Related papers: Structural transition states explored with minimal…
A simple approach is proposed to investigate the protein structure. Using a low complexity model, a simple pairwise interaction and the concept of global optimization, we are able to calculate ground states of proteins, which are in…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest…
Grain microstructures are crucial to the mechanical properties, performance, and often lifetime of metallic components. Hence, the prediction of grain microstructures emerging from solidification processes at relevant macroscopic scale is…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo…
A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2)…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic protein models. Our study investigated both the biophysics of conformational transitions as well as the possibility of increasing…
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…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
Global optimization of transition paths in complex atomic scale systems is addressed in the context of misfit dislocation formation in a strained Ge film on Si(001). Such paths contain multiple intermediate minima connected by minimum…
A coarse-grained cellular automaton is proposed to simulate traffic systems. There, cells represent road sections. A cell can be in two states: jammed or passable. Numerical calculations are performed for a piece of square lattice with open…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid domains linked by generalized (rotational and stretching) harmonic springs. We present a method to obtain the elastic parameters and overdamped…