Related papers: Exploring the Protein G Helix Free Energy Surface …
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Hydrophobic interactions are central to biological self-assembly and soft matter organization, yet their microscopic origins remain debated. A key hallmark is the strengthening of attraction between hydrophobic solutes with increasing…
When a liquid melt is cooled, a glass or phase transition can be obtained depending on the cooling rate. Yet, this behavior has not been clearly captured in energy landscape models. Here a model is provided in which two key ingredients are…
We consider a general incompressible finite model protein of size M in its environment, which we represent by a semiflexible copolymer consisting of amino acid residues classified into only two species (H and P, see text) following Lau and…
Topological freezing is a well known problem in lattice simulations: with shrinking lattice spacing a transition between topological sectors becomes increasingly improbable, leading to a problematic increase of the autocorrelation time…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
Thermoelectric metamaterials featuring width modulation through constrictions (constricted geometries) have emerged as a promising approach for improving heat management and thermoelectric performance. Through a combination of theoretical…
We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…
The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility…
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic…
In this study, we investigate the energy landscape of the Ising and Potts models on fixed and finite but large three-dimensional (3D) lattices where no external field exists and quantitatively characterize the metastable behavior of the…
The preferential formation of one solid over the other, as it precipitates out from the melt at specific temperatures, is often explained by invoking a competition between thermodynamic and kinetic control. A quantitative theory, however,…
The water dynamics, as characterized by the local hydrophobicity (LH), is investigated for tetrameric hemoglobin and dimeric melittin. For the T0 to R0 transition in Hb it is found that LH provides additional molecular-level insight into…
Rapid and accurate assessment of protein structural models is essential for protein structure prediction and design. Great progress has been made in this regard, especially by recent development of ``knowledge-based'' potentials. Various…
We propose two metadynamics (MetaD)-based methodologies for efficiently mapping free energy surfaces (FESs) of multiple interacting carriers diffusing in crystalline solids. Our approaches circumvent the challenges of high-dimensional…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
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…