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Publications in other journals ranked by Ministry of Science and Higher Education
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Affiliation to IPPT PAN

1.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

2.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.0, 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.0, 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

3.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

4.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

5.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

6.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.

7.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