly of Magnetic Nanocolloids, Frontiers of Nanoscience 13 23 (2019)

59 Hanqing Wang, Jure Dobnikar*, Jürgen Horbach, Active microrheology in two-dimensional magnetic networks, Soft Matter 15 4437-4444 (2019); COVER IMAGE

58 Tao Li, J. Klebes, Jure Dobnikar*, Paul S. Clegg*, Morphology Evolution of a Particle-Stabilized Binary-Component System, Chem. Commun. 55 5575 (2019)

57  T. Li, A. Schofield, K. Chen, J. Thijssen, J. Dobnikar*, P. Clegg*, Particle-Stabilized Janus Emulsions that Exhibit pH-Tunable Stability, Chem. Commun. 55 5773 (2019); COVER IMAGE

56  Xinli Gao, Song Hong, Zhiping Liu, Tongtao Yue, Jure Dobnikar*, Xianren Zhang*, Membrane potential drives direct translocation of cell-penetrating peptides, Nanoscale 11, 1949-1958 (2019)

55  T. Curk, P. Wirnsberger, J. Dobnikar*, D. Frenkel*, A. Saric*, Controlling cargo trafficking in multicomponent membranes, Nano Letters 18 (9) 5350-5356 (2018) ; COVER IMAGE

54 T. Curk, U. Bren, J. Dobnikar*, Bonding interactions between ligand-decorated colloidal particles, Mol. Phys. 116 (21-22) 3392-3400 (2018)

53 T. Curk, J. Dobnikar*, D. Frenkel*, Design principles for superselectivity using multivalent interactions; in R. Haag, J. Huskens, L. Prins, B.J. Ravoo (Editors), Multivalency: Concepts, Research & Applications, John Wiley & Sons Ltd (2018)

52 Q. Xiao, Y. Liu, Z. Guo, Z. Liu, D. Frenkel*, J. Dobnikar*, X. Zhang*, What experiments on pinned nanobubbles can tell about the critical nucleus for bubble nucleation, Eur. Phys. J. E 40 114 (2017)

51 E.Y. Lee, T. Takahashi, T. Curk, J. Dobnikar*, R.L. Gallo*, G.C.L. Wong*, Crystallinity of Double-Stranded RNA-Antimicrobial Peptide Complexes Modulates Toll-Like Receptor 3-Mediated Inflammation, ACS Nano 11 (12) 12145–12155 (2017)

50 T. Curk, J. Dobnikar*, D. Frenkel*, Optimal multivalent targeting of membranes with many distinct receptors, Proc. Nat. Ac. Sci. USA 114 (28) 7210-7215 (2017)

49 Y. Brill-Karniely*, F. Jin, G.C.L. Wong*, D. Frenkel, J. Dobnikar*, Emergence of complex behavior in coordination of type IV pili, Scientific Reports; in press (2017) 

48 K. Ioannidou, M. Kanduc, L. Li, D. Frenkel, J. Dobnikar*, E. Del Gado*, Crucial effect of earlystage gelation on mechanical properties of cement, Nature Communications 7 12106 (2016) 

47 B. Zhang, X. Chen, J. Dobnikar*, Z. Wang, X. Zhang, Spontaneous Wenzel to Cassie dewetting transition on structured surfaces, Phys. Rev. Fluids 1 073904 (2016) 

46 J. Wei, F. Song, J. Dobnikar*, Assembly of superparamagnetic filaments in external field, Langmuir 32 9321 (2016) 

45 T. Mohoric, G. Kokot, N. Osterman, A. Snezhko, A. Vilfan, D. Babic, J. Dobnikar*, Dynamic Assembly of Magnetic Colloidal Vortices, Langmuir 32 5094 (2016) 

44 E.Y. Lee, C.K. Lee, N.W. Schmidt, F. Jin, R. Lande, T. Curk, A. Kaplan, D. Frenkel, J. Dobnikar, M. Gilliet, and G.C.L. Wong, A review of immune amplification via ligand clustering by self-assembled liquid-crystalline DNA complexes, Adv. Col. Int. Sci. 232 17 (2016) 

43 T. Mohoric, J. Dobnikar*, J. Horbach, Two-dimensional magnetic colloids under shear, Soft Matter 12 3142 (2016); FRONT COVER 

42 J. Wei, J. Dobnikar, T. Curk, F. Song, The effect of attractive interactions and macromolecular crowding on crystallins association, PLoS One 11 e0151159 (2016) 

41 T. Curk, J. Dobnikar*, D. Frenkel, Rational design of molecularly imprinted polymers, Soft Matter 12 35 (2016); FRONT COVER 

40 N.W. Schmidt, F. Jin, R. Lande, T. Curk, W. Xian, L. Frasca, D. Frenkel, J. Dobnikar*, M. Gilliet*, G.C.L. Wong*, Antimicrobial-peptide-DNA complexes amplify TLR9 activation via liquidcrystalline ordering, Nature Materials 14 696 (2015) 

39 D. Dean, J. Dobnikar, A. Naji, R. Podgornik (Editors): Electrostatics of Soft and Disordered Matter, Pan Stanford Publishing Pte. Ltd.Singapore (2014) 

38 T. Curk, F. Martinez-Veracoechea, D. Frenkel and J. Dobnikar*: Nanoparticle organization in sandwiched polymer brushes, Nano Letters 2617 (2014) 

37 K. Müller, N.Osterman, D. Babić, C.N. Likos, J. Dobnikar*, A. Nikoubashman*: Pattern formation and coarse-graining in 2D colloids driven by multiaxial magnetic fields, Langmuir  18 5088 (2014) 

36 F. Martinez-Veracoechea, B.M. Mognetti, S. Angioletti-Uberti, P. Varilly, D. Frenkel, J. Dobnikar*, Designing stimulus-sensitive colloidal walkers, Soft Matter 10 3463 (2014) 

35 T. Curk, D. Marenduzzo, and J. Dobnikar*: Chemotactic sensing towards ambient and secreted attractant drives collective behaviour of E. coli, PLoS One 8 e74878 (2013) 

34 T. Curk, F. Martinez-Veracoechea, D. Frenkel, and J. Dobnikar*: Collective ordering of colloids in grafted polymer layers, Soft Matter 5565 (2013) 

33 J. Dobnikar*, A. Snezhko, and A. Yethiraj: Emergent colloidal dynamics in electromagnetic fields, Soft Matter 9 3693 (2013) 

32 J. Dobnikar*, T. Curk, F. J. Martinez-Veracoechea, and D. Frenkel: Slow colloidal dynamics in polymer brushes, AIP Conf. Proc. 1518 391 (2013) 

31 S. El Shawish, E. Trizac, and J. Dobnikar*: Phase behaviour of colloidal assemblies on 2D corrugated substrates, J. Phys.: Condens. Matter 24 284118 (2012) 

30 T. Curk, A. de Hough, F.J. Martinez-Veracoechea, E. Eiser, D. Frenkel, J. Dobnikar, M. Leunissen: Layering, freezing, and re-entrant melting of hard spheres in soft confinement,Phys. Rev. E 85 021502 (2012) 

29 B.M. Mognetti, P. Varilly, S. Angioletti-Uberti, F.J. Martinez-Veracoechea, J. Dobnikar, M. Leunissen, D. Frenkel: Predicting DNA-mediated colloidal pair interactions, PNAS 109 E378 (2012) 

28 T. Curk, F. Matthäus, Y. Brill-Karniely, J. Dobnikar*: Coarse graining E. coli chemotaxis: from multi-flagella propulsion to logarithmic sensing, Adv. Exp. Med. Biol. 736 381 (2012)

27 F. Matthäus, M.S. Mommer, T. Curk, J. Dobnikar*: On the origin and characteristics of noiseinduced Lévy Walks of E. Coli, PLoS ONE e18623 (2011) 

26 S. Y. Lee, K. J. Webb, S. M. Clarke, M. O'Sullivan, and Jure Dobnikar: Low Salinity Oil Recovery: Increasing Understanding of the Underlying Mechanisms of Double Layer Expansion,Proceedings of the 16th EAGE meeting, Cambridge (2011) 

25 S. El Shawish, J. Dobnikar*, E. Trizac: Colloidal ionic complexes on periodic substrates: Ground-state configurations and pattern switching, Phys. Rev. E 83 041403 (2011) 

24 E. Trizac, S. El Shawish, J. Dobnikar: Dimeric and dipolar ground state orders in colloidal molecular crystals, An. Acad. Bras. Cienc. 82 87 (2010) 

23 N. Osterman, I. Poberaj, J. Dobnikar*, D. Frenkel, P. Ziherl* and D. Babić*: Field-induced selfassembly of suspended colloidal membranes, Phys. Rev. Lett. 103 228301 (2009); 

22 F. Mattheus, M. Jagodič, and J. Dobnikar*: E. coli Super-diffusion and Chemotaxis – Search Strategy, Precision and Motility, Biophys. J. 97 946 (2009) 

21 M. Kanduč, J. Dobnikar*, R. Podgornik*: Counterion-mediated electrostatic interactions between helical molecules, Soft Matter 5 868 (2009) 

20 J. Dobnikar*, J. Fornleitner, G. Kahl: Ground states of model core-softened colloids, J. Phys.: Condens. Matter 20 494220 (2008) 

19 J. Baumgartl, J. Dietrich, C. Bechinger, J. Dobnikar, H.H.von Grünberg: Phonon dispersion curves of two-dimensional colloidal crystals: on the wavelength dependence of friction, Soft Matter 4 2199 (2008); FRONT COVER 

18 S. El Shawish, J. Dobnikar*, E. Trizac: Ground states of colloidal molecular crystals on periodic substrates, Soft Matter 4 1491 (2008) 

17 N. Osterman, D. Babic*, I. Poberaj, J. Dobnikar*, P. Ziherl*: Observation of Condensed Phases of Quasiplanar Core-Softened Colloids, Phys. Rev. Lett. 99 248301 (2007) 

16 E. Trizac, L. Belloni, J. Dobnikar*, R. Castañeda-Priego, H.H. von Grünberg: Macroion virial contribution to the osmotic pressure in charge-stabilized colloidal suspensions, Phys. Rev. E 75 011401 (2007) 

15 J. Dobnikar*, P. Ziherl: Stability of the hexagonal lattice of charged colloids, J. Mol. Liquids 173 131-132 (2007) 

14 J. Dobnikar*, R. Castañeda-Priego, H.H von Grünberg, E. Trizac: Testing the relevance of effective interaction potentials between highly charged colloids in suspension, New J. Phys. 277 (2006) 

13 S. Bleil, H.H. von Grünberg, J. Dobnikar*, R. Castaneda-Priego, C. Bechinger: Strain-induced domain formation in two-dimensional colloidal systems, Europhys. Lett. 73 450 (2006) 

12 Brunner M., Dobnikar J.*, von Grünberg H.H., Bechinger C.*: Direct measurement of threebody interactions amongst charged colloids, Phys. Rev. Lett. 92 078301 (2004) 

11 Dobnikar J.*, Brunner M., von Grünberg H.H., Bechinger C.: Three-body interactions in colloidal systems, Phys. Rev. E 69 031402 (2004) 

10 Dobnikar J.*, Halozan D., Brumen M., von Grünberg H.H., Rzehak R.: Poisson-Boltzmann Brownian dynamics of charged colloids in suspension, Computer Phys. Comm. 159 73 (2004) 

9 Dobnikar J.*, M. Brunner, J. Baumgartl, C. Bechinger and H.H. von Grünberg: Three- and fourbody interactions in colloidal systems, Proceedings of SPIE 5514, 340 (2004) 

8 Dobnikar J.*, Chen Y., Rzehak R. von Grünberg H.H.: Many-body interactions and the melting of colloidal crystals, J. Chem. Phys. 119 (9) 4971 (2003) 

7 Dobnikar J.*, Rzehak R., von Grünberg H.H.: Effect of many-body interactions on solid-liquid phase behaviour of charge-stabilized colloidal suspensions, Europhys. Lett. 61 695 (2003) 

6 Dobnikar J.*, Chen Y., Rzehak R., von Grünberg H.H.: Many-body interactions in colloidal suspensions, J. Phys.: Condens. Matter 15 S263 (2003) 

5 Podgornik R., Dobnikar J.*: Casimir and pseudo-Casimir interactions in confined polyelectrolytes, J. Chem.Phys. 115 1951 (2001) 

4 Dobnikar J., Podgornik R.: Pseudo-Casimir force in confined nematic polymers, Europhys. Lett 53 735 (2001) 

3 Robnik M., Dobnikar J.*, Prosen T.: Energy level statistics in the transition regime between integrability and chaos for systems with broken antunitary symmetry, J. Phys. A: Math. Gen. 32 1427 (1999) 

2 Robnik M., Prosen T., Dobnikar J.*: Multi-component random model of diffusion in chaotic systems, J. Phys. A: Math. Gen. 32 1147 (1999) 

1 Robnik M., Dobnikar J.*, Rapisarda A., Prosen T., Petkovšek M.: New universal aspects of diffusion in strongly chaotic systems, J. Phys. A: Math. Gen. 30 L803 (1997)

科研活动

I am broadly interested in studying organization of soft and biological matter and the unifying physical principles behind new materials design and complex biological processes. I use methods of theoretical physics and statistical mechanics to develop theoretical models and perform multiscale modeling of systems such as self-assembly and dynamics of complex colloids (e.g.  charged, magnetic, polymer-nanoparticle mixtures…), collective motility  of bacteria, and the role of multivalent binding in super-selective  targeting, molecular recognition, and functioning of immune system.  My work is usually interdisciplinary and related to experiments  performed by my international collaborators. Recently, I have  contributed to important achievements in topics that are shortly  outlined below.

Multivalent binding & selectivity. In (PNAS 2017), we  used computer simulations and statistical physics to formulate a theory  for targeting multicomponent receptor profiles by probe particles. We  derived simple design rules for optimal multivalent targeting. The key  finding is that selectivity can only be achieved by coating the  particles with many ligands that bind only weakly to the receptors: the  optimal ligand-receptor binding free energy is only about kBT.  The design rules discovered here are conceptually different from the  traditional approaches in biomedicine, which are based on identifying  antibodies that strongly and monovalently bind to the cell markers. Our  work suggests that instead of antibodies that cannot be selective, the  efficiency of cancer treatment could be greatly enhanced by using  multivalent particles. A related question, how to selectively transport particles through the cell membrane, has been addressed in another study (Nano Letters 2018).  We found a novel robust mechanism for controlling cargo trafficking by  adjusting the membrane composition. The presence of inert membrane  components with small spontaneous curvature dramatically influences  cargo endocytosis, so curved lipids, such as cholesterol, or  asymmetrically included proteins and tethered sugars can actively  participate in the control of endocytosis.

New approach to genome detection. Our study (PNAS 2020)  uses computer simulations to suggest how to detect pathogen DNA in a  simple and efficient way – using probes that bind weakly all over the  target DNA and exploit the concept of super-selectivity. We  computationally designed probes, which can distinguish between viral and  bacterial genome, and even between very similar strands of E. coli  bacterium. This work has a potential to result in a new fast and  economic disease detection method, which is urgently needed in the  present-day situation.

Viral DNA prefers to be compartmentalized. In a recent work (PRL 2019),  we addressed the problem of packing DNA molecules inside the viral  capsids. We postulated a simplified model of an elastic filament  confined to a sphere with three competing interactions: elasticity,  excluded volume, and spherical confinement. This simple model gives rise  to a surprisingly great deal of complexity. We observed that compartmentalization into multiple domains  is always preferred to a single domain (inverted spool) proposed in  previous works. Multidomain ordering is known from the structure of  chromatin, where the complex protein-DNA interactions drive the  segregation of DNA. Here, we have shown that it can emerge in a much  simpler and smaller system, in the absence of specific structural  constraints. Our results give a general context in which viral DNA  packing can be discussed, offering fresh insight into the fundamental  mechanisms that govern this process.

Physics of immune system activation. In (Nature Materials 2015), we  report on collaborative research combining statistical mechanics,  computer simulations, and experiments to elucidate physical principles  behind immune system activation. We have shown that receptor activation  leading to inflammatory immune response is intimately related to the  structure of self-assembled peptide-DNA complexes. We observed similar  mechanisms in RNA clusters activating TLR-3 receptors (ACS Nano 2018) and in other systems (preprint 2020).  Our findings elucidate how non-specific interactions are turned into  specific through multivalency and that immune response could be  modulated deterministically.

Dynamic assembly of comlex colloids.    I studied dynamic assembly of magnetic colloids as a novel tool to  control the structure formation in complex colloidal suspensions (Soft Matter 2019, Lnagmuir 2016, Soft Matter 2016, Langmuir 2016).  A problem where fundamental physical mechanism is related is cement  hydration. Perhaps surprisingly, soft matter nano physics plays a  crucial role in developing material macroscopic strength. The complexity  of the problem is in the fact that during the setting of the cement –  due to the on-going chemical reactions – the nanoparticle interactions  are varying with time. We discovered (Nature Commun. 2016)  a subtle relation between this non-equilibrium process and the  underlying thermodynamics, which will enable efficient design of novel  green formulations of cement. We also studied (Nano Letters 2014, Soft Matter 2014)  grafted polymer layers infiltrated by colloidal nanoparticles. The  observed microphase separation is potentially interesting for  applications in micro-sensing, surface characterization, photovoltaics,  antifouling, filtration and catalysis.




合作情况

有一个广阔的国际合作网络。主要的合作对象是:Daan Frenkel (剑桥大学),Gerard Wong (加州大学洛杉矶分校)Anand Yethiraj (圣约翰岛)Emanuela Del Gado and Peter Olmsted (乔治城大学) Alexey Snezhko (阿尔贡国家实验室) Erik Luijten (西北大学), Emmanuel Trizac, Lyderic Bocquet, Benjamin Rotenberg (巴黎) Christos Likos (维也纳), Jürgen Horbach (杜塞尔多夫) Clemens Bechinger (斯图加特) Davide Marenduzzo (爱丁堡) Ignacio Pagonabarraga (巴塞罗那) Franziska Matthäus (海德尔堡) Dušan Babić, Matej Praprotnik, Vojko Vlachy, Primož Ziherl and Rudi Podgornik (卢布亚尔那).  


指导学生

   
指导学生

指导了/正在指导:10位博士,6位学士,6位硕士研究生和10位博士后

现在的研究团队中有3位博士后,5位博士研究生和几位长期的访问学者