20170426 plan 
12:00, Sala: S3 im. W. Fiszdona, piętro III mgr Marek Bukowicki IPPT PANDynamics 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. 
20170320 
14:30, Sala: S3 im. W. Fiszdona, piętro III dr inż. Marta Grodzik Zakład Nanobiotechnologii, SGGWAntyglejakowa terapia grafenem  nadzieje i obawy 
20170111 
12:30, Sala: S3 im. W. Fiszdona, piętro III dr Gustavo Abade Institute of Geophysics, University of WarsawActive 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 modecoupling 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 forcethinning 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. 
20161221 
12:30, Sala: S3 im. W. Fiszdona, piętro III dr Karol Makuch Instytut Chemii Fizycznej PANSpeed of flow of nonwetting droplets in capillaries of circular crosssection 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.

20161214 
12:30, Sala: S3 im. W. Fiszdona, piętro III dr Paweł Żuk IPPT PANOn 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".

20161116 
12:30, Sala: S3 im. W. Fiszdona, piętro III Damian Zaremba IPPT PANDesign 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 Artix7. Thesis is a part of work in project of student scientific group "BioSon". 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 FrontEnd 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. 
20161109 
12:30, Sala: S3 im. W. Fiszdona, piętro III Chris Trombley, M.Sc. IPPT PANInteraction 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. 
20161026 
12:30, Sala: S3 im. W. Fiszdona, piętro III dr Marta Waclawczyk IGF UWLie point symmetries and invariant solutions of equations for turbulence statistics Although the evolution of turbulent velocity field is governed by the deterministic NavierStokes 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 nth equation for npoint 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 Liegroup 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. 
20161019 
12:30, Sala: S3 im. W. Fiszdona, piętro III dr Filippo Pierini
Stimuliresponsive liquid crystal hydrogel implants by electrospinning technique The aim of the project is to develop stimuliresponsive 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 stimulisensitive 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. 
20161019 
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. 
20160713 
12:30, Sala: S3 im. W. Fiszdona, piętro III Piotr Bełdowski Instytut Matematyki i Fizyki, Uniwersytet TechnologicznoPrzyrodniczy w BydgoszczyParadigms of micellesinvolving lubrication: brushes and hydrated (bio)surfaces 
20160622 
12:30, Sala: S3 im. W. Fiszdona, piętro III Sławomir Białecki seminarium w ramach przeglądów wyników doktorantów IPPT PAN w 2015/16Fale i oscylacje wapniowe w komórce biologicznej Na seminarium omówię rozwiązania w postaci fali biegnącej dla układu równań parabolicznych opisujących dynamikę wapnia dla różnych wartości współczynników dyfuzji buforów wolnych i 'uwapniowanych'. Przedstawię również pewne własności rozwiązań równań reakcji dyfuzji na sferze dla szczególnej postaci członu źródłowego. 
20160615 
12:30, Sala: S3 im. W. Fiszdona, piętro III Paramita Chatterjee seminarium w ramach przeglądów wyników doktorantów IPPT PAN w 2015/16Mathematical analysis of a model of avian limb formation A study on the existence and properties of solutions to a model describing the morphodynamic galectin patterning network of the developing avian limb skeleton derived in [1]. And a review of chondrogenic pattern formation in developing limb.
[1] "Modeling the morphodynamic galectin patterning network of the developing avian limb skeleton" by the authors T. Glimm, S. A. Newman, R. Bhat 
20160615 
13:30, Sala: S3 im. W. Fiszdona, piętro III Marek Bukowicki seminarium w ramach przeglądów wyników doktorantów IPPT PAN w 2015/16Dynamika symetrycznego układu giętkich cząstek opadających w lepkim płynie Na seminarium przedstawiona zostanie dynamika dwóch elastycznych cząstek opadających w lepkim płynie. Zostaną przedstawione wyniki dla cząstek o różnej giętkości i kształcie. W zależności od tych parametrów obserwowane jest odpychanie lub przyciąganie hydrodynamiczne pomiędzy cząstkami.

20160608 
12:30, Sala: S3 im. W. Fiszdona, piętro III Paweł Czyż graduated from XIV LO Staszic in WarsawBottle oscillators What is common for clocks, human hearts and... diverted bottles filled with water? All of them exhibit oscillations! In our work we analysed so called "bottle oscillators" and obtained a mathematical model describing them. In addition, we investigated more complicated systems with many bottles linked in a big oscillator! 
20160601 
12:30, Sala: S3 im. W. Fiszdona, piętro III prof. Krzysztof Kuczera Departments of Chemistry and Molecular Biosciences The University of Kansas Lawrence USA Modeling passive membrane permeation of aromatic dipeptides Umbrella sampling simulations are used to study the passive permeation of three aromatic dipeptides – Nacetylphenylalanineamide (NAFA), Nacetyltyrosineamide (NAYA) and Nacetyltryptophanamide (NATA)  through a 1,2dioleoylsnglycero3phospocholine (DOPC) lipid bilayer. We model the structure, dynamics and interactions of the peptides as a function of z, the distance from lipid bilayer. The calculated profiles of the potential of mean force show two strong effects – preferential binding of each of the three peptides to the lipid interface and large free energy barriers in the membrane center. Surprisingly, computed translational diffusion coefficients D(z) change very little with reaction coordinate and are also quite similar for the three peptides studied. In contrast calculated values of sidechain rotational correlation times τ_{rot}(z) show extremely large changes with peptide membrane insertion – values become 100 times larger in the headgroup region and 10 times larger at interface and in membrane center, relative to solution. The peptides’ conformational freedom becomes systematically more restricted as they enter the membrane, sampling α and β and C7_{eq} basins in solution, α and C7_{eq} at the interface and C7_{eq} only in the center. Residual waters of solvation remain around the peptides even in the membrane center. Overall, our study provides an improved microscopic understanding of passive peptide permeation through membranes, especially on the sensitivity of rotational diffusion to position relative to the bilayer.

20160518 
12:30, Sala: S3 im. W. Fiszdona, piętro III Karol Nienałtowski seminarium w ramach przeglądów wyników doktorantów IPPT PAN w 2015/16Sensitivity and identifiability analysis in quantitative biology dynamical models Dynamical models in quantitive biology are characterised by much more complex structures and substantially larger sets of parameters than models used in physics and engineering. Moreover available experiments usually provide limited set of data, which corresponds to fragments of studied systems. This leads to nonidentifiability of parameters that cannot be estimated from experimental data. In consequence the reliability of used models is limited and our knowledge of studied processes is misrepresented.
Therefore, my work is focused on understanding how parameter values and their mutual relationships determine a model behaviour. The sensitivity analysis provides tools that allow to rigorously investigate how individual parameter values (input) impact a defined quantitative characteristics of model behaviour (output). On the other hand analysis of parameters collinearity insight of joint parameters impact on the model dynamics.
Basing this both concepts we have developed techniques for verifying locally identifiability of individual parameters in large dynamical models, which contain even hundreds of parameters. Nowadays my research is directed to exploit local findings in problems of experimental design and model reduction. 
20160516 
16:15, Sala: S3 im. W. Fiszdona, piętro III Monika Kurpas Politechnika ŚląskaModelowanie układu p53 w odpowiedzi na jedno i dwuniciowe uszkodzenie DNA Podwójnoniciowe uszkodzenia DNA wykrywane są przez moduł ATM a pojedynczoniciowe fragmenty DNA przez moduł ATR. Obydwa szlaki aktywują białko p53 zaangażowane w regulację cyklu komórkowego, naprawę DNA i apoptozę. Pomiędzy szlakami ATM i ATR istnieją zależności. Przykładowo proces resekcji podwójnoniciowych uszkodzeń DNA skutkuje aktywacją modułu ATR. W ramach badań zostały stworzone: model ATM oparty na danych eksperymentalnych, model ATR, wstępny łączony model ATMATR uwzględniający proces resekcji podwójnoniciowych uszkodzeń DNA oraz wstępny model ATR połączony z modelem cyklu komórkowego. Otrzymane wyniki znajdują potwierdzenie w literaturze biologicznej. 
20160511 
12:30, Sala: S3 im. W. Fiszdona, piętro III Sylwia Pawłowska seminarium w ramach przeglądów wyników doktorantów IPPT PAN w 2015/16Eksperymentalna analiza dynamiki nano obiektów zawieszonych w cieczy A work focused on the mobility of the nanoobjects suspended in fluid. The research activity is centred on issues of hydrodynamic diameter of spherical particles that is affected by several factors such as the environment (ionic strength of the solution), the steric and ionic impact and the scale or slip effect on the particlefluid interaction. Knowledge of the hydrodynamic diameter of nanoparticles or biological macromolecules in a given environmental conditions is essential to determine the diffusion of the tested nanoobjects in the studied environment (e.g. body and intracellular fluids). The subject has been expanded to include the study of the influence of the structure of more morphologically complex nanomaterials as well as the strong deformability shown by hydrogel nanofilaments. These objects produced using coaxial electrospinning have been characterized by evaluating their mechanical properties (persistence length, Young's modulus), the rheological behaviour under the influence of thermal fluctuations (Brownian motion) and the morphology (AFM). The defined nanofilaments has been also analysed inside microchannels where a pulsed liquid flow allows to simulate the living body conditions. These studies will help to determine the impact that periodic movements have on the conformational changes of these nanofilaments. Conducted experiments can be helpful in understanding and assessing the behaviour of flexible nanofilaments, thereby helping to understand and explain the physical phenomena responsible for the coiling and bending dynamic of the long molecular objects, such as DNA and proteins. No doubt the existence of similar mechanical properties (ratio of persistence length to contour length) between DNA molecules and hydrogel nanofilaments supports the possibility of using them as models object in order to eliminate the disadvantages associated with the small size of DNA molecules. The presented research can help to verify the existing simulation models of Brownian dynamics in micro and nanoscale for spherical objects, highly deformable filaments and macromolecules. Understanding the relationship between microstructure and macroscopic properties of the filaments flow opens the possibility of designing nanoobjects capable to travel in crowded body fluids in order to selectively delivery drugs into the target area or reach specific local tissues with the aim of helping their regeneration. 