Research in Biophysics, Soft Materials and Pattern Formation

The soft matter and biophysics group started at LCE in September 2000. In general, the research is geared towards the interface between condensed matter physics, biology and material science. The great diversity of these systems, ranging, for instance, from complexes of DNA and cationic liposomes used in gene transfer to unexpected morphological evolution of polymers under shear flow and to pattern formation in biological processes, provides new challenges in both fundamental and applied research.

Typically, biological processes take place under non-equilibrium conditions. Modeling these processes provides many theoretical challenges since eventually the validity of equilibrium concepts, such as universality and scaling laws, breaks down. It is important to study their range of validity, and how the emergence of new time and length scales, and possibly a steady state, is manifested in dynamical systems. A good example of that is the shear flow behavior of complex fluids where the dynamics of order-disorder transition depends intimately on the application of shear. As vast number of industrial processes involve complex fluids and polymer mixtures under shear flow conditions, it is clear that a better theoretical understanding of these processes has immediate practical applications.

Another challenge arises from the interdisciplinary nature of these problems. A strong interaction between theory, computation, and experiments is essential in order to get insight of into the physical mechanisms producing these complex, often collective, phenomena. A clear example of this is the study of lipoplexes, i.e., the formation and behavior of DNA-cationic liposome complexes. There exists a large amount of experimental data, and in vivo experiments have shown that clinical application of lipoplexes is effective and safe. However, the processes and physical mechanisms, e.g., those involving interactions of electrostatic origin, that control the formation of these complex structures are not well established. Theoretical studies and, in particular, simulational studies, have the potential of helping to characterize better these complex processes.

The studies introduced below briefly describe our efforts in soft matter and biophysics. For details and up-to-date information, please see the corresponding project home page as given in connection of each project.

The group has been very active during its young life and at the end 2003 the Biological Physics Team consisting of our group together with Dr. Ilpo Vattulainen’s group at the Laboratory of Physics was selected as a Helsinki University of Technology Young Center of Excellence for 2004-2005 (in Finnish: tutkimuksen kärkiryhmä).


Computer Simulations of a Polymer Chain under Shear Flow

Researchers: Markus Miettinen, Mikko Karttunen, Michael Patra and Ilpo Vattulainen*
*Laboratory of Physics and Helsinki Institute of Physics, HUT

Project home page: http://www.lce.hut.fi/research/polymer/

The effect of shear flow on rhelogical properties of polymer mixtures is of great interest because the nonequilibrium nature of the problem makes it theoretically and computationally difficult. On the other hand, looking from the practical point of view, industrial processes often involve polymer mixtures under shear flow. A better theoretical knowledge of how to, e.g., control viscosity and phase separation would have immediate consequences in developing more efficient processes.

Dissolved polymer chains are known to undergo a globule to open coil transition as the solvent quality changes from poor to good. Likewise, it has been found out that an individual polymer chain undergoes a collapsing – stretching behaviour when the solute is exposed to shear. In this study, we look into the combined effect of shear flow and solvent properties to the conformational changes of the polymer chain.

The first part of the study has concentrated on the effect of solvent quality, i.e., studying the properties of a freely floating chain as a function of solubility. This offers a sturdy reference for the second part, which will introduce applying shear to the system. The chain properties will be measured as a function of both the shear strength and the solvent quality.

The solvent is modeled explicitly by monomers interacting with each other through a Lennard-Jones -type (LJ) potential. The polymer model is made up of a few dozen LJmonomers freely jointed together by nonlinear FENE-springs. The first part of the study will be performed by carrying out Molecular Dynamics (MD) simulations in three dimensions, changing the solvent properties by modifying the interaction coefficients of the LJ-potential. The second part shall consist of Nonequilibrium Molecular Dynamics (NEMD) simulations using the SLLOD algorithm with Lees-Edwards boundary conditions for implementing the shear.

Figure 30

Figure 30: Stretching and collapsing of a single molecule under shear flow.


Dissipative Particle Dynamics Studies of Coarse-grained Polymer Systems

Researchers: Petri Nikunen, Mikko Karttunen, and Ilpo Vattulainen*
*Laboratory of Physics and Helsinki Institute of Physics, HUT

Project home page: http://www.softsimu.org/

The physics of polymeric liquids has been a problem of considerable interest in recent years. From a modeling point of view, these systems are problematic due to the fact that numerous phenomena take place at mesoscopic time and length scales, which are not accessible by detailed simulation techniques such as molecular dynamics. To overcome this problem, a number of “coarse-grained” approaches have been suggested and developed to simplify the underlying microscopic model without changing the essential physics.

One candidate to work with is the dissipative particle dynamics method. It is a particlebased simulation technique which suits particularly well for studies of soft condensed matter systems. Due to this, it has been applied to various systems, including the structure of lipid bilayers, self-assembly, and the formation of polymer-surfactant complexes. In our project, we concentrate on methodological aspects of this method, and apply it e.g. to vesicle formation (figure below).

Figure 31

Figure 31: Formation of a vesicle. Time goes from left to right, top row illustrating the vesicle from outside and bottom row from inside.


Structural and Electrical Properties of Self-Organizing Biomaterials

Researchers: Ilkka Tittonen1 , Harri Lipsanen2, Paavo Kinnunen3, Kimmo Kaski and Adrian Sutton
1Meteorology Research Institure, HUT
2Optoelectronics Laboratory, HUT
3Institute of Biomedicine, University of Helsinki

This project addresses the synthesis, characterization and modelling of self-assembling biomolecular systems based on lipids and their complexes with proteins. The variety, stability and relative ease of synthesizing these systems offer considerable potential for the development of novel electronic, magnetic and optical device technologies. We shall explore the experimental and theoretical principles underlying the synthesis and electronic properties of a well-targeted subset of these materials. We have chosen to focus on polymerized superstructures of phospholipid vesicles and cytochrome c. The cytochrome c is a very well characterized stable peripheral protein. We have recently found that the liposomes undergo a self-assembly process in the presence of cytochrome c forming bundles of threads in rope-like polymerized structures. Both cytochrome c and several naturally occurring lipids, as well as man-made lipid derivatives, are commercially available in pure form. Such derivatives include those functionalized groups that lead to the formation of very large stable polymerized structures. It is the combination of the self-assembly, functionalization and stability of these materials that make them attractive candidates for the replacement of semiconductor device technologies over the next decade..

Figure 32

Figure 32: Haem iron coordination in cytochrome c.

Figure 33

Figure 33: Structure of cytochrome c from mammalian mitochondria. Haem shown by yellow.


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