A new approach in implementing classical molecular dynamics simulation for parallel computers has enabled a simulation to be carried out on a protein with explicit representation of water an order of magnitude longer than previously reported and will soon enable such simulations to be carried into the microsecond time range. We have used this approach to study the folding of the villin headpiec...

Binding of a solvated peptide A1 ((1)E (2)P (3)L (4)Q (5)L (6)K (7)M) with a graphene sheet is studied by a coarse-grained computer simulation involving input from three independent simulated interaction potentials in hierarchy. A number of local and global physical quantities such as energy, mobility, and binding profiles and radius of gyration of peptides are examined as a function of tempera...

Nearly thirty years ago, Daoud and de Gennes derived the scaling predictions for the linear polymer chains trapped in a slit with dimension close to the Kuhn length; however, these predictions have yet to be compared with experiments. We have fabricated nanoslits with vertical dimension similar to the Kuhn length of ds-DNA (110nm) using standard photolithography techniques. Fluorescently labele...

A static light scattering (SLS) study of bovine serum albumin (BSA) mixtures with two anionic graft copolymers of poly(sodium acrylate-co-sodium 2-acrylamido-2-methyl-1-propanesulphonate)-graft-poly(N,N-dimethylacrylamide), with a high composition in poly(N,N-dimethylacrylamide) (PDMAM) side chains, revealed the formation of oppositely charged complexes, at pH lower than 4.9, the isoelectric po...

We analyze a system consisting of two spherical particles immersed in a polydispersed polymer solution under theta conditions. An exact theory is developed to describe the potential of mean force between the spheres for the case where the polymer molecular weight dispersity is described by the Schulz-Flory distribution. Exact results can be derived for the protein regime, where the sphere radiu...

The bioactivity of galectin-1 in cell growth regulation and adhesion prompted us to answer the questions whether ligand presence and a shift to an aprotic solvent typical for bioaffinity chromatography might alter the shape of the homodimeric human lectin in solution. We used small angle neutron and synchrotron x-ray scattering studies for this purpose. Upon ligand accommodation, the radius of ...

Hydration structures around F-actin and myosin subfragment-1 (S1), which play central roles as counterparts in muscle contraction, were investigated by small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS). The radius of gyration of chymotryptic S1 was evaluated to be 41.3±1.1 Å for SAXS, 40.1±3.0 Å for SANS in H2O, and 37.8±0.8 Å for SANS in D2O, respectively. The value...

We use Brownian dynamics computer simulations to investigate single-chain dynamics in a semidilute polymer solution undergoing a steady, uniform shear flow. In the presence of the shear flow, the system used in the present study exhibits anisotropic structure factors, often referred to as butterfly patterns, which rotate with increasing shear rate [P. P. Jose and G. Szamel, J. Chem. Phys. 127, ...

Single-molecule measurements of polymer elasticity are powerful, direct probes of both biomolecular structure and principles of polymer physics. Recent work has revealed low-force regimes in which biopolymer elasticity is understood through blob-based scaling models. However, the small tensions required to observe these regimes have the potential to create measurement biases, particularly due t...

Small angle X-ray scattering (SAXS) measurements coupled to a stopped-flow device has permitted the observation of the kinetics of Fe(III) oxyhydroxide (FeOx) formation and transformation from around 1 s to 30 min after initiation under environmentally relevant conditions at pH 3. The Unified Model approach was used to determine the evolution of multiple key parameters (particle scattering mass...