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computational molecular biophysics

J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences, Prague

What We Do

We try to decipher how biological systems work at nanoscale by employing computer simulations. We investigate models of biosystems at the level of molecules by employing modern computational tools. More specifically, we perform computer simulations of time-dependent behavior of small fragments of biological systems consisting of hundreds of thousands of individual chemical molecules. Such simulations act as 'computational supermicroscope' that enables us to look at biosystems at the nanometer length-scale and up to microsecond time-scale.

Why We Do It

Our goal is to understand biological systems in detail. This can be achieved only by knowing how the underlying molecular nature of these systems determines their structure and function. The main goal is not merely to understand nature but to further use this knowledge, for instance, for design of biomimicking artificial constructs, drug design, or nanotechnological applications.

What Systems We Investigate

We study several classes of biological systems. Our main focus is on lipid- and protein-containing models.

- First, we study lipid bilayers. Such bilayers are main constituents of cellular membranes, for instance, the plasma membrane that encloses each living cell and acts as a complex, partially permeable barrier between the cell and its environment. learn more...

- Second, we are interested in the thin layer of lipids that covers the ocular surface of human eye, so called Tear Film Lipid Layer. Its main function is reduction of the surface tension of the tear film/air interface. learn more...

- Third, we look at lipid mono- and multilayers at water/air boundary. We are mainly interested in lipid monolayers in the context of the lung surfactant. //learn more...

- Fourth, we look how short transmembrane peptides behave in cell membranes. Some of the membrane proteins that span across cell membrane have relatively simple trnasmembrane domains that are able to modulate protein's behavior. //learn more...


What Methods We Use

We perform computer simulations, mainly classical molecular dynamics (MD). Specialized, highly parallelized software is used, and computations are performed at supercomputers in computational centers or locally at modern computer clusters. Regarding software, we moslty use the GROMACS code (>>). We also employ quantum chemical calculations both for force field parameterization and for combined quantum-classical simulations. We do a lot of coding/scripting, mainly with Python (>>). For visualization we primarily employ the VMD code (>>).


Join Us

We are looking for talented people, mainly PhD and master students, to join our lab.


Lipid Bilayers

Lipid bilayers bilayers are main constituents of cell membranes which enclose each living cell and act as complex, partialy permeable berriers between the cell and its environment. Each living cell transfers various material in and out across its cellular membrane. Moreover, bacteria and viruses always encounter the membrane when attacking a cell. Similarly, if we want to transport a drug molecule into a cell we must find a way to transfer it across the membrane. These three examples show why it is crucial to gain a molecular-level understanding of lipid membranes.


Tear Film Lipid Layer

Tear Film Lipid Layer is a thin layer of lipids that covers the ocular surface of human eye. Its main function is reduction of the surface tension of the tear film/air interface. Moreover, the presence of the TFLL prevents rapid evaporation of water from the underlying water aqueous phase. TFLL deficiencies lead to evaporative dry eye syndrome, one of the commonly reported eye ailments. Despite its vital role for eye function, the structure and other properties of TFLL at the molecular level are essentially unknown and only recently studied. We recently constructed a computational model of the TFLL and currently we employ it to investigate structure and dynamics of the TFLL.


Lipid Mono- and Multilayers

Lipid mono- and multilayers at water/air boundary are interesting preliminarily in the context of the lung surfactant. The gas exchange in lungs occurs through a layer of lipids that covers the surface of lung alveoli cells. This lipid layer is a first line of defense between air and the organism and is prone to a damage by such environmental factors as free radicals and air pollutants. On the other hand, this barrier is relatively easy to cross and may serve as convenient drug delivery path. This is why we try to better understand lipid monolayers at the level of individual molecules.


Transmembrane Peptides

Some of the membrane proteins that span across cell membrane have a relatively simple transmembrane domain that still is able to control protein's behavior. Moreover, this domain is directly interacting with membrane lipids, hence it influences membrane properties. Similarly, the lipid-protein interactions modulate protein behavior. These issues cannot be understood without a knowledge about lipid-protein interactions at the level of individual chemical moieties.