Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics

Smoothing the potential energy surface for structure optimization is a general and commonly applied strategy. We propose a combination of soft-core potential energy functions and a variation of the diffusion equation method to smooth potential energy surfaces, which is applicable to complex systems such as protein structures; The performance of the method was demonstrated by comparison with simulated annealing using the refinement of the undecapeptide Cyclosporin A as a test case. Simulations were repeated many times using different initial conditions and structures since the methods are heuristic and results are only meaningful in a statistical sense.

Bone mineral and calcium accretion during puberty

We measured bone mineral content (BMC) and estimated calcium accretion in children to provide insight into dietary calcium requirements during growth. Anthropometric measurements were done semiannually and whole-body BMC was measured annually by dual-energy X-ray absorptiometry for 4 y in 228 children (471 scans in 113 boys and 507 scans in 115,girls). Mean values for BMC, skeletal area, and height were calculated for 1-y age groups from 9.5 to 19.5 y of age. Cross-sectional analysis of the pooled data gave peak height velocity and peak BMC velocity (PBMCV) and the ages at which these occurred (13.3 y in boys and 11.4 y in girls). PBMCV did not peak until 1.2 y after peak height velocity in boys and 1.6 y after peak height velocity in girls. Within 3 y on either side of PBMCV, boys had consistently higher BMC and BMC velocity compared with girls and the discrepancy increased steadily through puberty. Three years before PBMCV, BMC Values in girls were 69% of those in boys; 3 y after peak height velocity this proportion fell to 51%. PBMCV was 320 g/y in boys and 240 g/y in girls. Under the assumption that bone mineral is 32.2% calcium, these values corresponded to a daily calcium retention of 282 mg in boys and 212 mg in girls. Individual Values could be much greater. In one boy in a group of six subjects for whom there were enough data for individual analysis through puberty, PBMCV was 555 g Ca/y or 490 mg Ca/d. Such high skeletal demands for calcium require large dietary calcium intakes and such requirements may not be met immediately in some children.

Non-equilibrium energy and momentum accommodation coefficients of Ar atoms scattered from Ni(001) in the thermal regime: A molecular dynamics study

Molecular dynamics simulations are used to study energy and momentum transfer of low-energy Ar atoms scattered from the Ni(001) surface. The investigation concentrates on the dependence of these processes on incident energy, angles of incidence and surface temperature. Energy transfer exhibits a strong dependence on the surface temperature, at incident energies below 500 meV, and incident angles close to specular incidence. Above 500 meV, the surface temperature dependence vanishes, and a limiting value in the amount of energy transferred to the surface is attained. Momentum exchange is investigated in terms of tangential and normal components. Both components exhibit a weak surface temperature dependence, but they have opposite behaviours at all incidence angles. In each component, momentum can be lost or gained following the interaction with the surface. (C) 1997 Elsevier Science B.V.

Quantum signatures of chaos in the dynamics of a trapped ion

We show how a nonlinear chaotic system, the parametrically kicked nonlinear oscillator, may be realized in the dynamics of a trapped, laser-cooled ion, interacting with a sequence of standing-wave pulses. Unlike the original optical scheme [G. J. Milburn and C.A. Holmes, Phys. Rev. A 44, 4704 (1991)], the trapped ion enables strongly quantum dynamics with minimal dissipation. This should permit an experimental test of one of the quantum signatures of chaos: irregular collapse and revival dynamics of the average vibrational energy.

Cell cycle model to describe animal cell size variation and lag between cell number and biomass dynamics

The use of cell numbers rather than mass to quantify the size of the biotic phase in animal cell cultures causes several problems. First, the cell size varies with growth conditions, thus yields expressed in terms of cell numbers cannot be used in the normal mass balance sense. Second, experience from microbial systems shows that cell number dynamics lag behind biomass dynamics. This work demonstrates that this lag phenomenon also occurs in animal cell culture. Both the lag phenomenon and the variation in cell size are explained using a simple model of the cell cycle. The basis for the model is that onset of DNA synthesis requires accumulation of G1 cyclins to a prescribed level. This requirement is translated into a requirement for a cell to reach a critical size before commencement of DNA synthesis. A slower gl-owing cell will spend more time in G1 before reaching the critical mass. In contrast, the period between onset of DNA synthesis and mitosis, tau(B), is fixed. The two parameters in the model, the critical size and tau(B), were determined from eight steady-state measurements of mean cell size in a continuous hybridoma culture. Using these parameters, it was possible to predict with reasonable accuracy the transient behavior in a separate shift-up culture, i.e., a culture where cells were transferred from a lean environment to a rich environment. The implications for analyzing experimental data for animal cell culture are discussed. (C) 1997 John Wiley & Sons, Inc.

Calcium potassium tris(oxalato-O-1, O-2)-chromate(III) pentahydrate

The Cr-III atom in CaK[Cr(C2O4)(3)].5H(2)O, has a regular octahedral geometry with three oxalato groups completing the coordination, Both the calcium and potassium cations are coordinated to the O atom of the oxalate group.