J. A. McCammon

Brownian dynamics with hydrodynamic interactions

A method for simulating the Brownian dynamics of N particles with the inclusion of hydrodynamic interactions is described. The particles may also be subject to the usual interparticle or external forces (e.g., electrostatic) which have been included in previous methods for simulating Brownian dynamics of particles in the absence of hydrodynamic interactions. The present method is derived from the Langevin equations for the N particle assembly, and the results are shown to be consistent with the corresponding Fokker–Planck results. Sample calculations on small systems illustrate the importance of including hydrodynamic interactions in Brownian dynamics simulations. The method should be useful for simulation studies of diffusion limited reactions, polymer dynamics, protein folding, particle coagulation, and other phenomena in solution.

Protein structural fluctuations during a period of 100 ps.

A RECENT 9-ps molecular dynamics simulation1 of the bovine pancreatic trypsin inhibitor (PTI) at 295 K revealed a rich variety of motional phenomena at the atomic level on a picosecond time scale. To obtain information about longer time processes, and to characterise more accurately the short time results, a 96-ps dynamical simulation of PTI at an average temperature of 306 K has been completed with the techniques used previously1; an extended equilibration period of 72 ps before simulation served to eliminate internal stresses. Analysis of the present simulation has confirmed most of the conclusions of the earlier study but has shown in addition that there are significant features of the dynamics that can be observed only over a longer period, ∼100 ps.

Acute Metabolic Responses in Myxedema to Large Doses of Intravenous L-Thyroxine

Abstract Two comparable groups of noncomatose hypothyroid patients were given large doses of intravenous L-thyroxine. Group I was given an initial mean injection of 428 µg L-thyroxine and then 100 ...

Nonsteady hydrodynamics of biopolymer motions

Many biopolymers undergo conformational fluctuations in which large subunits move relative to each other under the influence of significant mechanical restoring forces. It is shown that nonsteady hydrodynamic effects may be important in the solvent response to such macromolecular motions. This result is in marked contrast to the familiar case of conformational fluctuations of random coil polymers, which move under the influence of weak entropic forces. The nonsteady solvent response is shown to affect the details of the biopolymer motion and to produce special qualitative features in the Raman light scattering spectrum of such macromolecules.Many biopolymers undergo conformational fluctuations in which large subunits move relative to each other under the influence of significant mechanical restoring forces. It is shown that nonsteady hydrodynamic effects may be important in the solvent response to such macromolecular motions. This result is in marked contrast to the familiar case of conformational fluctuations of random coil polymers, which move under the influence of weak entropic forces. The nonsteady solvent response is shown to affect the details of the biopolymer motion and to produce special qualitative features in the Raman light scattering spectrum of such macromolecules.

Internal dynamics of proteins. Short time and long time motions of aromatic sidechains in PTI

Theoretical approaches to the internal dynamics of proteins are outlined and illustrated by application to the aromatic sidechain motions of tyrosines in the bovine pancreatic trypsin inhibitor. High frequency torsional oscillations are obtained from a molecular dynamics simulation, while the longer time ring rotations are analyzed by use of adiabatic energy minimization and special transition-state trajectory techniques.