20180710 plan 
12:30, Sala: S3 im. W. Fiszdona, piętro III Abhyudai Singh, Associate Professor University of Delaware, Newark, DESystems Biology in Single Cells: A Tale of Two Viruses In the noisy cellular environment, expression of genes has been shown to be stochastic across organisms ranging from prokaryotic to human cells. Stochastic expression manifests as celltocell variability in the levels of RNAs/proteins, in spite of the fact that cells are genetically identical and are exposed to the same environment. Development of computationally tractable frameworks for modeling stochastic fluctuations in gene product levels is essential to understand how noise at the cellular level affects biological function and phenotype. I will introduce stateoftheart computational tools for stochastic modeling, analysis and inferences of biomolecular circuits. Mathematical methods will be combined with experiments to study infection dynamics of two viral systems in single cells. First, I will show how stochastic expression of proteins results in intercellular lysis time and viral burst size variations in the bacterial virus, lambda phage. Next, I will describe our efforts in stochastic analysis of the Human Immunodeficiency Virus (HIV) genetic circuitry. Our results show that HIV encodes a noisy promoter and stochastic expression of key viral regulatory proteins can drive HIV into latency, a drugresistant state of the virus. 
20180627 plan 
11:30, Sala: S3 im. W. Fiszdona, piętro III Karol Nienałtowski IPPT PANBayesian approach to reconstruction of time series from snapshot data Seminarium w ramach przeglądu wyników doktorantów w 2017/2018
Fluorescent live imaging (FLI) has become a powerful technique in studies at the singlecell level. One of its key advantages is the ability to measure quantities of interest, e.g. protein levels, over time in the same cell. Most often however reliable quantitative measurements require timeconsuming and costly preparation of cells, e.g. stable transfection with a fluorescent protein. An alternative approach is the highthroughput immunocytofluorescence (ICF) microscopy that uses fluorescent antibodies to detect molecules of interests. Unfortunately, the latter method is limited to fixed (dead) cells, what leads to the loss of information regarding correlations over time. Therefore, the question arises, whether the missing information could be augmented using a tailored statistical technique. Here, we propose a Bayesian approach to reconstruct timeseries of the heterogeneous behaviour of single cells from snapshot data. Timeseries are described as a Gaussian process (GP) with the mean and variance of ICF data and the correlations between timepoints are augmented with a prior. The covariance matrix of the GP is modeled using the inverseWishart distribution with a prior described by kernel covariance functions. The possibility to reconstruct timeseries is useful in studies of various dynamic processes in single cells. Here, the method allowed us for more accurate estimation of information transfer in the JAKSTAT pathway. 
20180627 plan 
12:00, Sala: S3 im. W. Fiszdona, piętro III Damian Zaremba IPPT PANModular microfluidic geometries for passive manipulations on droplets Seminarium w ramach przeglądu wyników doktorantów w 2017/2018
Microfluidics is still a new and rapidly growing field of science and has the potential to influence subject areas from chemical synthesis and biological analysis to optics and information technology. Dropletbased microfluidic is the branch of this field, where we use two immiscible fluids. The first liquid is used to produce droplets. Most often it is water and its mixtures. The second liquid is most often fluorinated oil (FC40, HFE7500) or hexadecane. This liquid is used to push droplets through complex microfluidics channels. Twophase flows have a lot of interesting physical phenomena and these phenomena can be used to complex manipulations on droplets in microfluidics. Changing the geometry of microfluidic structures, e.g. by adding a slit or an obstacle, significantly changes the behavior of flowing drops in the channels. I'll present the comprehensive study of the geometry of microfluidic components which can manipulate on droplets and next I'll show the new approach to the construction of microfluidic devices using these geometries. 
20180627 plan 
12:30, Sala: S3 im. W. Fiszdona, piętro III Chris Trombley IPPT PANCharged Particles Sedimenting Under Gravity In A Viscous Fluid Seminarium w ramach przeglądu wyników doktorantów w 2017/2018 
20180411 
12:30, Sala: S3 im. W. Fiszdona, piętro III S. Kondrat Department of Complex Systems, Institute of Physical Chemistry, WarsawModelling diffusion and reactions in biologically relevant systems There are many aspects of modelling biologically relevant systems, but often two main physical processes occurring are diffusion and reactions. In this talk, I will focus on modelling diffusion inside living cells, emphasizing its main features and challenges. I shall also outline an approach attempting to incorporate diffusion and reactions into a single multiscale simulation framework, and I will discuss a few applications ranging from enzyme kinetics to population dynamics. 
20180404 
12:30, Sala: S3 im. W. Fiszdona, piętro III mgr Marek Jerzy Grądzki The Institute of Geophysics, Polish Academy of SciencesInfluence of diffusion on magnetic buoyancy instability Magnetic buoyancy instability (MBI) is believed to plays an important role in the evolution of magnetic fields in astrophysical objects, especially stars. Probably it is also present in the Earth's core. In the case of the Sun observations indicate that the strong toroidal magnetic field emerges from deep regions to the surface and create sunspots or solar prominences. MBI is a probable mechanism of this phenomenon, while magnetic and thermal diffusion are processes important for dynamics of systems with this type of instability. During the presentation I will show the results of analytical and numerical approach to the problem. 
20180110 
12:30, Sala: S3 im. W. Fiszdona, piętro III Valentina Grippo Warsaw UniversityLipidic cubic phase for hosting enzymes and improving their catalytic activity 
20171220 
12:30, Sala: S3 im. W. Fiszdona, piętro III Paweł NałęczJawecki
Potential in discrete stochastic systems and connections with game theory In this seminar I will present the main points of my Bachelor thesis. I will show what potential can be in the context of sotchastic, an how to deal with it a manner which is both precise and intuitive (at least for me). This will lead to an exact connection between spacially discrete and continuous processes. In the end, I hope to show how the introduced methods can be applied to evolutionary games. 
20171206 
12:30, Sala: S3 im. W. Fiszdona, piętro III Dr Robert Owczarek University of New MexicoA story on knotted links between knots, links, the associated invariants, and Chebyshev/Fibonacci/Lucas invariants Topology has become very important in studying condensed matter systems recently to the extent that it is one of the most popular games in town. My interest in topology grew up during studies of vortices in superfluid helium and their role in the phase transition between normal and superfluid helium. Knotted and linked vortex structures proved to contribute to the transition. Such structures are mathematically described by various knot and link invariants, which I will discuss briefly in seminar. Examples of invariants include Alexander polynomial, Fox tricoloring, Jones polynomial, Khovanov homology. An intriguing and puzzling fact in studies of knot invariants is appearance of Chebyshev polynomials in various roles. I will try to make a small step forward in understanding of this role, and as a byproduct I will propose a generalization of Chebyshev polynomials so that they include the standard Chebyshev polynomials, Lucas polynomials, and Fibonacci polynomials (and yes, the latter are related to Fibonacci series) as special cases. This generalization opens a way to a generalization of the Jones polynomial in the sense I will discuss in the seminar, and perhaps more, though I am not going to go that far in this seminar. 
20171025 
12:30, Sala: S3 im. W. Fiszdona, piętro III dr Filippo Pierini IPPT PANElectrospinning of conjugated polymer nanofibers: research challenges and applications Conjugated polymers are a class of organic macromolecules with large πconjugated polymer chains due to a backbone chain of alternating double and singlebonds. The highly electrondelocalized structures generated by the overlapping of porbitals create systems with fascinating electronic and optical properties. Conjugated polymer nanomaterials have been shown to be promising for advanced organic electronic, photovoltaic and biomedical applications. Electrospinning is the most efficient technique for elongating and aligning polymer chains to form nanofibers with a welldefined structure. This technique is particularly interesting in order to fabricate continuous polymer 1D nanostructures with controllable composition, structure and properties. Chemical and physical properties of conjugated polymer nanofibers could be modulated by controlling their hierarchical structure by way of electrospinning [13]. The major challenge in the development of these materials has been obtaining a balance between polymer properties and spinnability. During this seminar, a brief overview of conjugated polymer material properties will be presented. In the second part, principles of the electrospinning of conjugated polymer will be discussed. Finally, recent results on the development of electrospun nanofiberbased devices and their applications will be demonstrated [4]. REFERENCES [1] F. Pierini et al., “Electrospun poly(3hexylthiophene)/poly(ethylene oxide)/graphene oxide composite nanofibers: effects of graphene oxide reduction", Polymers for Advanced Technologies, 27 (2016) 1465–1475. [2] F. Pierini et al., “Comparison between inorganic geomimetic chrysotile and multiwalled carbon nanotubes for the preparation of onedimensional conducting polymer nanocomposites”, Fibers and Polymers, 16, (2015) 426433. [3] F. Pierini et al., "Electrospun polyanilinebased composite nanofibers: tuning the electrical conductivity by tailoring the structure of thiolprotected metal nanoparticles", Journal of Nanomaterials, 6142140 (2017) 10. [4] F. Pierini et al., “Singlematerial organic solar cells based on electrospun fullerenegrafted polythiophene nanofibers” Macromolecules, 50, 13 (2017) 49724981. 
20171018 
12:30, Sala: S3 im. W. Fiszdona, piętro III dr inż. Izabela Piechocka IPPT PANThe effect of shear flow on fibrin clot structure and fibrinplatelets interactions Fibrin and platelets are the two main components involved in blood clot formation, preventing bleeding and promoting wound repair. In vivo, the formation of blood clots takes place in the presence of flowing blood that exerts a continuous shear force on the whole structure, influencing its mechanical properties such as extensibility and resistance. The exact role of the shear flow in bulk organization of fibrin networks and in fibrinplatelet interactions at the nanometer scale still remains, however, unexplored. Here, by bring together parallelplate flow chamber (PPFC) together with confocal microscope, we plan to follow in situ changes in fibrin network structure at the bulk level and the level of individual fibrin filaments. By using combination of PPFC together with superresolution microscopy techniques such as stimulated emission depletion microscopy (STED) or stochastic optical reconstruction microscopy (STORM), we plan to uncover the role of shear flow in spatial organization of fibrinplatelet adhesion receptors. Such fibrinplatelets model system will closely mimics the in vivo
situation of blood clots, providing a crucial insight into the role of shear flow in the extracellular matrix (ECM)cell interactions which is important in light of the biological function of blood clots. 
20171011 
12:30, Sala: S3 im. W. Fiszdona, piętro III dr hab. Piotr Korczyk IPPT PANSelfcounting droplets and other microfluidic curiosities Integrated logic elements with embedded digital operations into the structure of the device has been successfully implemented in electronics, becoming one of the pillars of the information revolution.About one decade ago Manu Prakash demonstrated, that single fundamental logic operations can be implemented in the twophase microfluidic flows due to the utilization of nonlinearity introduced by surface interactions. Those findings raised a hope that further integration of these base units would enable construction of architectures inducing programmed cascades of digital operations on droplets or bubbles. That approach would pave the way for autonomous microfluidic systems with all analytical procedures hardwired into the structure of the device. However, until now there is a lack of examples of realization of that promising idea.Herein we show the new approach to the construction of microfluidic geometries, which perform the logic operations on sequences of droplets. We explain the working principles and, what is most important, we demonstrate that those single units can be successfully arranged into larger systems performing sequences of operations. Finally, we demonstrate the examples of encoding of the digital procedures of counting of droplets in both binary and decimal systems. In our microfluidic architectures, some of the droplets flowing into the counter play a role of indicators and their positions correspond directly to the current count of all flowing droplets. Such microfluidic counters can be arranged in series to count a custom number of droplets. We show and test a few construction of the counters, which can count reliably up to 1000 droplets. Presented devices show the fascinating aspect of microfluidics, where continuous flows of liquids crossed in microfluidic junction spontaneously transform into the discrete droplets and then these droplets perform digital computations. 
20170929 
12:30, Sala: S3 im. W. Fiszdona, piętro III Prof. Jochen Rink Max Planck Institute of Molecular Cell Biology and Genetics Dresden, GermanyPattern establishment and scaling in planarians Planarian flatworms are astonishing creatures. They have the ability to regenerate complete and perfectly proportioned individuals from tiny tissue fragments. They grow when fed and literally shrink when starving, continuously varying their body size between less than one mm and several cm in length. Abundant pluripotent adult stem cells serve as sole source of new cells and their continuous divisions continuously renew all organismal cell types. Such unique biology epitomizes a fascinating challenge: How to regenerate, maintain and scale form and function of a triploblastic body plan? My lab approaches this problem from multiple angles, including the patterning systems specifying the body plan, the multilevel control of organismal growth dynamics and via the comparative analysis of our large live collection of planarian species. We recently found that the planarian A/P axis is patterned by a selforganizing Wnt gradient deployed from the tail tip, which exists in mutual antagonism with a similar patterning system deployed from the head. Current work addresses the transformation of the signaling gradients into cell fate choices and the evolutionary changes in the signaling network that ultimately explain why some planarians regenerate, while others do not. 
20170926 
10:30, Sala: S3 im. W. Fiszdona, piętro III Chris Trombley IPPT PANStability And Earnshaw’s Theorem In A Viscous Fluid Seminarium w ramach przeglądu wyników doktorantów uzyskanych w 2016/17. 
20170913 
12:30, Sala: S3 im. W. Fiszdona, piętro III Paramita Chatterjee IPPT PANMathematical analysis of a limb growth model Seminarium w ramach przeglądu wyników doktorantów uzyskanych w 2016/17.
Vertebrate limb development is an important example of organogenesis. In [1], Glimm and coauthors proposed a new model related to bone formation based upon the results of an experimental paper [2]. It diﬀers signiﬁcantly from any previously discussed model of growing limb. In [2], a crucial role of new morphogens regulating the cells aggregation and bone formation during avian limb growth has been reported. The main mathematical feature of the Glimm’s model is that it is described by a system of equations which are neither parabolic nor hyperbolic. Here we propose a possible approach of the model analysis.
1. T. Glimm, R. Bhat, S.A. Newman, Modeling the morphodynamic galectin patterning network of the developing avian limb skeleton,J.Theor. Biol.,346(2014), pp. 86108.
2. Bhat, R., Lerea, K.M., Peng, H., Kaltner, H., Gabius, H.J., Newman, S.A., A regulatory network of two galectins mediates the earliest steps of avian limb skeletal morphogenesis, BMC developmental biology, 11(1), (2011), 1. 
20170628 
12:30, Sala: S3 im. W. Fiszdona, piętro III prof. Jerzy Bławzdziewicz Department of Mechanical Engineering, Texas Tech University, Lubbock, TX, USAGeometry and mechanics in soft biological matter: an analysis of nematode locomotion and fruit ﬂy morphogenesis The interplay between geometry and mechanical forces plays a subtle but very important role in diverse biological systems. In our ﬁrst example we will focus on locomotion of the nematode C. elegans in 2D and 3D environments. We will investigate optimization and neuromuscular control of nematode gait patterns in diﬀerent media; we also discuss the geometry and biomechanics of its turning maneuvers. The second example will center on the formation of embryonic architecture during fruit ﬂy morphogenesis; in our analysis we argue that mechanical feedback is crucial for robustness of morphogenetic movements.

20170621 
12:30, Sala: S3 im. W. Fiszdona, piętro III mgr Karol Nienałtowski IPPT PANQuantitative methods for analysing cellular signalling Seminarium w ramach przeglądu wyników doktorantów uzyskanych w 2016/17.
The complexity of biochemical signalling induce usage a combination of tailored experimental measurements with quantitative approaches for better understanding signalling mechanisms. My research is focused on: (1) development software for quantification of highthrougput single cellmeasurements and (2) mathematical methodology for analysing signalling mechanisms. We proposed nonparametric modelling method for reconstructing trajectory of cellular response to the stimuli from singlecell snapshot data. Moreover, we work on developing stochastic models of interferones signalling in normal cell lines of human lung epithelium as well as in human nonsmall cell lung cancer cell lines that combine intrinsic and extrinsic sources of cellular variability. During the seminar I will present previous results of my PhD project and plan of work for the next year. 