A parameterization has been performed of the biologically important sterols cholesterol, ergosterol, and lanosterol for the CHARMM27 all-atom molecular mechanics force field. An automated parameterization method was used that involves fitting the potential to vibrational frequencies and eigenvectors derived from quantum-chemical calculations. The partial charges were derived by fitting point ch...

We demonstrate a self-contained methodology for predicting conductance histograms of atomic and molecular junctions. Fast classical molecular-dynamics simulations are combined with accurate density functional theory calculations predicting both quantum transport properties and molecular-dynamics force field parameters. The methodology is confronted with experiments on atomic-sized indium nanoju...

this paper studies the effect of flexible linear torso on the dynamics of passive quadruped bounding. a reduced-order passive and conservative model with linear flexible torso and springy legs is introduced. the model features extensive spine deformation during high-speed bounding, resembling those observed in a cheetah. fixed points corresponding to cyclic bounding motions are found and calcul...

In this paper we investigate the spatiotemporal dynamics of a diatomic fluid undergoing zero mean oscillatory flow in a slit pore. The study is based on nonequilibrium molecular dynamics simulations together with two limiting solutions to the Navier-Stokes equations which include the effect of molecular rotation. By examining the viscoelastic properties of the system we can estimate the extent ...

Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model syste...

We have employed molecular dynamics (MD) simulation to investigate, with atomic details, the structural dynamics and energetics of three major ATPase states (ADP, APO, and ATP state) of a human kinesin-1 monomer in complex with a tubulin dimer. Starting from a recently solved crystal structure of ATP-like kinesin-tubulin complex by the Knossow lab, we have used flexible fitting of cryo-electron...

phage elisa is a common method to confirm binding of obtained phages from phage display technique to related antigens. enzyme-conjugated antibody directed against the major capsid protein (pviii) or enzyme-conjugated secondary antibody against the primary antibody is used as a detection system in phage elisa. we have suggested to express an acid phosphatase (sapm) enzyme on m13 pix minor coat p...

We develop a hierarchical solution (PFfit) for fitting an atomic structure to a density map. We use scoring functions that account for steric clashes while maximizing the degree of fit between the protein and the density map, a non-uniform rotationally exhaustive Fourier-based search scheme, and a flexibility model that parametrizes shear and hinge bending motions available to each protein doma...