Final Report Biophysics 2012

Objective: State of the art report on a biophysics-related research topic highlighting relevant applications of high impact or the advances needed in the field.

Maximum length: 10 pages including bibliography (1.5 space, Times New Roman 12 or equivalent) The report should consist of an introduction, a description of the problematic, a stateof-the art on the topic and the aspects that need further research contributions Projects are due in my mailbox (DF secretary) no later than 17:00 h Thursday 24 May (last class of the semester). Oral presentations will be one week later on 31 May 2012.

Evaluation criteria 1. Originality of the subject 2. Organization and written quality 3. Bibliography - Recent publications citation 4. Oral presentation (max 8 min / project): clarity of presentation of the problem of current knowledge, and achievements in the field.

COMPUTATIONAL BIOPHYSICS
Structural studies of Biomolecules: explore the underlying physical mechanism of structural formation, folding dynamics and protein-protein interaction 1. 2. 3. 4. 5. 6. 7. mathematical patterning of cells in 2D to yield 3D cellular organization Tumor growth Lipid membranes Bone remodeling Myocardial remodeling Mechanism of cell migration within tissues (as in cancer malignant tumours) Myxobacteria (soil inhabiting bacteria which produce and export chemotherapy drugs, antibiotics,) Other tissue remodeling

CELLS AND TISSUE ENGINEERING AND BIOMATERIALS

Target therapeutics, Cellular analogues and drug delivery 1. Study of lipid mixtures(e.g., sphingomyelin-colesterol); self-assembly 2. Membrane proteins and lipoproteins 3. Application of lipid films in biomedical nanotechnology 4. Lipid raft formation 5. design of model bilayer surfaces with engineered binding affinity 6. immunoliposomes 7. Protein-DNA interactions 8. Evolving self-assembling proteins, such as nanocages 9. Interaction of lung surfactant with nanoparticles 10. Structure and function of pulmonary surfactant 11. Protein-DNA interactions - Structure, function and nucleocytoplasmic traffic of nuclear protein 12. nanocarriers 13. Dynamics of bleb formation (apoptosis, cancer,) 14. Mechanism of cell deformation - dynamics of bleb nucleation and instability of the cell membrane adhesion 15. Transdermal drug delivery 16. cell-based therapies: biomimetic materials 17. Membrane electroporation 18. Synthetic tissue engineering tissue transplantation 19. Synthetic scaffold seeded with patients stem cells (tissue, organ 20. Artificial organs (heart, kidney,..) 21. Nanoparticles-based carriers for drug delievery

Dynamics of tissue growth Numerical simulation for elastic, adhesive and contractile stresses at the cell membranes (growth anisotropy, cell division and morphology of the growing tissue)

Dynamics of cell adhesion 1. Analytical and numerical approaches 2. Dynamics of cell rolling in blood flow 3. Cooperative effects of molecular motors pulling on fluid-like cargoes 4. Collective dynamics of small clusters of motors pulling on vesicles or membrane tubes 5. Numerical simulation of equations for ratchet-like motors 6. Monte Carlo simulation of discrete random walkers and analytical calculations in different approximations 7. Modelling of monomeric kinesin, a motor which is known to work collectively for long-range transport in axons 8. Motor traffic disorders that are associated to most neurodegenerative diseases organization of molecules on drug delivery vehicles relative to cell membrane receptors

BIO-NANOSENSOR DEVELOPMENT AND APPLICATIONS The primary challenge in these systems is not the sensors themselves, but the connections and interfaces to the outside world, both with regard to fluidics (sample handling) and electronics or optics (signal output). The high-density electronics and optics appear available, but high-density microfluidic systems are just beginning to come online. Overall, these types of arrangements are likely to lead to inexpensive screening for multiple diseases or biomolecule states in a simultaneous fashion, which should quickly change the way in which medicine is practiced. In any case, the impact of nanoscale sensors will have a profound effect on medical, food, and environmental testing. Applications, techniques, and microfluidic interfacing for nanoscale biosensing Interaction of magnetic nanoparticles with lipid membrane and cancer cells controlling biological processes and diseases Micro and nanofabricated substrates to control enzyme mediated molecular selfassembly 5. topographical and biochemical patterns designed to precisely position enzymes and control the assembly of small peptide molecules into well-defined nanofibers (nanofabrication techniques, lithographic techniques, and small molecule manipulation) 1. 2. 3. 4.

DISSECT THE EPIGENOME OF HUMAN CELLS How variants of the genomic DNA sequence and mRNA that are encountered among different individuals might influence gene function, transcriptional regulation, nuclear organization, development and disease (cardiovascular, metabolic disorders and neuropsychiatric conditions). These are relevant modifications to the genome that do not involve a change in the nucleotide sequence 1. genome-wide charts of epigenome features 2. development of computational and mathematical approaches to define and characterize epigenomic features 3. statistical approaches to study the effects of common human genetic variation on chromatin and 4. transcriptional activity in the human genome 5. Transcriptome and proteome analysis

REACTION DYNAMICS OF LIGHT-ACTIVATED DRUGS FOR CANCER THERAPIES 1. High-sensitivity and high-resolution time-resolved femtosecond laser spectroscopic techniques for real time studies of reaction dynamics of lightactivated drugs.

2. Real-time observation of light activated reactions in drugs for cancer therapies including photodynamic therapy, radiotherapy and their combination with chemotherapy. 3. Molecular pathways that lead to the formation of highly reactive radicals such as singlet oxygen and uracil that then mediate biological effects such as DNA damage and cell death. DESIGN OF NOVEL NEAR-INFRARED (NIR) SENSITIVE PHOTODYNAMIC THERAPY
DRUGS

1. Towards more effective drugs and clinical tests 2. photochemistry, photobiology and biological effects of light activated drugs 3. single-photon activated drugs for cancer therapy .

MRI BASED DIAGNOSTICS AND RADIATION DOSIMETRY

Pathological Iron Deposits Iron overload diseases are very common around the globe. These diseases cause iron to be deposited within tissues. Detection and measurement of iron deposits in organs, liver, heart, pancreas,

Neuronal activity and calcium imaging

CARDIOVASCULAR IMAGING Optical coherent tomography Intravascular ultrasound (RF analysis) - Interaction of a pathogens with cell membranes PLASMA HEALTH CARE Regenerative medicine Desinfection/sterilization Cell growth HUMAN PATHOLOGIES 1. Amyloidogenesis: Amyloid fibril formation and toxicity in relation to Alzheimers disease 2. Prion protein toxicity

OTHER SUBJECTS 1. Plasmodium falciparum infection - resistance and sensitization to antimalarials 2. Virus glycoproteins that induce cell fusion and membrane permeabilization (e.g., HIV, Ebola,) 3. Antigenic and inhibitory agents 4. Cell-cell communication 5. Noise exposure and health effects 6. Artificial gravity sustaining life in space Effect of gravity on cells and body structures (cell division, bone, muscles, heart, lungs, metabolism,) Biomechanics and motor control Bio-inspired robotics Orthopedics Acoustics. Vision