Related papers: Soliton driven relaxation dynamics and universalit…
The WW domain of the human Pin1 protein for its simple topology and the large amount of experimental data is an ideal candidate to assess theoretical approaches to protein folding. The purpose of the present work is to compare the…
In a recent Letter, Gutin, Abkevich, and Shakhnovich (GAS) reported on a series of dynamical Monte Carlo simulations on lattice models of proteins. Based on these highly simplified models, they found that four different potential energies…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
When described by a low-dimensional reaction coordinate, the rates of protein folding are determined by a subtle interplay between free-energy barriers and friction. While it is commonplace to extract free-energy profiles from molecular…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
We propose to combine a mean field approach with all atom molecular dynamics into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic level precision. As an example we investigate…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
We present a new hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of spherical colloidal particles. The solvent is modeled on the level of the lattice-Boltzmann method while the…
On approaching the glass transition, the microscopic kinetic unit spends increasing time rattling in the cage of the first neighbours whereas its average escape time, the structural relaxation time $\tau_\alpha$, increases from a few…
We report a single-copy tempering method for simulating large complex systems. In a generalized ensemble, the method uses runtime estimate of the thermal average energy computed from a novel integral identity to guide a continuous…
Determining the folding core of a protein yields information about its folding process and dynamics. The experimental procedures for identifying the amino acids which make up the folding core include hydrogen-deuterium exchange and…
Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively…
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…