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Piotr E. Marszalek, Professor of Mechanical Engineering and Materials Science and Director of Graduate Studies

 

Piotr E. Marszalek

My research focuses on investigating relationships between structural and mechanical properties of biopolymers (polysaccharides, DNA, proteins), which I study at a single molecule level. My main approaches are experimental scanning probe microscopy techniques and computational methods involving Molecular Dynamics simulations and ab initio quantum mechanical calculations. The ultimate goal of this research is to understand the above-mentioned relationships at an atomic level and to apply the knowledge gained towards elucidating basic phenomena such as: molecular recognition that mediates interactions between proteins and sugars, mechanotransduction that underlies mechanical sensing and hearing in all organisms, and protein folding that is fundamental to all biology. Our DNA research is aimed at exploiting atomic force microscopy techniques to develop new ultra-sensitive assays for detecting and examining DNA damage, the process underlying carcinogenesis, and to increase our mechanistic understanding of DNA damage and repair processes. This research, in addition to its basic science aspects will lay a foundation for the future use of AFM technologies in the nanoscale DNA diagnostics with a potential to directly benefit human health.

Contact Info:
Office Location:  3387 CIEMAS, Durham, NC 27708
Office Phone:  (919) 660-5381
Email Address: send me a message

Teaching (Fall 2017):

  • ME 331L.001, THERMODYNAMICS Synopsis
    Hudson 207, TuTh 01:25 PM-02:40 PM
  • ME 331L.01L, THERMODYNAMICS Synopsis
    Teer 106, Th 08:30 AM-09:45 AM
  • ME 331L.02L, THERMODYNAMICS Synopsis
    SEE INSTRU, Th 08:30 AM-11:20 AM
  • ME 331L.03L, THERMODYNAMICS Synopsis
    Teer 106, Th 10:05 AM-11:20 AM
Teaching (Spring 2018):
  • ME 555.01, ADVANCED TOPICS Synopsis
    Hudson 218, TuTh 03:05 PM-04:20 PM

Education:

Ph.D.Electrotechnical Institute (Poland)1991
M.S.University of Warsaw (Poland)1985

Specialties:

Nanomaterial manufacturing and characterization
Nanoscale/microscale computing systems
Materials
Nanoscience
Polymer and Protein Engineering

Research Interests:

Current projects: Investigating conformations of single polysaccharides and nucleic acids by AFM, An AFM Study of DNA damage and Repair, Nanoscale DNA Diagnostics by Single Molecule AFM, Nanomechanics of Spiral Proteins

The invention of the atomic force microscope (AFM) in 1986 by Binnig, Quate and Gerber (Phys. Rev. Lett. 56, 930) started a revolution in many branches of science by realizing an unprecedented possibility to visualize and manipulate individual molecules under ambient conditions including water, which is critical for most studies involving bio-molecules. Biomolecular studies are therefore, in my opinion one of the main beneficiaries of this seminal invention. I was very fortunate to start my AFM research in 1997, the year, which marked great progress in AFM-based single-molecule force spectroscopy of proteins and polysaccharides. From the very beginning of my AFM work I experienced a particular appeal to polysaccharides research. This is because the wealth of information contained in their AFM measured force-extension relationships with totally unanticipated deviations from the entropic elasticity of simple polymers prompted me to believe that many interesting and quite fundamental observations can soon be made by studying polysaccharides elasticity. Protein mechanics is, in my opinion, another area of great potential because investigating the elastic properties of individual proteins promises to make significant contributions to the understanding of mechanotransduction, which is a process that underlies such important and basic phenomena as a sense of touch and hearing in all organisms. In addition, investigating mechanical unfolding and refolding reactions of individual proteins can contribute to elucidating the mechanism of protein folding, which is fundamental to all biology. More recently I initiated a new area of research by applying the AFM-based technology to study DNA damage and repair. While my polysaccharide and protein research is extremely rewarding by continuously offering quite fundamental observations and discoveries to be made, the new DNA research promises in addition even a greater scientific fulfillment through its possible contributions to medicine and human health.

Areas of Interest:

Force-induced conformational transitions of polysaccharides
Relationships between DNA damage and nanomechanics
Detecting DNA damage by Atomic Force Microscopy
Mechanical unfolding and refolding of repeat proteins

Keywords:

AFM • Alcohols • Algorithms • Alternative Splicing • Amino Acid Motifs • Amino Acid Substitution • Amino Acids • Amylopectin • Amylose • Animals • Anisotropy • Ankyrin Repeat • Ankyrins • Antibodies • Anura • Artifacts • Base Pairing • Binding Sites • Biocompatible Materials • Biomechanics • Biophysics • Butanols • Calcium • Calibration • Calixarenes • Calmodulin-Binding Proteins • Calorimetry • Carbohydrate Conformation • Carbohydrate Sequence • Carbohydrates • Carbon • Carrageenan • Cell Adhesion Molecules • Cellulose • Cloning, Molecular • Computer Simulation • Crystallization • Deoxyribodipyrimidine Photo-Lyase • Deoxyribonuclease (Pyrimidine Dimer) • Dextrans • Diffusion • Dimerization • DNA • DNA damage • DNA Damage • DNA Fingerprinting • DNA mechanics • DNA Methylation • DNA, Superhelical • Dose-Response Relationship, Radiation • Drug Carriers • Elasticity • Electrolytes • Electrophoresis, Agar Gel • Electroporation • Entropy • Enzyme Stability • Escherichia coli • Extracellular Matrix • Fibronectins • force spectroscopy • Glucans • Glucose • Glycine • Glycosides • Gold • Histidine • Humans • Hydrogen Bonding • Hydrogen-Ion Concentration • Immunoglobulins • Iodine • Isomerism • Kinetics • Lasers • Lichens • Light • Lysine • Macromolecular Substances • Maltose • Mast Cells • Materials Testing • Mathematics • Mechanical Processes • Mechanoreceptors • Membrane Potentials • Micelles • Micromanipulation • Microscopy, Atomic Force • Microscopy, Scanning Probe • Models, Biological • Models, Chemical • Models, Molecular • Models, Statistical • Models, Theoretical • Molecular Conformation • Molecular Dynamics Simulation • Molecular Sequence Data • Molecular Structure • Monte Carlo Method • Motion • Muscle Proteins • Mutagenesis • Mutation, Missense • Myocardium • Nanoparticles • Nanostructures • Nanotechnology • Neoplasms • Nervous System • Neurons • Nucleic Acid Conformation • Oligonucleotides • Oxidation-Reduction • Particle Size • Pectins • Peptide Fragments • Peptides • Phenotype • Physical Stimulation • Plants • Plasmids • Point Mutation • Poly A • Polydeoxyribonucleotides • Polymerase Chain Reaction • Polyproteins • polysaccharide conformations • Polysaccharides • Polyubiquitin • Proline • Proteasome Endopeptidase Complex • Protein Binding • Protein Conformation • Protein Denaturation • Protein Engineering • Protein Folding • Protein Kinases • protein mechanics • Protein Refolding • Protein Renaturation • Protein Stability • Protein Structure, Secondary • Protein Structure, Tertiary • Protein Unfolding • Proteins • Proto-Oncogene Proteins • Pyrimidine Dimers • Quantum Theory • Radiation Dosage • Recombinant Fusion Proteins • Recombinant Proteins • Repetitive Sequences, Amino Acid • Reproducibility of Results • RNA • Scattering, Radiation • Sensitivity and Specificity • Sepharose • Signal Processing, Computer-Assisted • Signal Transduction • Silicon • single molecule • Software • Solutions • Solvents • Spectrum Analysis • Spherocytosis, Hereditary • Steered Molecular Dynamics • Stochastic Processes • Streptavidin • Stress, Mechanical • Structure-Activity Relationship • Surface Properties • Temperature • Tenascin • Tensile Strength • Thermodynamics • Time Factors • Transient Receptor Potential Channels • Ubiquitin • Ultraviolet Rays • Viral Proteins • Viscosity • Water

Representative Publications   (More Publications)

  1. Ke, C; Humeniuk, M; S-Gracz, H; Marszalek, PE, Direct measurements of base stacking interactions in DNA by single-molecule atomic-force spectroscopy., Physical Review Letters, vol. 99 no. 1 (July, 2007), pp. 018302, ISSN 0031-9007 [17678193], [doi]  [abs]
  2. Lee, G; Abdi, K; Jiang, Y; Michaely, P; Bennett, V; Marszalek, PE, Nanospring behaviour of ankyrin repeats., Nature, vol. 440 no. 7081 (March, 2006), pp. 246-249 [16415852], [doi]  [abs]
  3. Ke, C; Jiang, Y; Rivera, M; Clark, RL; Marszalek, PE, Pulling geometry-induced errors in single molecule force spectroscopy measurements., Biophysical Journal, vol. 92 no. 9 (May, 2007), pp. L76-L78, ISSN 0006-3495 [17324999], [doi]  [abs]
  4. Jiang, Y; Ke, C; Mieczkowski, PA; Marszalek, PE, Detecting ultraviolet damage in single DNA molecules by atomic force microscopy., Biophysical Journal, vol. 93 no. 5 (September, 2007), pp. 1758-1767, ISSN 0006-3495 [17483180], [doi]  [abs]
  5. Zhang, Q; Marszalek, PE, Identification of sugar isomers by single-molecule force spectroscopy., Journal of the American Chemical Society, vol. 128 no. 17 (May, 2006), pp. 5596-5597, ISSN 0002-7863 [16637601], [doi]  [abs]
  6. Lee, G; Nowak, W; Jaroniec, J; Zhang, Q; Marszalek, PE, Nanomechanical control of glucopyranose rotamers., Journal of the American Chemical Society, vol. 126 no. 20 (May, 2004), pp. 6218-6219, ISSN 0002-7863 [15149204], [doi]  [abs]
  7. Marszalek, PE; Lu, H; Li, H; Carrion-Vazquez, M; Oberhauser, AF; Schulten, K; Fernandez, JM, Mechanical unfolding intermediates in titin modules., Nature, vol. 402 no. 6757 (November, 1999), pp. 100-103, ISSN 0028-0836 [10573426], [doi]  [abs]
  8. Marszalek, PE; Oberhauser, AF; Pang, YP; Fernandez, JM, Polysaccharide elasticity governed by chair-boat transitions of the glucopyranose ring., Nature, vol. 396 no. 6712 (December, 1998), pp. 661-664, ISSN 0028-0836 [9872313], [doi]  [abs]