Most recent publications

For a complete list of publications (1990 - 2016) please click here.

Hanson, K. L., Fulga, F., Dobroiu, S., Solana, G., Kašpar, O., Tokárová, V., Nicolau, D.V., Polymer surface properties control the function of heavy meromyosin in dynamic nanodevices, Biosensors and Bioelectronics (2016) More

The actin-myosin system, responsible for muscle contraction, is also the force-generating element in dynamic nanodevices operating with surface-immobilized motor proteins. These devices require materials that are amenable to micro- and nano-fabrication, but also preserve the bioactivity of molecular motors. The complexity of the protein-surface systems is greatly amplified by those of the polymer-fluid interface; and of the structure and function of molecular motors, making the study of these interactions critical to the success of molecular motor-based nanodevices. We measured the density of the adsorbed motor protein (heavy meromyosin, HMM) using quartz crystal microbalance; and motor bioactivity with ATPase assay, on a set of model surfaces, i.e., nitrocellulose, polystyrene, poly(methyl methacrylate), and poly(butyl methacrylate), poly(tert-butyl methacrylate). A higher hydrophobicity of the adsorbing material translates in a higher total number of HMM molecules per unit area, but also in a lower uptake of water, and a lower ratio of active per total HMM molecules per unit area. We also measured the motility characteristics of actin filaments on the model surfaces, i.e., velocity, smoothness and deflection of movement, determined via in vitro motility assays. The filament velocities were found to be controlled by the relative number of active HMM per total motors, rather than their absolute surface density. The study allowed the formulation of the general engineering principles for the selection of polymeric materials for the manufacturing of dynamic nanodevices using protein molecular motors.

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Kašpar, O., Zhang, H., Tokárová, V., Boysen, R. I., Suñé, G. R., Borrise, X., Murano, F.P., Hearn, M. T. W., Nicolau, D.V., "Confinement of water droplets on rectangular micro/nano-arrayed surfaces", Lab Chip, 16, 2487-2493 (2016) More

Nearly perfect confinement, i.e., no spill over, of nanodroplets by rectangular hydrophilic patches surrounded by surfaces with high hydrophobicity. Confinement areas: a) 3 μm x 3 μm, b) 1 μm x 1 μm, and c) 0.5 μm x 0.5 μm. The repellent feature of the surrounding hydrophobic walls is stronger for smaller confining areas, e.g., manifested by the central positioning of the nanodroplets in smaller confining rectangles, as opposed to nanodroplets touching the hydrophobic walls for larger confining areas. Note: The aspect ratio of Z-axis has been increased to ensure better droplet visibility. The X, Y and Z values represent range of measured area.

Micro-patterned surfaces with alternate hydrophilic and hydrophobic rectangular areas effectively confine water droplets down to attolitre volumes. The contact angle, volume, and geometry of the confined droplets as a function of the geometry and physico-chemical properties of the confining surfaces have been determined by phenomenological simulations, validated by atomic force microscopy measurements. The combination between experiments and simulations can be used for the purposeful design of arrays with surface-addressable hydrophobicity employed in digital microfluidics and high-throughput screening nanoarrays.

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Nicolau, D. V. Jr., Lard, M., Korten, T., Van Delft, F. C. M. J. M., Persson, M., Bengtsson, E., Månsson, A., Diez, S., Linke H., Nicolau, D.V., Parallel computation with molecular-motor-propelled agents in nanofabricated networks. PNAS, 2016, doi:10.1073/pnas.1510825113 More

The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecular motor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NP-complete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.

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Asenova, E., Lin, H. Y., Fu, E., Nicolau, D. V. Jr., Nicolau, D.V. "Optimal Fungal Space Searching Algorithms", IEEE Transactions on NanoBioscience, PP, 1 (2016) More

directional memoryPrevious experiments have shown that fungi use an efficient natural algorithm for searching the space available for their growth in micro-confined networks, e.g., mazes. This natural ‘master’ algorithm, which comprises two ‘slave’ sub-algorithms, i.e., collision-induced branching and directional memory, has been shown to be more efficient than alternatives, with one, or the other, or both sub-algorithms turned off. In contrast, the present contribution compares the performance of the fungal natural algorithm against several standard artificial homologues. It was found that the space-searching fungal algorithm consistently outperforms uninformed algorithms, such as Depth-First-Search (DFS). Furthermore, while the natural algorithm is inferior to informed ones, such as A*, this under-performance does not importantly increase with the increase of the size of the maze. These findings suggest that a systematic effort of harvesting the natural space searching algorithms used by microorganisms is warranted and possibly overdue. These natural algorithms, if efficient, can be reverse-engineered for graph and tree search strategies.

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Filipponi, L., Livingston, P., Kašpar, O., Tokárová, V., Nicolau, D.V., "Protein patterning by microcontact printing using pyramidal PDMS stamps", Biomedical Microdevices 18, 1-7 (2016) More

Micro-contact printing, μCP, is a well-established soft-lithography technique for printing biomolecules. μCP uses stamps made of Poly(dimethylsiloxane), PDMS, made by replicating a microstructured silicon master fabricated by semiconductor manufacturing processes. One of the problems of the μCP is the difficult control of the printing process, which, because of the high compressibility of PDMS, is very sensitive to minute changes in the applied pressure. This over-sensitive response leads to frequent and/or uncontrollable collapse of the stamps with high aspect ratios, thus decreasing the printing accuracy and reproducibility. Here we present a straightforward methodology of designing and fabricating PDMS structures with an architecture which uses the collapse of the stamp to reduce, rather than enlarge the variability of the printing. The PDMS stamp, organized as an array of pyramidal micro-posts, whose ceiling collapses when pressed on a flat surface, replicates the structure of the silicon master fabricated by anisotropic wet etching. Upon application of pressure, depending on the size of, and the pitch between, the PDMS pyramids, an air gap is formed surrounding either the entire array, or individual posts. The printing technology, which also exhibits a remarkably low background noise for fluorescence detection, may find applications when the clear demarcation of the shapes of protein patterns and the distance between them are critical, such as microarrays and studies of cell patterning.

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Nguyen, M.T., Chaffee, A.L., Boysen, R.I., Nicolau, D.V., Hearn, M.T.W., A versatile modelling approach to determine the hydrophobicity of peptides at the atomic level. Molecular Simulation, 2016. 42(4): p. 257-269 More

article_1This study describes a versatile computational method to determine the hydrophobicity of small peptides at the atomic level. Free energies of transfer for individual atoms in peptide structures were derived, utilising two specifically defined parameters: (i) the water-excluding distance to define the dynamic interface between a peptide solute and its surrounding solvent and (ii) the corresponding hydrophobicity index as a relative measure for water occlusion/repulsion. The method was tested on a range of small peptide models (Ac-X-NH2, G-X-G, Ac-WL-X-LL and Ac-GG-X-GG-NH2) and several derivatives of these structures, whereby X was any of the 20 most common amino acids that naturally occur in polypeptides or proteins. The advantage of this new method lies in its versatility, ease to implement and capability to provide information on the hydrophobicity characteristics at the atomic level. The approach also encapsulates the impact of factors that influence these properties, but which have hitherto been difficult to accurately quantify, e.g. steric hindrance or proximity effects due to nearby polarised atoms. The method is not conditional on the knowledge of hydrophobicity parameters from the literature and does not require a sophisticated computer software/hardware to enable the atomic solvent-accessible surface areas or other hydrophobicity parameters to be de novo obtained.

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Van Zalinge, H., Ramsey, L.C., Aveyard, J., Persson, M., Mansson, A., Nicolau, D.V., Surface-Controlled Properties of Myosin Studied by Electric Field Modulation. Langmuir, 2015. 31(30): p. 8354-8361 More

The efficiency of dynamic nanodevices using surface-immobilized protein molecular motors, which have been proposed for diagnostics, drug discovery, and biocomputation, critically depends on the ability to precisely control the motion of motor-propelled, individual cytoskeletal filaments transporting cargo to designated locations. The efficiency of these devices also critically depends on the proper function of the propelling motors, which is controlled by their interaction with the surfaces they are immobilized on. Here we use a microfluidic device to study how the motion of the motile elements, i.e., actin filaments propelled by heavy mero-myosin (HMM) motor fragments immobilized on various surfaces, is altered by the application of electrical loads generated by an external electric field with strengths ranging from 0 to 8 kVm–1. Because the motility is intimately linked to the function of surface-immobilized motors, the study also showed how the adsorption properties of HMM on various surfaces, such as nitrocellulose (NC), trimethylclorosilane (TMCS), poly(methyl methacrylate) (PMMA), poly(tert-butyl methacrylate) (PtBMA), and poly(butyl methacrylate) (PBMA), can be characterized using an external field. It was found that at an electric field of 5 kVm–1 the force exerted on the filaments is sufficient to overcome the frictionlike resistive force of the inactive motors. It was also found that the effect of assisting electric fields on the relative increase in the sliding velocity was markedly higher for the TMCS-derivatized surface than for all other polymer-based surfaces. An explanation of this behavior, based on the molecular rigidity of the TMCS-on-glass surfaces as opposed to the flexibility of the polymer-based ones, is considered. To this end, the proposed microfluidic device could be used to select appropriate surfaces for future lab-on-a-chip applications as illustrated here for the almost ideal TMCS surface. Furthermore, the proposed methodology can be used to gain fundamental insights into the functioning of protein molecular motors, such as the force exerted by the motors under different operational conditions.

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Hajne, J., Hanson, K.L., van Zalinge, H., Nicolau, D.V., Motility of actin filaments on micro-contact printed myosin patterns. IEEE Transactions on Nanobioscience, 2015. 14(3): p. 313-322 More

Protein molecular motors, which convert, directly and efficiently, chemical energy into motion, are excellent candidates for integration in hybrid dynamic nanodevices. To integrate and use the full potential of molecular motors in these devices, their design requires a quantitative and precise prediction of the fundamental mechanical and physicochemical features of cytoskeletal proteins operating in artificial environments. In that regard, the behavior of protein molecular motors constructs in/on nano-confined spaces or nanostructured surfaces that aim to control their motility is of critical interest. Here, we used a standard gliding motility assay to study the actin filaments sliding on a surface comprising heavy mero myosin (HMM) micro- and nano-patterns. To print HMM, we used negative tone, micro contact printing of a blocking protein (bovine serum albumin, BSA) on a nitrocellulose surface, followed by specific adsorption of HMM on BSA-free surfaces. While the large BSA-free patterns allowed for selective confinement of actin filaments motility, the BSA-stamped areas displayed intricate nano-sized HMM patterns, which enabled a deeper analysis of the nano-mechanics of actomyosin motility in confined spaces.

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Ramsey, L., Schroeder, V., van Zalinge, H., Berndt, M., Korten, T., Diez, S., Nicolau, D.V., Control and gating of kinesin-microtubule motility on electrically heated thermo-chips. Biomedical Microdevices, 2014. 16(3): p. 459-463 More

First lab-on-chip devices based on active transport by biomolecular motors have been demonstrated for basic detection and sorting applications. However, to fully employ the advantages of such hybrid nanotechnology, versatile spatial and temporal control mechanisms are required. Using a thermo-responsive polymer, we demonstrated a temperature controlled gate that either allows or disallows the passing of microtubules through a topographically defined channel. The gate is addressed by a narrow gold wire, which acts as a local heating element. It is shown that the electrical current flowing through a narrow gold channel can control the local temperature and as a result the conformation of the polymer. This is the first demonstration of a spatially addressable gate for microtubule motility which is a key element of nanodevices based on biomolecular motors.

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Nicolau, D.V. Jr., Paszek, E., Fulga, F., Nicolau, D.V., Mapping hydrophobicity on the protein molecular surface at atom-level resolution. PLoS ONE, 2014. 9(12) More

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 Å, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced “leopard skin”-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions, can capture processes that are otherwise obscured to the amino acid-based formalism.

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Wilson, R., Cossins, A., Nicolau, D. V., Missailidis, S., The selection of DNA aptamers for two different epitopes of thrombin was not due to different partitioning methods. Nucleic Acid Therapeutics, 2013. 23(1): p. 88-92 More


The Selection of DNA Aptamers for Two Different Epitopes of Thrombin Was Not Due to Different Partitioning MethodsNearly all aptamers identified so far for any given target molecule have been specific for the same binding site (epitope). The most notable exception to the 1 aptamer per target molecule rule is the pair of DNA aptamers that bind to different epitopes of thrombin. This communication refutes the suggestion that these aptamers exist because different partitioning methods were used when they were selected. The possibility that selection of these aptamers was biased by conflicting secondary structures was also investigated and found not to contribute. The preparation of protein-coated magnetic beads for systematic evolution of ligands by exponential enrichment (SELEX) and the different specificities of the thrombin aptamers for the α and β forms of thrombin are also reported.

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Nicolau, D. V., Paszek, E., Fulga, F., Nicolau Jr, D. V., Protein Molecular Surface Mapped at Different Geometrical Resolutions. PLoS ONE, 2013. 8(3) More

Many areas of biochemistry and molecular biology, both fundamental and applications-orientated, require an accurate construction, representation and understanding of the protein molecular surface and its interaction with other, usually small, molecules. There are however many situations when the protein molecular surface gets in physical contact with larger objects, either biological, such as membranes, or artificial, such as nanoparticles. The contribution presents a methodology for describing and quantifying the molecular properties of proteins, by geometrical and physico-chemical mapping of the molecular surfaces, with several analytical relationships being proposed for molecular surface properties. The relevance of the molecular surface-derived properties has been demonstrated through the calculation of the statistical strength of the prediction of protein adsorption. It is expected that the extension of this methodology to other phenomena involving proteins near solid surfaces, in particular the protein interaction with nanoparticles, will result in important benefits in the understanding and design of protein-specific solid surfaces.

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Bartolini, M., Naldi, M., Nicolau, D. V., Van Delft, F. C. M. J. M., Van Zijl, J., Snijder, J., Van Den Heuvel, E. F. C., Naburgh, E. P., Calonghi, N., Andrisano, V., Fluorescence biosensing micropatterned surfaces based on immobilized human acetylcholinesterase. Analytical and Bioanalytical Chemistry, 2013. 405(2-3): p. 795-804 More

Fluorescence biosensing micropatterned surfaces basedHuman acetylcholinesterase (AChE) is a widely studied target enzyme in drug discovery for Alzheimer's disease (AD). In this paper we report evaluation of the optimum structure and chemistry of the supporting material for a new AChE-based fluorescence sensing surface. To achieve this objective, multilayered silicon wafers with spatially controlled geometry and chemical diversity were fabricated. Specifically, silicon wafers with silicon oxide patterns (SiO(2)/Si wafers), platinum-coated silicon wafers with SiO(2) patterns (SiO(2)/Pt/Ti/Si wafers), and Pt-coated wafers coated with different thicknesses of TiO(2) and SiO(2) (SiO(2)/TiO(2)/Pt/Ti/Si wafers) were labelled with the fluorescent conjugation agent HiLyte Fluor 555. Selection of a suitable material and the optimum pattern thickness required to maximize the fluorescence signal and maintain chemical stability was performed by confocal laser-scanning microscopy (CLSM). Results showed that the highest signal-to-background ratio was always obtained on wafers with 100 nm thick SiO(2) features. Hence, these wafers were selected for covalent binding of human AChE. Batch-wise kinetic studies revealed that enzyme activity was retained after immobilization. Combined use of atomic-force microscopy and CLSM revealed that AChE was homogeneously and selectively distributed on the SiO(2) microstructures at a suitable distance from the reflective surface. In the optimum design, efficient fluorescence emission was obtained from the AChE-based biosensing surface after labelling with propidium, a selective fluorescent probe of the peripheral binding site of AChE.

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Journal publications

  1. Boysen, R. I., Schwarz, L. J., Nicolau, D. V., Hearn, M. T., Molecularly imprinted polymer membranes and thin films for the separation and sensing of biomacromolecules. Journal of Separation Science 2017. 40: p. 314–335. 
  2. Hanson, K.L., et al., Polymer surface properties control the function of heavy meromyosin in dynamic nanodevices. Biosensors and Bioelectronics, 2016.
  3. Kašpar, O., et al., Confinement of water droplets on rectangular micro/nano-arrayed surfaces, Lab Chip, 2016. 16: p. 2487-2493.
  4. Nicolau, D. V.  Jr., et al., Parallel computation with molecular-motor-propelled agents in nanofabricated networks. PNAS, 2016, doi:10.1073/pnas.1510825113.
  5. Asenova, E.,  Lin, H. Y., Fu, E.,  Nicolau, D. V. Jr., Nicolau, D. V. Optimal Fungal Space Searching Algorithms. IEEE Transactions on NanoBioscience, 2016. PP(99): p. 1.
  6. Filipponi, L., et al., Protein patterning by microcontact printing using pyramidal PDMS stamps. Biomedical Microdevices, 2016. 18: p. 1-7.
  7. Nguyen, M.T., et al., A versatile modelling approach to determine the hydrophobicity of peptides at the atomic level. Molecular Simulation, 2016. 42(4): p. 257-269.
  8. Van Zalinge, H., et al., Surface-Controlled Properties of Myosin Studied by Electric Field Modulation. Langmuir, 2015. 31(30): p. 8354-8361.
  9. Hajne, J., et al., Motility of actin filaments on micro-contact printed myosin patterns. IEEE Transactions on Nanobioscience, 2015. 14(3): p. 313-322.
  10. Ramsey, L., et al., Control and gating of kinesin-microtubule motility on electrically heated thermo-chips. Biomedical Microdevices, 2014. 16(3): p. 459-463.
  11. Nicolau, D.V., et al., Mapping hydrophobicity on the protein molecular surface at atom-level resolution. PLoS ONE, 2014. 9(12).
  12. Wilson, R., et al., The selection of DNA aptamers for two different epitopes of thrombin was not due to different partitioning methods. Nucleic Acid Therapeutics, 2013. 23(1): p. 88-92.
  13. Nicolau, D.V., et al., Protein Molecular Surface Mapped at Different Geometrical Resolutions. PLoS ONE, 2013. 8(3).
  14. Bartolini, M., et al., Fluorescence biosensing micropatterned surfaces based on immobilized human acetylcholinesterase. Analytical and Bioanalytical Chemistry, 2013. 405(2-3): p. 795-804.
  15. Van Zalinge, H., et al., Actin filament motility induced variation of resonance frequency and rigidity of polymer surfaces studied by quartz crystal microbalance. Langmuir, 2012. 28(42): p. 15033-15037.
  16. Komaromy, A.Z., et al., Arrays of nano-structured surfaces to probe the adhesion and viability of bacteria. Microelectronic Engineering, 2012. 91: p. 39-43.
  17. Wilson, R. and D.V. Nicolau, Separation-free detection of biological molecules based on plasmon-enhanced fluorescence. Angewandte Chemie - International Edition, 2011. 50(9): p. 2151-2154.
  18. Van Zalinge, H., et al., Nanoscale electrode gaps to study single molecule conduction. Microelectronic Engineering, 2011. 88(8): p. 2707-2709.
  19. Held, M., C. Edwards, and D.V. Nicolau, Probing the growth dynamics of Neurospora crassa with microfluidic structures. Fungal Biology, 2011. 115(6): p. 493-505.
  20. Bartolini, M., et al., Kinetic characterization of amyloid-beta 1-42 aggregation with a multimethodological approach. Analytical Biochemistry, 2011. 414(2): p. 215-225.
  21. Nicolau, D.V., et al., Protein immobilisation on micro/nanostructures fabricated by laser microablation. Biosensors and Bioelectronics, 2010. 26(4): p. 1337-1345.
  22. Li, S., et al., Bacterial adhesion to toroidal nano-structures from poly(styrene)-block-poly(tert-butyl acrylate) diblock copolymer thin films. Microelectronic Engineering, 2010. 87(5-8): p. 715-718.
  23. Held, M., et al., Microfluidics structures for probing the dynamic behaviour of filamentous fungi. Microelectronic Engineering, 2010. 87(5-8): p. 786-789.
  24. Fulga, F. and D.V. Nicolau, Simulation of the nanostructuring of surfaces under ion-beam bombardment. Microelectronic Engineering, 2010. 87(5-8): p. 1455-1457.
  25. Dobroiu, S., et al., Laser-assisted structuring of metal-polymer bilayers for protein patterning. Microelectronic Engineering, 2010. 87(5-8): p. 1190-1194.
  26. Binz, M., et al., Motility of bacteria in microfluidic structures. Microelectronic Engineering, 2010. 87(5-8): p. 810-813.
  27. Aveyard, J., et al., Microfabricated magnetic bead polydimethylsiloxane microarrays. Microelectronic Engineering, 2010. 87(5-8): p. 760-764.
  28. Vasina, E.N., et al., The BAD project: Data mining, database and prediction of protein adsorption on surfaces. Lab on a Chip - Miniaturisation for Chemistry and Biology, 2009. 9(7): p. 891-900.
  29. Komaromy, A., et al., Micro-structures modulate bacterial cell viability and attachment. Microelectronic Engineering, 2009. 86(4-6): p. 1431-1434.
  30. Held, M., et al., Dynamic behaviour of microorganisms on microstructures. Microelectronic Engineering, 2009. 86(4-6): p. 1455-1458.
  31. Held, M., C. Edwards, and D. Nicolau, Fungal intelligence; Or on the behaviour of microorganisms in confined micro-environments. Journal of Physics: Conference Series, 2009. 178.
  32. Fulga, F. and D.V. Nicolau, Consequences of non-standard bleaching on microlithographic performance. Microelectronic Engineering, 2009. 86(4-6): p. 783-786.
  33. Filipponi, L., et al., Microbeads on microposts: An inverted architecture for bead microarrays. Biosensors and Bioelectronics, 2009. 24(7): p. 1850-1857.
  34. Nicolau Jr, D.V., et al., 'Extremotaxis': Computing with a bacterial-inspired algorithm. BioSystems, 2008. 94(1-2): p. 47-54.
  35. Nicolau, D.V., et al., Surface hydrophobicity modulates the operation of actomyosin-based dynamic nanodevices (Langmuir (2007) 23 (10846-10854)). Langmuir, 2008. 24(8): p. 4420.
  36. Ivanova, E.P., et al., Staleya guttiformis attachment on poly(tert-butylmethacrylate) polymeric surfaces. Micron, 2008. 39(8): p. 1197-1204.
  37. Nicolau, D.V., et al., Surface hydrophobicity modulates the operation of actomyosin-based dynamic nanodevices. Langmuir, 2007. 23(21): p. 10846-10854.
  38. Bakewell, D.J.G. and D.V. Nicolau, Protein linear molecular motor-powered nanodevices. Australian Journal of Chemistry, 2007. 60(5): p. 314-332.
  39. Sawant, P.D. and D.V. Nicolau, Hierarchy of DNA immobilization and hybridization on poly-L-lysine: An atomic force microscopy study. Smart Materials and Structures, 2006. 15(1): p. S99-S103.
  40. Sawant, P.D. and D.V. Nicolau, Nano-topographic evaluation of highly disordered fractal-like structures of immobilized oligonucleotides using AFM. Materials Science and Engineering B: Solid-State Materials for Advanced Technology, 2006. 132(1-2): p. 147-150.
  41. Sawant, P.D., P. Livingston, and D.V. Nicolau, Microablation of gold nanolayers by direct write lithography. Journal of Physics: Conference Series, 2006. 34(1): p. 22-27.
  42. Ivanova, E.P., et al., A comparative study between the adsorption and covalent binding of human immunoglobulin and lysozyme on surface-modified poly(tert-butyl methacrylate). Biomedical Materials, 2006. 1(1): p. 24-32.
  43. Ivanova, E.P., et al., Characterization of unusual alkaliphilic gram-positive bacteria isolated from degraded brown alga thalluses. Mikrobiolohichnyǐ zhurnal (Kiev, Ukraine : 1993), 2006. 68(4): p. 10-20.
  44. Ivanova, E.P., et al., ATP level variations in heterotrophic bacteria during attachment on hydrophilic and hydrophobic surfaces. International Microbiology, 2006. 9(1): p. 37-46.
  45. Hanson, K.L., et al., Fungi use efficient algorithms for the exploration of microfluidic networks. Small, 2006. 2(10): p. 1212-1220.
  46. Sawant, P.D., et al., Hierarchy of DNA immobilization and hybridization on poly-L-lysine using an atomic force microscopy study. Journal of Nanoscience and Nanotechnology, 2005. 5(6): p. 951-957.
  47. Sawant, P.D. and D.V. Nicolau, Line and two-dimensional fractal analysis of micrographs obtained by atomic force microscopy of surface-immobilized oligonucleotide nano-aggregates. Applied Physics Letters, 2005. 87(22): p. 1-3.
  48. Martinez-Neira, R., et al., A novel biosensor for mercuric ions based on motor proteins. Biosensors and Bioelectronics, 2005. 20(7): p. 1428-1432.
  49. Watson, G.S., et al., Interactions of poly(amino acids) in aqueous solution with charged model surfaces - Analysis by colloidal probe. Biosensors and Bioelectronics, 2004. 19(11): p. 1355-1362.
  50. Nicolau Jr, D.V. and D.V. Nicolau, Simulation of the motility of filaments on surfaces functionalised with molecular motors. Current Applied Physics, 2004. 4(2-4): p. 316-319.
  51. Kalinovskaya, N.I., et al., Low-molecular-weight, biologically active compounds from marine Pseudoalteromonas species. Current Microbiology, 2004. 48(6): p. 441-446.
  52. Ivanova, E.P., et al., Poly(L-lysine)-mediated immobilisation of oligonucleotides on carboxy-rich polymer surfaces. Biosensors and Bioelectronics, 2004. 19(11): p. 1363-1370.
  53. Ivanova, E.P., et al., Shewanella affinis sp. nov., isolated from marine invertebrates. International Journal of Systematic and Evolutionary Microbiology, 2004. 54(4): p. 1089-1093.
  54. Ivanova, E.P., et al., Characterization of Pseudoalteromonas distincta-like sea-water isolates and description of Pseudoalteromonas aliena sp. nov. International Journal of Systematic and Evolutionary Microbiology, 2004. 54(5): p. 1431-1437.
  55. Ivanova, E.P., et al., Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina). International Journal of Systematic and Evolutionary Microbiology, 2004. 54(2): p. 475-480.
  56. Ivanova, E.P., et al., Shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water. International Journal of Systematic and Evolutionary Microbiology, 2004. 54(4): p. 1083-1087.
  57. Ivanova, E.P., et al., Erratum: Shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water (International Journal of Systematic and Evolutionary Microbiology vol. 54 (1083-1087)). International Journal of Systematic and Evolutionary Microbiology, 2004. 54(6): p. 2441.
  58. Ivanova, E.P., et al., Brevibacterium celere sp. nov., isolated from degraded thallus of a brown alga. International Journal of Systematic and Evolutionary Microbiology, 2004. 54(6): p. 2107-2111.
  59. Ivanova, E.P., et al., Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. International Journal of Systematic and Evolutionary Microbiology, 2004. 54(3): p. 705-711.
  60. Ivanova, E.P., et al., Bacillus algicola sp. nov., a novel filamentous organism isolated from brown alga Fucus evanescens. Systematic and Applied Microbiology, 2004. 27(3): p. 301-307.
  61. Blach, J.A., et al., A mechanistic approach to tip-induced nano-lithography of polymer surfaces. Thin Solid Films, 2004. 459(1-2): p. 95-99.
  62. Watson, G.S., et al., Surface topography and surface chemistry of radiation-patterned P(tBuMA) - Analysis by atomic force microscopy. Polymer International, 2003. 52(9): p. 1408-1414.
  63. Watson, G.S., et al., Poly(amino acids) at Si-oxide interfaces - Bio-colloidal interactions, adhesion and 'conformation'. Colloid and Polymer Science, 2003. 282(1): p. 56-63.
  64. Nicolau Jr, D.V., F. Fulga, and D.V. Nicolau, Impact of protein adsorption on the geometry of microfluidics devices. Biomedical Microdevices, 2003. 5(3): p. 227-233.
  65. Ivanova, E.P., et al., Occurrence and diversity of mesophilic Shewanella strains isolated from the North-West Pacific Ocean. Systematic and Applied Microbiology, 2003. 26(2): p. 293-301.
  66. Ivanova, E.P., et al., Shewanella fidelis sp. nov., isolated from sediments and sea water. International Journal of Systematic and Evolutionary Microbiology, 2003. 53(2): p. 577-582.
  67. Ivanova, E.P., et al., Shewanella waksmanii sp. nov., isolated from a sipunculla (Phascolosoma japonicum). International Journal of Systematic and Evolutionary Microbiology, 2003. 53(5): p. 1471-1477.
  68. Ivanova, E.P., et al., Ecophysiological variabilities in ectohydrolytic enzyme activities of some Pseudoalteromonas species, P. citrea, P. issachenkonii, and P. nigrifaciens. Current Microbiology, 2003. 46(1): p. 6-10.
  69. Gorshkova, N.M., et al., Marinobacter excellens sp. nov., isolated from sediments of the Sea of Japan. International Journal of Systematic and Evolutionary Microbiology, 2003. 53(6): p. 2073-2078.
  70. Wright, J., et al., Micropatterning of myosin on O-acryloyl acetophenone oxime (AAPO), layered with bovine serum albumin (BSA). Biomedical Microdevices, 2002. 4(3): p. 205-211.
  71. Pham, D., et al., Effects of polymer properties on laser ablation behaviour. Smart Materials and Structures, 2002. 11(5): p. 668-674.
  72. Nicolau Jr, D.V., et al., A C library for simulating P systems. Fundamenta Informaticae, 2002. 49(1-3): p. 241-248.
  73. Mahanivong, C., et al., Manipulation of the motility of protein molecular motors on microfabricated substrates. Biomedical Microdevices, 2002. 4(2): p. 111-116.
  74. Ivanova, E.P., et al., Pseudoalteromonas ruthenica sp. nov., isolated from marine invertebrates. International Journal of Systematic and Evolutionary Microbiology, 2002. 52(1): p. 235-240.
  75. Ivanova, E.P., et al., Pseudoalteronomas translucida sp. nov. and Pseudoalteromonas paragorgicola sp. nov., and emended description of the genus. International Journal of Systematic and Evolutionary Microbiology, 2002. 52(5): p. 1759-1766.
  76. Ivanova, E.P., et al., Detection of coccoid forms of Sulfitobacter mediterraneus using atomic force microscopy. FEMS Microbiology Letters, 2002. 214(2): p. 177-181.
  77. Ivanova, E.P., et al., Tolerance to cadmium of free-living and associated with marine animals and eelgrass marine gamma-proteobacteria. Current Microbiology, 2002. 44(5): p. 357-362.
  78. Ivanova, E.P., et al., Pseudomonas extremorientalis sp. nov., isolated from a driking water reservoir. International Journal of Systematic and Evolutionary Microbiology, 2002. 52(6): p. 2113-2120.
  79. Ivanova, E.P., et al., Two species of culturable bacteria associated with degradation of brown algae Fucus evanescens. Microbial Ecology, 2002. 43(2): p. 242-249.
  80. Fulga, F., et al., Interrogation of the dynamics of magnetic microbeads on the meso-scale via electromagnetic detection. Smart Materials and Structures, 2002. 11(5): p. 722-727.
  81. Cao, J., et al., Study of atomic force microscopy force-distance curves by simulation using the Connolly surface for proteins. Smart Materials and Structures, 2002. 11(5): p. 767-771.
  82. Cao, J., et al., Predicting surface properties of proteins on the Connolly molecular surface. Smart Materials and Structures, 2002. 11(5): p. 772-777.
  83. Ivanova, E.P., et al., Shewanella japonica sp. nov. International Journal of Systematic and Evolutionary Microbiology, 2001. 51(3): p. 1027-1033.
  84. Nicolau, D.V., Mechanisms for protein micro/nano-patterning on photopolymer substrates. Proceedings of SPIE - The International Society for Optical Engineering, 2000. 3912: p. 114-119.
  85. Nicolau, D.E., et al., Nanotechnology at the crossroads: The hard or the soft way? Microelectronics Journal, 2000. 31(7): p. 611-616.
  86. Nicolau, D.V., et al., Negative and positive tone protein patterning on e-beam/deep-UV resists. Langmuir, 1999. 15(11): p. 3845-3851.
  87. Nicolau, D.V., et al., Protein patterning via radiation-assisted surface functionalization of conventional microlithographic materials. Colloids and Surfaces A: Physicochemical and Engineering Aspects, 1999. 155(1): p. 51-62.
  88. Nicolau, D.V., et al., Patterning neuronal and glia cells on light-assisted functionalised photoresists. Biosensors and Bioelectronics, 1999. 14(3): p. 317-325.
  89. Nicolau, D.V., et al., Actin motion on microlithographically functionalized myosin surfaces and tracks. Biophysical Journal, 1999. 77(2): p. 1126-1134.
  90. Nicolau, D.V., et al., Protein patterning using bilayer lithography and confocal microscopy. Proceedings of SPIE - The International Society for Optical Engineering, 1999. 3678(I): p. 602-607.
  91. Nicolau, D.V. and S. Yoshikawa, Molecular modelling of Me2+(8-hydroxy-quinolinate)2 complexes using ZINDO and ESSF methods. Journal of Molecular Graphics and Modelling, 1998. 16(2): p. 83-96.
  92. Nicolau, D.V. and S. Yoshikawa, Molecular modelling of Me2+ (8-hydroxy-quinolinate)2 complexes using ZINDO and ESSF methods. Journal of Molecular Graphics and Modelling, 1998. 16(2): p. 99.
  93. Nicolau, D.V., et al., Micron-sized protein patterning on diazonaphthoquinone/novolak thin polymeric films. Langmuir, 1998. 14(7): p. 1927-1936.
  94. Ivanova, E.P., et al., Impact of conditions of cultivation and adsorption on antimicrobial activity of marine bacteria. Marine Biology, 1998. 130(3): p. 545-551.
  95. Ivanova, E.P., et al., Phenotypic diversity of Pseudoalteromonas citrea from different marine habitats and emendation of the description. International Journal of Systematic Bacteriology, 1998. 48(1): p. 247-256.
  96. Nicolau, D.V., et al., Bio-microlithography: UV- and E-beam patterning of bioactive molecules. Journal of Photopolymer Science and Technology, 1996. 9(4): p. 645-652.
  97. Nicolau, D.V., et al., Technique for combinatorial drug release screening using microlithographic thin polymeric films. Proceedings of the Controlled Release Society, 1996(23): p. 809-810.
  98. Nicolau, D.V., et al., Control of the neuronal cell attachment by functionality manipulation of diazo-naphtho-quinone/novolak photoresist surface. Biosensors and Bioelectronics, 1996. 11(12): p. 1237-1252.
  99. Nicolau, D.V. and M.V. Dusa, The application of the in-situ dyeing effect to an image reversal resist. Microelectronic Engineering, 1990. 11(1-4): p. 557-560.