Seminaria Zakładu Biosystemów i Miękkiej Materii

Pawińskiego 5b

kolor czcionki + kolor tła = plan do 7 dni.

2018-11-22
 plan 
12:30, Sala: S3 im. W. Fiszdona, piętro III
Rachel Rigby
MRC Weatherall Institute of Molecular Medicine
University of Oxford

Characterisation of the heterogeneity of human type I IFNs

2018-10-17 12:30, Sala: S3 im. W. Fiszdona, piętro III
Prof. Andrzej Nowicki
IPPT PAN

The value of flow mediated dilation in prediction of vascular disorders

There is growing interest in the application of non-invasive clinical tools allowing to assess the endothelial function, preceding atherosclerosis. A comparison of 7-12 MHz and 20 MHz scanners for flow mediated dilation (FMD) and shear rate (SR) measurements in radial artery is reported. The experiments in vitro using closely spaced food plastic foils proved over three times better resolution of the high frequency 20 MHz scanner (<0.1 mm) over the 7-12 MHz one. Also the sensitivity of the external single transducer 20 MHz pulse Doppler proved to be over 20 dB better (in terms of SNR) than the pulse Doppler incorporated into linear 7-12 MHz linear array. These results justified designing of a high-frequency scanning system consisting of a 20 MHz linear array transducer combined with 20 MHz pulsed Doppler probe to validate its usefulness in estimation of the degree of radial artery FMD and SR after 5 minutes of reactive hyperaemia.

In the pilot studies, 12 healthy volunteers (38–71 yr old) and 14 patients (36–77 yr old) with chronic coronary artery disease (CAD) were included. The diagnosis of chronic CAD was based on the presence of symptoms of stable angina or a positive myocardial ischemia stress test. The Imaging/Doppler system was modified by adding the single element 20 MHz pulse Doppler with a sample volume size being equal 0.3 mm axially and 0.8 mm laterally, to the linear array transducer, providing to high precision FMD and SR measurements. The normalization of FMD to shear rate is done by dividing the peak FMD by the accumulated value of shear rate area under the curve.

Statistically significant differences between the two groups were confirmed by a Wilcoxon-Mann-Whitney test for both FMD and FMD/SR (p-values < 0.01). AUCs of ROC curves for FMD and FMD/SR were greater than 0.9. The results confirm the usefulness of the proposed measurements of radial artery FMD and SR in differentiation of normal subjects from those with chronic coronary artery disease.

2018-10-08 14:00, Sala: S3 im. W. Fiszdona, piętro III
Francesca Petronella
Institute for Chemical Physical Processes, Italian National Council of Research

Smart nanomaterials: a new route towards novel environmental and biological applications

Nanostructured materials exhibit outstanding size/shape dependent properties that make them extremely promising in several application fields. Fundamental features that include (but are not limited to) their optical response, thermodynamic behaviour, plasmonic, magnetic and catalytic properties can be modulated by varying nanocrystal size and shape, without altering their chemical composition.1 Furthermore, synthesis routes as well as characterization techniques have rapidly evolved thus enabling to rationally design, synthesize process and organise nanomaterials. In this perspective, they can be regarded as building blocks that allow to achieve structures with compelling complexity; hence providing nanostructured materials properly addressable to target applications.2 The present contribution aims at sharing the experience, gained by the Bari Division of CNR-IPCF, on the development of synthetic strategies for preparation of colloidal nanocrystal based materials (metal, semiconductors and oxides), and tailoring their physical and chemical properties towards photocatalytic3, optoelectronic,4 environmental,5 (bio)sensing and biomedical applications.6 The ultimate goal is to organize the prepared nano-objects in mesoscopical structures to be integrated in advanced functional materials and devices.

1. Alivisatos, A. P., Perspectives on the Physical Chemistry of Semiconductor Nanocrystals. The Journal of Physical Chemistry 1996, 100 (31), 13226-13239.
2. Curri, M. L.; Comparelli, R.; Striccoli, M.; Agostiano, A., Emerging methods for fabricating functional structures by patterning and assembling engineered nanocrystals. Physical Chemistry Chemical Physics 2010, 12 (37), 11197-11207.
3. Petronella, F.; Truppi, A.; Ingrosso, C.; Placido, T.; Striccoli, M.; Curri, M. L.; Agostiano, A.; Comparelli, R., Nanocomposite materials for photocatalytic degradation of pollutants. Catalysis Today 2017, 281 (Part 1), 85-100.
4. Ingrosso, C.; Bianco, G. V.; Pifferi, V.; Guffanti, P.; Petronella, F.; Comparelli, R.; Agostiano, A.; Striccoli, M.; Palchetti, I.; Falciola, L.; Curri, M. L.; Bruno, G., Enhanced photoactivity and conductivity in transparent TiO2 nanocrystals/graphene hybrid anodes. Journal of Materials Chemistry A 2017, 5 (19).
5. Petronella, F.; Pagliarulo, A.; Striccoli, M.; Calia, A.; Lettieri, M.; Colangiuli, D.; Curri, M.; Comparelli, R., Colloidal Nanocrystalline Semiconductor Materials as Photocatalysts for Environmental Protection of Architectural Stone. Crystals 2017, 7 (1), 30.
6. Depalo, N.; Iacobazzi, R. M.; Valente, G.; Arduino, I.; Villa, S.; Canepa, F.; Laquintana, V.; Fanizza, E.; Striccoli, M.; Cutrignelli, A.; Lopedota, A.; Porcelli, L.; Azzariti, A.; Franco, M.; Curri, M. L.; Denora, N., Sorafenib delivery nanoplatform based on superparamagnetic iron oxide nanoparticles magnetically targets hepatocellular carcinoma. Nano Research 2017, 10 (7), 2431-2448.

2018-09-19 11:00, Sala: S3 im. W. Fiszdona, piętro III
Paramita Chatterjee
IPPT PAN

Mathematical analysis of a new model of bone pattern formation

The study of vertebrate limb development is an important example of organogenesis connected with limb bud growth and shaping as well as on its skeleton formation. This process has been modeled by many authors. We tried to explain some mathematical properties of a relatively new model of this phenomenon designed by T. Glimm et al. in a paper from 2014. The most widely used mathematical scenario of pattern formation in biology, among them the formation of chonrogenetic pattern, is the Turing bifurcation. In our publication from 2016, we use this method to study the bacterial patterns driven by chemotaxis and patterns on the sphere, which can correspond to some other biological phenomena.

2018-08-08 12:30, Sala: S3 im. W. Fiszdona, piętro III
Paramita Chatterjee
IPPT PAN

Analysis of a model of avian limb formation

Seminarium w ramach przeglądu wyników doktorantów w 2017/2018

Mathematical analysis of a system of mixed parabolic-hyperbolic equations proposed in (Glimm, Newman, 2014). The model was designed to describe the process of bone formation pattern during chicken embryo morphogenesis. In our study, we propose some simplifications making the model more convenient to analyze, in particular reducing it to a standard system of reaction-diffusion equations.

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
IPPT PAN

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
IPPT PAN

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
IPPT PAN

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.

2018-01-10
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.

ArchiwumSeminaria 1996-2010
Strona Zakładu