Related papers: Folding Trp-cage to NMR resolution native structur…

We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…

Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways…

We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…

Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…

We describe the results obtained from an improved model for protein folding. We find that a good agreement with the native structure of a 46 residue long, five-letter protein segment is obtained by carefully tuning the parameters of the…

The structure of the self-cleaving hairpin ribozyme is well characterized, and its folding has been examined in bulk and by single-molecule fluorescence, establishing the importance of cations, especially magnesium in the stability of the…

The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…

Coarse-grained (CG) molecular dynamics simulations extend the length and time scale of atomistic simulations by replacing groups of correlated atoms with CG beads. Machine-learned coarse-graining (MLCG) has recently emerged as a promising…

Atomistic force fields that are tuned to describe folded proteins predict overly compact structures for intrinsically disordered proteins (IDPs). To correct this, improvements in force fields to better model IDPs are usually paired with…

In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…

The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental…

We propose a criterion for optimal parameter selection in coarse-grained models of proteins, and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM…

We report on atomistic simulation of the folding of a natively-knotted protein, MJ0366, based on a realistic force field. To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate…

We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…

We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…

Recent developments in specialized computer hardware have greatly accelerated atomic level Molecular Dynamics (MD) simulations. A single GPU-attached cluster is capable of producing microsecond-length trajectories in reasonable amounts of…

Many single molecule experiments for molecular motors comprise not only the motor but also large probe particles coupled to it. The theoretical analysis of these assays, however, often takes into account only the degrees of freedom…

The structure and mechanical properties of a simple two-dimensional model of a cohesive powder are investigated by molecular dynamics simulations. Micromechanical ingredients involve elasticity, friction, a short range attraction and,…

Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…

We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…