Seminaria Zakładu Biosystemów i Miękkiej Materii

Pawińskiego 5b

kolor czcionki + kolor tła = plan do 7 dni.

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.

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.

2017-06-28 12:30, Sala: S3 im. W. Fiszdona, piętro III
prof. Jerzy Bławzdziewicz
Department of Mechanical Engineering,
Texas Tech University, Lubbock, TX, USA

Geometry 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.

2017-06-21 12:30, Sala: S3 im. W. Fiszdona, piętro III
mgr Karol Nienałtowski

Quantitative 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 high-througput single cell-measurements and (2) mathematical methodology for analysing signalling mechanisms. We proposed non-parametric modelling method for reconstructing trajectory of cellular response to the stimuli from single-cell 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 non-small 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.

2017-06-14 12:30, Sala: S3 im. W. Fiszdona, piętro III
Professor Krzysztof Kuczera
Departments of Chemistry and Molecular Biosciences
The University of Kansas, Lawrence, USA

Modeling peptide solvation by denaturing and protective co-solvents

2017-04-26 12:00, Sala: S3 im. W. Fiszdona, piętro III
mgr Marek Bukowicki

Dynamics of settling pairs of elastic particles at low Reynolds number regime

I will discuss dynamics of symmetric pairs of particles, settling in viscous fluid. Results for two regimes will be presented: the system of rigid particles, where periodic solutions are observed, and the system of elastic particles.

2017-03-20 14:30, Sala: S3 im. W. Fiszdona, piętro III
dr inż. Marta Grodzik
Zakład Nanobiotechnologii, SGGW

Antyglejakowa terapia grafenem - nadzieje i obawy

2017-01-11 12:30, Sala: S3 im. W. Fiszdona, piętro III
dr Gustavo Abade
Institute of Geophysics, University of Warsaw

Active microrheology in a colloidal glass of hard spheres

The talk will address the dynamics of a probe particle driven by a constant force through a colloidal glass of hard spheres. This nonequilibrium and anisotropic problem is investigated using a new implementation of the mode-coupling approximation with multiple relaxation channels and Langevin dynamics simulations. An important feature of the system is the critical force, above which the probe delocalizes. Friction coefficients of delocalized probes decrease with force, indicating force-thinning behavior. Probe van Hove functions predicted by the theory show exponential tails reminiscent of an intermittent dynamics of the probe. This scenario is microscopically supported by simulations.

2016-12-21 12:30, Sala: S3 im. W. Fiszdona, piętro III
dr Karol Makuch
Instytut Chemii Fizycznej PAN

Speed of flow of non-wetting droplets in capillaries of circular cross-section

We measure mobility of long droplets in circular microfluidic channels. Using oil as a continuous phase and aqueous solutions of glycerol with die as droplet phase, we determine mobility for the range of values of the capillary number Ca∈(〖10〗^(-5),〖10〗^(-2) ) and ratio of viscosities of the droplet and continuous phase λ∈(0.25,10). To explain the results of our experiments, we also introduce approximate method of calculation of the speed of viscous droplets. This theoretical approach is based on lubrication approximation.

2016-12-14 12:30, Sala: S3 im. W. Fiszdona, piętro III
dr Paweł Żuk

On the viscosity of rigid models of molecules

The viscosity of complex fluids very strongly depends on their composition. For many medical and technological applications it is important to know how does the macroscopic viscosity change with the shape of suspended molecules. We will show ho to calculate the viscosity of macromolecules modeled as bead modes and treat some artificial problems that can be found in the literature like "the center of viscosity".

2016-11-16 12:30, Sala: S3 im. W. Fiszdona, piętro III
Damian Zaremba

Design of a control and signal processing module for an experimental research ultrasound system and its implementation in a FPGA device. - Master Thesis presentation

Aim of this thesis is design of a control and signal processing module of ultrasound 2D imaging system and its implementation in FPGA Xilinx Artix-7. Thesis is a part of work in project of student scientific group "Bio-Son". It is carried out at Faculty of Mechatronics, Warsaw University of Technology.
Task of the control module is configuration and synchronization of the signal processing modules, a user interface and peripheral devices embedded in the ultrasound system. It has been implemented as software running on an embedded system. Embedded system is based on Leon3/GRLIB project.
The signal processing module operates on a single line of RF signal. The RF signal is preprocessed in Front-End block and it is an output of the beamformer. Operations of filtration, various kinds of envelope detection and compression of an amplitude are used to processing this signal in implemented module.
The Research task was to examine accuracy of estimation envelope of RF signal and resources utilization of FPGA by proposed methods.

2016-11-09 12:30, Sala: S3 im. W. Fiszdona, piętro III
Chris Trombley, M.Sc.

Interaction of a Straight Line Current with a Superconducting Sphere

An analytical expression for a scalar potential for a current line near a grounded sphere is obtained. This is an exact solution for a model of a superconducting sphere in the Meissner state which gives expressions for not only the scalar potential, but also the magnetic field and the force. This solution is derived in a way analogous to the hydrodynamic problem of a spherical blockage near a vortex line in a potential flow. This method avoids both guesswork and complicated series expansions, and also results in simple expression for the solution. Once the solution is obtained, both its symmetries and its dependencies of the result on model parameters will be explained. The behavior as the line current approaches the sphere will also be explored.

12:30, Sala: S3 im. W. Fiszdona, piętro III
dr Marta Waclawczyk

Lie point symmetries and invariant solutions of equations for turbulence statistics

Although the evolution of turbulent velocity field is governed by the deterministic Navier-Stokes equations, due to its sensitivity to small variations in the initial and boundary conditions turbulent field may be treated as a stochastic field. For its statistical description joint probability density functions (pdf's) of velocities in different points of the flow are needed. Transport equations for such pdf's form a system of infinitely many equations where in the n-th equation for n-point pdf an unknown pdf in (n+1) points is present.
In the first part of the talk theoretical description of turbulent flows and mathematical analysis of the infinite system for pdf's with the use of the Lie-group method will be addressed.
Next, possible applications of this theoretical study to derive invariant solutions for turbulence statistics and invariant turbulence closures will be discussed.

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

Stimuli-responsive liquid crystal hydrogel implants by electrospinning technique

The aim of the project is to develop stimuli-responsive electrospun polymer hydrogel materials in order to produce implantable smart materials for biomedical applications.
Tissue engineering and drug delivery strategies have great potential for medical treatments of several diseases and injuries. Their applicability is limited by the lack of implanted materials adaptability to the specific biological tissue requirements over time.
The project is intended to produce soft and biocompatible stimuli-sensitive nanostructured hydrogel capable of releasing drugs and to be easily tunable applying external stimuli. The beneficial effects of the material softness will be assisted by the drug release that will minimize tissue inflammation and stimulate the growth of cells around the implant. The stiffness reduction and materials deformability is particularly appreciated in neural tissue treatments.
The proposed materials will be composed of a hydrogel and liquid crystal blend possessing the required biocompatibility, mechanical properties and ability to release drugs. The capability to change the material structure and biomolecule release properties applying external stimuli will be guarantee by the presence of liquid crystals into the polymer structure.

13:00, Sala: S3 im. W. Fiszdona, piętro III
dr inż. Paweł Nakielski

Investigation of blood clotting mechanism in contact with nanofibers

The main objective of the project is the analysis of blood clotting mechanisms in the contact with polymer nanofibers. Knowledge on platelets plug and fibrin clot formation is crucial in the assessment of hemostatic potential of wound dressings. Despite a large number of experiments carried out using polymer materials, coagulation mechanisms are still not fully understood. Therefore, the use of various synthetic polymers, their blends with natural polymers of confirmed hemostatic effect e.g. collagen and gelatine, and additionally nanofibers made of natural polymer chitosan, will be investigated for their potential to stop bleeding. Analysis of nanofibers’ surface modifications and its effect on wettability of the material and most importantly acceleration of platelets adhesion and aggregation will be an important objective of the project. Addition of drugs affecting coagulation cascade will help design delivery system acting locally and accelerating blood clot formation.

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