Search results for "Quantitative Biology::Biomolecules"

Linear chain surfactants at a planar interface: a comparative Monte Carlo study of several lattice models

1993

Linear chain surfactants in a densely packed arrangement (such as alkane chains in lipid monolayers in the “uniform tilt” structures) are described by a crude coarse-grained model where the endgroups grafted on the interface form a regular lattice and the chains are described by the bond fluctuation model with chains containing N = 4 effective monomers only. Square-well interactions between the monomers are studied for both the attractive and repulsive case for three choices of the interaction range. None of these models exhibits a structure with uniform tilt. For attractive interactions the last bond has a strong tendency to fold back thus leading to a very high density close to the interf…

1988

Deviations in the determination of the unperturbed dimensions of polymers arising in ternary polymer systems (solvent (1)/solvent (2)/polymer) can be explained by the inaccurate use of an interaction parameter independent of polymer molecular weight. On this basis, a new formalism for the calculation of the second virial coefficient from intrinsic viscosity is proposed. This formalism was tested (and compared with well established formalisms) for all ternary polymer systems with simultaneous intrinsic viscosity and second virial coefficient data in the literature.

The Boson Peak of Amyloid Fibrils: Probing the Softness of Protein Aggregates by Inelastic Neutron Scattering

2014

Proteins and polypeptides are characterized by low-frequency vibrations in the terahertz regime responsible for the so-called "boson peak". The shape and position of this peak are related to the mechanical properties of peptide chains. Amyloid fibrils are ordered macromolecular assemblies, spontaneously formed in nature, characterized by unique biological and nanomechanical properties. In this work, we investigate the effects of the amyloid state and its polymorphism on the boson peak. We used inelastic neutron scattering to probe low-frequency vibrations of the glucagon polypeptide in the native state and in two different amyloid morphologies in both dry and hydrated sample states. The dat…

Calculation of phase diagrams not requiring the derivatives of the Gibbs energy demonstrated for a mixture of two homopolymers with the corresponding…

1995

A method is presented which allows the calculation of phase diagrams (spinodal, binodal and tie lines) on the basis of the Gibbs energy of mixing ΔG. No derivatives of ΔG with respect to the composition variables are required. This method is particularly useful in cases where the composition dependence of ΔG is very complex and no analytical representation of the derivatives can be given. The method is applied to a ternary mixture of two homopolymers with a copolymer consisting of the same monomers. The sequence distribution of the copolymer is kept constant between random and purely alternating, and phase diagrams are calculated for different chemical compositions of the copolymer. The com…

Thermodynamics of a polymer blend solution system studied by gel permeation chromatography and viscosity

1999

Binary and ternary interaction parameters and their derivatives have been calculated with the Flory-Huggins formalism developed for a ternary polymer system. The equilibrium compositions of the ternary system tetrahydrofuran/polybutadiene/polystyrene that forms two phases in equilibrium at 25°C have been used to solve the binodal equations. With this set of parameters, the viscosimetric interaction parameters have been computed. For the sake of comparison, the experimental viscosimetric parameter has been determined from intrinsic viscosity data of a polymer (3) in a "binary solvent" (solvent + polymer (2)). It has been clearly shown that composition-dependent parameters are necessary to re…

Polymer Incompatibility Caused by Different Molecular Architectures: Modeling via Chain Connectivity and Conformational Relaxation

2009

The calculation of phase diagrams for blends of linear and branched polymers made up of identical monomeric units is modeled using an approach that subdivides the mixing process into two steps: i) contact formation between the different components, keeping their chain conformations and the volume of the system constant; and, ii) relaxation of the macromolecules into their equilibrium state by molecular rearrangements. It is assumed that step (ii) causes shape-induced polymer incompatibility and that the degree of branching can be quantified in terms of the volumes the isolated coils of the branched polymer occupy in relation to the volume the linear product with the same molecular weight oc…

Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser.

2014

Light absorption can trigger biologically relevant protein conformational changes. The light-induced structural rearrangement at the level of a photoexcited chromophore is known to occur in the femtosecond timescale and is expected to propagate through the protein as a quake-like intramolecular motion. Here we report direct experimental evidence of such ‘proteinquake’ observed in myoglobin through femtosecond X-ray solution scattering measurements performed at the Linac Coherent Light Source X-ray free-electron laser. An ultrafast increase of myoglobin radius of gyration occurs within 1 picosecond and is followed by a delayed protein expansion. As the system approaches equilibrium it underg…

Intrinsic Acidity of Surface Sites in Calcium Silicate Hydrates and Its Implication to Their Electrokinetic Properties

2014

Calcium Silicate Hydrates (C–S–H) are the major hydration products of portland cement paste. The accurate description of acid–base reactions at the surface of C–S–H particles is essential for both understanding the ion sorption equilibrium in cement and prediction of mechanical properties of the hardened cement paste. Ab initio molecular dynamics simulations at the density functional level of theory were applied to calculate intrinsic acidity constants (pKa’s) of the relevant ≡SiOH and ≡CaOH2 groups on the C–S–H surfaces using a thermodynamic integration technique. Ion sorption equilibrium in C–S–H was modeled applying ab initio calculated pKa’s in titrating Grand Canonical Monte Carlo simu…

Computer simulation of bottle-brush polymers with flexible backbone: good solvent versus theta solvent conditions.

2011

By Molecular Dynamics simulation of a coarse-grained bead-spring type model for a cylindrical molecular brush with a backbone chain of $N_b$ effective monomers to which with grafting density $\sigma$ side chains with $N$ effective monomers are tethered, several characteristic length scales are studied for variable solvent quality. Side chain lengths are in the range $5 \le N \le 40$, backbone chain lengths are in the range $50 \le N_b \le 200$, and we perform a comparison to results for the bond fluctuation model on the simple cubic lattice (for which much longer chains are accessible, $N_b \le 1027$, and which corresponds to an athermal, very good, solvent). We obtain linear dimensions of …

Exploring Chemical Reactivity in Enzyme Catalyzed Processes Using QM/MM Methods: An Application to Dihydrofolate Reductase

2015

Enzymes are the catalysts used by living organisms to accelerate chemical processes under physiological conditions. In this chapter, we illustrate the current view about the origin of their extraordinary rate enhancement based on molecular simulations and, in particular, on methods based on the combination of Quantum Mechanics and Molecular Mechanics potentials which provide a solution to treat the chemical reactivity of these large and complex molecular systems. Computational studies on Dihydrofolate Reductase have been selected as a conductor wire to present the evolution and difficulties to model chemical reactivity in enzymes. The results discussed here show that experimental observatio…