Author Archives: Ondrej Kaspar


May 25 – Unconventional Computing

The actin-myosin system

Attention Everyone,

mark your calendar and watch online

Wednesday, May 25, 2016 – 4:30pm to 5:30pm

Dan V. Nicolau will present ‘Unconventional Computing’ at Stanford University.

Additional info: here + video

About the talk:

Many important mathematical problems, ranging from cryptography, network routing, and protein folding, require the exploration a large number of candidate solutions. Because the time required for solving these problems grows exponentially with their size, electronic computers, which operate sequentially, cannot solve them in a reasonable timeframe. Unfortunately, the parallel-computation approaches proposed so far, e.g., DNA-, and quantum-computing, suffer from fundamental and practical drawbacks, which prevented their successful implementation. On the other hand, biological entities, from microorganisms to humans, process information in parallel, routinely, for essential tasks, such as foraging, searching for available space, competition, and cooperation. However, aside of their sheer complexity, parallel biological processes are difficult to harness for artificial parallel computation because of a fundamental difference: biological entities process analog information, e.g., concentration gradients, whereas computing devices require the processing of numbers. This subtle, but important difference between artificial and biological computation, together with the opportunity to operate biocomputation with large numbers of (small) biological agents, opens three possible avenues for development.

Biological IT. The first opportunity relies on the study of the natural procedures used by biological agents, e.g., for space search and partitioning, chemotaxis, etc., followed by the translation of these procedures in abstract mathematical algorithms. These bioinspired algorithms can be then benchmarked against standard analogues used for similar tasks, and, if appropriate, improved and implemented. Along this development avenue, which is conceptually similar to other biomimetics efforts, such as biomimetic materials, we have shown that fungi used exquisitely efficient algorithms for search for available space; and that the chemotaxis procedures used by bacteria can be used to find edges of geometrical patterns.

Biosimulation. The second opportunity relies on the capacity of using large numbers of biological agents to explore complex networks which mimic real traffic situations. This line of development has been almost entirely dedicated to the study of network optimization performed by amoeboid organisms, e.g., Physarum, placed in geometrically confined environments which also contain chemotactic ‘cues’, e.g., larger concentrations of nutrients in set coordinates. This physical simulation of traffic networks resulted in many studies assessing the optimality of real traffic networks in many countries.

Biocomputation with biological agents in networks. Finally, the third, and arguably the most exciting development consists in the use of very large number of agents exploring purposefully-designed microfluidics networks. For instance, we reported the foundations of a 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, agents, e.g., 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.

The lecture will conclude with a perspective on the computation and simulation using biological entities in microfluidics structures, weighing the opportunities and challenges offered by various technological avenues.


e mrs

E-MRS 2016 Spring Meeting

emrs 2

Meet Us at the 2016 E-MRS Spring Meeting in Lille (France) from May 2 to 6

The conference will include 31 parallel symposia, 3 workshops & tutorials, one plenary session, one exhibition and much more. All technical sessions and non-technical events will be held at Lille Grand Palais.

V. Tokárová – Solving geometrical problems with bacteria

oral presentation is scheduled for 03/05/2016 – 16h15 – session B6.5


O. KašparConfinement of water nanodroplets on micro/nano chessboard-like patterned surfaces

poster presentation is scheduled for 03/05/2016 – 17h35 – session B.P4.15




Parallel computation with molecular-motor-propelled agents in nanofabricated networks

Who’s talking about our research? Please click here!

Overview of attention for article published in Proceedings of the National Academy of Sciences of the United States of America, February 2016

Score: In the top 5% of all research outputs scored by Altmetric


“The digital age is dawning. The bio computer will make digital look like the abacus.

Science MArch

Science – Replacing electrons with filaments

Science MArch


Replacing electrons with filaments

Science  11 Mar 2016:
Vol. 351, Issue 6278, pp. 1163-1164
DOI: 10.1126/science.351.6278.1163-g



Hot off the press

Parallel computation with molecular-motor-propelled agents in nanofabricated networks

Dan V. Nicolau Jr., Mercy Lard, Till Korten, Falco C. M. J. M. van Delft, Malin Persson, Elina Bengtsson, Alf Månsson, Stefan Diez, Heiner Linke and Dan V. Nicolau

Freely available online through the PNAS open access option


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.

Actin filaments exploring the {2, 5, 9} device. The movie shows a time lapse of 200 typical fluorescence micrographs of actin filaments (shown in white) moving through a network (shown in blue) encoding the SSP with the set {2, 5, 9}. Exits labeled with green numbers represent correct results, and magenta numbers represent incorrect results. Below each exit, the number of actin that has arrived there is shown in white. The image of the network was obtained from an optical micrograph of the device and cropped to fit to the fluorescence image. Blurred objects passing over the network are actin filaments floating by in the solution. A background subtraction and contrast enhancement was performed evenly across the images with the use of ImageJ (


Hot off the press

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.

This article is open access - enjoy it! :)


BµF Team