"Open for Collaborations"
(Tissue mechanics, Microfluidics, Soft matter & AI based microscopy)
Hello! I am a Postdoctoral Fellow in the Haase Group of Dr. Kristina Haase, EMBL Barcelona.
Dr. Amir Raoof, Utrecht University
I work at the interfaces of biofluidmechanics, microfluidics, engineering design and multiphysics based computational modeling for tissue vascularization. This enjoyable curiosity-driven multidisciplinary projects, keeps my week days super active. Usually, I start my day with simulation (8-10), chicken embryo or cell culture (10-12), microscopy (13-15) and data analysis (15-17). I get super excited, when I see "live moving objects under microscope" - that made my interest towards biomechanics and vascularization. Also, I feel more convergence with my postdoc project, about my expertise, research interest and career goals. Currently I am interested in exploring opportunities to make mechanically stable microtissues with perfusable and tunable vessel structures compatible with clinical testing.
Apart from research, I appreciate and participate in public speaking and science communication events (like FameLab, Science Cafe) to promote science to the general audience and being creative when it comes to cooking, drawing and making crafts from recycled items. As a outgoing person, I enjoy organizing social events and very active in Twitter.
Postdoctoral Fellow|EIPOD Marie-Curie
I work on a self-designed multidisciplinary project "HEAT" in the lab of Dr. Kristina Haase, partnering with Dr. Nicoletta Petridou and Dr. Amir Raoof. In a nutshell, the project HEAT explores the possibilities of engineering, tissue-specific vascularized microtissues for clinical testing. More details will be updated soon in a separate link...
As a part of PhD mobility, I visited the Professor Roeland Merks group and trained with the cellular Potts model. This experience allows me to develop a framework to couple Multiphysics models involving chemical gradients (growth factors), matrix degradation, and fluid flow with cellular potts model. Also I initiated a new collaboration between Leiden University and Twente University.
Under the supervision of Dr. Moritz Kreysing, I worked on spatial fractionation of RNA in an inhomogeneous temperature gradient. This project deals with origin of life experiments combined with computer simulations and wet lab techniques. As a part of my Master's thesis, I developed a prototype that can generate microscale temperature gradients within a glass capillary. Using this prototype we could fractionate biomolecules such as DNA, RNA.
Erasmus Trainee Scholarship
As a part of my Master's mobility, I worked at UCB on cell culture optimization and bioreactor systems for monoclonal antibody production. In particular, I studied the efficiency and functionality of CHO cells over long-term passages. Also compared the cells functionality between multiple culture systems of varying scales such as T-flasks, mini-bioreactor, 1L, 10L and 200L. For this work, I received "Focused Recognition Award"for enabling my team to make data-driven decision on the cell line assessment study.
Under the supervision of Dr. Moritz Kreysing, I worked on modeling and simulation of microscale thermophoresis and microfluidics gradient generators for biological applications. Later I extended this work, to my Master's thesis assignment.
Scientific Research Assistant
Under the supervision of Professor Philip Russell, I worked on nanoelectrodes fabrication, where I selectively fill the gold and aluminum metals inside the hollow-core photonic crystal fibers. Later I extended this work, as a part of the mini - thesis for which I integrated microfluidics and photonic crystal fibers for biosensing and particle guidance applications. Also, I presented this work at the International symposium, which gave me the "Best Scientific Poster Award".
Design Engineer R&D
During my time at SITAR, I developed Lab-on-chip devices for medical applications and biowarfare agent detection. Also I received expert training with COMSOL Multiphysics software.
Sales Engineer Trainee
I take care of pre-sales activities of liquid handling consumables mainly single-channel, multichannel pipettes (both manual and electronic).
Bachelor Thesis Internship
For my bachelor's thesis assignment, I worked on the quantification of Ibuprofen in human plasma samples by the HPLC method. During my time there, I also participated in "mock audits" of FDA assessment.
UNIVERSITY OF TWENTE, ENSCHEDE,
Topic: "Engineering tools to study and tune the vascular organization".
Mechanical signals have a strong effect on vascular development and organization. However, there exists no proper tool to study their influence on vascular organization. Under the supervision of Dr. Jeroen Rouwkema, I am working towards creating efficient engineering tools to probe, perturb and predict the evolution of vascular networks in invivo, invitro and insilico models.
I studied Elite Master's Program "Advanced Materials and Processes" focusing on biomaterials and advanced processes as specialization. This study program allows me to gain fundamental knowledge about biophysics and materials design for biological applications. Moreover, coolest thing during this study program, I had a good chance to talk with students from multidisciplinary and multicultural backgrounds which pay out in many collaborative projects.
ANNA UNIVERSITY, INDIA
I studied Biotechnology in "Adhiyamaan College of Engineering" focusing on molecular cell biology and bioprocesses as specialization. This study program allows me to gain basic knowledge about cell biology and bioreactor operations. Moreover, this study program provide me a chance to work in various research institutions and biopharmaceutical industry.
Post Graduate Diploma
LIFE SCIENCE FOUNDATION, INDIA
I studied a PGDBT course via online focuses on nanotechnology. This study program allows me to gain basic knowledge about nanobiotechnology concepts and their applications.
Blood flow microscopy
To be clinically effective, engineered tissues should be mechanically stable with surgical compatibility and have a multiscale hierarchical organization resembling vascular tree. Apart from organization, mechanical properties such as blood flow velocity, patency and vascular permeability are important parameters that control vascular structures in remodeling and maturation phase. This proposal uses the optical techniques such as laser speckle contrast imaging (LSCI), laser Doppler perfusion imaging (LDPI) and monitoring (LDPM) and side-stream dark field imaging to explore and quantify the influence of mechanical signals on vascular organization, both within transparent chick embryo culture systems and engineered tissue models.
(Cell-based computational models)
Using cellular potts model, this proposal models the vascular network in a virtual microfluidic device setting. From the cells seeded in a virtual hydrogel lattice and with cells interacting with local environment, vascular network structures emerge. The shapes of arising structures are studied and correlated to calculated properties and parameter values. New experimental boundary conditions and external vascular endothelial growth factor sources are added to the model framework. We anticipate our model framework to be a starting point for more sophisticated experimental driven insilico testing tool for tissue engineereing applications.
Transparent biological culture systems
Adding vascular network to engineered tissues is an important step for the clinical application of these tissues. However, in order for such networks to perform, they need to have a physiological organization. This proposal hypothesizes that fluid flow shear stress on the outside of a vascular network can control vascular organization. To test this hypothesis, a transparent artificial eggshell with which directed fluid flow pattern can be applied, will be used in a chick embryo model. When the hypothesis holds true, the results of this project will provide us with an extra tool to control vascular organization in engineered tissues.
Biomimetic physiological structures (Mathematical models)
With biomimetic scaffolds, environment close to the natural extracellular matrix of organs can be created in which cells could be guided to create new tissue with appropriate function. However, in order to create such scaffolds, spatial distribution of seeds with appropriate pore geometry, interconnectivity and number of seeds should be precisely evaluated. This proposal involves the application of voronoi based generative algorithmic model for designing 3D biological models particularly human cancellous bone. By altering the spatial distribution of seeds the mechanical strength of the scaffold will change. In order to determine the influence of spatial seed distribution on the scaffolds mechanical strength, the models will undergo virtual compression loading. To quantify this change, finite element modeling (FEM) will be used to evaluate the prototypes of biological cancellous bone scaffolds based on strain, stress and total deformation.
P Padmanaban, A Chizari, T Knop, J Zhang, VD Trikalitis, B Koopman, W Steenbergen, J Rouwkema Assessment of flow within developing chicken vasculature and biofabricated vascularized tissues using multimodal imaging techniques, 2021, Scientific Reports
M Kaya, F Stein, P Padmanaban, Z Zhang, Khalil I S M, S Misra Visualization of micro-agents and surroundings by real-time multicolor fluorescence microscopy, 2022, Scientific Reports