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Publications in other journals ranked by Ministry of Science and Higher Education
Conference publications indexed in the Web of Science Core Collection
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Affiliation to IPPT PAN

1.Korczyk P.M., van Steijn V., Błoński S., Zaremba D., Beattie D.A., Garstecki P., Accounting for corner flow unifies the understanding of droplet formation in microfluidic channels, Nature Communications, ISSN: 2041-1723, DOI: 10.1038/s41467-019-10505-5, Vol.10, No.1, pp.2528-1-9, 2019
Korczyk P.M., van Steijn V., Błoński S., Zaremba D., Beattie D.A., Garstecki P., Accounting for corner flow unifies the understanding of droplet formation in microfluidic channels, Nature Communications, ISSN: 2041-1723, DOI: 10.1038/s41467-019-10505-5, Vol.10, No.1, pp.2528-1-9, 2019

Abstract:
While shear emulsification is a well understood industrial process, geometrical confinement in microfluidic systems introduces fascinating complexity, so far prohibiting complete understanding of droplet formation. The size of confined droplets is controlled by the ratio between shear and capillary forces when both are of the same order, in a regime known as jetting, while being surprisingly insensitive to this ratio when shear is orders of magnitude smaller than capillary forces, in a regime known as squeezing. Here, we reveal that further reduction of—already negligibly small—shear unexpectedly re-introduces the dependence of droplet size on shear/capillary-force ratio. For the first time we formally account for the flow around forming droplets, to predict and discover experimentally an additional regime—leaking. Our model predicts droplet size and characterizes the transitions from leaking into squeezing and from squeezing into jetting, unifying the description for confined droplet generation, and offering a practical guide for applications.

2.Komorowski M., Tawfik D.S., The Limited Information Capacity of Cross-Reactive Sensors Drives the Evolutionary Expansion of Signaling, Cell Systems, ISSN: 2405-4712, DOI: 10.1016/j.cels.2018.12.006, Vol.8, No.1, pp.76-85.e6, 2019
Komorowski M., Tawfik D.S., The Limited Information Capacity of Cross-Reactive Sensors Drives the Evolutionary Expansion of Signaling, Cell Systems, ISSN: 2405-4712, DOI: 10.1016/j.cels.2018.12.006, Vol.8, No.1, pp.76-85.e6, 2019

Abstract:
Signaling systems expand by duplications of various components, be it receptors or downstream effectors. However, whether and how duplicated components contribute to higher signaling capacity is unclear, especially because in most cases, their specificities overlap. Using information theory, we found that augmentation of capacity by an increase in the copy number is strongly limited by logarithmic diminishing returns. Moreover, counter to conventional biochemical wisdom, refinements of the response mechanism, e.g., by cooperativity or allostery, do not increase the overall signaling capacity. However, signaling capacity nearly doubles when a promiscuous, non-cognate ligand becomes explicitly recognized via duplication and partial divergence of signaling components. Our findings suggest that expansion of signaling components via duplication and enlistment of promiscuously acting cues is virtually the only accessible evolutionary strategy to achieve overall high-signaling capacity despite overlapping specificities and molecular noise. This mode of expansion also explains the highly cross-wired architecture of signaling pathways.

Keywords:
paralog expansion, gene duplication, allostery, cooperativity, biochemical signal processing, information capacity

3.Bobrowski A., Lipniacki T., Robin-type boundary conditions in transition from reaction-diffusion equations in 3D domains to equations in 2D domains, Journal of Differential Equations, ISSN: 0022-0396, DOI: 10.1016/j.jde.2019.08.022, Vol.268, No.1, pp.239-271, 2019
Bobrowski A., Lipniacki T., Robin-type boundary conditions in transition from reaction-diffusion equations in 3D domains to equations in 2D domains, Journal of Differential Equations, ISSN: 0022-0396, DOI: 10.1016/j.jde.2019.08.022, Vol.268, No.1, pp.239-271, 2019

Abstract:
We consider a singular limit of diffusion equations in 3D domains of thickness converging to zero. In the 2D limit the resulting reaction-diffusion equation has a source term resulting from the Robin-type boundary conditions imposed on boundaries of the original 3D domain. The proposed approach can be applied to constructing approximate solutions of diffusion problems in thin planar, cylindrical, or spherical layers between two membranes. As an example we refer to the problem of activation of B lymphocytes, which typically have large nuclei and a thin cytoplasmic layer which can be considered as a spherical shell. For this example, assuming additionally axial symmetry we provide a rigorous convergence theorem in the language of semigroups of operators.

Keywords:
Semigroups of operators, Degenerate convergence, Singular perturbation, Boundary conditions, Thin layers, Signaling pathways, Phosphorylation–dephosphorylation cycle

4.Nakielski P., Pierini F., Blood interactions with nano- and microfibers: recent advances, challenges and applications in nano- and microfibrous hemostatic agents, Acta Biomaterialia, ISSN: 1742-7061, DOI: 10.1016/j.actbio.2018.11.029, Vol.84, pp.63-76, 2019
Nakielski P., Pierini F., Blood interactions with nano- and microfibers: recent advances, challenges and applications in nano- and microfibrous hemostatic agents, Acta Biomaterialia, ISSN: 1742-7061, DOI: 10.1016/j.actbio.2018.11.029, Vol.84, pp.63-76, 2019

Abstract:
Nanofibrous materials find a wide range of applications, such as vascular grafts, tissue-engineered scaffolds, or drug delivery systems. This phenomenon can be attributed to almost arbitrary biomaterial modification opportunities created by a multitude of polymers used to form nanofibers, as well as by surface functionalization methods. Among these applications, the hemostatic activity of nanofibrous materials is gaining more and more interest in biomedical research. It is therefore crucial to find both materials and nanofiber structural properties that affect organism responses. The present review critically analyzes the response of blood elements to natural and synthetic polymers, and their blends and composites. Also assessed in this review is the incorporation of pro-coagulative substances or drugs that can decrease bleeding time. The review also discusses the main animal models that were used to assess hemostatic agent safety and effectiveness.

Keywords:
Blood-biomaterial interactions, Coagulation, Electrospinning, Nanofibers, Platelets, Hemorrhage

5.Ekiel-Jeżewska M.L., Adamczyk Z., Bławzdziewicz J., Streaming Current and Effective ζ-Potential for Particle-Covered Surfaces with Random Particle Distributions, The Journal of Physical Chemistry C, ISSN: 1932-7447, DOI: 10.1021/acs.jpcc.8b10068, Vol.123, No.6, pp.3517-3531, 2019
Ekiel-Jeżewska M.L., Adamczyk Z., Bławzdziewicz J., Streaming Current and Effective ζ-Potential for Particle-Covered Surfaces with Random Particle Distributions, The Journal of Physical Chemistry C, ISSN: 1932-7447, DOI: 10.1021/acs.jpcc.8b10068, Vol.123, No.6, pp.3517-3531, 2019

Abstract:
A detailed theoretical and experimental study is presented concerning the streaming current and the derivative effective ζ-potential for a planar surface covered by a monolayer of adsorbed particles. Precise simulation results are obtained for the equilibrium and random-sequential-adsorption (RSA) distributions of monodisperse spherical particles interacting via the excluded-volume potential. The streaming current is calculated in the thin-double-layer regime for all physically accessible particle area fractions. The results are expressed as a linear combination of the interface and particle contributions DI and DP weighted by the interface and particle ζ-potentials ζI and ζP. We find that in the area-fraction regime where both particle distributions exist, the equilibrium and RSA results for the streaming current are nearly indistinguishable. Our numerical data show that DI exponentially decays to zero when the particle area fraction θ is increased, whereas DP exponentially tends to a linear behavior. The results are described (with the accuracy better than 1.5% of the maximal value) by the exponential and linear plus exponential approximations, with only one fitting parameter. The numerical and theoretical predictions are in agreement with experimental data obtained for a wide range of ζ-potentials of the interface and the particles. Results obtained for a rough surface with spherical asperities indicate that the roughness can reduce the effective ζ-potential (as evaluated from the streaming current) by more than 25%; this prediction is also confirmed by experiments.

6.Pręgowska A., Kaplan E., Szczepański J., How Far can Neural Correlations Reduce Uncertainty? Comparison of Information Transmission Rates for Markov and Bernoulli Processes, International Journal of Neural Systems, ISSN: 0129-0657, DOI: 10.1142/S0129065719500035, Vol.29, No.8, pp.1950003-1-13, 2019
Pręgowska A., Kaplan E., Szczepański J., How Far can Neural Correlations Reduce Uncertainty? Comparison of Information Transmission Rates for Markov and Bernoulli Processes, International Journal of Neural Systems, ISSN: 0129-0657, DOI: 10.1142/S0129065719500035, Vol.29, No.8, pp.1950003-1-13, 2019

Abstract:
The nature of neural codes is central to neuroscience. Do neurons encode information through relatively slow changes in the firing rates of individual spikes (rate code) or by the precise timing of every spike (temporal code)? Here we compare the loss of information due to correlations for these two possible neural codes. The essence of Shannon’s definition of information is to combine information with uncertainty: the higher the uncertainty of a given event, the more information is conveyed by that event. Correlations can reduce uncertainty or the amount of information, but by how much? In this paper we address this question by a direct comparison of the information per symbol conveyed by the words coming from a binary Markov source (temporal code) with the information per symbol coming from the corresponding Bernoulli source (uncorrelated, rate code). In a previous paper we found that a crucial role in the relation between information transmission rates (ITRs) and firing rates is played by a parameter s, which is the sum of transition probabilities from the no-spike state to the spike state and vice versa. We found that in this case too a crucial role is played by the same parameter s. We calculated the maximal and minimal bounds of the quotient of ITRs for these sources. Next, making use of the entropy grouping axiom, we determined the loss of information in a Markov source compared with the information in the corresponding Bernoulli source for a given word length. Our results show that in the case of correlated signals the loss of information is relatively small, and thus temporal codes, which are more energetically efficient, can replace rate codes effectively. These results were confirmed by experiments.

Keywords:
Shannon information theory, information source, information transmission rate, firing rate, neural coding

7.Senapati S., Poma Bernaola A., Cieplak M., Filipek S., Park P., Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes, Analytical Chemistry, ISSN: 0003-2700, DOI: 10.1021/acs.analchem.9b00546, Vol.91, No.11, pp.7226-7235, 2019
Senapati S., Poma Bernaola A., Cieplak M., Filipek S., Park P., Differentiating between Inactive and Active States of Rhodopsin by Atomic Force Microscopy in Native Membranes, Analytical Chemistry, ISSN: 0003-2700, DOI: 10.1021/acs.analchem.9b00546, Vol.91, No.11, pp.7226-7235, 2019

Abstract:
Membrane proteins, including G protein-coupled receptors (GPCRs), present a challenge in studying their structural properties under physiological conditions. Moreover, to better understand the activity of proteins requires examination of single molecule behaviors rather than ensemble averaged behaviors. Force–distance curve-based AFM (FD-AFM) was utilized to directly probe and localize the conformational states of a GPCR within the membrane at nanoscale resolution based on the mechanical properties of the receptor. FD-AFM was applied to rhodopsin, the light receptor and a prototypical GPCR, embedded in native rod outer segment disc membranes from photoreceptor cells of the retina in mice. Both FD-AFM and computational studies on coarse-grained models of rhodopsin revealed that the active state of the receptor has a higher Young’s modulus compared to the inactive state of the receptor. Thus, the inactive and active states of rhodopsin could be differentiated based on the stiffness of the receptor. Differentiating the states based on the Young’s modulus allowed for the mapping of the different states within the membrane. Quantifying the active states present in the membrane containing the constitutively active G90D rhodopsin mutant or apoprotein opsin revealed that most receptors adopt an active state. Traditionally, constitutive activity of GPCRs has been described in terms of two-state models where the receptor can achieve only a single active state. FD-AFM data are inconsistent with a two-state model but instead require models that incorporate multiple active states.

Keywords:
Nanoindentation, Rhodopsin, GPCR, membrane, biophysics, AFM, active, inactive, molecular dynamics, coarse graining, Go-like model

8.Jetka T., Nienałtowski K., Winarski T., Błoński S., Komorowski M., Information-theoretic analysis of multivariate single-cell signaling responses, PLOS COMPUTATIONAL BIOLOGY, ISSN: 1553-7358, DOI: 10.1371/journal.pcbi.1007132, Vol.15, No.7, pp.e1007132-1-23, 2019
Jetka T., Nienałtowski K., Winarski T., Błoński S., Komorowski M., Information-theoretic analysis of multivariate single-cell signaling responses, PLOS COMPUTATIONAL BIOLOGY, ISSN: 1553-7358, DOI: 10.1371/journal.pcbi.1007132, Vol.15, No.7, pp.e1007132-1-23, 2019

Abstract:
Mathematical methods of information theory appear to provide a useful language to describe how stimuli are encoded in activities of signaling effectors. Exploring the information-theoretic perspective, however, remains conceptually, experimentally and computationally challenging. Specifically, existing computational tools enable efficient analysis of relatively simple systems, usually with one input and output only. Moreover, their robust and readily applicable implementations are missing. Here, we propose a novel algorithm, SLEMI—statistical learning based estimation of mutual information, to analyze signaling systems with high-dimensional outputs and a large number of input values. Our approach is efficient in terms of computational time as well as sample size needed for accurate estimation. Analysis of the NF-κB single—cell signaling responses to TNF-α reveals that NF-κB signaling dynamics improves discrimination of high concentrations of TNF-α with a relatively modest impact on discrimination of low concentrations. Provided R-package allows the approach to be used by computational biologists with only elementary knowledge of information theory.

9.Poma Bernaola A., Guzman V.H., Li M.S., Theodorakis P.E., Mechanical and thermodynamic properties of Aβ42, Aβ40, and α-synuclein fibrils: a coarse-grained method to complement experimental studies, Beilstein Journal of Nanotechnology, ISSN: 2190-4286, DOI: 10.3762/bjnano.10.51, Vol.10, pp.500-513, 2019
Poma Bernaola A., Guzman V.H., Li M.S., Theodorakis P.E., Mechanical and thermodynamic properties of Aβ42, Aβ40, and α-synuclein fibrils: a coarse-grained method to complement experimental studies, Beilstein Journal of Nanotechnology, ISSN: 2190-4286, DOI: 10.3762/bjnano.10.51, Vol.10, pp.500-513, 2019

Abstract:
We perform molecular dynamics simulation on several relevant biological fibrils associated with neurodegenerative diseases such as Aβ40, Aβ42, and α-synuclein systems to obtain a molecular understanding and interpretation of nanomechanical characterization experiments. The computational method is versatile and addresses a new subarea within the mechanical characterization of heterogeneous soft materials. We investigate both the elastic and thermodynamic properties of the biological fibrils in order to substantiate experimental nanomechanical characterization techniques that are quickly developing and reaching dynamic imaging with video rate capabilities. The computational method qualitatively reproduces results of experiments with biological fibrils, validating its use in extrapolation to macroscopic material properties. Our computational techniques can be used for the co-design of new experiments aiming to unveil nanomechanical properties of biological fibrils from a point of view of molecular understanding. Our approach allows a comparison of diverse elastic properties based on different deformations , i.e., tensile (YL), shear (S), and indentation (YT) deformation. From our analysis, we find a significant elastic anisotropy between axial and transverse directions (i.e., YT > YL) for all systems. Interestingly, our results indicate a higher mechanostability of Aβ42 fibrils compared to Aβ40, suggesting a significant correlation between mechanical stability and aggregation propensity (rate) in amyloid systems. That is, the higher the mechanical stability the faster the fibril formation. Finally, we find that α-synuclein fibrils are thermally less stable than β-amyloid fibrils. We anticipate that our molecular-level analysis of the mechanical response under different deformation conditions for the range of fibrils considered here will provide significant insights for the experimental observations.

Keywords:
Alzheimer disease, Parkinson disease, β-amyloid, α-synuclein, molecular dynamics, AFM, indentation, elasticity, protein, fibrils, assemblies, soft matter, Young modulus

10.Enayati M.S., Neisiany R.E., Sajkiewicz P., Behzad T., Denis P., Pierini F., Effect of nanofiller incorporation on thermomechanical and toughness of poly (vinyl alcohol)-based electrospun nanofibrous bionanocomposites, Theoretical and Applied Fracture Mechanics, ISSN: 0167-8442, DOI: 10.1016/j.tafmec.2018.11.006, Vol.99, pp.44-50, 2019
Enayati M.S., Neisiany R.E., Sajkiewicz P., Behzad T., Denis P., Pierini F., Effect of nanofiller incorporation on thermomechanical and toughness of poly (vinyl alcohol)-based electrospun nanofibrous bionanocomposites, Theoretical and Applied Fracture Mechanics, ISSN: 0167-8442, DOI: 10.1016/j.tafmec.2018.11.006, Vol.99, pp.44-50, 2019

Abstract:
The current work studies the electrospun poly (vinyl alcohol) (PVA) nanofibers and its nanocomposites including nanohydroxy apatite (nHAp) and nHAp/cellulose nanofibers (CNFs), emphasizing the impact of nanofillers on the toughness of nanofibers. PVA nanofibers were incorporated with 10 wt% of nHAp and then various amounts of CNF were added to subsequent PVA/nHAp fibrous nanocomposites. The morphology of nonwoven mats was studied by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). While neat PVA nanofibers were smooth and uniform in thickness, the nanofiller loading resulted in thinner fibers with less uniformity. Furthermore, the thermal properties of the nonwoven network of fibers were characterized employing thermogravimetric analysis (TGA). Although the maximum loss mass temperature of PVA was partially reduced upon addition of nanofillers, the onset of decomposition was not altered. The mechanical characterizations were performed using static tensile and dynamic mechanical analysis (DMA). Compared to neat PVA mats, the tensile test of nanocomposites mats demonstrated the significant increase in Young’s modulus; however, strain at break was dramatically reduced. In addition, the fracture work was assessed from the area under the stress-strain curve, which showed brittleness of fibrous nanocomposites due to the nanofiller incorporation. Field emission SEM (FE-SEM) was employed to scan the fracture surface of stretched fibers. The increase in modulus of electrospun mats was also shown by DMA in frequency mode. In parallel, both tensile test and DMA confirmed the change in fracture of PVA fibers from a tough to brittle mode, due to the nanofiller addition.

Keywords:
Electrospun nanocomposites, Nanofillers, Toughness, Mechanical properties

11.Pręgowska A., Proniewska K., van Dam P., Szczepański J., Using Lempel-Ziv complexity as effective classification tool of the sleep-related breathing disorders, Computer Methods and Programs in Biomedicine, ISSN: 0169-2607, DOI: 10.1016/j.cmpb.2019.105052, Vol.182, pp.105052-1-7, 2019
Pręgowska A., Proniewska K., van Dam P., Szczepański J., Using Lempel-Ziv complexity as effective classification tool of the sleep-related breathing disorders, Computer Methods and Programs in Biomedicine, ISSN: 0169-2607, DOI: 10.1016/j.cmpb.2019.105052, Vol.182, pp.105052-1-7, 2019

Abstract:
Background and objective
People suffer from sleep disorders caused by work-related stress, irregular lifestyle or mental health problems. Therefore, development of effective tools to diagnose sleep disorders is important. Recently, to analyze biomedical signals Information Theory is exploited. We propose efficient classification method of sleep anomalies by applying entropy estimating algorithms to encoded ECGs signals coming from patients suffering from Sleep-Related Breathing Disorders (SRBD).

Methods
First, ECGs were discretized using the encoding method which captures the biosignals variability. It takes into account oscillations of ECG measurements around signals averages. Next, to estimate entropy of encoded signals Lempel–Ziv complexity algorithm (LZ) which measures patterns generation rate was applied. Then, optimal encoding parameters, which allow distinguishing normal versus abnormal events during sleep with high sensitivity and specificity were determined numerically. Simultaneously, subjects’ states were identified using acoustic signal of breathing recorded in the same period during sleep.

Results
Random sequences show normalized LZ close to 1 while for more regular sequences it is closer to 0. Our calculations show that SRBDs have normalized LZ around 0.32 (on average), while control group has complexity around 0.85. The results obtained to public database are similar, i.e. LZ for SRBDs around 0.48 and for control group 0.7. These show that signals within the control group are more random whereas for the SRBD group ECGs are more deterministic. This finding remained valid for both signals acquired during the whole duration of experiment, and when shorter time intervals were considered. Proposed classifier provided sleep disorders diagnostics with a sensitivity of 93.75 and specificity of 73.00%. To validate our method we have considered also different variants as a training and as testing sets. In all cases, the optimal encoding parameter, sensitivity and specificity values were similar to our results above.

Conclusions
Our pilot study suggests that LZ based algorithm could be used as a clinical tool to classify sleep disorders since the LZ complexities for SRBD positives versus healthy individuals show a significant difference. Moreover, normalized LZ complexity changes are related to the snoring level. This study also indicates that LZ technique is able to detect sleep abnormalities in early disorders stage.

Keywords:
Information theory, Lempel-Ziv complexity, Entropy, ECG, Sleep-related breathing disorders, Randomness

12.Grabowski F., Czyż P., Kochańczyk M., Lipniacki T., Limits to the rate of information transmission through the MAPK pathway, JOURNAL OF THE ROYAL SOCIETY INTERFACE, ISSN: 1742-5689, DOI: 10.1098/rsif.2018.0792, Vol.16, No.152, pp.20180792-1-10, 2019
Grabowski F., Czyż P., Kochańczyk M., Lipniacki T., Limits to the rate of information transmission through the MAPK pathway, JOURNAL OF THE ROYAL SOCIETY INTERFACE, ISSN: 1742-5689, DOI: 10.1098/rsif.2018.0792, Vol.16, No.152, pp.20180792-1-10, 2019

Abstract:
Two important signalling pathways of NF-κB and ERK transmit merely 1 bit of information about the level of extracellular stimulation. It is thus unclear how such systems can coordinate complex cell responses to external cues. We analyse information transmission in the MAPK/ERK pathway that converts both constant and pulsatile EGF stimulation into pulses of ERK activity. Based on an experimentally verified computational model, we demonstrate that, when input consists of sequences of EGF pulses, transmitted information increases nearly linearly with time. Thus, pulse-interval transcoding allows more information to be relayed than the amplitude–amplitude transcoding considered previously for the ERK and NF-κB pathways. Moreover, the information channel capacity C, or simply bitrate, is not limited by the bandwidth B = 1/τ, where τ ≈ 1 h is the relaxation time. Specifically, when the input is provided in the form of sequences of short binary EGF pulses separated by intervals that are multiples of τ/n (but not shorter than τ), then for n = 2, C ≈ 1.39 bit/h; and for n = 4, C ≈ 1.86 bit/h. The capability to respond to random sequences of EGF pulses enables cells to propagate spontaneous ERK activity waves across tissue.

Keywords:
cellular signal transduction, pulsatile stimulation, pulse-interval transcoding, bandwidth, representation problem

13.Gruziel-Słomka M., Kondratiuk P., Szymczak P., Ekiel-Jeżewska M.L., Stokesian dynamics of sedimenting elastic rings, SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/c9sm00598f, Vol.15, pp.7262-7274, 2019
Gruziel-Słomka M., Kondratiuk P., Szymczak P., Ekiel-Jeżewska M.L., Stokesian dynamics of sedimenting elastic rings, SOFT MATTER, ISSN: 1744-683X, DOI: 10.1039/c9sm00598f, Vol.15, pp.7262-7274, 2019

Abstract:
We consider elastic microfilaments which form closed loops. We investigate how the loops change shape and orientation while settling under gravity in a viscous fluid. Loops are circular at the equilibrium. Their dynamics are investigated numerically based on the Stokes equations for the fluid motion and the bead–spring model of the microfilament. The Rotne–Prager approximation for the bead mobility is used. We demonstrate that the relevant dimensionless parameter is the ratio of the bending resistance of the filament to the gravitation force corrected for buoyancy. The inverse of this ratio, called the elasto-gravitation number [scr B, script letter B], is widely used in the literature for sedimenting elastic linear filaments. We assume that [scr B, script letter B] is of the order of 104–106, which corresponds to easily deformable loops. We find out that initially tilted circles evolve towards different sedimentation modes, depending on [scr B, script letter B]. Very stiff or stiff rings attain almost planar, oval shapes, which are vertical or tilted, respectively. More flexible loops deform significantly and converge towards one of several characteristic periodic motions. These sedimentation modes are also detected when starting from various shapes, and for different loop lengths. In general, multi-stability is observed: an elastic ring converges to one of several sedimentation modes, depending on the initial conditions. This effect is pronounced for very elastic loops. The surprising diversity of long-lasting periodic motions and shapes of elastic rings found in this work gives a new perspective for the dynamics of more complex deformable objects at micrometer and nanometer scales, sedimenting under gravity or rotating in a centrifuge, such as red blood cells, ring polymers or circular DNA.

14.Pręgowska A., Casti A., Kaplan E., Wajnryb E., Szczepański J., Information processing in the LGN: a comparison of neural codes and cell types, BIOLOGICAL CYBERNETICS, ISSN: 0340-1200, DOI: 10.1007/s00422-019-00801-0, Vol.113, No.4, pp.453-464, 2019
Pręgowska A., Casti A., Kaplan E., Wajnryb E., Szczepański J., Information processing in the LGN: a comparison of neural codes and cell types, BIOLOGICAL CYBERNETICS, ISSN: 0340-1200, DOI: 10.1007/s00422-019-00801-0, Vol.113, No.4, pp.453-464, 2019

Abstract:
To understand how anatomy and physiology allow an organism to perform its function, it is important to know how information that is transmitted by spikes in the brain is received and encoded. A natural question is whether the spike rate alone encodes the information about a stimulus (rate code), or additional information is contained in the temporal pattern of the spikes (temporal code). Here we address this question using data from the cat Lateral Geniculate Nucleus (LGN), which is the visual portion of the thalamus, through which visual information from the retina is communicated to the visual cortex. We analyzed the responses of LGN neurons to spatially homogeneous spots of various sizes with temporally random luminance modulation. We compared the Firing Rate with the Shannon Information Transmission Rate , which quantifies the information contained in the temporal relationships between spikes. We found that the behavior of these two rates can differ quantitatively. This suggests that the energy used for spiking does not translate directly into the information to be transmitted. We also compared Firing Rates with Information Rates for X-ON and X-OFF cells. We found that, for X-ON cells the Firing Rate and Information Rate often behave in a completely different way, while for X-OFF cells these rates are much more highly correlated. Our results suggest that for X-ON cells a more efficient “temporal code” is employed, while for X-OFF cells a straightforward “rate code” is used, which is more reliable and is correlated with energy consumption.

Keywords:
Shannon information theory, Cat LGN, ON–OFF cells, Neural coding, Entropy, Firing rate

15.Zaremba D., Błoński S., Marijnissen M.J., Korczyk P.M., Fixing the direction of droplets in a bifurcating microfluidic junction, MICROFLUIDICS AND NANOFLUIDICS, ISSN: 1613-4982, DOI: 10.1007/s10404-019-2218-x, Vol.23, pp.55-1-18, 2019
Zaremba D., Błoński S., Marijnissen M.J., Korczyk P.M., Fixing the direction of droplets in a bifurcating microfluidic junction, MICROFLUIDICS AND NANOFLUIDICS, ISSN: 1613-4982, DOI: 10.1007/s10404-019-2218-x, Vol.23, pp.55-1-18, 2019

Abstract:
We present a novel type of microfluidic bifurcating junctions which fixes the droplet’s route. Unlike in regular junctions, where a droplet chooses one of two outputs depending on the (often instantaneous) flow distribution, our modifications direct droplets only to one preferred outlet. As we show, this solution works properly regardless of the variations of flow distribution in a wide range of its amplitude. Such modified junctions allow for the encoding of the droplet’s traffic in the geometry of the device. We compare in a series of experiments different junctions having channels of uniform square cross section. Our observations revealed that a small, local modification of the junction in the form of an additional shallow slit imposes a significant consequence for the flow of droplets at an entire microfluidic network’s scale. Another interesting and helpful feature of these new junctions is that they keep the integrity of long droplets, unlike regular junctions, which tend to split long droplets. Our experimental investigations revealed a complex transformation of the long droplet during its transfer through the modified junction. We show that this transformation resembles the Baker’s transform and can be used for the enhancement of mixing inside the droplets. Finally, we show two examples of microfluidic devices where the deterministic character of these modified junctions is utilized to obtain new, non-trivial functionalities. This approach can be used for the engineering of microfluidic devices with embedded procedures replacing active elements like valves or magnetic/electric fields.

Keywords:
Droplet, Microfluidics, Two-phase, Manipulations