Dr. Thorsten-Lars Schmidt in his lab

Thorsten-Lars Schmidt

Physics
Assistant Professor
Campus:
Kent
Contact Information
Phone:
330-672-0356

Biography

*** I'm hiring! ***

1) Undergraduate or graduate research or rotation projects with foci in single-molecule biophysics, molecular biology or biochemistry are available.

2) PhD projects: Several projects are available for students from various backgrounds including physics, chemistry (polymer chemistry, physical chemistry, or biochemistry), and biology (molecular), bioengineering or related subjects.
If you are not admitted to a graduate program at Kent State, yet: Please be aware that at US universities, students need to be accepted to a graduate program, do some courses and pass “candidacy exams” prior to starting full-time research for their PhD project. Typically, you will also be a teaching assistant in a course or lab during the semester. If your previous degree is not in Physics, you may also check the graduate programs of the "Biomedical Sciences" program, particularly the Cell & Molecular Biology program, or the Chemical Physics Interdisciplinary Program.

 


Research

Why building with DNA?

Schmidt Lab Experimental Biophysics, Biology, Chemistry

DNA is a unique polymer. It is the information storage molecule of all known life forms, and can be used to build up almost arbitrary structures and patterns out of DNA. These structures can be functionalized with a large variety of inorganic nanoparticles, small molecules or large biomolecules such as proteins and antibodies. Our group is leveraging this programmability to engineer nanoarchitectures and tools for applications in biophysics, molecular biology, nanophotonics and nanomedicine. Moreover, we are developing scalable “next-generation DNA synthesis” methods.

 

DNA-encircled lipid bilayers

DNA encircled lipid bilayer Iric Schmidt et al DEB Nanodisc Nanosale 2018

Lipid bilayers and lipid-associated proteins play a crucial role in biology. As in vivo studies and manipulation of single molecules are inherently difficult, several membrane-mimetic systems have been developed to enable investigation of lipidic phases, lipid-protein interactions, membrane protein function and membrane structure in vitro. We leverage the unique programmability of DNA nanotechnology to create DNA-encircled bilayers (DEBs). DEBs provide an unprecedented control over size and allows the orthogonal functionalizations and arrangement of engineered membrane nanoparticles.[Nanoscale 2018].

Outlook: We want to use DEBs as a tool for biophysical investigation of lipid phases and lipid-associated proteins and complexes including structure determination of membrane proteins. Moreover, we explore lipid-DNA interactions further and will use DNA structures anchored to supported lipid bilayers to investigate interactions of molecules with cells.

 

DNA-based plasmonic devices

Plasmonic waveguides Schmidt Gür DNA nanotechnology

The field of plasmonics exploits the interaction of light with nanoscale metallic structures to confine, guide and manipulate light on scales below the diffraction limit. Plasmonic structures exhibit significant potential for applications including quantum optics, sensing, and short-distance optical communication (a). Towards this goal, we demonstrated the precise, robust, and high-yield assembly of gold nanoparticles on DNA origami templates (b).  [ACS Nano 2016].

More recently, we realized energy propagation through such a self-assembled waveguide to a fluorescent nanodiamond and out coupling of energy. We analyzed the waveguiding at a single-device level by electron energy loss spectroscopy (c) and cathodoluminescence imaging spectroscopy. Our work visually demonstrates the realization of nanometer-precise light manipulation and energy conversion. [Nano Lett. 2018].

Finally, these closely spaced gold nanoparticles create a strong plasmonic hotspot for the sensing of molecules. [Nano Lett. 2019].

 

Triangulated DNA origami and nanomechanical actuators

Tetrahedral Truss DNA Nanostructure Matthies Schmidt

In the macroscopic world, stiff and material-efficient structures such as construction cranes and high voltage transmission towers are usually built from triangulated wireframe structures. We extended the DNA origami concept to generate a series of triangulated trusses. These provide defined cavities that we seek to fill with functional elements. [Nano Lett. 2016].

 
Gap filling Polymerase, DNA origami, Actuator, Agarwal, Schmidt et al ACS nano 2018
actuator Nanoscale 2019

By introducing single-stranded regions edges of the wireframe trusses, the structures are heavily deformed due to the entropic spring forces contracting the single-stranded region. The gaps can be filled by a gap filling polymerase (such as the T4 polymerase) or the addition of the missing oligonucleotides, thus creating a nanomechanical actuator. [ACS Nano 2018].

Outlook: This principle shall be the basis for stimuli-responsive mechanical nano devices in photonics or for applications in molecular biology. Moreover, we wish to determine biophysical properties such as their bending and torsional stiffness with super-resolution microscopy.

 

Nanomedicine

Nanomedicine gold nanoparticles gliablastoma cancer stem cells photothermal therapy Goncalves Schmidt

An important goal in nanomedicine is the synthesis of smart designer nanoparticles, which show a lower renal clearance compared to conventional drugs and increase specificity to malignant cells. Cancer stem cells (CSCs) are responsible for drug resistance, tumor recurrence, and metastasis in several cancer types, making their eradication a primary objective in cancer therapy. In a collaboration project lead by Dr. Goncalves-Schmidt, gold nanorods were functionalized with nestin-binding peptides that specifically recognize Glioblastoma multiforme stem cells for photothermal therapy. [Acta Biomaterialia  2017] and [Biomat. Sci. 2018].

Outlook: Building up on our experience with gold nanoparticle based cell uptake, we will develop sophisticated and more complex functionalized DNA structures for drug delivery or as diagnostic and therapeutic devices.

 

Stabilizing DNA structures for nanomedicine

Polyplex Micelle Agarwal Angewandte Chemie 2016

A main drawback of structural DNA nanotechnology is the instability of structures in biological environments. We developed a protection strategy based on block copolymer micellization which stabilizes DNA structures in biological or low-salt environments. [Angew. Chem. 2017].

Outlook: We will use this protection to enhance DNA-based nanomedicines.

 

“Next-generation” DNA synthesis methods

Synthetic oligonucleotides (short single-stranded DNA) and genes (long double-stranded DNA) are the main cost factor for many studies in DNA nanotechnology, genetics and synthetic biology. Inexpensive chip-synthesized oligonucleotide libraries can contain hundreds of thousands of distinct sequences, however only at sub-femtomole quantities per strand. We developed a selective oligonucleotide amplification method based on rolling circle amplification (RCA) with a 10-1000-fold cost-reduction compared to synthetic oligonucleotides or competing amplification methods such as PCR. [Nat. Commun. 2015].

Outlook: We have recently extended our method for de novo gene synthesis. This will allow us to design custom scaffolds, and testing design principles that influence the folding kinetics and yields.

 

Other future directions

More multi-disciplinary projects are being followed at the interface of physics, biology, chemistry and nanoscale engineering. For example, we want to learn about the mechanobiology of cell-cell contacts. Please inquire.

 

Group

Schmidt Lab 2019

Current group members:

  • Praneetha Sundar Prakash (research assistant, PhD candidate Biomedical Sciences)
  • Brady Weber (research assitant)
  • Soumya Chandrasekhar (research assistant, PhD candidate, Chemical Physics Interdisciplinary Program)

Alumni:

Years Name Degree Now
2019 Yusuke Sato Postdoc Assistant Professor, Tohoku University, Sendai
2019 Parastoo Maleki Postdoc University of Texas, Austin
2019 Alamgir Kabir Master's PhD student, Toledo
       
Dresden      
2014-2017 Fatih Nadi Gür PhD. Postdoc at LMU Munich
2014-2018 Michael Matthies Master's and PhD. Postdoc at Arizona State University
2014-2018 Nayan P. Agarwal Master's and PhD. Postdoc at Massachussets Institute of Technology
2015-2018 Bastian Joffroy PhD. Researcher at DKMS Dresden
2015-2019 Katarina Iric PhD. Postdoc at TU Dresden
2014-2015 Hafesudeen Sahabudeen Master's PhD candidate at TU Dresden
2014-2016 Simon Ahrens Technitian Paternity leave
2014-2015 Yavuz Uca Master's PhD candidate at Charite Berlin
2015-2016 Jingjing Ye Master's PhD candidate at U. Leipzig
2015-2016 Eric Wiener Master's PhD candidate at U. Leipzig
2017 Ashwin Karthick Winter intern PhD candidate Aalto University
2016-2017 Shikhar Gupta Master's PhD candidate at U. Leipzig
2016-2017 Foram M. Joshi Master's PhD candidate at TU Dresden
2017-2018 Olga Aftenieva Master's PhD candidate at TU Dresden
2017-2018 Kristin Joffroy Technitian Researcher at DKMS Dresden
2017-2018 Diana Goncalves-Schmidt Postdoc Postdoc at Kent State University
2018 Chloe Jones Summer intern PhD candidate
       

 

Further Reading

For more information, I recommend this 3-hour lecture (iBiology) by William Shih:

https://www.youtube.com/watch?v=Ek-FDPymyyg

https://www.youtube.com/watch?v=noWkRxKYBhU

https://www.youtube.com/watch?v=5cmg1oa4-fg

or a current review on structural DNA nanotechnology such as: DNA Origami: Scaffolds for Creating Higher Order Structures.

 

Teaching Spring 2020

DNA nanotechnology and single-molecule biophysics (PHY 40095 = CRN 17016 = 50095 = CRN 21393). Mon 2:15-3:55 and Wed 2:15-3:05 ISB 040.

Students who don't need this course for credit could audit selected topics. Please inquire by email.


 

Education

2013-2018 Group leader, Cluster of Excellence cfaed (Center for Advancing Electronics Dresden), Dresden, Germany, 2010-2013: Postdoctoral research fellow at the Wyss Institute for Biologically Inspired Engineering at Harvard (Boston, MA) with Lynen fellowship from the Alexander von Humboldt foundation, 2010: PhD from Goethe University Frankfurt (Germany), 2000-2005: Chemistry (Diploma) at University of Bonn (Germany) and Oviedo (Spain)

Publications

  • https://scholar.google.com/citations?authuser=1&user=2UtidW0AAAAJ

Affiliations

Department of Physics; Full PI of the Chemical Physics Interdisciplinary program

Awards/Achievements

  • 2018: Outstanding Mentor Award by the Dresden International PhD Program

Research Institutes and Initiatives

Advanced Materials and Liquid Crystal Institute