Seminaria Zakładu Biosystemów i Miękkiej Materii

Pawińskiego 5b

kolor czcionki + kolor tła = plan do 7 dni.

2018-07-10 12:30, Sala: S3 im. W. Fiszdona, piętro III
Abhyudai Singh, Associate Professor
University of Delaware, Newark, DE

Systems 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 cell-to-cell 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 state-of-the-art 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 drug-resistant state of the virus.

2018-06-27 11:30, Sala: S3 im. W. Fiszdona, piętro III
Karol Nienałtowski

Bayesian 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 single-cell 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 time-consuming and costly preparation of cells, e.g. stable transfection with a fluorescent protein. An alternative approach is the high-throughput 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 correlation​s​ ​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 time-series of the heterogeneous behaviour of single cells​ from snapshot data.​ ​Time-series are described as a Gaussian process (GP) with the mean and variance ​of ICF data and the correlations between time-points ​are augmented with a prior.​ ​The covariance matrix of ​the ​GP ​is modeled ​using the inverse-Wishart distribution with a prior described by kernel covariance functions. ​The possibility to reconstruct time-series 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 JAK-STAT pathway.

2018-06-27 12:00, Sala: S3 im. W. Fiszdona, piętro III
Damian Zaremba

Modular 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. Droplet-based 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 (FC-40, HFE-7500) or hexadecane. This liquid is used to push droplets through complex microfluidics channels.
Two-phase 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.

2018-06-27 12:30, Sala: S3 im. W. Fiszdona, piętro III
Chris Trombley

Charged Particles Sedimenting Under Gravity In A Viscous Fluid

Seminarium w ramach przeglądu wyników doktorantów w 2017/2018
2018-04-11 12:30, Sala: S3 im. W. Fiszdona, piętro III
S. Kondrat
Department of Complex Systems,
Institute of Physical Chemistry, Warsaw

Modelling 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.

2018-04-04 12:30, Sala: S3 im. W. Fiszdona, piętro III
mgr Marek Jerzy Grądzki
The Institute of Geophysics, Polish Academy of Sciences

Influence 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.

12:30, Sala: S3 im. W. Fiszdona, piętro III
Valentina Grippo
Warsaw University

Lipidic cubic phase for hosting enzymes and improving their catalytic activity

2017-12-20 12:30, Sala: S3 im. W. Fiszdona, piętro III
Paweł Nałęcz-Jawecki

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.

2017-12-06 12:30, Sala: S3 im. W. Fiszdona, piętro III
Dr Robert Owczarek
University of New Mexico

A 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.

12:30, Sala: S3 im. W. Fiszdona, piętro III
dr Filippo Pierini

Electrospinning of conjugated polymer nanofibers: research challenges and applications

Conjugated polymers are a class of organic macromolecules with large π-conjugated polymer chains due to a backbone chain of alternating double- and single-bonds. The highly electron-delocalized structures generated by the overlapping of p-orbitals 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 well-defined 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 [1-3]. 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 nanofiber-based devices and their applications will be demonstrated [4].


[1] F. Pierini et al., “Electrospun poly(3-hexylthiophene)/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 one-dimensional conducting polymer nanocomposites”, Fibers and Polymers, 16, (2015) 426-433.

[3] F. Pierini et al., "Electrospun polyaniline-based composite nanofibers: tuning the electrical conductivity by tailoring the structure of thiol-protected metal nanoparticles", Journal of Nanomaterials, 6142140 (2017) 10.

[4] F. Pierini et al., “Single-material organic solar cells based on electrospun fullerene-grafted polythiophene nanofibers” Macromolecules, 50, 13 (2017) 4972-4981.

2017-10-18 12:30, Sala: S3 im. W. Fiszdona, piętro III
dr inż. Izabela Piechocka

The effect of shear flow on fibrin clot structure and fibrin-platelets 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 fibrin-platelet interactions at the nanometer scale still remains, however, unexplored.

Here, by bring together parallel-plate 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 super-resolution 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 fibrin-platelet adhesion receptors.

Such fibrin-platelets 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.

2017-10-11 12:30, Sala: S3 im. W. Fiszdona, piętro III
dr hab. Piotr Korczyk

Self-counting 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 two-phase 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 hard-wired 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.

2017-09-29 12:30, Sala: S3 im. W. Fiszdona, piętro III
Prof. Jochen Rink
Max Planck Institute of Molecular Cell Biology and Genetics
Dresden, Germany

Pattern 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 multi-level 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 self-organizing 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.

2017-09-26 10:30, Sala: S3 im. W. Fiszdona, piętro III
Chris Trombley

Stability And Earnshaw’s Theorem In A Viscous Fluid

Seminarium w ramach przeglądu wyników doktorantów uzyskanych w 2016/17.
2017-09-13 12:30, Sala: S3 im. W. Fiszdona, piętro III
Paramita Chatterjee

Mathematical 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.

ArchiwumSeminaria 1996-2010
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