Search results for "Energy landscape"
showing 10 items of 37 documents
Dynamical properties of myoglobin in an ultraviscous water-glycerol solvent investigated with elastic neutron scattering and FTIR spectroscopy
2018
Abstract Proteins have distinctive dynamical properties, characterized by the fluctuations of protein molecules among the different minima of their energy landscape. These fluctuations, progressively activated for temperature values larger than ~180 K, lead to a steep increase in the temperature dependence of all measurable dynamical properties. This phenomenon is known as Protein Dynamical Transition and, in spite of the intense studies due to its importance in protein function and to the relation with the fascinating fundamental thermodynamics of complex systems, many aspects of it are not yet clearly understood. Among these, the relationship with the properties of the external solvent an…
Force probe simulations using an adaptive resolution scheme
2021
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In force probe molecular dynamics (FPMD) simulations, one pulls one end of the molecule with a constant velocity in order to induce the relevant conformational transitions. Since the extended configuration of the system has to fit into the simulation box together with the solvent such simulations are very time consuming. Here, we apply a hybrid scheme in which the solute is treated with atomistic resolution and the solvent molecules far away from the solute a…
Limits of stability in supported graphene nanoribbons subject to bending
2016
Graphene nanoribbons are prone to in-plane bending even when supported on flat substrates. However, the amount of bending that ribbons can stably withstand remains poorly known. Here, by using molecular dynamics simulations, we study the stability limits of 0.5-1.9 nm wide armchair and zigzag graphene nanoribbons subject to bending. We observe that the limits for maximum stable curvatures are below ~10 deg/nm, in case the bending is externally forced and the limit is caused by buckling instability. Furthermore, it turns out that the limits for maximum stable curvatures are also below ~10 deg/nm, in case the bending is not forced and the limit arises only from the corrugated potential energy…
Energy and entropy barriers of two-level systems in argon clusters: An energy landscape approach
1999
Abstract Free argon clusters containing up to 160 atoms have been studied by means of a numerical algorithm for finding thousands of adjacent minima connected through a first-order saddle point. Many minimum-saddle-minimum systems have been found to be good candidates for forming two-level systems. The ground state splitting has been evaluated by taking into account both energy and entropy barriers. The role of the latter in auenching or enhancing the ground state splitting is discussed with the aid of a simple model potential.
On the polymer physics origins of protein folding thermodynamics
2016
A remarkable feature of the spontaneous folding of many small proteins is the striking similarity in the thermodynamics of the folding process. This process is characterized by simple two-state thermodynamics with large and compensating changes in entropy and enthalpy and a funnel-like free energy landscape with a free-energy barrier that varies linearly with temperature. One might attribute the commonality of this two-state folding behavior to features particular to these proteins (e.g., chain length, hydrophobic/hydrophilic balance, attributes of the native state) or one might suspect that this similarity in behavior has a more general polymer-physics origin. Here we show that this behavi…
Mechanically interlocked calix[4]arene dimers display reversible bond breakage under force.
2009
The physics of nanoscopic systems is strongly governed by thermal fluctuations that produce significant deviations from the behaviour of large ensembles1,2. Stretching experiments of single molecules offer a unique way to study fundamental theories of statistical mechanics, as recently shown for the unzipping of RNA hairpins3. Here, we report a molecular design based on oligo calix[4]arene catenanes—calixarene dimers held together by 16 hydrogen bridges—in which loops within the molecules limit how far the calixarene nanocapsules can be separated. This mechanically locked structure tunes the energy landscape of dimers, thus permitting the reversible rupture and rejoining of the individual n…
Collective properties of hydration: long range and specificity of hydrophobic interactions
1997
We report results of molecular dynamics (MD) simulations of composite model solutes in explicit molecular water solvent, eliciting novel aspects of the recently demonstrated, strong many-body character of hydration. Our solutes consist of identical apolar (hydrophobic) elements in fixed configurations. Results show that the many-body character of PMF is sufficiently strong to cause 1) a remarkable extension of the range of hydrophobic interactions between pairs of solute elements, up to distances large enough to rule out pairwise interactions of any type, and 2) a SIF that drives one of the hydrophobic solute elements toward the solvent rather than away from it. These findings complement re…
Phycocyanobilin in solution – a solvent triggered molecular switch
2014
We present a computational investigation of the conformational response of phycocyanobilin (PCB) to the ability of solvents to form hydrogen bonds. PCB is the chromophore of several proteins in light harvesting complexes. We determine the conformational distributions in different solvents (methanol and hexamethylphosphoramide HMPT) by means of ab initio molecular dynamics simulations and characterize them via ab initio calculations of NMR chemical shift patterns. The computed trajectories and spectroscopic fingerprints illustrate that the energy landscape is very complex and exhibits various conformations of similar energy. We elucidate the strong influence of the solvent characteristics on…
Two-state protein-like folding of a homopolymer chain
2010
Many small proteins fold via a first-order "all-or-none" transition directly from an expanded coil to a compact native state. Here we study an analogous direct freezing transition from an expanded coil to a compact crystallite for a simple flexible homopolymer. Wang-Landau sampling is used to construct the 1D density of states for square-well chains of length 128. Analysis within both the micro-canonical and canonical ensembles shows that, for a chain with sufficiently short-range interactions, the usual polymer collapse transition is preempted by a direct freezing or "folding" transition. A 2D free-energy landscape, built via subsequent multi-canonical sampling, reveals a dominant folding …
Ground states of ultrasoft particles with attractions: a genetic algorithm approach
2009
International audience; We analyze in detail the ground-state structure of model systems of athermal star polymers with an additional, tunable attraction that may result from dispersion or depletion forces. To perform a free, unbiased search in the space spanned by the crystal parameters, we employ genetic algorithms, which are enhanced with respect to previous versions in their ability to find stable structures that occupy very narrow basins of attraction in the energy landscape. Application of this method brings about a very large variety of ground states for star polymers with attractions, in particular for the case of intermediate functionalities and strong, short-range attractive force…