Category: Biophysics

In Silico Biomechanical Analysis for Surgical Planning

Soruce: http://complexsystems.khas.edu.tr/ , https://nodds.khas.edu.tr/node/115

Women in 3D Printing

I was the guest of Women in 3D Printing this week.

The full-page is on this page: https://womenin3dprinting.com/banu-kose/

Thanks to Nora Toure for all the great work she has done and for bringing us together.

Read more »

Institute of Physics / Challenges in Cardiocascular Flow

A joint meeting showcasing current work addressing the complex challenges in cardiac flow modeling, particularly focusing on the work of early career researchers (source).

Physics

Liquid State Physics in Turkey

22. Liquid State Symposium (22. Sıvı Hal Senpozyumu) took place on 7th December 2018 in Piri Reis University.
It was very proud to be together with the physicist academics I knew and admired since my undergraduate years.
I find myself lucky to see the Prof. Zehra Akdeniz that I have always admired and exemplified. I could finally meet Prof. Nihat Berker who is not only a famous physicist but also an intellectual on comparative literature readings.

Thanks to Dr. Ozan Sarıyer and Dr. Gulsen Evingur for organizing this meeting.

The symposium program link

Prof Pekkan presented biological flow researches of his lab, and I presented a sample case of a pediatric aortic blood flow comparison study which is done with the great help of Dr. Ece Salihoglu.

Virtual Physiological Human Conference 2018 / Zaragoza

Conference Web Link

8th World Congress of Biomechanics / Pekkan Lab

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Doctorate Diploma

Certificate of Honour / Doctorate Program of Biomedical Engineering and Bioinformatics

Laser Doppler Velocimetry

Laser Doppler velocimetry is used in hemodynamics research as a technique to partially quantify blood flow in human tissues such as skin. Within the clinical environment, the technology is often referred to as laser Doppler flowmetry (LDF). The beam from a low-power laser (usually a laser diode) penetrates the skin sufficiently to be scattered with a Doppler shift by the red blood cells and return to be concentrated on a detector. These measurements are useful to monitor the effect of exercise, drug treatments, environmental, or physical manipulations on targeted micro-sized vascular areas.

The laser Doppler vibrometer is being used in clinical otology for the measurement of tympanic membrane (eardrum), malleus (hammer), and prosthesis head displacement in response to sound inputs of 80- to 100-dB sound-pressure level. It also has potential use in the operating room to perform measurements of prosthesis and stapes (stirrup) displacement.

20. National Liquid State Physics Symposium 16 December 2016

20. National Symposium on  Liquid State Physics was held in Piri Reis University.

The symposium was obtaining various studies about liquids as water and climate change, simulating strait systems, oceans, spin glass phases, liquid crystals, serum transferring,  swollen gells, GO composites, metals with  glass-like structure, super hidrophobic polistren and, biofluids {yes, this was mine ;) }.

It was an incontrovertible experience for me that i could meet new studies in the field and spend nameable times with  physics authors.

Many thanks to organizing comitee (especially to Gülşen Evingür) and Sevtap Yıldız Özbek.

The website of the symposium is here.

Simulate the Physiology & Understand the Pathology

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Computational Life is a young company which has the specialty on computational flow simulations and mathematical models for the medical technology field.

The validated software Digital Avatar Platform (DAP) of Computational Life is modeling human and animal body mathematically. It is testing physiological scenarios for drugs, medical devices and treatment methods.

Circulation system, cerebrospinal fluids, transport of pharmaceutical products throughout the body can be simulated for the human and animal body with DAP. It can also be modified due to the experiment.

They replied to me with a very warm and energetic mood when I wrote them. It is great that there are enthusiastic people in the medical technology field. I am sure that I will hear more about the news of Computational Life in the next days.

Thanks to Christian Contarino, Davide Chieco and Carlo Rivis for their innovative platform which brings a great help for clinicians, researchers, and engineers.

Please check their website for more information.

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ICPT – GEFIK 2016

I had chance to present my works to authors and answer the questions of young curious physicisits at GEFIK2016 in Ege University. Discussing about medical physics and classical mechanics with physicists was a peerless experience.

3D Printed Aorta

A pediatric aorta model reconstructed from the 3D CT images.

‘Go with the flow’ by Victoria Stoll

The British Heart Foundation (BHF) announced the winners of its annual ?Reflections of Research? image competition, reflecting the charity?s research into heart and circulatory disease.
The winning image ? titled ?Go with the flow,? by Victoria Stoll, a BHF-funded researcher at the University of Oxford ? captures the blood flowing within an adult heart frozen in time. Blood flows within the main pumping chambers (ventricles) of the heart and the vessels leaving the heart. The blue flow is blood that lacks oxygen and is travelling to the lungs. The red flow is blood that has been through the lungs and received oxygen and is now ready to be pumped around the body.
Stoll is using this type of imaging, four-dimensional cardiac magnetic resonance imaging (MRI), to look at the blood flow in four dimensions within the hearts of people with heart failure, whose hearts are not pumping effectively. She has already found that in people with severe heart failure the blood flows around the heart in a more disordered and disrupted pattern.

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6ISCOMS 2017 at University of Groningen

Many thanks to University Medical Center Groningen for the oral sessions and workshops of 3D Lab, LVAD treatment, Dissection of Brain, CABG treatment, IV Injections and Nuclear Medicine.

Me in FU Fluids Lab and The Oxygenator from IMAEH (2013)

PRINT THYSELF

This sort of procedure is becoming more and more common among doctors and medical researchers. Almost every day, I receive an e-mail from my hospital?s press office describing how yet another colleague is using a 3-D printer to create an intricately realistic surgical model?of a particular patient?s mitral valve, or finger, or optic nerve?to practice on before the actual operation. Surgeons are implanting 3-D-printed stents, prosthetics, and replacement segments of human skull. The exponents of 3-D printing contend that the technology is making manufacturing more democratic; the things we are choosing to print are becoming ever more personal and intimate. This appears to be even more true in medicine: increasingly, what we are printing is ourselves.

Source: Newyorker

Trando Med

Trando Med will attend MEDICA 2017 in the Dusseldorf Germany from 13-16 November 2017. The booth is Hall 13 Booth F 9-05

Measure Your Blood Flow

The inventors of the new ?epidermal electronic? sensor system say it is ready for use in a clinical setting, specifically for monitoring skin health, for example in patients who have recently had skin grafts. They say down the road it may also be possible to use it inside the body. In a recent demonstration, the researchers showed that the device can record accurate data from human subjects about the flow of blood in larger vessels, specifically veins in the forearm, as well as in the network of tiny vessels near the surface of the skin.

Compared with state-of-the-art methods for noninvasively measuring blood flow, which rely on optical systems or ultrasound technology, the new sensor is much simpler and less expensive, says John Rogers, one of the inventors and a professor of materials science and engineering at the University of Illinois at Urbana-Champaign. More importantly, he says, it is much less sensitive to motion thanks to the way it ?intimately laminates? to the skin.

Characteristics of the blood flow in any given tissue are a good indicator of that tissue?s health. Some conditions, like infection and inflammation, can lead to an increase in local blood flow, whereas others, like atherosclerosis, heart failure, and diabetes, can cause a decrease. If doctors could precisely and even continuously monitor this flow, they could better tailor care to individual patients and conditions.

Source

3D Printing for Pediatric Cardiothoracic Surgeons

‘Having worked in product development for the past few years, Dr. Enrique Garcia had seen what 3D printers were capable of and began investigating the possibilities for creating models for pediatric cardiologists to use before an operation. She began by asking surgeons from around the country what they thought of the idea. To say that their response was overwhelmingly positive is an understatement. The value of this idea was immediately apparent.’

‘Pediatric heart surgery is the hardest thing that I can imagine a person doing. A surgeon doesn’t know what he’s going to see until he opens a child?s chest. Every heart is different and every cardiopathy is different,? said Garcia. ?A baby?s heart is the size of a walnut, and surgeons need to go in and move around structures that are as small and thin as a human hair, and they’re doing it with their own two hands. And all of this is occurring against a ticking clock.’

‘Having something in your hands, and being able to turn it any way you want, and to be able to cut and open it up and see the inside; and to be able to physically hold it, to feel it, is something that can?t be replicated on a computer.’

Read More in the source.

cSound

Researchers have created software that can model internal organs in ‘extreme 4D’.
The system, dubbed cSound, is currently being used by cardiologist Bijoy Khandheria, who has been fixing broken hearts for more than three decades.

Dr Khandheria describes the images as ‘exquisite’, and says it’s like opening up someone’s chest and watching their heart beat.’

‘Traditionally, ultrasound has allowed us to see the heart but not in as much detail as we might like,’ he said.
‘We used the signal to image the heart layer by layer, almost like a butcher using a knife, and then mentally splice the layers together to see the whole picture’.
Dr Khandheria and his colleagues at Aurora St Luke’s Medical Center in Milwaukee, have recently started ‘extreme 4D’ software.
The images are so clear that it allows doctors to see how blood swirls around clots in arteries.
This can then be used to measure the severity of blood leakage around the valves and assess the damages.
‘It’s almost as if I took out the valve and started turning it with my hands,’ said Dr Khandheria.

Read more

3D-Printed Artificial Heart Test / #ETH Zurich

Carol Malnati

“- I wanted to be someone that encouraged young women to get involved in math, science, and engineering.”

Today, she’s doing just that.

As a product development engineer in the Medtronic cardiovascular division, Carol has been doing what she loves for more than 25 years. She provided critical technical expertise for the company’s first implantable cardioverter defibrillator and continues to collaborate with engineering teams and physicians to find new ways of doing things.

But on top of her day job, she has taken on another commitment – overseeing the Women in Science and Engineering (WISE) Initiative at the company.

Beginning in the spring of 2017, Medtronic introduced another opportunity that taps into an often overlooked talent pool.  Careers 2.0 is a “returnship” program designed to provide paid internships for female engineers looking to get back into STEM-related careers. Research suggests close to 25 percent of women in engineering careers leave the industry by age 30, citing work culture or family commitments.

“This is a way to bring these talented women back into our technical and managerial ranks,” says Carol. “We are very excited about providing this amazing pool of talent an opportunity at Medtronic.”

“Overall, I want to inspire women,” says Carol. “Whatever your passion is; clean air, fighting hunger, or improving healthcare. Behind the biggest challenges of humanity, there’s an engineer working to find a solution.”

Source

The special session for the women in the field of cardiovascular surgery – The 64th Istanbul ESCVS

International Congress of the European Society for Cardiovascular and Endovascular Surgery (ESCVS) will be held on March 26th – 29th, 2015 in İstanbul in collaboration with International Congress of Update Cardiology and Cardiovascular Surgery.

The congress scientific program includes a session for women in cardiovascular surgery which will be held on March 28th.

Abstract Submission Deadline
December 22, 2014
…………………………………………..
Notification of Abstract Acceptance
January 2, 2015
…………………………………………..
Early Registration
until November 7, 2014

ESCVS 2015 Web Site

IFG26 – Statistical Physics Days

26th Statistical Physics Days were held in İzmir Institute of Technology.

During the program organization, Prof. Nejat Bulut’s dedication and careful attention to every detail was so amazing that it will be a very nice experience in my mind.

It was an honor to be among the successful physicist academicians and to listen to their work. It was also my chance that I had the opportunity to talk about my own practice and find the opportunity to discuss it with very precious professors.

K. Banu Kose

Starfish Medical – VivitroLabs – ProtomedLabs – Marseille – France


Ece Tutsak (Left) – Banu Köse(Middle) – Vincent Garitey(Right)

The Horizon for Mechanical Circulatory Support

Filmed at the 2014 STS Annual Meeting in Orlando, Florida, this roundtable discussion focuses on mechanical circulatory support. John Kern moderates the discussion with Pavan Atluri and Francis Pagani. The panelists discuss mechanical circulatory support, LVAD therapy, and heart transplantation. The discussion concludes with thoughts on the future of mechanical circulatory support.

Source:  CTS

Female ‘Clinician Engineer Hub’ Webinar Series

Welcoming you all to our upcoming female Clinician Engineer Hub Webinar series for this July.

‘Clinician Engineer Hub was born in a collaboration between clinicians and independent research groups at the Queen Elizabeth Hospital Birmingham, Imperial College London, and King’s College London. This international hub is a non-profit organization that aims to bring together the clinical and biomedical engineering field and provide talented medical students and clinicians exposure to the world of clinical medicine, the challenges doctors face in diagnosing and treating patients, and how to potentially solve these issues with cutting edge engineering solutions.’

‘The hub allows medical students and clinicians fascinated by pathophysiology to understand the current diagnostic and treatment gaps in the clinical field and design effective solutions based on solid engineering principles. It will be revolutionary for your career with the unique opportunity to receive mentorship across world-renowned academic centers in the UK and abroad.’

Thanks Dr. Neel Sharma  for bringing such a team together!

[on Twitter:  https://twitter.com/clinicengine , on Web : https://clinicianengineer.com/ ]

Clinical Engineering Lecture in Beykent University

Clinical Engineering

Lecture

VOKSEL 3D Event in Istanbul

Voksel’s Anatomical Modeling, Surgical Planning, 3D Printing with Engineer – Surgeon Collaboration Training‘ was held on 23rd February in Istanbul.

I had the chance to share my experiences in image processing and modeling with the participants. I would like to thank Kerem Girgin, Erbil Oğuz, Samet Serbest and Cansu Çeltik from Voksel. It was great to be a part of Voksel team, and meeting with the participants who were aware of the benefits of interdisciplinary collaborations and patient-specific planning very well.

Surgical Planning and 3D Printing Meeting

3D Bio-Printing Project of Sabancı University

For the first time in the world, tissue structures were created by using self-supported live cells in a 3D bio-printer from medical images in the 3D Tissue and Organ Printing Project.

Sabancı University Faculty of Engineering and Natural Sciences? Manufacturing Systems Program professor Bahattin Koç and his stedents; Can Küçükgül, Saime Burçe Özler, Forough Hafezi printed artificial tissue construct at the Nanotechnology Research and Application Center (SUNUM) using self-supported live cells in a  3D bio-printing system.

The 3D Tissue and Organ Printing Project team used live human dermal fibroblast cells as bio-ink to print a part of aortic tissue.  Human blood vessel tissue consists of mainly three types of cells: fibroblast, endothelial  and smooth muscle.  Fibroblast cells are the main cells of connective tissues.  They synthesize the extracellular matrix and collagen protein needed for tissues.  Endothelium is the thin inner layer of cells of blood vessels.  Smooth muscle cells are found in inner organs such as blood vessels, esophagus and intestines.  The scientists continue their efforts to maturate the blood vessel tissue created by fibroblasts as well as endothelial and smooth muscle cells in a bioreactor.

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17th U.S. National Congress on Theoretical & Applied Mechanics

Every four years since 1950 the leading mechanics researchers  have convened the U.S. National Congress on Theoretical and Applied Mechanics. All mechanics researchers and students are invited for the 17th  Congress on the beautiful Big Ten campus at Michigan State University. The sessions will be held at the Kellogg Hotel and Conference Center on Michigan State University’s campus.

Many thanks to Seungik Baek for his kind invite us Cardiovascuar Mechanics Minisymposia:

The goal of this minisymposium is to provide the state of the art in theoretical and computational methods applied to the cardiovascular mechanics including computational and constitutive modeling, theoretical vascular mechanics analysis, and cardiovascular design technologies. Topics may include, but are not limited to cardiovascular fluid and/or solid mechanics, cardiovascular diseases and treatment, optimization techniques. We believe that you would be an excellent contributor to this session based on your many exceptional works in the fields of theoretical and computational mechanics to cardiovascular problems.

The 14th Annual International Symposium on Congenital Heart Disease

The 14th Annual International Symposium on Congenital Heart Disease will feature a world-class faculty of domestic and international experts in Cardiology, Cardiac Critical Care, Cardiac Surgery, Nursing, Hospital Administration, and Ethics. This year the conference will focus on Diseases of the Cardiac Valves from the Fetus to the Adult. The program will include didactic, case-based, and interactive presentations as well as pathologic heart specimens and practical workshops. Special tracks dedicated to cardiovascular nursing and hospital administration will be included making this a truly team-based symposium.

Click for the Symposium Web Page.

Click for Symposium Document.

The World Congress of Biomechanics (WCB) 2014

Registration and abstract submission are now open for The World Congress of Biomechanics (WCB) 2014. The World Congress is the most comprehensive global meeting on all topics related to biomechanics and is held once every four years. The next meeting will be in Boston, Massachusettson July 6-11, 2014.

Submission Timeline

  • November 15, 2013 ? January 15, 2014. Due to limited podium presentation slots, early submission recommended.
  • Student Paper Competition sponsored by ASME Bioengineering Division; requires abstract submission by currently enrolled students at the BS, MS, and PhD levels

Submissions for podium and poster presentations include any area of biomechanics and related areas, including bioheat transfer, biomaterials, ergonomics, medical devices, new testing devices and technologies, and tissue engineering. In particular, biomechanical studies ranging from the molecular level (e.g., DNA mechanics and mechanotransduction) to whole organisms (e.g., from animal flight to human sports biomechanics) are welcome.

Abstracts should be submitted on-line at http://wcb2014.com/event-info/call-for-papers/ and will be reviewed on a continuous basis. Early submission is encouraged! Note that WCB2014 follows a US holiday weekend (July 4, Independence Day) that may affect your travel plans.

Functional blood vessels regenerated in vivo from human induced pluripotent stem cells

Vasculogenesis ? the process of blood vessel formation through a de novo production of endothelial cells (ECs, or those forming a thin layer lining the interior surface of blood and lymphatic vessels) ? is a vital tool in regenerative medicine, tissue engineering, and, in particular, the battle against vascular disease, the leading cause of mortality in the United States. (More than one in three Americans (36.9%) suffer from heart disease, and by 2030, an estimated 116 million people in the United States (40.5%) will have some form of cardiovascular disease.) More specifically, generating functional, long-lasting vasculogenic cells is a key but elusive component in human induced pluripotent stem (hiPS) research. Recently, however, researchers at Harvard University and Massachusetts General Hospital successfully generated endothelial cells from healthy donors’ hiPS cells to form stable functional blood vessels in vivo. Moreover, they developed an approach to generate mesenchymal precursor cells (MPCs, or multipotent stromal, or connective tissue, cells that can differentiate into a variety of cell types including perivascular cells ? another component of vessel wall) from hiPS cells in parallel, and also generated functional blood vessels in vivo using these endothelial and multipotent stromal derived cells from the same hiPS cell line. Beyond this, and in terms of clinical translation, the team successfully generated ECs and MPCs from Type 1 Diabetic patient-derived hiPS cell lines and also used them to generate blood vessels in vivo.

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6.Istanbul Symposium: The Progresses and Conclusions on The Life Support Systems in Turkey /2013

The International Society for Pediatric Mechanical Cardiopulmonary Support organized 6.Istanbul Symposium: The Proggresses and Conclucions on The Life support Systems in Turkey /2013 Dr. Siyami Ersek Chest & Cardiovascular Surgery Training & Research Hospital.

Click for comitee members, speakers and panel topics.

All partipiants had a sertificate and the english translation of Aydın Aytaç’s book named Life Dedicated to The Heart.

I specially thank Atıf Akçevin for his advises and supports to my research topic and of course Kerem Pekkan and Ahmet Şaşmezel for their kind favors.

Making a window for drug delivery in the blood-brain barrier

Normally, the circulatory system of the body is isolated by tight junctions between the endothelial cells of the capillaries inside the brain. There is also a thick basement membrane composed of matrix proteins, as well as astrocytic endfeet surrounding the capillaries. Nutrients required by the brain, such as glucose and amino acids, are actively transported across this barrier by specific membrane-bound transporter proteins. There are also specific efflux pumps, that remove certain molecules that might occasionally breach the BBB. Endoscopically accessing the brain through the nose has made many difficult surgeries routine. Removing tumors from normally inaccessible regions, like the pituitary, can now be done with little risk. Typically these procedures require removal of intervening dura mater and arachnoid membrane, which creates a significant communication between the inside of the nose and the surface of the brain. To seal up the gap, nasal mucosal grafts are harvested from the nasal septum. When healed, these grafts can potentially provide a means to bypass the BBB and permit high molecular weight or polar molecules to get into the brain. To determine the diffusion capacity of transplanted nasal mucosa, the researchers applied fluorescent rhodamine-dextran molecules of different sizes to a mouse graft model. Dextran polymer molecular weights of 20, 40 and 500 kDa were tested. All three weights showed significant penetration into the brain which peaked at around 72 hours. The grafts proved to be water tight, immunocompetent, and permanent, suggesting they may be a viable way to create a drug-permeable window for humans. The trans-olfactory drug delivery route has been studied previously in rats, and it was found that nerve growth factor (NGF) could be absorbed in significant doses. Unfortunately, these finding failed to translate into a clinical success in humans. One reason for the the failure may be due to the relatively small size and distribution of the olfactory mucosa in humans. The researchers in the present study did look at the striatum, a region important for the treatment of Parkinson’s disease. They found penetration of fluorescent dextran into this region, suggesting potential therapeutic benefit in humans may be possible. Intranasal drug delivery to the CNS is currently utilized in Parkinson’s treatment to deliver apomorphine, although its ultimate utility has been controversial. The mucosal graft procedure described here would have to be further vetted before it would ready for actual clinical trials. One concern would be the possibility for sinus or other infection to propagate through the graft, particular over longer periods of time. Convection and natural CSF circulation is also different in the brains of mice and humans, in addition to the disparity of scale. However when contrasted with the infection risk inherent in using catheters or cannulas to deliver drugs into the brain, the transplanted olfactory mucosa route has plenty of appeal.

More information: Bleier BS, Kohman RE, Feldman RE, Ramanlal S, Han X (2013) Permeabilization of the Blood-Brain Barrier via Mucosal Engrafting: Implications for Drug Delivery to the Brain. PLoS ONE 8(4): e61694. doi:10.1371/journal.pone.0061694

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Air pollution and hardening of arteries

The researchers, led by Sara Adar, John Searle Assistant Professor of Epidemiology, University of Michigan School of Public Health, and Joel Kaufman, Professor of Environmental and Occupational Health Sciences and Medicine, University of Washington, found that higher concentrations of fine particulate air pollution (PM2.5) were linked to a faster thickening of the inner two layers of the common carotid artery, an important blood vessel that provides blood to the head, neck, and brain. They also found that reductions of fine particulate air pollution over time were linked to slower progression of the blood vessel thickness. The thickness of this blood vessel is an indicator of how much atherosclerosis is present in the arteries throughout the body, even among people with no obvious symptoms of heart disease. “Our findings help us to understand how it is that exposures to air pollution may cause the increases in heart attacks and strokes observed by other studies,” Adar said.

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5th ISTANBUL SYMPOSIUM: BIOENGINEERING APPROACHES ON PEDIATRIC CARDIOVASCULAR MEDICINE

Scientific Co-Chairs are Kerem Pekkan, PhD & Akif Ündar, PhD

Invitation to Attend

The 5th Istanbul Symposium is intended for medical and engineering students, nurses,
scientists, pediatric heart surgeons, engineers, cardiologists, intensivists, neonatologists,
anesthesiologists, neurologists, pediatric perfusionists, respiratory therapists, residents
and fellows. All are invited and encouraged to attend.

Koç University, Engineering Auditorium ( Mühendislik Oditoryumu ) / 19 April 2013

European Society of Cardiology Congress 2013 / Amsterdam

  • The new translational initiative Science in Practice’ will provide clinicians with insights on where the field is going in the future and basic scientists with a critically important context for future work.
  • General practitioners, nurses and other allied professionals: reduced fee to participate in the general cardiology update programme on Saturday 31 August as an introduction to the ESC Congress 2013.
  • For the first time delegates will be able to follow the ?Guidelines into Practice (GIP)? track ,  designed to support cardiologists in the implementation of the Guidelines in their daily practice.

Click for Congress Home Page

International Conference on Integrated Medical Imaging in Cardiovascular Diseases / Vienna

The International Atomic Energy Agency (IAEA) announces its intention to hold the International Conference on Integrated Medical Imaging in Cardiovascular Diseases (IMIC2013). Cardiovascular diseases (CVDs) are an important sub-group of non-communicable diseases and are one of the main priorities in the health care systems of many IAEA Member States. Medical imaging, including molecular nuclear medicine, is extremely important in that it offers strategic advantages in both diagnostic and therapeutic decision making. It provides inputs for diagnosis, staging, treatment, prognosis and follow-up in the management of CVDs. Medical imaging includes techniques such as single photon emission computed tomography (SPECT), positron emission tomography (PET), echocardiography, computed tomography (CT), and magnetic resonance imaging (MRI). These techniques provide an excellent opportunity to understand the pathology of individual patients and can therefore serve to facilitate tailored clinical management. Each imaging modality has its advantages and limitations which need to be understood properly by health care professionals dealing with CVDs. Many Member States are actively using, have recently implemented or are planning to acquire these technologies.

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International Congress of Cardiovascular Technologies /Algarve

Extended Abstract Submission and Complete Paper Submission: April 24, 2013
Authors Notification: June 17, 2013
Camera Ready and Registration: July 8, 2013

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Wireless device powers implanted blood-pressure sensor, eliminating batteries

Researchers at A*STAR Institute of Microelectronics in Singapore are developing a prototype wireless device that powers an implanted blood-pressure sensor, eliminating the need to recharge or replace a battery.

The microscale electronic sensor monitors blood flow through artificial blood vessels. Surgeons use these prosthetic grafts to bypass diseased or clogged blood vessels in patients experiencing restricted blood supply, for example.

Over time, however, the graft can also become blocked. To avoid complete failure, blood flow through the graft must be monitored regularly, but existing techniques are slow and costly.

Monitoring blood flow rate inside prosthetic vascular grafts enables early detection of graft degradation and prevention of graft failure.

The implant is powered by a handheld external reader, which uses inductive coupling to wirelessly transfer energy. The team developed an ultralow-power application-specific integrated circuit (ASIC) for the implant designed for low-power (21.6 ?W) use.

The sensors are based on piezoresistive silicon nanowires. As blood flows over the sensor, the associated mechanical stresses induce a measurable increase in electrical resistance, proportional to the flow pressure.

?Our flow sensor system achieves an ultra-low power consumption of 12.6 microwatts,? said A*STAR?s Jia Hao Cheong, who heads the project. To achieve that the sensor transmits its data to the handheld reader passively, by backscattering some of the incoming energy. ?We have tested our system with 50-millimeter-thick tissue between the external coil and implantable coil, and it successfully extracted the pressure data from the implantable device.?

?The next step of the project is to integrate the system and embed it inside a graft for an experimental animal,? Cheong said.

Source: http://www.kurzweilai.net

Infant brain controls blood flow differently

?The control of blood flow in the brain is very important,? says Elizabeth Hillman, associate professor of biomedical engineering and of radiology, who led the research study in her Laboratory for Functional Optical Imaging at Columbia University.

?Not only are regionally specific increases in blood flow necessary for normal brain function, but these blood-flow increases form the basis of signals measured in fMRI, a critical imaging tool used widely in adults and children to assess brain function,? says Hillman. ?Many prior fMRI studies have overlooked the possibility that the infant brain controls blood flow differently.?

Functional magnetic resonance imaging, or fMRI, is one of several brain-imaging methods that measure changes in blood flow to detect the presence and location of neuronal activity. In adults, blood-flow increases occur in specific regions of the brain during a particular task like moving your hand or reacting to a stimulus.

?We found that the immature brain does not generate localized blood-flow increases in response to stimuli,? says Mariel Kozberg, a neurobiology MD-PhD candidate and lead author of the paper published in the Proceedings of the National Academy of Sciences. ?By tracking changes in blood-flow control with increasing age, we observed the brain gradually developing its ability to increase local blood flow and, by adulthood, generate a large blood-flow response.?

Hillman says the findings suggest that vascular development may be an important new factor to consider in normal and abnormal brain development.

The team used a unique high-speed, high-resolution imaging approach that takes advantage of the different absorption spectra of deoxygenated and oxygenated hemoglobin in order to determine changes in the concentrations of each.

The researchers found that, with increasing age, there was a gradual development of a localized increase in blood flow, while a strong, delayed decrease in flow was consistently present. Only by adulthood was the positive increase able to balance the decrease in flow.

?Our results suggest that the infant brain might not be able to generate localized blood-flow increases, even if there is neuronal activity occurring, and that the development of blood-flow control occurs in parallel with early neuronal development,? says Kozberg.

?This could suggest that fMRI studies of infants and children may be detecting changes in both vascular and neuronal development?in fact, vascular development may be an important new factor to consider in normal and abnormal brain development.?

The team also found that the younger age groups were highly sensitive to blood pressure increases in response to stimulation and that these increases can cause large increases in blood flow across the brain.

?This finding indicates that the newborn brain is also unable to regulate its overall blood-flow levels,? Kozberg explains. ?This could explain earlier fMRI results in infants and children that were sometimes positive and sometimes negative, because it is difficult to tell whether blood pressure increases are occurring in infants and children. This result suggests that great care should be taken in setting stimulus thresholds in young subjects.?

The researchers add that, since the newborn brain appears to be able to sustain itself without tightly controlled blood flow, their findings suggest that the infant brain may be intrinsically more resistant to damage due to a lack of oxygen than the adult brain.

?This could be an important property to understand, both in terms of understanding how best to treat blood-flow problems in the newborn infant brain, which can cause lifelong problems such as cerebral palsy, and to potentially better understand how to treat the adult brain in conditions such as stroke,? Hillman observes.

This research was supported by grants and student fellowships from the National Institute of Neurological Disorders and Stroke, the National Eye Institute, the National Science Foundation, the National Defense Science and Engineering Graduate Fellowship, the Medical Scientist Training Program, and the Human Frontier Science Program.

SourceColumbia University

Blood plasma

Blood plasma is placed between two plates and the plates then drawn apart. High-speed cameras fitted with high-resolution microscope lenses capture the formation of threads and drops, demonstrating that blood plasma exhibits both viscous and elastic behavior when deformed and that it does not behave like water. Credit: Christof Schäfer, Phys. Rev. Lett. 110, 2013, 078305. Copyright (2013) by the American Physical Society

Read more at: http://medicalxpress.com/news/2013-02-blood-thicker-waterand-plasma-video.html#jCp

Researchers show how blood vessels regroup after stroke

Growth factors released by oxygen-starved cells prompt nearby endothelial cells, which line blood vessels, to grow into new networks. Researchers at Rice University are working to understand how to direct the process in the brains of stroke and disease patients. Credit: Qutub Lab/Rice University Rice scientists simulate “robot” cells to study the development of microvascular systems in the brain. The goal is to find a way to direct the development of vessels that feed oxygen-starved cells in stroke and neurodegenerative disease patients.

Read more at: http://medicalxpress.com/news/2013-02-blood-vessels-regroup.html#jCp

5th ISTANBUL SYMPOSIUM: BIOENGINEERING APPROACHES ON PEDIATRIC CARDIOVASCULAR MEDICINE

5th ISTANBUL SYMPOSIUM: BIOENGINEERING APPROACHES ON PEDIATRIC CARDIOVASCULAR MEDICINE – Koç University, Sevgi Gönül Auditorium – 21 December 2012

Scientific Co-Chairs are Kerem Pekkan, PhD & Akif Ündar, PhD

Invitation to Attend

The 5th Istanbul Symposium is intended for medical and engineering students, nurses,
scientists, pediatric heart surgeons, engineers, cardiologists, intensivists, neonatologists,
anesthesiologists, neurologists, pediatric perfusionists, respiratory therapists, residents
and fellows. All are invited and encouraged to attend.

Invited Faculty

Mehmet A. Ağırbaşlı, MD Dept. of Cardiology, Marmara University, Istanbul, Türkiye
Atıf Akçevin, MD Dept. of Cardiovascular Surgery, Medipol University, Istanbul, Türkiye
Tijen Alkan-Bozkaya, MD Dept. of Cardiovascular Surgery, Medipol University, Istanbul, Türkiye
Ihsan Bakır, MD Istanbul Mehmet Akif Ersoy Thoracic and Cardiovascular
Surgery Training and Research Hospital, Istanbul, Türkiye
Hakan Ceyran, MD Istanbul Koşuyolu Heart Hospital, Cardiovascular Surgery,
Istanbul, Türkiye
Sertaç Haydın, MD Istanbul Mehmet Akif Ersoy Thoracic and Cardiovascular
Surgery Training and Research Hospital, Istanbul, Türkiye
Ender Ödemiş, MD Istanbul Mehmet Akif Ersoy Thoracic and Cardiovascular
Surgery Training and Research Hospital, Istanbul, Türkiye
Kerem Pekkan, PhD Şevket Ruacan, MD, Dept. Of Mechanical Engineering, Koc University, Istanbul,
Türkiye
Dean, College of Medicine, Koç University, Istanbul, Türkiye
Ayda Türköz, MD Başkent University, Department of Anethesiology, Istanbul,
Türkiye
Rıza Türköz, MD Başkent University, Department of Cardiovascular Surgery,
Istanbul, Türkiye
Akif Ündar, PhD Penn State Hershey Pediatric Cardiovascular Research
Center, Penn State Hershey College of Medicine, Penn State
Hershey Children’s Hospital, Hershey, PA, USA
Songül Yaşar Yıldız, PhD Candidate Dept. of Bioengineeering, Marmara University,
Istanbul, Türkiye)
TBA (Koç University, School of Nursing, Istanbul, Türkiye

3
SCIENTIFIC PROGRAM
9:00 ? 9:20 am Welcome ? Kerem Pekkan, PhD& Şevket Ruacan, MD, Dean, College of Medicine, Koç University,
Istanbul, Türkiye
9:20 ? 10:00 am ABC’s of Pediatric Cardiovascular Research for Medical and
Engineering Students
Akif Ündar, PhD ? Penn State Hershey Pediatric Cardiovascular
Research Center, Penn State Hershey College of Medicine, Penn
State Hershey Children’s Hospital, Hershey, PA, USA
10:00 ? 11:00 am Key Note Lecture – Applications of Computational Fluid Dynamics to
solve pediatric cardiovascular problems
Kerem Pekkan, PhD, (Dept. Of Mechanical Engineering, Koc
University, Istanbul, Türkiye)
Introduction: Akif Ündar, PhD
11:00 ? 11: 15 am Break
11:15 am ? Noon CASE STUDY: Novel fenestration designs for controlled venous flow
shunting in failing Fontans with systemic hypertension
Cardiac Surgeon: Definition of the problem – Rıza Türköz, MD
(Başkent University, Department of Cardiovascular Surgery, Istanbul,
Türkiye)
Scientist: Suggested Solution – Kerem Pekkan, PhD
12:00 ? 13:30 pm Lunch
13:30 ? 14:00 pm What are the "real" problems for pediatric cardiac patients in
Türkiye? Why multi-disciplinary approach is necessity, not an option?
Atıf Akçevin, MD (Dept. of Cardiovascular Surgery, Medipol
University, Istanbul)
14:00 ? 15:30 pm PANEL: Importance of Multidisciplinary Team Approach to Improve
the Outcomes During and After Neonatal and Pediatric
Cardiopulmonary Bypass Procedures in Türkiye
Moderators: Atıf Akçevin, MD and Ihsan Bakır, MD

4
Pediatric Cardiologists’ Perspective – Ender Ödemiş, MD (Istanbul
Mehmet Akif Ersoy Thoracic and Cardiovascular Surgery Training and
Research Hospital, Istanbul, Türkiye) (20 min)
Pediatric Cardiac Surgeons’ Perspective – Hakan Ceyran, MD (Istanbul
Koşuyolu Heart Hospital, Cardiovascular Surgery, Istanbul, Türkiye)
(20 min)
Pediatric Anesthesiologists’ Perspective – Ayda Türköz, MD (Başkent University, Department of Anethesiology, Istanbul, Türkiye)
(20 min)
Pediatric Nurses’ Perspective – TBA (Koç University, School of Nursing, Istanbul, Türkiye (20 min)
15:30 ? 16:00pm Break
16:00 ? 18:00pm PANEL: Pediatric ECLS Systems & Novel Techniques and Methods to
Minimize the Injury during neonatal/Pediatric Cardiopulmonary
Bypass Procedures
Moderators: Hakan Ceyran, MD and Rıza Türköz, MD
Pediatric Extracorporeal Life Support Systems in Türkiye ? 2012
Update –
Sertaç Haydın, MD (Istanbul Mehmet Akif Ersoy Thoracic and
Cardiovascular Surgery Training and Research Hospital, Istanbul,
Türkiye)
Monitoring Biomarkers After Pediatric Cardiac Surgery: A New
Paradigm in the Horizon, Mehmet A. Ağırbaşlı, MD (Dept. of
Cardiology, Marmara University, Istanbul, Türkiye)
Extremophiles for cardiovascular research – Songül Yaşar Yıldız, PhD
Candidate (Dept. of Bioengineeering, Marmara University, Istanbul,
Türkiye)
Impact of Pulsatile Perfusion on Clinical Outcomes of Neonates and
infants with Complex Pathologies undergoing Cardiopulmonary
Bypass Procedures ?
Tijen Alkan-Bozkaya, MD (Dept. of Cardiovascular Surgery, Medipol
University, Istanbul)

5
Importance of Neonatal/Pediatric oxygenators with or without
Arterial Filters for capturing microemboli during CPB procedures –
Akif Ündar, PhD
18:00pm Closing Remarks – Kerem Pekkan, PhD

A Primer on Computational Simulation in Congenital Heart Disease for the Clinician

Interest in the application of engineering methods to problems in congenital heart disease has
gained increased popularity over the past decade. The use of computational simulation to
examine common clinical problems including single ventricle physiology and the associated
surgical approaches, the effects of pacemaker implantation on vascular occlusion, or
delineation of the biomechanical effects of implanted medical devices is now routinely
appearing in clinical journals within all pediatric cardiovascular subspecialties. In practice,
such collaboration can only work if both communities understand each other?s methods and
their limitations. This paper is intended to facilitate this communication by presenting in the
context of congenital heart disease (CHD) the main steps involved in performing
computational simulation – from the selection of an appropriate clinical question/problem to
understanding the computational results, and all of the ?black boxes? in between.

More

Handmade Glass Anatomical Models by Farlow’s Scientific Glassblowing

Gary Farlow can make art out of arteries. He and his team of 10 at Farlow?s Scientific Glassblowing are able to transform the body?s vasculature?and nearly all of its other parts?into an ornate borosilicate glass sculpture, from the heart?s ventricles to the brain?s circle of Willis. ?We do almost every part of the body,? Farlow says. ?It can take a pretty artistic mind to make some of these things.? With the help of cardiologists, the team creates custom see-through systems for science and medical training.

Their anatomically correct models can be designed to simulate blood flow, teach placement of catheters and angioplasty devices, or simply test or demo new surgical gizmos. Individual arteries, veins, and capillaries are shaped and fused together, one at a time. Ground-glass joints are added at the exposed ends so a head, say, can be connected to the carotid arteries should customers want to expand their model. A full-body setup could cost $25,000, so don?t get any bright ideas about using one as a brandy decanter.

4th Istanbul Symposium: Pediatric Support Systems and Pediatric Cardiopulmonary Bypass

The 4th Pediatric Support Systems and Pediatric Cardiopulmonary

Bypass Symposium will be held on 28th July 2012

at Istanbul Mehmet Akif Ersoy

Thoracic & Cardiovascular Surgery Training and Research Hospital.

.

3th International VIB Ph.D. Symposium VIBes on Biosciences 2012

?The VIBes 2012 Organizing Committee has the pleasure to invite all Ph.D. Students to the 3rd edition of the VIB Ph.D. symposium ?VIBes in Biosciences 2012?, which will take place from 5 to 7 September 2012 in the city of Ghent (Belgium).

The VIBes 2012 program kicks off with several workshop sessions on the scientific publication process and soft skills training. The scientific program consists of two days of lectures by world-class scientists, covering a broad range of topics from immunology and molecular biology to cybernetics and biomedical engineering. Selected speakers will also discuss career opportunities and share insights on how to succeed in science.
VIBes 2012 will again be a very international event as we will provide up to 50 international (i.e. not working in Belgium) Ph.D. students with free attendance to the symposium, free accommodation as well as a limited amount of travel grants.

Registration is now open at www.vibes2012.org
Places are limited and provided on a first-come-first-serve basis.

The VIBes2012 Organizing Committee
Jonas Bethuyne, Miguel Lopez Cardoso, Eleonora Billi, Nathan De Geyter, Lynn Elton, Matthieu Moisse, Christina Müller, Julie Mutert, Zeynep Okray, Ioanna Petta, Sebastian Proost, Dariusz Ratman, Tim Snoek, Lorin Spruyt, Suresh Subedi, Joemar Taganna, Arun Kumar Tharkeshwar, Koen Tyberghein and Rajesh Vyas?

Engineered microvessels provide 3-D test bed for human diseases

University of Washington bioengineers have developed the first structure to grow small human blood vessels, creating a 3-D test bed that offers a better way to study disease, test drugs and perhaps someday grow human tissues for transplant.

?In clinical research you just draw a blood sample,? said first author Ying Zheng, a UW research assistant professor of bioengineering. ?But with this, we can really dissect what happens at the interface between the blood and the tissue. We can start to look at how these diseases start to progress and develop efficient therapies.?

Zheng first built the structure out of the body?s most abundant protein, collagen, while working as a postdoctoral researcher at Cornell University. She created tiny channels and injected this honeycomb with human endothelial cells, which line human blood vessels.

During a period of two weeks, the endothelial cells grew throughout the structure and formed tubes through the mold?s rectangular channels, just as they do in the human body.

When brain cells were injected into the surrounding gel, the cells released chemicals that prompted the engineered vessels to sprout new branches, extending the network. A similar system could supply blood to engineered tissue before transplant into the body.

After joining the UW last year, Zheng collaborated with the Puget Sound Blood Center to see how this research platform would work to transport real blood.

Microfluidic vessel networks (credit: Y. Zheng et al./PNAS)

The engineered vessels could transport human blood smoothly, even around corners. And when treated with an inflammatory compound, the vessels developed clots, similar to what real vessels do when they become inflamed.

The system also shows promise as a model for tumor progression. Cancer begins as a hard tumor but secretes chemicals that cause nearby vessels to bulge and then sprout. Eventually tumor cells use these blood vessels to penetrate the bloodstream and colonize new parts of the body.

When the researchers added to their system a signaling protein for vessel growth that?s overabundant in cancer and other diseases, new blood vessels sprouted from the originals. These new vessels were leaky, just as they are in human cancers.

?With this system we can dissect out each component or we can put them together to look at a complex problem. We can isolate the biophysical, biochemical or cellular components. How do endothelial cells respond to blood flow or to different chemicals, how do the endothelial cells interact with their surroundings, and how do these interactions affect the vessels? barrier function? We have a lot of degrees of freedom?,? Zheng said.

The system could also be used to study malaria, which becomes fatal when diseased blood cells stick to the vessel walls and block small openings, cutting off blood supply to the brain, placenta or other vital organs.

?I think this is a tremendous system for studying how blood clots form on vessels walls, how the vessel responds to shear stress and other mechanical and chemical factors, and for studying the many diseases that affect small blood vessels,? said co-author Dr. José López, a professor of biochemistry and hematology at UW Medicine and chief scientific officer at the Puget Sound Blood Center.

Future work will use the system to further explore blood vessel interactions that involve inflammation and clotting. Zheng is also pursuing tissue engineering as a member of the UW?s Center for Cardiovascular Biology and the Institute for Stem Cell and Regenerative Medicine.

Ref.: Ying Zheng et al., In vitro microvessels for the study of angiogenesis and thrombosis, PNAS, May 29, 2012

Source

3D blood vessels could aid artificial organs

Growing artificial organsMovie Camera might help solve the transplantation shortage, but one major hurdle still exists: it is difficult to get blood vessels to grow all the way through a large organ. A gel that allows blood vessels to grow in precise shapes and respond to human cells in a manner similar to natural vessels might help jumpstart that process.

Ying Zheng at the University of Washington in Seattle and colleagues injected human endothelial cells ? which line blood vessels ? into tiny channels within a collagen gel.

The endothelial cells spread throughout the channels, which were only micrometres in width, and formed hollow, three-dimensional tubes, or microvessels. When the researchers pumped blood into the system, it moved through the microvessels without sticking. It could even flow smoothly around 90 degree bends.

The researchers then added a series of proteins involved in inflammation. They found that the proteins caused the blood to clot inside the microvessels, just as it would in the body. Because the system reacted to these stimuli in the same way as a natural vascular system would, Zheng says, it might one day be useful for screening drugs.

When the group injected human brain and muscle cells into the gel, along with proteins that stimulate blood vessel growth, the microvessels showed that they could branch and integrate with the two types of tissue.

Because the channels can be directed into any shape, bioengineer Linda Griffith of Massachusetts Institute of Technology is hopeful that the system can model complex vascular systems such as the blood-brain barrier, which is difficult to study in living animals. Additionally, she adds, researchers could study how cancers metastasise by putting other cell types, such as bone or liver cells, into the channels along with cancerous cells.

Zheng says that the next step is to use the system as a starting point for an artificial organ. Drawing the channels in the right shape will allow the organ to have an adequate blood supply throughout.

Journal reference: Proceedings of the National Academy of Sciences

Source

Large-Scale Simulation of Human Blood Is Boon to Personalized Medicine

Having a virtual copy of a patient’s blood in a computer would be a boon to researchers and doctors. They could examine a simulated heart attack caused by blood clotting in a diseased coronary artery and see if a drug like aspirin would be effective in reducing the size of such a clot.

“Blood platelets are like computers in that they integrate many signals and make a complex decision of what to do,” said senior author Scott Diamond, professor of chemical and biomolecular engineering in the School of Engineering and Applied Science. “We were interested to learn if we could make enough measurements in the lab to detect the small differences that make each of us unique. It would be impossible to do this with the cells of the liver, heart or brain. But we can easily obtain a tube of blood from each donor and run tests of platelet calcium release.”

Read More

ITU BIOTECH’12

ITU BIOTECH ’12 Student Congres is at İTÜ Ayazağa Campus Süleyman Demirel Congres Center for two days ( 9-10 April).

KUSOM Research Meeting, January 24th, 2012 (Dr. Kerem Pekkan)

KOÇ UNIVERSITY SCHOOL OF MEDICINE

SEMINAR

Tuesday, January 24th, 2012

******************************************************************

Speaker : Dr. Kerem Pekkan; Assistant Professor in Carnegie Mellon University’s Biomedical and Mechanical Engineering Departments

Title : High-speed multi-phase blood cell flow using confocal scanning microscopy for the development of next-generation blood damage models

Time : 16.00 (Refreshments will be served at 15.45)

Place : SOS B 21

High-speed multi-phase blood cell flow using confocal scanning microscopy for the development of next-generation blood damage models
Abstract: Measurement of multi-phase micro-scale morphology and fluid flow in the advanced microscopy environment represents a major step toward assessing blood element damage in medical devices and understanding the developmental role of hemodynamics in congenital heart defects. For improved medical devices with very low blood damage and platelet activation, three-dimensional, time-lapsed cellular deformation and fluid-induced mechanical red blood cell (RBC) loading must be quantified. In particular, investigating near-wall regions of high flow blood-wetted micro-components in cardiovascular devices is critical. Unfortunately, most relevant prior research is limited to very low flow speeds and to non-physiologic hematocrit (Ht) levels, due to limited optical access at higher RBC concentrations. Towards this objective a time-resolved, confocal microPIV technique that simultaneously measures velocities of high Ht (48%) human RBC and the plasma with high temporal (16,000 Hz) and spatial resolution in in vitro micro-fabricated channels has been developed. This technique integrates advanced confocal microscopy with in-house long wavelength fluorescent dyes. For the first time in literature, confocal velocimetry allowed deep measurements in optically opaque physiological high-Ht blood where measures of cell-cell and cell-plasma interactions (tracked with sub-micron fluorescent particles) and membrane phase unsteadiness have been reported. The method is further applied to pulsatile great vessel microcirculation using transgenically labeled zebrafish embryonic blood and endothelial cells, where average velocities can reach up to ~5 mm/s through short vessel sections, requiring advanced high-speed imaging. We demonstrated that individual RBC flow and dynamic crowded cell morphology can be acquired in microscopic aortic arches with high spatial resolution and record temporal resolution (resulting 175 full frames/sec). The limitations of the state-of-the art confocal hardware and configurations will also be reviewed.

The 6th IASTED International Conference on Biomechanics

Biomechanics encompasses a wide variety of subjects, including motion analysis and orthopaedics, as well as the study of cardiovascular, respiratory, musculoskeletal, and other systems. The Sixth IASTED International Conference on Biomechanics (BioMech 2011) will provide the opportunity for researchers and specialists to connect with others within their area of study as well as with those in the larger field of biomechanics.

Conference

News

Seminar

Structure and Dynamics of Bio-Networks: Robustness of Metabolic Networks

Prof. Hawoong Jeong ( Korea Advanced Institute of Science and Technology, Taejon, KOREA )

Istanbul Technical Univercity Physics Department – Friday, 27 May 2011 – 15:45

Seminars 13th April_1

Bogazici University Physics Department, Feza Gursey Seminar Room

13 April 2011 Wednesday 15:30

Deniz Sezer, Sabancı University

Towards understanding of protein conformational changes through simulations of biomolecular and spin dynamics.

One of the most ambitious aims in molecular biophysics?pursued both experimentally and theoretically?is to understand in atomistic detail the functionally relevant conformational transitions of biological molecules. More specifically, the goal is to identify the relevant conformations on the basis of their free energies and to characterize the sequence and time scales of the transitions between these conformations. In principle, this could be achieved computationally through moleculardynamics (MD) simulations. In practice, MD simulations, like any other model, rely on approximations and have their own inherent limitations. Therefore, direct comparison of the MD simulations with experimental data is essential. Among the experimental methods that probe the structure and dynamics of biomolecules electron spin resonance (ESR) spectroscopy provides rich information [1-3]. For example, ESR spectroscopy revealed the open conformations of a potassium channel [4] and a mechanosensitive channel [5] for which only the closed conformations were available from X-ray crystallography. In spite of the utility of ESR spectra, however, their interpretation in terms of the underlying molecular properties is not always unambiguous.

In this talk I will argue that the atomistic picture required for the conclusive interpretation of ESR data can be effectively obtained from MD simulations. In return, the experimental spectra can provide a stringent validation of the MD simulations, thus addressing concerns regarding their limitations. An unambiguous, quantitative comparison of these two techniques can be achieved by calculating the measured ESR spectra directly from the MD simulations. Naturally, such prediction of ESR spectra from ?first principles? poses many challenges. The systematic approach followed in addressing these challenges will be presented. The developed methodology will be illustrated in the context of a spin-labeled protein [6] and a DNA fragment labeled simultaneously with two spin labels [7].
[1] P. P. Borbat, A. J. Costa-Filho, K. A. Earle, J. K. Moscicki, and J. H. Freed. Electron spin resonance in studies of membranes and proteins. Science, 291:266-269, 2001.
[2] Linda Columbus and Wayne L. Hubbell. A new spin on protein dynamics. TIBS, 27:288-295, 2002.
[3] Gail E. Fanucci and David S. Cafiso. Recent advances and applications of site-directed spin labeling. Curr. Opin. Struct. Biol., 16:644-653, 2006.
[4] E. Perozo, D. M. Cortes, and L. G. Cuello. Structural Rearrangements Underlying K+-Channel Activation Gating. Science, 285:73?78, 1999.
[5] E. Perozo, D. M. Cortes, P. Sompornpisut, A. Kloda, and B. Martinac. Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Nature, 418:942?948, 2002.
[6] Deniz Sezer, Jack H. Freed, and Beno?ıt Roux. Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations. J. Am. Chem. Soc., 131(7): 2597-2605, 2009.
[7] Deniz Sezer and Snorri Th. Sigurdsson. Simulating electron spin resonance spectra of macromolecules labeled with two dipolar-coupled nitroxide spin labels from trajectories (submitted).

Biographical sketch
Deniz Sezer studied Electrical Engineering and Physics at Bo?gazi¸ci University, graduating in 1998. He obtained his Master?s degree in Physics from the same university in 2000. Between 2000 and 2008 he was a graduate student in the Physics department at Cornell University. During this period he worked successively at the following departments (institutions): Physics (Cornell University), Physiology and Biophysics (Graduate School of Medical Sciences of Cornell University), and Biochemistry and Molecular Biology (The University of Chicago). His PhD research was conducted in the group of Prof. Beno?ıt Roux, who is mostly known for his computational work on potassium channels. From early 2008 until the end of 2009 Deniz was a postdoctoral researcher in the Institute of Physical and Theoretical Chemistry at the University of Frankfurt. There he worked in the group of Prof. Thomas Prisner, who is pushing the limits of electron spin resonance (ESR) spectroscopy by developing new methodologies for the characterization of biomolecular systems. Since February 2010 Deniz is a faculty member in the Faculty of Engineering and Natural Sciences at Sabancı University, where he teaches courses in Structural Biology, Biophysics, and Mathematical Methods for Scientists and Engineers. During both his doctoral and postdoctoral research Deniz worked on the development of computational tools that make possible the interpretation of ESR experiments of biomolecules in terms of their atomic structure and dynamics. He continues working in this direction at Sabancı University.

Frankfurt Euro Biotechnology Congress