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For the purpose of molecular dynamics simulations of large biopolymers we have developed a new method to accelerate the calculation of long-range pair interactions (e.g. Coulomb interaction). The algorithm introduces distance classes to schedule updates of non-bonding interactions and to avoid unnecessary computations of interactions between particles which are far apart. To minimize the error caused by the updating schedule, the Verlet integration scheme has been modified. The results of the method are compared to those of other approximation schemes as well as to results obtained by numerical integration without approximation. For simulation of a protein with 12 637 atoms our approximation scheme yields a reduction of computer time by a factor of seven. The approximation suggested can be implemented on sequential as well as on parallel computers. We describe an implementation on a (Transputer-based) MIMD machine with a systolic ring architecture.

Quasi-elastic neutron scattering (QENS) was employed to study the molecular dynamics of three structurally related sterols, namely, cholesterol, lanosterol, and ergosterol. Oriented bilayers of dipalmitoylphosphatidylcholine (DPPC) were investigated at 40 mol % sterol content and at three temperatures (20, 36, and 50 degrees C) for two energy resolutions. Data analysis was concentrated on a direct comparison of the out-of-plane and the in-plane high-frequency motions of the three sterols in terms of their rates and amplitudes. The (spatially restricted) diffusive motion of the three sterols in the two directions was characterized by diffusion constants in the range of (5-30) x 10(-12) x m(2) x s(-1), with a significantly faster rate of diffusion along the membrane normal, resulting in a diffusional anisotropy, D(a). At low temperature (20 degrees C), cholesterol showed the highest value (D(a) = 4.5), while lanosterol gave the lowest one (D(a) = 2.0). At high temperature (50 degrees C), ergosterol diffusion had the highest diffusion anisotropy (D(a) = 2.0) compared to lanosterol (D(a) = 1.8) and cholesterol (D(a) = 1.6). Most interestingly, cholesterol showed at all three temperatures an amplitude of its out-of-plane-motion of 1.0-1.1 nm, more than a factor of 3 higher than measured for the other two sterols. This finding suggests that the short alkyl chain of the cholesterol molecule may cross at high frequency the bilayer midplane, while the other two sterols remain confined within the geometrical limits of each monolayer leaflet. The results provide an example of how slight structural alterations of sterols can affect their molecular dynamics in bilayers, which in turn may be relevant to the membrane micromechanical properties.

Within molecular dynamics simulations of protein᎐solvent systems the exact evaluation of long-range Coulomb interactions is computationally demanding and becomes prohibitive for large systems. Conventional truncation methods circumvent that computational problem, but are hampered by serious artifacts concerning structure and dynamics of the simulated systems. To avoid these artifacts we have developed an efficient and yet sufficiently accurate approximation scheme which combines the structure-Ž .w adapted multipole method SAMM C. Niedermeier and P. Tavan, J. Chem. Ž .x Phys., 101, 734 1994 with a multiple-time-step method. The computational effort for MD simulations required within our fast multiple-time-step structure-Ž . adapted multipole method FAMUSAMM scales linearly with the number of particles. For a system with 36,000 atoms we achieve a computational speed-up by a factor of 60 as compared with the exact evaluation of the Coulomb forces. Extended test simulations show that the applied approximations do not seriously affect structural or dynamical properties of the simulated systems.

For the purpose of molecular dynamics simulations of large biopolymers we have built a parallel computer with a systolic loop architecture, based on Transputers as computational units, and have programmed it in Occam 11. The computational nodes of the computer are linked together in a systolic ring. The program based on this .topology for large biopolymers increases its computational throughput nearly linearly with the number of computational nodes. The program developed is closely related to the simulation programs CHARMM and XPLOR, the input files required (force field, protein structure file, coordinates) and output files generated (sets of atomic coordinates representing dynamic trajectories and energies) are compatible with the corresponding files of these programs. Benchmark results of simulations of biopolymers comprising 66, 568, 3 634, 5 797 and 12 637 atoms are compared with XPLOR simulations on conventional computers (Cray, Convex, Vax). These results demonstrate that the software and hardware developed provide extremely cost effective biopolymer simulations. We present also a simulation (equilibrium of X-ray structure) of the complete photosynthetic reaction center of Rhodopseudomonus viridis (12 637 atoms). The simulation accounts for the Coulomb forces exactly, i.e. no cutoff had been assumed.

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In polarized infrared (IR) absorption experiments, dichroic values are used to study the structure and orientation of lipid molecules. From computer simulations, we obtained angular distributions of IR transition moment (TM) orientations of the stretch vibrations of CH 2 groups of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholin (POPC) lipid bilayers in the gel (L/~) and fluid (L a) phases. From these distributions, we calculated dichroic absorption values, as well as order parameters. We established a connection between the dichroic ratio R am, which is measured in IR-ATR setups, with the dichroic ratio D and the order parameter Szz.The calculated values compare well with experimental results for the fluid phase. In addition, we computed angular distributions of transition moments with respect to the tail director orientation for the gel and the fluid phases. Only small differences were found between the distributions in the symmetric stretch orientation, the asymmetric stretch orientation, and the C-H bond orientation of CH 2 groups. The distributions of tail directors of POPC showed average tilts of 14.7 ° in the gel phase and 32.9 ° in the fluid phase. We developed a theory which makes it possible to calculate average tilt angles of tail directors in the gel phase from dichroic absorption values obtained from IR measurements for a wide range of lipids. Legendre coefficients were calculated from TM distributions. Order parameters, defined as the second Legendre polynomial, were found to closely approximate the TM distribution in lipid bilayers in the fluid phase.

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