This paper is a review of our previous work on the field of possible ways of prebiotic evolution. We propose an algorithm providing sequences of model proteins with rapid folding into a given native conformation. Thermodynamical analysis shows that the increase in speed is matched by an increase in stability: the evolved sequences are much more stable in their native conformation than the initi...

The Prisoner's Dilemma has long been considered the paradigm for studying the emergence of cooperation among selfish individuals. Because of its importance, it has been studied through computer experiments as well as in the laboratory and by analytical means. However, there are important differences between the way a system composed of many interacting elements is simulated by a digital machine...

Hydromagnetic processes play an important role in many astrophysical systems (e.g. stars, galaxies, accretion discs). This is because the medium is hot enough to be partially or fully ionized. Because of the huge scales involved the medium is usually turbulent, provided there is an instability (shear, convection) facilitating the cascading of energy down to small scales. In turbulence research ...

The aim of this paper is to assist researchers in understanding the dynamics of simulation models that have been implemented and can be run in a computer, i.e. computer models. To do that, we start by explaining (a) that computer models are just input-output functions, (b) that every computer model can be re-implemented in many different formalisms (in particular in most programming languages),...

Computer simulation holds great promise to significantly complement experiment as a tool for biological and biophysical characterization. Simulations offer the promise of atomic spatial detail with femtosecond temporal resolution. However, the application of computational methodology has been greatly limited due to fundamental computational challenges: put simply, for much of what one would wan...

Title of dissertation: COMPUTER SIMULATIONS OF PROTEIN FOLDING Aram Davtyan, Doctor of Philosophy, 2013 Dissertation directed by: Professor Garegin A. Papoian Department of Chemistry and Institute for Physical Science and Technology Understanding how proteins fold and interact with each other is key to understanding virtually all biological processes. Recent advances in computer power and model...

Lipid nanoparticles (LNP) are promising soft matter nanomaterials for drug delivery applications. In spite of their interest, little is known about the supramolecular organization of the components of these self-assembled nanoparticles. Here, we present a molecular dynamics simulation study, employing the Martini coarse-grain forcefield, of self-assembled LNPs made by tripalmitin lipid in water...

We report recent progress in computer simulations of quantum systems described in the path-integral formulation. For the example of the φ quantum chain we show that the accuracy of the simulation may greatly be enhanced by a combination of multigrid update techniques with a refined discretization scheme. This allows us to assess the accuracy of a variational approximation.

Monte Carlo simulations of electroptical devices based on a nematic Lebwohl-Lasher liquid crystal model with suitable boundary conditions are presented. The simplicity of the model allows an investigation of various effects like the influence of an external field strength and that of anchoring at the oriented surfaces of the display cell. Moreover suitable order parameters are introduced to fac...