Homepage Andreas Hanke - Department of Physics UT Brownsville

Biophysics & Nanoscience @ UT Brownsville

Group Leader:

Andreas Hanke, Assistant Professor of Physics

Students:

Graduate:

Maria Akhmanova (Ph.D. student at Moscow State University, on visit at UTB spring 2009 & 2010)

Marco Milan

Undergraduate:

Sigrid Andrea Razo Moreno

Lauro Salazar

Former students:

Moatez Eldib

Martha Gabriela Ochoa

Erick Vallarino

Mailing Address:

Department of Physics and Astronomy
University of Texas at Brownsville
80 Fort Brown
Brownsville, TX 78520

Office Address: Engineering, Science & Technology, Office 1.318

Phone: (956) 882-6682

Fax: (956) 882-6726

e-mail: hanke@phys.utb.edu

Research Interests: Biophysics and Nanoscience

I am theoretical physicist by training and have worked in the fields of mesoscopic quantum systems, soft condensed matter physics, and biological physics. My current plans are to build up a theory division in the fields of biophysics and nanoscience at the Physics Department of UT Brownsville. The scope of my research is to develop new theoretical models relevant to molecular cell biology and nanoscience and to validate these models with experimental data for systems such as cell membranes, proteins, DNA, RNA, and their interactions. My research is highly interdisciplinary in nature, involving Statistical Physics, Biology, Computer Science, and Math.

Casimir force in nanomechanical systems

Jointly with H. B. Chan (University of Florida)

Student: Lauro Salazar

The increasing miniaturization of nanomechanical systems requires an understanding of fundamental forces on the nanoscale. When the distance between metallic or dielectric surfaces is reduced to the submicron range, forces of pure quantum electrodynamical origin emerge. This force was first predicted 1948 by H. B. G. Casimir for two infinitely extended, perfectly conducting, electrically neutral plates in vacuum. The Casimir force can be understood as resulting from the modification of the quantum fluctuations of the electromagnetic field in vacuum by the presence of boundaries. Due to its nature as a fluctuation-induced force, the Casimir force has a strong dependence on both the geometry and the optical properties of the interacting bodies.

In 2001, Ho Bun Chan and collaborators at Bell Labs pioneered experiments that demonstrated the possibility of using the Casimir force as an actuation force of micromechanical components. These experiments establish the importance of quantum electrodynamical effects in micro- and nanomechanical systems (MEMS and NEMS), hence the convergence of fundamental physics and real world technological applications. Concurrently with this development, significant progress has been made in the last decade in predicting the Casimir force for complex geometries and materials, as often encountered in actual nanomechanical systems.

In this project we calculate the Casimir force for given material and geometry of nanomechanical components in the framework of the Lifshitz theory. To this end we use the electromagnetic stress tensor, which is evaluated via the fluctuation-dissipation theorem in terms of imaginary-frequency Green’s functions. This approach to calculate the Casimir force, developed in theory by Dzyaloshinskii in 1961, allows one to resort to well-developed methods in computational electromagnetics; see Stephen Johnson’s group at MIT and Casimir calculations in Meep.

We currently apply this method to calculate the Casimir force between a gold-coated sphere and an array of nanoscale rectangular silicon trenches, for which experimental data are available by Ho Bun Chan’s group [H. B. Chan et al, Phys. Rev. Lett. 101, 030401 (2008)]. The Green’s function is calculated using finite-difference methods in the frequency domain (FDFD) and time-domain (FDTD, see Meep). The results will be validated by experimental data provided by Ho Bun Chan’s group. This project is a collaboration with the MIT group and Ho Bun Chan.

Setup of the experiment to measure the Casimir force between a gold sphere
and a silicon surface with nanoscale trench arrays using a micromechanical
torsional oscillator [H. B. Chan et al, Phys. Rev. Lett. 101, 030401 (2008)].
Inset: Electron micrograph of the silicon trenches (image courtesy Ho Bun Chan).

Recent Publications

Andreas Hanke, Casimir force waves induced by non-equilibrium fluctuations between vibrating plates (2009), E-print arXiv:0912.3325

We study the fluctuation-induced, time-dependent force between two plates immersed in a fluid driven out of equilibrium mechanically by harmonic vibrations of one of the plates. Considering a simple Langevin dynamics for the fluid, we explicitly calculate the fluctuation-induced force acting on the plate at rest. The time-dependence of this force is characterized by a positive lag time with respect to the driving, indicating a finite speed of propagation of stress through the medium, reminiscent of waves. We obtain two distinctive contributions to the force, where one may be understood as directly emerging from the corresponding force in the static case, while the other is related to resonant dissipation in the cavity between the plates.

Left: Two parallel plates separated by a varying distance L(t). Plate 1 is at rest while plate 2 is vibrating in z-direction. The plates are immersed in a fluctuating fluid with long-ranged correlations. We are interested in the fluctuation-induced, time-dependent force F(t) on plate 1.

Right: Force F(t) on plate 1, normalized by its value for plates at rest, for given model parameters (black line). The harmonic driving of plate 2 is shown as the blue line. For the given parameters, the lag time is 0.15 s, indicating a finite speed of propagation of the fluctuation-induced force through the medium.

Biophysics – from single molecules to biological function

Currently I work as Principal Investigator on two major research projects which are funded by AFOSR (SPRING) and NIH (SCORE) programs:

1) Studies of single biomolecules: DNA conformational changes and protein binding

Jointly with S. D. Levene (UT Dallas) and M. C. Williams (Northeastern University)

Students: Marco Milan, Sigrid Moreno

Structural transitions of DNA and docking of proteins on DNA are fundamental processes in molecular biology. Understanding these processes on a single-molecule level is essential for our understanding of gene function and control, and may find application in DNA-based sensors and other emerging nanotechnology.

Stretching on individual DNA molecules in single molecule force spectroscopy can be used to induce a helix-coil transition in double-stranded DNA. Within a certain range of stretching forces, only local denaturing of the DNA duplex, or "bubble formation", occurs. The interaction of these localized regions of unwound DNA with single-strand-specific DNA binding proteins can then be probed under a wide range of conditions using new experimental techniques. Our collaborator Mark Williams and his group at Northeastern University is able to measure the forces required to stretch single DNA molecules by using an optical tweezers instrument with high precision. In our lab at UTB we study also force-induced transitions and conformational changes caused by DNA-binding proteins. A state-of-the-art Veeco Nanoscope IV Scanning Probe Microscope with PicoForce Module is available for imaging at atomic resolution and force measurements in the piconewton range.

2) Sequence-dependent unwinding in superhelical DNA

Jointly with S. D. Levene (UT Dallas)

Sequence-dependent unwinding of DNA is an integral aspect of many biological processes such as gene regulation, DNA replication, and DNA repair. DNA unwinding is facilitated by negative supercoiling, which provides a ubiquitous source of free energy that augments the unwinding free energy accompanying the interactions of many proteins with their cognate DNA sequences. Although much is known about sequence-dependent unwinding in linear DNA molecules, our present understanding of the effects of supercoiling on localized, sequence-dependent melting transitions in DNA is at best semi-quantitative.

The DNA of virtually all terrestrial organisms is negatively supercoiled. Negative supercoiling is regulated in prokaryotes by DNA gyrase; eukaryotes lack gyrase but maintain negative supercoiling through winding of DNA around nucleosomes and interactions with DNA-unwinding proteins. Large regions of mammalian chromosomes appear to be organized into negatively supercoiled, topologically independent domains. Therefore, understanding the interplay of supercoiling and local helical structure is essential to a complete understanding of biological mechanisms in higher organisms. Recent developments in biophysical theory provide an opportunity to develop a detailed and quantitative framework for analyzing localized DNA-unwinding transitions in superhelical domains.

In our research we will use a fusion of numerical simulations of superhelical conformation and a statistical-mechanical treatment of sequence-dependent transitions in DNA to develop a comprehensive biophysical model for supercoiling-dependent DNA unwinding. The theoretical model will be validated by comparing predictions of the theory for several DNA sequences with experimental data from plasmid DNAs and supercoiled DNA minicircles that contain 2-aminopurine substitutions as spectroscopic probes of local unwinding.

Recent Publications

[1] R. Metzler, T. Ambjornsson, A. Hanke, and H. C. Fogedby, Single DNA denaturation and bubble dynamics, J. Phys.: Condens. Matter 21, 034111 (2009).

[2] L. Shokri, B. Marintcheva, M. Eldib, A. Hanke, I. Rouzina, and M. C. Williams, Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA, Nucl. Acids Res. 36, 5668 (2008).

[3] A. Hanke, Martha G. Ochoa, and R. Metzler, Denaturation transition of stretched DNA, Phys. Rev. Lett. 100, 018106 (2008); E-print arXiv:0709.2958.

[4] R. Metzler, T. Ambjornsson, A. Hanke, and S. Levene, Single DNA conformations and biological function, Review article, J. Comp. Theor. Nanoscience 4, 1 (2007); E-print physics/0609139.

Development

I wrote my diploma thesis with Prof. W. Zwerger at the Physics Department at the Ludwig Maximilians University Munich, Germany, on a topic of mesoscopic quantum systems. In my PhD thesis with Prof. S. Dietrich at the University of Wuppertal, Germany, now at the Max Planck Institute for Metal Research in Stuttgart, I studied fluctuation-induced entropic forces between colloidal particles. After my PhD I went to MIT for my post-doctoral studies where I worked with Prof. M. Kardar on problems of nanoscience and biological physics. In November and December 2001 I visited the group of Prof. M. Schick in Seattle, before I moved to a Postdoctoral Position in Prof. John Cardy's group at the University of Oxford. From October 2002 until July 2003 I worked as Research Associate in the group of Prof. U. Seifert in Stuttgart where I worked on problems of single molecule biophysics. In August 2003 I returned with a Marie Curie Fellowship to John Cardy\222s group at the University of Oxford. In March 2004 I finally moved to my present position as Assistant Professor at the Physics & Astronomy Department at The University of Texas at Brownsville. I am also Adjunct Assistant Professor at the Physics Department at The University of Texas at Dallas and my research includes summer appointments at the Dallas NanoTech Institute.

Teaching

F 2004: PHYS 5321 - Classical Mechanics (Graduate Course)

S 2005: PHYS 4320 - Quantum Mechanics (Undergraduate Course)

F 2005: PHYS 5322 – Electrodynamics II (Graduate Course at UT Dallas via distance video conferencing)

S 2006: PHYS 4380 – Thermodynamics and Statistical Mechanics (Undergraduate Course)

F 2006: PHYS 5461 – Quantum Mechanics (Graduate Course)

S 2007: PHYS 1302 – General Physics II (Undergraduate Course)

F 2007: PHYS 5364 – Thermodynamics and Statistical Mechanics (Graduate Course)

S 2008: PHYS 5321 – Classical Mechanics (Graduate Course)

F 2009: PHYS 1302 – General Physics II (Undergraduate Course)

S 2009: PHYS 3320 – Thermodynamics and Statistical Mechanics (Undergraduate Course)

F 2009: PHYS 5330 – Thermodynamics and Statistical Mechanics (Graduate Course)