1. LUO, Binbin, ZIWEI, Wang, CURK, Tine, WATSON, Garrett, LIU, Chang, KIM, Ahyoung, OU, Zihao, LUIJTEN, Erik, CHEN, Qian. Unravelling crystal growth of nanoparticles. Nature nanotechnology. [Online ed.]. 2023, vol. 18, str. 589-595, ilustr. ISSN 1748-3395. DOI: 10.1038/s41565-023-01355-w. [COBISS.SI-ID 176820995]
projekt: We thank J. Kim for useful discussions. Z.W. gratefully acknowledges support from a Ryan Fellowship and the International Institute for Nanotechnology at Northwestern University. This material is based on work supported by the US Department of Energy, Ofice of Science, Ofice of Basic Energy Sciences, Division of Materials Sciences and Engineering, under award nos. DE-SC0020723 and DE-SC0020885. G.W. was supported by the National Science Foundation Graduate Research Fellowship under grant no. DGE-1842165 and T.C. by the EU’s Horizon 2020 programme under Marie Skłodowska-Curie Fellowship no. 845032

Crystal growth from nanoscale constituents is a ubiquitous phenomenon in biology, geology and materials science. Numerous studies have focused on understanding the onset of nucleation and on producing high-quality crystals by empirically sampling constituents with different attributes and varying the growth conditions. However, the kinetics of post-nucleation growth processes, an important determinant of crystal morphology and properties, have remained underexplored due to experimental challenges associated with real-space imaging at the nanoscale. Here we report the imaging of the crystal growth of nanoparticles of different shapes using liquid-phase transmission electron microscopy, resolving both lateral and perpendicular growth of crystal layers by tracking individual nanoparticles. We observe that these nanoscale systems exhibit layer-by-layer growth, typical of atomic crystallization, as well as rough growth prevalent in colloidal systems. Surprisingly, the lateral and perpendicular growth modes can be independently controlled, resulting in two mixed crystallization modes that, until now, have received only scant attention. Combining analytical considerations with molecular dynamics and kinetic Monte Carlo simulations, we develop a comprehensive framework for our observations, which are fundamentally determined by the size and shape of the building blocks. These insights unify the understanding of crystal growth across four orders of magnitude in particle size and suggest novel pathways to crystal engineering.

2. BRUCKNER, Eric P., CURK, Tine, ĐORĐEVIĆ, Luka, ZIWEI, Wang, YANG, Yang, QIU, Ruomeng, DANNENHOFFER, Adam J., SAI, Hiroaki, KUPFENBERG, Jacob, PALMER, Liam C., LUIJTEN, Erik, STUPP, Samuel I. Hybrid Nanocrystals of Small Molecules and Chemically Disordered Polymers. ACS nano. 2022, vol. 16, no. 6, str. 8993-9003. ISSN 1936-0851. DOI: 10.1021/acsnano.2c00266. [COBISS.SI-ID 141057283]

3. ROYCHOUDHURY, Appan, ALLEN, Rosalind J., CURK, Tine, FARRELL, James, MCALLISTER, Gina, TEMPLETON, Kate, BACHMANN, Till T. Amplification Free Detection of SARS-CoV-2 Using Multi-Valent Binding. ACS sensors. 8 Dec. 2022, vol. 7, iss. 12, str. 3692–3699, ilustr. ISSN 2379-3694. DOI: 10.1021/acssensors.2c01340. [COBISS.SI-ID 140892675]

4. CURK, Tine, YUAN, Jiaxing, LUITEN, Erik. Accelerated simulation method for charge regulation effects. Journal of chemical physics. [Online ed.]. 2022, vol. 156, 13 str. ISSN 1089-7690. DOI: 10.1063/5.0066432. [COBISS.SI-ID 98048515]

5. CURK, Tine, DUBACHEVA, Galina V., BRISSON, Alain R., RICHTER, Ralf P. Controlling Superselectivity of Multivalent Interactions with Cofactors and Competitors. Journal of the American Chemical Society : JACS. 2022, vol. 144, no. 38, str. 17346–17350. ISSN 0002-7863. DOI: 10.1021/jacs.2c06942. [COBISS.SI-ID 140962051]

6. CURK, Tine, LUIJTEN, Erik. Charge regulation effects in nanoparticle self-assembly. Physical review letters. [Print ed.]. 2021, vol. 126, iss. 13, str. 138003-1 - 138003-6. ISSN 0031-9007. https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.126.138003, DOI: 10.1103/PhysRevLett.126.138003. [COBISS.SI-ID 58108931]

7. CURK, Tine, BRACKLEY, Chris A., FARRELL, James Daniel, ZHONGYANG, Xing, JOSHI, Darshana, DIREITO, Susana, BREN, Urban, ANGIOLETTI-UBERTI, Stefano, DOBNIKAR, Jure, EISER, Erika, FRENKEL, Daan, ROSALIND J., Alen. Computational design of probes to detect bacterial genomes by multivalent binding. Proceedings of the National Academy of Sciences of the United States of America. 2020, vol. 117, no. 16, str. 8719-8726, graf. prikazi. ISSN 0027-8424. DOI: 10.1073/pnas.1918274117. [COBISS.SI-ID 23106326]

8. DUBACHEVA, Galina V., CURK, Tine, FRENKEL, Daan, RICHTER, Ralf P. Multivalent recognition at fluid surfaces: the interplay of receptor clustering and superselectivity. Journal of the American Chemical Society : JACS. 2019, vol. 141, no. 6, str. 2577-2588. ISSN 0002-7863. DOI: 10.1021/jacs.8b12553. [COBISS.SI-ID 22368534]

9. CURK, Tine, FARRELL, James Daniel, DOBNIKAR, Jure, PODGORNIK, Rudolf. Spontaneous domain formation in spherically confined elastic filaments. Physical review letters. [Print ed.]. 2019, vol. 123, iss. 4, str. 047801-1 - 047801-6. ISSN 0031-9007. https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.123.047801, DOI: 10.1103/PhysRevLett.123.047801. [COBISS.SI-ID 22938390]

10. HENRICH, Oliver, GUTIÉRREZ FOSADO, Yair Augusto, CURK, Tine, OULDRIDGE, Thomas E. Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications. The European physical journal. E, Soft matter. May 2018, vol. 41, issue 5, str. 1-16. ISSN 1292-8941. DOI: 10.1140/epje/i2018-11669-8. [COBISS.SI-ID 22374678]

11. CURK, Tine, BREN, Urban, DOBNIKAR, Jure. Bonding interactions between ligand-decorated colloidal particles. Molecular Physics. [Print ed.]. 2018, vol. 116, iss. 21/22, str. 3392-3400. ISSN 0026-8976. DOI: 10.1080/00268976.2018.1503354. [COBISS.SI-ID 21615382]

12. CURK, Tine, WIRNSBERGER, Peter, DOBNIKAR, Jure, FRENKEL, Daan, ŠARIĆ, Anđela. Controlling cargo trafficking in multicomponent membranes. Nano letters. 2018, vol. 18, iss. 9, str. 5350-5356, ilustr. ISSN 1530-6992. DOI: 10.1021/acs.nanolett.8b00786. [COBISS.SI-ID 22373910]

13. LEE, Ernest Y., TAKAHASHI, Toshiya, CURK, Tine, DOBNIKAR, Jure, GALLO, Richard L., WONG, Gerard C. L. Crystallinity of double-stranded RNA-antimicrobial peptide complexes modulates toll-like receptor 3-mediated inflammation. ACS nano. 2017, vol. 11, iss. 12, str. 12145-12155, ilustr. ISSN 1936-086X. https://pubs.acs.org/doi/pdf/10.1021/acsnano.7b05234, DOI: 10.1021/acsnano.7b05234. [COBISS.SI-ID 527000601]

Double-stranded RNA (dsRNA) induces production of pro-inflammatory cytokines in normal human epidermal keratinocytes (NHEK) by specific binding to endosomal Toll-like receptor-3 (TLR3). Recently, it has been shown that hyperactivation of TLR3 in psoriatic keratinocytes by dsRNA can occur in the presence of human antimicrobial peptide (AMP) LL37. Here, we combine synchrotron X-ray scattering, microscopy, computer simulations, and measurements of NHEK cytokine production to elucidate a previously unanticipated form of specific molecular pattern recognition. LL37 and similar %-helical AMPs can form pro-inflammatory nanocrystalline complexes with dsRNA that are recognized by TLR3 differently than dsRNA alone. dsRNA complexes that activate IL-6 production in NHEK and those that do not are both able to enter cells and co-localize with TLR3. However, the crystallinity of these AMP-dsRNA complexes, specifically the geometric spacing between parallel dsRNA and the repeat number of ordered dsRNA, strongly influences the level of TLR3 activation. Crystalline complexes that present dsRNA at a spacing that matches with the steric size of TLR3 can recruit and engage multiple TLR3 receptors, driving receptor clustering and immune amplification, whereas crystalline complexes that exhibit poor steric matching do not. Reverse-transcription quantitative PCR of IL-6 during siRNA knockdown of TLR3 confirms that cytokine production is due to TLR3: High levels of IL-6 transcription are observed for sterically matched complexes without TLR3 knockdown, whereas such activity is abrogated with TLR3 knockdown.

14. CURK, Tine, DOBNIKAR, Jure, FRENKEL, Daan. Optimal multivalent targeting of membranes with many distinct receptors. Proceedings of the National Academy of Sciences of the United States of America. [Online ed.]. 2017, vol. 114, no. 28, str. 7210-7215, ilustr. ISSN 1091-6490. http://www.iop.cas.cn/xwzx/kydt/201707/P020170703429098795360.pdf, DOI: 10.1073/pnas.1704226114. [COBISS.SI-ID 526561561]

Cells can often be recognized by the concentrations of receptors expressed on their surface. For better (targeted drug treatment) or worse (targeted infection by pathogens), it is clearly important to be able to target cells selectively. A good targeting strategy would result in strong binding to cells with the desired receptor profile and barely binding to other cells. Using a simple model, we formulate optimal design rules for multivalent particles that allow them to distinguish target cells based on their receptor pro- file. We find the following: (i) It is not a good idea to aim for very strong binding between the individual ligands on the guest (delivery vehicle) and the receptors on the host (cell). Rather, one should exploit multivalency: High sensitivity to the receptor density on the host can be achieved by coating the guest with many ligands that bind only weakly to the receptors on the cell surface. (ii) The concentration profile of the ligands on the guest should closely match the composition of the cognate membrane receptors on the target surface. And (iii) irrespective of all details, the effective strength of the ligand%receptor interaction should be of the order of the thermal energy kBT, where T is the absolute temperature and kB is Boltzmann%s constant. We present simulations that support the theoretical predictions. We speculate that, using the above design rules, it should be possible to achieve targeted drug delivery with a greatly reduced incidence of side effects.

15. WEI, Jiachen, DOBNIKAR, Jure, CURK, Tine, SONG, Fan. The effect of attractive interactions and macromolecular crowding on crystallins association. PloS one. 2016, vol. 11, iss. 3, [13 str.], ilustr. ISSN 1932-6203. http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0151159&type=printable, DOI: 10.1371/journal.pone.0151159. [COBISS.SI-ID 526561049]

In living systems proteins are typically found in crowded environments where their effective interactions strongly depend on the surrounding medium. Yet, their association and dissociation needs to be robustly controlled in order to enable biological function. Uncontrolled protein aggregation often causes disease. For instance, cataract is caused by the clustering of lens proteins, i.e., crystallins, resulting in enhanced light scattering and impaired vision or blindness. To investigate the molecular origins of cataract formation and to design efficient treatments, a better understanding of crystallin association in macromolecular crowded environment is needed. Here we present a theoretical study of simple coarse grained colloidal models to characterize the general features of how the association equilibrium of proteins depends on the magnitude of intermolecular attraction. By comparing the analytic results to the available experimental data on the osmotic pressure in crystallin solutions, we identify the effective parameters regimes applicable to crystallins. Moreover, the combination of two models allows us to predict that the number of binding sites on crystallin is small, i.e. one to three per protein, which is different from previous estimates. We further observe that the crowding factor is sensitive to the size asymmetry between the reactants and crowding agents, the shape of the protein clusters, and to small variations of intermolecular attraction. Our work may provide general guidelines on how to steer the protein interactions in order to control their association.

16. CURK, Tine, DOBNIKAR, Jure, FRENKEL, Daan. Rational design of molecularly imprinted polymers. Soft matter. 2016, vol. 12, str. 35-44, ilustr. ISSN 1744-6848. http://pubs.rsc.org/en/content/articlepdf/2016/sm/c5sm02144h, DOI: 10.1039/c5sm02144h. [COBISS.SI-ID 525410073]

Molecular imprinting is the process whereby a polymer matrix is cross-linked in the presence of molecules with surface sites that can bind selectively to certain ligands on the polymer. The cross-linking process endows the polymer matrix with a chemical "memory", such that the target molecules can subsequently be recognized by the matrix. We present a simple model that accounts for the key features of this molecular recognition. Using a combination of analytical calculations and Monte Carlo simulations, we show that the model can account for the binding of rigid particles to an imprinted polymer matrix with valence-limited interactions. We show how the binding multivalency and the polymer material properties affect the efficiency and selectivity of molecular imprinting. Our calculations allow us to formulate design criteria for optimal molecular imprinting.

17. SCHMIDT, Nathan W., JIN, Fan, LANDE, Roberto, CURK, Tine, XIAN, Wujing, LEE, Calvin, FRASCA, Loredana, FRENKEL, Daan, DOBNIKAR, Jure, GILLIET, Michel, WONG, Gerard C. L. Liquid-crystalline ordering of antimicrobial peptide-DNA complexes controls TLR9 activation. Nature Materials. [Online ed.]. 2015, vol. 14, str. 696-700, ilustr. ISSN 1476-4660. http://www.nature.com/nmat/journal/v14/n7/full/nmat4298.html, DOI: 10.1038/nmat4298. [COBISS.SI-ID 525410585]

Double-stranded DNA (dsDNA) can trigger the production of type I interferon (IFN) in plasmacytoid dendritic cells (pDCs) by binding to endosomal Toll-like receptor-9 (TLR9; refs 1, 2, 3, 4, 5). It is also known that the formation of DNA%antimicrobial peptide complexes can lead to autoimmune diseases via amplification of pDC activation1, 2. Here, by combining X-ray scattering, computer simulations, microscopy and measurements of pDC IFN production, we demonstrate that a broad range of antimicrobial peptides and other cationic molecules cause similar effects, and elucidate the criteria for amplification. TLR9 activation depends on both the inter-DNA spacing and the multiplicity of parallel DNA ligands in the self-assembled liquid-crystalline complex. Complexes with a grill-like arrangement of DNA at the optimum spacing can interlock with multiple TLR9 like a zipper, leading to multivalent electrostatic interactions that drastically amplify binding and thereby the immune response. Our results suggest that TLR9 activation and thus TLR9-mediated immune responses can be modulated deterministically.

18. DUBACHEVA, Galina V., CURK, Tine, AUZÉLY-VELTY, Rachel, FRENKEL, Daan, RICHTER, Ralf P. Designing multivalent probes for tunable superselective targeting. Proceedings of the National Academy of Sciences of the United States of America. [Online ed.]. 2015, vol. 112, iss. 18, str. 5579-5584, ilustr. ISSN 1091-6490. http://www.pnas.org/content/112/18/5579.full.pdf, DOI: 10.1073/pnas.1500622112. [COBISS.SI-ID 525409561]

Specific targeting is common in biology and is a key challenge in nanomedicine. It was recently demonstrated that multivalent probes can selectively target surfaces with a defined density of surface binding sites. Here we show, using a combination of experiments and simulations on multivalent polymers, that such "superselective" binding can be tuned through the design of the multivalent probe, to target a desired density of binding sites. We develop an analytical model that provides simple yet quantitative predictions to tune the polymer's superselective binding properties by its molecular characteristics such as size, valency, and affinity. This work opens up a route toward the rational design of multivalent probes with defined superselective targeting properties for practical applications, and provides mechanistic insight into the regulation of multivalent interactions in biology. To illustrate this, we show how the superselective targeting of the extracellular matrix polysaccharide hyaluronan to its main cell surface receptor CD44 is controlled by the affainity of individual CD44-hyaluronan interacions.

19. GERNIER, Robin de, CURK, Tine, DUBACHEVA, Galina V., RICHTER, Ralf P., MOGNETTI, Bortolo M. A new configurational bias scheme for sampling supramolecular structures. Journal of chemical physics. [Online ed.]. 2014, vol. 141, iss. 24, str. 244909-1-244909-11, ilustr. ISSN 1089-7690. http://scitation.aip.org/content/aip/journal/jcp/141/24/10.1063/1.4904727, DOI: 10.1063/1.4904727. [COBISS.SI-ID 525201945]

We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias scheme of Siepmann and Frenkel and is powered by the possibility of changing the topology of the supramolecular network by a non-local Monte Carlo algorithm. Such a plan is accomplished by a multi-scale modelling that merges coarse-grained simulations, describing the typical polymer conformations, with experimental results accounting for free energy terms involved in the reactions of the active sites. We test the new algorithm for a system of DNA coated colloids for which we compute the hybridisation free energy cost associated to the binding of tethered single stranded DNAs terminated by short sequences of complementary nucleotides. In order to demonstrate the versatility of our method, we also consider polymers functionalized by receptors that bind a surface decorated by ligands. In particular, we compute the density of states of adsorbed polymers as a function of the number of ligand%receptor complexes formed. Such a quantity can be used to study the conformational properties of adsorbed polymers useful when engineering adsorption with tailored properties. We successfully compare the results with the predictions of a mean field theory. We believe that the proposed method will be a useful tool to investigate supramolecular structures resulting from direct interactions between functionalized polymers for which efficient numerical methodologies of investigation are still lacking.

20. DUBACHEVA, Galina V., CURK, Tine, MOGNETTI, Bortolo M., AUZÉLY-VELTY, Rachel, FRENKEL, Daan, RICHTER, Ralf P. Superselective targeting using multivalent polymers. Journal of the American Chemical Society. [Online ed.]. 2014, vol. 136, iss. 5, str. 1722-1725. ISSN 1520-5126. http://pubs.acs.org/doi/pdf/10.1021/ja411138s, DOI: 10.1021/ja411138s. [COBISS.SI-ID 519911961]

Despite their importance for material and life sciences, multivalent interactions between polymers and surfaces remain poorly understood. Combiningrecent achievements of synthetic chemistry and surface characterization, we have developed a well-defined and highly specific model system based on host/guest interactions. We use this model to study the binding of hyaluronic acid functionalized with host molecules to tunable surfaces displaying different densities of guest molecules. Remarkably, we find that the surface density of bound polymer increases faster than linearly with the surface density of binding sites. Based on predictions from a simple analytical model, we propose that this superselective behavior arises from a combination of enthalpic and entropic effects upon binding of nanoobjects to surfaces, accentuated by the ability of polymer chains to interpenetrate.

21. CURK, Tine, MARTINEZ-VERACOECHEA, Francisco J., FRENKEL, Daan, DOBNIKAR, Jure. Nanoparticle organization in sandwiched polymer brushes. Nano letters. 2014, vol. 14, iss. 5, str. 2617-2622, ilustr. ISSN 1530-6992. http://pubs.acs.org/doi/abs/10.1021/nl500449x?prevSearch=curk&searchHistoryKey=, DOI: 10.1021/nl500449x. [COBISS.SI-ID 520213529]

The organization of nanoparticles inside grafted polymer layers is governed by the interplay of polymer-induced entropic interactions and the action of externally applied fields. Earlier work had shown that strong external forces can drive the formation of colloidal structures in polymer brushes. Here we show that external fields are not essential to obtain such colloidal patterns: we report Monte Carlo and molecular dynamics simulations that demonstrate that ordered structures can be achieved by compressing a %sandwich% of two grafted polymer layers, or by squeezing a coated nanotube, with nanoparticles in between. We show that the pattern formation can be efficiently controlled by the applied pressure, while the characteristic length-scale, that is, the typical width of the patterns, is sensitive to the length of the polymers. Based on the results of the simulations, we derive an approximate equation of state for nanosandwiches.

22. CURK, Tine, MARENDUZZO, Davide, DOBNIKAR, Jure. Chemotactic sensing towards ambient and secreted attractant drives collective behaviour of E. coli. PloS one. 2013, vol. 8, no. 10, str. e4878-1-e4878-9. ISSN 1932-6203. http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0074878&representation=PDF, DOI: 10.1371/journal.pone.0074878. [COBISS.SI-ID 27381799]

We simulate the dynamics of a suspension of bacterial swimmers, which chemotactically sense gradients in either ambient or self-secreted attractants(e.g. nutrient or aspartate respectively), or in both. Unlike previous mean field models based on a set of continuum partial differential equations, our model resolves single swimmers and therefore incorporates stochasticity and effects due to fluctuations in the bacterial density field. The algorithm we use is simple enough that we can follow the evolution of colonies of up to over a million bacteria for timescales relevant to pattern formation for E. coli growing in semisolid medium such as agar, or in confinedgeometries. Our results confirm previous mean field results that the patterns observed experimentally can be reproduced with a model incorporating chemoattractant secretion, chemotaxis (towards gradients in the chemoattractant field), and bacterial reproduction. They also suggest that further experiments with bacterial strains chemotactically moving up both nutrient and secreted attractant field may yield yet more dynamical patterns.

23. CURK, Tine, MARTINEZ-VERACOECHEA, Francisco J., FRENKEL, Daan, DOBNIKAR, Jure. Collective ordering of colloids in grafted polymer layers. Soft matter. 2013, vol. 9, iss. 23, str. 5565-5571, ilustr. ISSN 1744-6848. http://pubs.rsc.org/en/content/articlepdf/2013/sm/c3sm50486g, DOI: 10.1039/C3SM50486G. [COBISS.SI-ID 519455513]

We present Monte Carlo simulations of colloidal particles pulled into grafted polymer layers by an external force. The insertion free energy for penetration of a single colloid into a polymer layer is qualitatively different for surfaces with an ordered and a disordered distribution of grafting points and the tendency of colloidal particles to traverse the grafting layer is strongly size dependent. In dense colloidal suspensions, under the influence of sufficiently strong external forces, colloids penetrate and form internally ordered, columnar structures spanning the polymer layer. The competition between the tendency for macro-phase separation of colloids and polymers and the elastic-like penalty for deforming the grafted layer results in the micro-phase separation, i.e. finite colloidal clusters characterized by a well-defined length scale. Depending on the conditions, these clusters are isolated or laterally percolating. The morphology of the observed patterns canbe controlled by the external fields, which opens up new routes for the design of thin structured films.

24. CURK, Tine, HOOGH, Anouk de, MARTINEZ-VERACOECHEA, Francisco J., EISER, Erika, FRENKEL, Daan, DOBNIKAR, Jure, LEUNISSEN, Mirjam E. Layering, freezing, and re-entrant melting of hard spheres in soft confinement. Physical review. E, Statistical, nonlinear and soft matter physics. [Online ed.]. 2012, vol. 85, iss. 2, str. 021502-1-021502-5. ISSN 1550-2376. http://link.aps.org/doi/10.1103/PhysRevE.85.021502, DOI: 10.1103/PhysRevE.85.021502. [COBISS.SI-ID 518221081]

Confinement can have a dramatic effect on the behavior of all sorts of particulate systems, and it therefore is an important phenomenon in many different areas of physics and technology. Here, we investigate the role played by the softness of the confining potential. Using grand canonical Monte Carlo simulations, we determine the phase diagram of three-dimensional hard spheres that in one dimension are constrained to a plane by a harmonic potential. The phase behavior depends strongly on the density and on the stiffness of the harmonic confinement. While we find the familiar sequence of confined hexagonal and square-symmetric packings, we do not observe any of the usual intervening ordered phases. Instead, the system phase separates under strong confinement, or forms a layered re-entrant liquid phase under weaker confinement. It is plausible that this behavior is due to the larger positional freedom in a soft confining potential and to the contribution that the confinement energy makes to the total free energy. The fact that specific structures can be induced or suppressed by simply changing the confinement conditions (e.g., in a dielectrophoretic trap) is important for applications that involve self-assembled structures of colloidal particles.

25. MATTHÄUS, Franziska, MOMMER, Mario S., CURK, Tine, DOBNIKAR, Jure. On the origin and characteristics of noise-induced Lévy Walks of E. Coli. PloS one. 2011, vol. 6, no. 4, str. e18623-1-e18623-8. ISSN 1932-6203. http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018623, Digitalna knjižnica Univerze v Mariboru – DKUM. [COBISS.SI-ID 25045031]

26. LEE, Ernest Y., LEE, Calvin, SCHMIDT, Nathan W., JIN, Fan, LANDE, Roberto, CURK, Tine, FRENKEL, Daan, DOBNIKAR, Jure, GILLIET, Michel, WONG, Gerard C. L. A review of immune amplification via ligand clustering by self-assembled liquid-crystalline DNA complexes. Advances in colloid and interface science. [Print ed.]. Jun. 2016, vol. 232, str. 17-24, ilustr. ISSN 0001-8686. http://www.sciencedirect.com/science/article/pii/S0001868616300471, DOI: 10.1016/j.cis.2016.02.003. [COBISS.SI-ID 526561305]

We examine how the interferon production of plasmacytoid dendritic cells is amplified by the self-assembly of liquid%crystalline antimicrobial peptide/DNA complexes. These specialized dendritic cells are important for host defense because they quickly release large quantities of type I interferons in response to infection. However, their aberrant activation is also correlated with autoimmune diseases such as psoriasis and lupus. In this review, we will describe howpolyelectrolyte self-assembly and the statistical mechanics ofmultivalent interactions contribute to this process. In a more general compass, we provide an interesting conceptual corrective to the common notion in molecular biology of a dichotomy between specific interactions and non-specific interactions, and show examples where one can construct exquisitely specific interactions using non-specific interactions.

27. DOBNIKAR, Jure, CURK, Tine. Nova pot za zdravljenje avtoimunskih bolezni?. Delo, Znanost : štirinajstdnevna znanstvena priloga časnika Delo. [Tiskana izd.]. 16. jul. 2015, letn. 57, št. 163, str. 16. ISSN 0350-7521, ISSN 1580-7584. [COBISS.SI-ID 525410841]

28. DOBNIKAR, Jure, CURK, Tine, MARTINEZ-VERACOECHEA, Francisco J., FRENKEL, Daan. Slow colloidal dynamics in polymer brushes. V: TOKUYAMA, Michio (ur.), OPPENHEIM, Irwin (ur.). 4th International symposium on slow dynamics in complex systems, Sendai, Japan, 2-7 December 2012 : keep going Tohoku. Melville (NY): American Institute of Physics, 2013. Str. 391-397, ilustr. AIP conference proceedings, 1518. ISBN 978-0-7354-1141-8. ISSN 1551-7616. http://proceedings.aip.org/resource/2/apcpcs/1518/1/391_1?isAuthorized=no, DOI: 10.1063/1.4794602. [COBISS.SI-ID 519458073]

We present Monte Carlo simulations of dense colloidal suspensions pulled into grafted polymer layers by external forces. The size-selectivity of the tendency of colloidal particles to traverse grafting layers is discussed. At weak external fields, large-enough colloids cannot penetrate the brush and form a liquid layer on top of it, while under the influence of sufficiently strong forces, a collective instability occurs and ordered structures spanningthe brush layer emerge. The formation of such structures is a slow process and we demonstrate that the particlesʼ kinetics can have a decisive role in their collective ordering.

29. CURK, Tine, DOBNIKAR, Jure, MARTINEZ-VERACOECHEA, Francisco J., FRENKEL, Daan. Collective ordering of colloids in poymer layers. V: Design of self-assembling materials, September 4, 2012 - September 7, 2012, University of Vienna, Austria. Lausanne: CECAM, 2012. Str. [15]. http://www.cecam.org/upload/files/file_1307.pdf. [COBISS.SI-ID 519459097]

30. RAVNIK, Vid, CURK, Tine, BREN, Urban. Selective targeting with multivalent polymers. V: PINTAR, Albin (ur.). Slovenski kemijski dnevi 2022 = 28th Annual Meeting of the Slovenian Chemical Society : zbornik povzetkov = book of abstracts : 21.-23. september 2022, Portorož, Portorose, Slovenija. Ljubljana: Slovensko kemijsko društvo, 2022. Str. 192. ISBN 978-961-95922-1-2. [COBISS.SI-ID 126544131]

31. CURK, Tine, MARTINEZ-VERACOECHEA, Francisco J., FRENKEL, Daan, DOBNIKAR, Jure. Collective ordering of colloids in grafted polymer layers. V: OSTERMAN, Natan (ur.), ZIHERL, Primož (ur.). Book of abstracts. Physics of Complex Colloids, Ljubljana, May 14-18, 2013. [S. l.: s. n.], 2013. Str. 110. [COBISS.SI-ID 519457561]

32. CURK, Tine, FRENKEL, Daan, DOBNIKAR, Jure. Design principles for super selectivity using multivalent interactions. V: HUSKENS, Jurriaan (ur.), et al. Multivalency : concepts, research & applications. 1st edition. Hoboken (NJ): J. Wiley & Sons, cop. 2018. Str. 75-101. ISBN 978-1-119-14349-9. https://arxiv.org/abs/1608.01222. [COBISS.SI-ID 527001113]

33. CURK, Tine, MATTHÄUS, Franziska, BRILL-KARNIELY, Yifat, DOBNIKAR, Jure. Coarse graining escherichia coli chemotaxis: from multi-flagella propulsion tologarithmic sensing. V: GORYANIN, Igor I. (ur.), GORYACHEV, Andrew B. (ur.). Advances in systems biology. New York [etc.]: Springer, cop. 2012. Str. 381-395. Advances in experimental medicine and biology, 736. ISBN 978-1-4419-7210-1, ISBN 978-1-4419-7209-5. ISSN 0065-2598. http://www.springerlink.com/content/978-1-4419-7210-1#section=1000406&page=1&locus=0. [COBISS.SI-ID 518220569]

34. CURK, Tine. Modelling multivalent interactions : [doctoral thesis]. Cambridge: University of Cambridge, Darwin College, 2016. 150 str. https://www.repository.cam.ac.uk/handle/1810/266916, DOI: 10.17863/CAM.12977. [COBISS.SI-ID 526563097]
nagrada: Preglova nagrada Kemijskega inštituta, 2017; Krkina nagrada, 2017

A Multivalent entity, which could represent a protein, nanoparticle, polymer, virus or a lipid bilayer, has the ability to form multiple bonds to a substrate. Hence, a multivalent interaction can be strong, even if the individual bonds are weak. However, much more interestingly, multivalency enables the design of highly specific interactions using non-specific individual bonds. We attempt to rationalise multivalent effects using simple physical models complemented with numerical simulations. Based on physiochemical characteristics of multivalent binders, we aim to predict the overall strength of interaction and its sensitivity to variation in parameters. We start with a simple model of homo-multivalency, where all bonds are equivalent. Such systems can exhibit a super-selective response, which denotes the high sensitivity of the strength of multivalent binding to the number of accessible binding sites on the target surface. We present a theoretical analysis of systems of multivalent particles and show that a certain degree of disorder is necessary for super-selective behaviour. Moreover, we formulate a set of simple design rules for multivalent interactions that yield optimal selectivity. In the second stage, we expand the model to hetero-multivalency, accounting for multiple distinct types of binding partners. We consider targeting of cells based on a density profile of different membrane receptors types and demonstrate, that speci city towards a desired receptor density profile can be obtained. Hence, cells can be reliably targeted in the absence of specific markers. Crucially, we show that for optimal selectivity, individual bonds must be weak. Finally, we add information about specific geometry and positions of binding sites on the multivalent entity. We focus on molecular imprinting; the process whereby a polymer matrix is cross-linked in the presence of template molecules. The cross-linking process endows the polymer matrix with a chemical %memory%, such that the target molecules can subsequently be recognised by the matrix. We show how the binding multivalency and the polymer material properties affect the efficiency and selectivity of molecular imprinting.

35. CURK, Tine. Urejanje koloidnih delcev na mehkih površinah : magistrsko delo = Colloidal ordering on soft coated surfaces : master thesis. Maribor: [T. Curk], 2012. 46 f., ilustr. Digitalna knjižnica Univerze v Mariboru – DKUM. [COBISS.SI-ID 19544584]

A grafted polymer layer can be used to prevent the deposition of colloidal particles on a solid surface. This thesis presents Monte Carlo simulations of hard-sphere colloids pushed to a polymer brush under the influence of external fields (e.g. gravity). For weak fields colloids can not penetrate the brush and the effective potential acting on a single colloid is approximately quadratic. The phase diagram of three-dimensional hard-sphere colloids, that in one dimension are constrained to a plane by a harmonic potential, is presented. Under the influence of sufficiently strong external fields colloids penetrate the brush and form internally ordered, columnar structures that span the polymer layer. The morphology of the patterns that form depends sensitively on the strength of the applied field. We propose a simple phenomenological theory that accounts for the main characteristics of the observed behaviour. The present results suggest a simple experimental method to determine the surface polymer coverage.

Polimerne krtačke varujejo površine pred adsorpcijo različnih delcev. V magistrskem delu predstavimo Monte Carlo simulacije koloidov, ki so pod vplivom zunanjih polj (npr. gravitacijskega polja) potisnjeni ob polimerno krtačko. Pri šibkih poljih koloidi ne morejo predreti krtačke in efektivni potencial, ki ga čuti posamezen koloid, je približno harmonski. Predstavljen je fazni diagram tridimenzionalnih koloidov, ki so v eni dimenziji omejeni na površino s harmonskim potencialom. Pod vplivom dovolj močnih polj lahko koloidi prodrejo v krtačko, kjer tvorijo urejene, stebraste strukture. Morfologija vzorcev, ki nastanejo, je občutljivo odvisna od poljske jakosti. Predlagamo enostavno fenomenološko teorijo, ki pojasni glavne značilnosti opaženega obnašanja. S predstavljenimi rezultati predlagamo dokaj enostavno eksperimentalno metodo za določitev površinske gostote sidranih polimerov.

36. CURK, Tine. Bakterijska kemotaksa : diplomski seminar na bolonjskem študijskem programu 1. stopnje Fizika. Maribor: [T. Curk], 2010. 25 f., ilustr., graf. prikazi. [COBISS.SI-ID 19483912]

37. CURK, Tine. Bakterijska kemotaksa : zaključni seminar na študijskem programu 1. stopnje Fizika. Maribor: [T. Curk], 2010. http://fizika.uni-mb.si/files/seminarji/10/Tine_Curk-bakterijska_kemotaksa.pdf. [COBISS.SI-ID 518220825]

38. CURK, Tine. Double exponential project code. [S. l.: s. n., 2018]. https://github.com/tc387/dexp. [COBISS.SI-ID 22406166]

39. BERTONCELJ, Blaž, CURK, Tine. Vpliv svetlobne onesnaženosti na rastline in živali : [raziskovalno področje] varstvo okolja : raziskovalna naloga. Maribor: Prva gimnazija Maribor, 2007. 39 f., ilustr. [COBISS.SI-ID 60586241]

40. BERTONCELJ, Blaž, CURK, Tine. Vpliv svetlobne onesnaženosti na rastline in živali : varstvo okolja : raziskovalna naloga. Maribor: Prva gimnazija Maribor, 2007. 39 f., ilustr. [COBISS.SI-ID 10232627]

41. BERTONCELJ, Blaž, CURK, Tine. Šolsko kosilo : zdravstvo : raziskovalna naloga. Maribor: Osnovna šola bratov Polančičev, 2003. 37 f., ilustr. [COBISS.SI-ID 13435144]

42. Biophysical journal. CURK, Tine (recenzent 2019). New York: Published for the Biophysical Society by the Rockefeller University Press, 1960-. ISSN 0006-3495. [COBISS.SI-ID 25099520]

43. ACS nano. CURK, Tine (recenzent 2016). Washington (DC): American Chemical Society. ISSN 1936-0851. http://pubs.acs.org/journals/ancac3/index.html. [COBISS.SI-ID 2217316]

44. Langmuir. CURK, Tine (recenzent 2016). Washington: American Chemical Society, 1985-. ISSN 0743-7463. [COBISS.SI-ID 3267855]