Biophysics
DNA-adsorption
DNA is the genetic building block of life on earth. After seven years all atoms in our body are renewed,
but the structure remains, be it older and wiser.
The secret of the stability of DNA is the naturation (binding) of its two monomer strands.
Under specific conditions, the strands can denaturate (unbind).
This is already needed for making a copy of DNA, but it can also occur in laboratory.
Adhesion of DNA to a wall will typically make the two strands stronger bound and lead to an unexpected
collective effect. We find a region of Borromean binding, where the potentials that
try to adsorb the individual strands to the wall are too weak to do so, while also
the interstrand potential is too weak to naturate (bind) the two strands.
Nevertheless, their combined effect may yield a bound state of naturated, adsorbed DNA. [L48]
A.E. Allahverdyan, Zh.S. Gevorkian, Chin-Kun Hu and Th.M. N., Molecular Motors
Molecular motors are proteins that move in the cells of our body along filaments,
like trains proceed along railroad tracks. They take care of transport inside cells,
muscle contraction and are involved in healing of wounds and fractures.
One example is the motor molecule kinesin, that moves on microtubules.
Typical progression speeds are one micron per second (a few milimeters per hour).
This explains why it takes weeks to heal fractures: the new material has to be transported
from the spine over a distance of about one meter at this slow speed.
[C32] Stefan Klumpp, Theo M. N. and Reinhard Lipowsky,
Movements of molecular motors: Ratchets, random walks and traffic phenomena,
Physica E 29, 380-389 (2005) or
cond-mat/0502527
[C31] Theo M. N., Stefan Klumpp and Reinhard Lipowsky,
Walks of molecular motors interacting with immobilized filaments,
Physica A 350, 2005 pp 122-130: Proceedings Conference: Biologically Motivated Statistical Physics and Related Problems,
Academia Sinica, Taipei, Taiwan, 22-26 June 2004. Also as cond-mat/0408655
[P63] Th.M. N., S. Klumpp and R. Lipowsky, Random walks of molecular motors arising
from diffusional encounters with immobilized filaments,
Physical Review E 69, 061911 (2004) [L40] Th.M.
N., R. Lipowsky and S. Klumpp, Walks of molecular motors in two and three
dimensions, Europhys. Lett. 58 , (2002) 469-474 [L39] R.
Lipowsky, S. Klumpp and Th.M. N., Random walks of cytoskeletal motors
in open and closed compartments, Phys.
Rev. Lett. 87 (2001) 108101
Neural networks are statistical mechanics models designed to understand, on a fundamental level,
how pattern storage and recovery could be organized in our brain. An important field was started by
Hopfield in the mid-seventies, where networks are considered of neurons that can be in one of two states,
firing or non-firing. A pattern is then a certain state with firing and non-firing neurons. Imporant issues are then: stability, recovery, adaptation, learning.
[C9] Th.M.
N. Why disorder influences life, in ``Dynamics of interfaces, surfaces
and membranes'', Les Houches series (Nova, New York 1993) pp 191-200
(The weapon shield of the "famiglia Borreomeo" contains three connected rings. When one is taken out,
the other two are also no longer bound, symbolizing the strength of cooporation.
Magicians often perform tricks based on this type of binding.)
Adhesion Induced DNA Naturation,
Phys. Rev. Lett. 96, 098302 (2006)
Selected for
Virtual Journal of Biological Physics Research -- March 15, 2006
My research on this subject is carried out with Stefan Klumpp and Reinhard Lipowsky of the Max Planck
Institute for Colloids and Interfaces in Golm, near Potsdam, near Berlin.
Whereas most research in the field of Brownian motors concentrates on the question
how these motors can propagate at all, we have studied their large scale motion, which is important
for their functioning in our body.
A press release on this work was issued by the Max Planck Society on May 3, 2005:
Motor Transport in Bio-Nano Systems
Proceedings Conference Frontiers of Quantum and Mesoscopic Thermodynamics, Prague, Czech Republic 26-29 July 2004.
Edited by Th.M. Nieuwenhuizen, P.D. Keefe and V. Spicka
[P65] S. Klumpp, Th.M. N. and R. Lipowsky, Self-organized density patterns
of molecular motors in arrays of cytoskeletal filaments,
Biophys. J. 88, 3118-3132 (2005).
Selected for: June
15, 2004 issue of Virtual Journal of Biological Physics Research.
Neural networks
The next work was done in collaboration with researchers from the University of Leuven, near Brussels.
[P61] D.
Bollé, Th M Nieuwenhuizen, I Pérez Castillo and T Verbeiren, A spherical
Hopfield model,
J. Phys. A: Math. Gen. 36 10269-10277, 2003
An old work