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Biomedical subjects

Peter Virnau

Publications and source records attributed to Peter Virnau.

6 recordsLinked to original sources
PubMed2006

Intricate knots in proteins: Function and evolution.

Our investigation of knotted structures in the Protein Data Bank reveals the most complicated knot discovered to date. We suggest that the occurrence of this knot in a human ubiquitin hydrolase might be related to the role of the enzyme in protein degradation. While knots are usually preserved among homologues, we also identify an exception in a transcarbamylase. This allows us to exemplify the function of knots in proteins and to suggest how they may have been created.

Bacterial Proteins↗
PubMed2005

Knots in globule and coil phases of a model polyethylene.

We examine the statistics of knots with numerical simulations of a simplified model of polyethylene. We can simulate polymers of up to 1000 monomers (each representing roughly three CH(2) groups), at a range of temperatures spanning coil (good solvent) and globule (bad solvent) phases. We quantify the abundance of knots in the globule phase and in confined polymers, and their rarity in the swollen phase. Since our polymers are open, we consider (and test) various operational definitions for knots, which are rigorously defined only for closed chains. We also associate a typical size with individual knots, which are found to be small (tight and localized) in the swollen phase but large (loose and spread out) in the dense phases.

Journal Article↗
PubMed2004

Phase behavior of n-alkanes in supercritical solution: a Monte Carlo study.

We present a coarse-grained model for n-alkanes in a supercritical solution, which is exemplified by a mixture of hexadecane and CO2. For pure hexadecane, the Monte Carlo simulations of the coarse-grained model reproduce the experimental phase diagram and the interfacial tension with good accuracy. For the mixture, the phase behavior sensitively depends on the compatibility of the polymer with the solvent. We present a global phase diagram with critical lines, which is in semiquantitative agreement with experiments. In this context we developed two computational schemes: The first adopts Wang-Landau sampling to the off-lattice grand canonical ensemble, the second combines umbrella sampling with an extrapolation scheme to determine the weight function. Additionally, we use Wertheim's theory (TPT1) to obtain the equation of state for our coarse-grained model of supercritical mixtures and discuss the behavior for longer alkanes.

Journal Article↗
PubMed2004

Calculation of free energy through successive umbrella sampling.

We consider an implementation of umbrella sampling in which the pertinent range of states is subdivided into small windows that are sampled consecutively and linked together. This allows us to simulate without a weight function or to extrapolate the results to the neighboring window in order to estimate a weight function. Additionally, we present a detailed error analysis in which we demonstrate that the error in umbrella sampling is controlled and, in the absence of sampling difficulties, independent of the window sizes. In this case, the efficiency of our implementation is comparable to a multicanonical simulation with a very good weight function, which in our scheme does not need to be known ahead of time. The analysis also allows us to detect sampling difficulties such as correlations between adjacent windows and provides a test of equilibration. We exemplify the scheme by simulating the liquid-vapor coexistence in a Lennard-Jones system.

Journal Article↗
PubMed2004

The evaporation/condensation transition of liquid droplets.

The condensation of a supersaturated vapor enclosed in a finite system is considered. A phenomenological analysis reveals that the vapor is found to be stable at densities well above coexistence. The system size at which the supersaturated vapor condenses into a droplet is found to be governed by a typical length scale which depends on the coexistence densities, temperature and surface tension. When fluctuations are neglected, the chemical potential is seen to show a discontinuity at an effective spinodal point, where the inhomogeneous state becomes more stable than the homogeneous state. If fluctuations are taken into account, the transition is rounded, but the slope of the chemical potential versus density isotherm develops a discontinuity in the thermodynamic limit. In order to test the theoretical predictions, we perform a simulation study of droplet condensation for a Lennard-Jones fluid and obtain loops in the chemical potential versus density and pressure. By computing probability distributions for the cluster size, chemical potential, and internal energy, we confirm that the effective spinodal point may be identified with the occurrence of a first order phase transition, resulting in the condensation of a droplet. An accurate equation of state is employed in order to estimate the droplet size and the coexisting vapor density and good quantitative agreement with the simulation data is obtained. The results highlight the need of an accurate equation of state data for the Laplace equation to have predictive power.

Journal Article↗