10 different force fields tested in microsecond MD

Secondary structure formation using 10 different force fields, E.A. Cino, W.-Y. Choy, M. Karttunen, submitted

Langmuir cover: biomineralization

Our biomineralization paper, combining experiments and Molecular Dynamics Simulations, got the front page!.

Biomineralization is abundant in nature, sea shells, bones, kideny stones and atherosclerotic plaque beeing examples of it. We disucss the importance of electrostatics over secondary structure in biomineralization.

“The Flexible Polyelectrolyte Hypothesis of Protein–Biomineral Interaction” in Langmuir made the cover page

Microsecond Molecular Dynamics

Elio's first paper combining isothermal titration and very extensive MD simulations of Prothymosin alpha (ProTα) and the Neh2 domain of Nuclear factor erythroid 2-related factor 2 (Nrf2) was just published. Features an exciting study of intrinsically disorderder proteins and their behavior.

Paper:  "Microsecond Molecular Dynamics Simulations of Intrinsically Disordered Proteins Involved in the Oxidative Stress Response",  PLoS One.

See our flickr site for movies: 1 and 2

Cashew - Coarse Approach Simulator for H- Bonding Effects in Water - free code available.

Modified 3D Mercedes-Benz (MB) model for water [Dias et al., J. Chem. Phys. (2009)]. Written in Fortran 90. The modified 3D-MD: coarse-grained water model for studying geometric effects in interactions of water with solutes, polymers, proteins etc. Both a serial and MPI versions are available.

Paper "A molecular dynamics implementation of the 3D Mercedes-Benz water model",  Computer Physics Communications 183, 363-369 (2011)

Code: Cashew

Ordering effects of cholesterol: 3-fold symmetry

MD simulations show the fundamental importance of cholesterol's methyl groups in inducing three-fold symmetry. Cholsterol is compared to de-methylated cholesterol and the relation to the Condesed Complex Model and Umbrella Model is discussed

Paper: "Cholesterol Induces Specific Spatial and Orientational Order in Cholesterol/Phospholipid Membranes", PLoS One.

Multi-microsecond MD of the Good Cholesterol

Our simulations show the important roles of different lipids for the structure of Higy Density Lipoprotein, HDL (also known as the Good Cholesterol). Simulations were done both with and without apoA-1. Th results may also be helpful in desgining self-assembling systems for drug delivery.

Paper: "Role of Lipids in Spheroidal High Density Lipoproteins", PLoS Comput. Biol.

Nanowire paper featured in APS' Physics Focus

Our simulations shows that water and ice behave very unexpectedly when different kind of naniwires are used moved through ice: one can even cut ice using a hydrophobic nanowire. One also sees interesting pinning-depinning behavior resembling dynamical critical phenomena as seen in, e.g. vortex lattices.

Paper: Cutting Ice: Nanowire Regelation, Phys Rev. Lett.

Teemu was interviewed for the APS Focus article

Nano: Time-resolved laser-induced incandescence

We use density functional theory to obtain interactions for metal nanoparticles and Ar, and use them in MD and MC calculations to simulate laser-energized nanopartices. We estimate thermal accommodation constants & other properties and establish a protocol for simulations that can be used to make reliable predictions for  TiRe-LII

"Accommodation Coefficients for TiRe Laser-Induced Incandescence Sizing of Ni Nanoparticles", J. Appl. Phys. B

Hydrophobicity & secondary structure

We focus on the importance of hydrophobicty in α helices and β sheets of small peptides. In particular, we found that desolvation barriers favor β sheets in collapsed conformations of polyalanine, polyvaline, polyleucine, and three fragments of amyloid peptides. Our results show the multifaceted role of hydrophobicity in secondary structure formation, a particularly important one being the α to β transition in amyloid peptides.

"Hydrophobic interactions in the formation of secondary structures in small peptides", Phys. Rev. E

Volkswagen Foundation awards Dias and Miettinen

Two of our alumni, Dr. Cristiano Dias (former PDF) and Dr. Markus Miettinen (former PhD student) receive prestigious 3-year grants from the Volkswagen Foundation to study hydrogen bond networks in protein folding at the Physics Department of the Freie Universität Berlin starting in early 2012.

Congratulations Cristiano and Markus!!

Carbon nanotubes and water: how to do it right

The importance charges and, in particular, simulation protocol is demonstrated. If not chosen carefully, one can obtain quite spectacular but physically incorrect results. In addition to carbon nanotubes, the results also apply to biological systems such as aquaporin and other passivce channels.

"Static charges cannot drive a continuous flow of water molecules through a carbon nanotube", Nature Nanotechnology

Old but still interesting: Lipid raft simulations

Biological membranes have different lipid environments. Lipid rafts are an example of such. Rafts have been suggested to be of particular importance for the functioning of proteins such as insulin receptors and ion channels. We have performed large-scale simulations of rafts (up to 100 ns and 15-20 nm in size). Our study shows, how rafts may regulate protein functions.

"Assessing the nature of lipid raft membranes", PLoS Comput. Biol. 2007.

Popular: Life on a raft floating on a sea of maple syrup

Bad Cholesterol (LDL): structure from MD

We performed multi-microsecond near-atomistic MD to study LDL. Despite its importance to health, the detailed structure is not known. This is lack structural information makes it difficult to understand LDL's function. We have combined experimental and theoretical data to construct LDL models. Our findings set the stage for further studies of LDL to better understand the various steps in the emergence of atherosclerosis.

Low density lipoprotein: structure, dynamics, and interactions of apoB-100 with lipids, Soft Matter

Cationic lipids (DOTAP) and free parameters

Cationic lipids are rare in nature but they are important for, e.g., drug transport and DNA translocation. We have developed a parameterization for DOTAP and study it is properties in detail. DOTAP shows interesting concentration dependent behavior. 

"Cationic DOTAP Lipid Bilayers: Atomistic Insight for Structure and Dynamics", J. Phys. Chem B

Parameters: see our "Downloads" page

Computational-experimental: ectopic calcification

We propose that matrix gla protein (MGP) prevents arterial calcification by adsorbing to growing hydroxyapatite (HA) crystals. We synthesized peptides covering the entire sequence of human MGP & studied effects of phosphorylation and different HA surfaces using both experiments and MD simulations. Our results suggest that MGP prevents arterial calcification by interactions (with HA) involving phosphate and gla residues.

"Matrix Gla Protein Inhibits Ectopic Calcification by a Direct Interaction with Hydroxyapatite Crystals", JACS

Molecular motors & actin: Aster formation

Fibrous active network structures whose properties are regulated by motor proteins, or simply motors, are fundamental to life. We present a full elastic and three dimensional model for such systems. The filament networks with motors shows rich patterns, that we argue, are important to cellular dynamics. Comparison with several independent experiments is also performed

"Aster formation and rupture transition in semi-flexible fiber networks with mobile cross-linkers", Soft Matter

Flower power: morphological instabilities

We study the formation of flower patters both theoretically and experimentally. We vary the length of ceramide chains (in DMPC matrix) in a Langmuir monolayer and see changes in the morphological behavior ranging from sphericla to seaweed-like. We relate such changes to diffusive instabilities.

"Lipid domain morphologies in phosphatidylcholine-ceramide monolayers", Langmuir

Micelle fission in atomistic detail: surface instability

These are the first atomistic simulations of fission of charged micelles (SDS). We propose that charges are important for the selction of the fission pathway which here proceeds via a Rayleigh instability. Understaning the fission pathway may help in developing methods to functionalize micelles.

"Micelle fission through surface instability and formation of an interdigitating stalk", JACS

​We are now on flickr.

Lots of visualizations, movies and pictures, with explanations are now available at our flickr site

         www.flickr.com/photos/softsimu

More material is being added (older stuff first) almost daily.

As for other social media, check out our Twitter stream.

Year 2011 ended on a high note:

Mohsen successfully defended his PhD thesis "Molecular Dynamics Studies of Interactions of Phospholipid membarens with Dehydroergosterol and Penetrating Peptides".

We also had a second graduation as Sepideh succesfully defended her MSc thesis,  "Molecular Dynamics Analysis of the Behaviour of Prolyl Oligopeptidase (POP) in the Presence of Z-Pro-Prolinal Inhibitor".

Congratulations to Sepideh and Mohsen!