Molecular dynamics study of interaction of dimyristoyl phosphotidyl choline with water

We present here results of molecular dynamics (MD) simulations on hydrated bilayers of 40 molecules of 1-2-dimyristoyl-sn-glycero-3-phosphatidyl choline (DMPC) in liquid crystalline (Lα) phase using two different models (i) with same (A) conformation for all DMPC molecules, (ii) with alternate rows having different (A and B reported in crystallographic studies on DMPC) conformations. The bilayers were hydrated using 776 and 1064 water molecules. Simulations have been carried out at 310K with AMBER 4.0 program, using united atom force field for 200 pico seconds (ps) after equilibration. During heating and equilibration constant pressure temperature (PT) conditions were maintained while in simulation of equillibrated bilayers constant volume temperature (VT) conditions were used. Subaveraged atomic coordinates were used to calculate geometric parameters of lipid molecules and lipid water interaction. Our results show larger flexibility of polar head group and glycerol region in Lα phase compared to gel or non-hydrated bilayers. Chain disorder was more towards end. Sn-2 chains were more disordered. Use of two types of starting conformations increased disorder. Trans fraction of chain torsional angle was higher in non-hydrated bilayer. However it was more disordered due to ‘swing’ movement of chains because of distortion in torsional angles α2 and 03 due to absence of water molecules. Trans fraction of the chains, order parameter and water penetration showed general agreement with the available experimental results. On the whole MD technique was found to be quite useful for depicting microscopic behaviour of liquid crystalline system and correlating the same with macroscopic changes observed experimentally.     

Polypeptide folding with off-lattice Monte Carlo dynamics: the method

The MC dynamics of an off-lattice all-atom protein backbone model with rigid amide planes are studied. The only degrees of freedom are the dihedral angle pairs of the C-atoms. Conformational changes are generated by Monte Carlo (MC) moves. The MC moves considered are single rotations (simple moves, SM's) giving rise to global conformational changes or, alternatively, cooperative rotations in a window of amide planes (window moves, WM's) generating local conformational changes in the window. Outside the window the protein conformation is kept invariant by constraints. These constraints produce a bias in the distribution of dihedral angles. The WM's are corrected for this bias by suitable Jacobians. The energy function used is derived from the CHARMM force field. In a first application to polyalanine it is demonstrated that WM's sample the conformational space more efficiently than SM's.Abbreviations CPU Central Processing Unit - MC Monte Carlo - MCD Monte Carlo Dynamics - MD Molecular Dynamics - RMS Root-Mean-Square - RMSD Root-Mean-Square-Deviation - SM Simple Move - WM Window Move     

Free Air Temperature Increase (FATI): a new tool to study global warming effects on plants in the field

A new technique, called Free Air Temperature Increase (FATI), was developed to artificially induce increased canopy temperature in field conditions without the use of enclosures. This acronym was chosen in analogy with FACE (Free Air CO₂ Enrichment), a technique which produces elevated CO₂ concentrations [CO₂] in open field conditions. The FATI system simulates global warming in small ecosystems of limited height, using infrared heaters from which all radiation below 800 nm is removed by selective cut-off filters to avoid undesirable photomorpho-genetic effects. An electronic control circuit tracks the ambient canopy temperature in an unheated reference plot with thermocouples, and modulates the radiant energy from the lamps to produce a 2.5°C increment in the canopy temperature of an associated heated plot (continuously day and night). This pre-set target differential is relatively-constant over time due to the fast response of the lamps and the use of a proportional action controller (the standard deviation of this increment was <1°C in a 3 week field study with 1007 measurements). Furthermore, the increase in leaf temperature does not depend on the vertical position within the canopy or on the height of the stand. Possible applications and alternative designs are discussed.     

Modeling of nitrogen transformations and translocations

Different submodels within complex model packages on N regimes-for plant N-uptake, net N-mineralization, nitrate leaching and microbial N immobilization-are critically reviewed mainly with regard to their prediction ability on the basis of three comparative papers. Only for some of the processes adequate statistical evaluation of the models was possible. Compared to the other statistically evaluable process, nitrate leaching, modeling of plant N-uptake yields the better results. Most models for mineralization use arbitrary approaches rather than empirical ones. Although only approximate estimates of N mineralisation were at hand, the models generally behave expectedly poor. Only one model-DAISY-out of 16 involved in the comparison uses an explicit microbial biomass sub-model including microbial growth, decline and maintenance terms. So DAISY is the only model coupling C and N cycles. But what is true for an individual model describing the C and N transformation of a lab incubation experiment seems to be valid for most of the complex simulation work on the C and N regimes: this model was said to be overparameterized with respect to the available data.     

A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci. I. Methodology

A Bayesian approach to the statistical mapping of Quantitative Trait Loci (QTLs) using single markers was implemented via Markov Chain Monte Carlo (MCMC) algorithms for parameter estimation and hypothesis testing. Parameter estimators were marginal posterior means computed using a Gibbs sampler with data augmentation. Variables sampled included the augmented data (marker-QTL genotypes, polygenic effects), an indicator variable for linkage, and the parameters (allele frequency, QTL substitution effect, recombination rate, polygenic and residual variances). Several MCMC algorithms were derived for computing Bayesian tests of linkage, which consisted of the marginal posterior probability of linkage and the marginal likelihood of the QTL variance associated with the marker.     

Structured modelling of animal cells

Recent advances in computer technology have promoted the design and use of detailed, computer-based models for biological systems. For many non-biological systems, the complexity of such simulations may be considered inappropriate and unwieldy, but in biological systems, and more specifically in animal cell culture, this level of complexity simply mimics what is only beginning to be understood about metabolic processs. With this in mind, we contend that complex, structured models are vital tools in the investigation of fundamental biological processes. An example of such a simulation, which describes the commercial production of therapeutic proteins by animal cell cultures, is considered.     

方差组分估计方法MIVQUE和REML的模拟比较

利用ＭｏｎｔｅＣａｒｌｏ方法,对４种数据结构进行了ＭＩＶＱＵＥ和ＲＥＭＬ两种方差组分估计方法的模拟比较。方差组分估计所用的模型为奶牛育种中常用的公畜模型,它包括场年季固定效应、公牛组固定效应和公牛随机效应。４种数据结构中最大的有１２８４７个观察值,场年季效应和公牛效应水平数分别为７７８和４７,它与北京市目前可利用的奶牛头胎产奶量记录资料相当。最小的数据结构只有２００个观察值,１４８个场年季和２０头公牛。比较指标为估计值的偏差和方差（理论的或根据１０００次重复模拟所得的经验值）。结果表明,对于较大样本的数据结构,两种方法差异很小,它们间的估计值的相关接近于１,偏差小于真值的１％,方差近似相等。对于较小样本的数据结构,ＭＩＶＱＵＥ则明显优于ＲＥＭＬ。本研究还表明,对于ＲＥＭＬ来说,类似数据结构１的样本已能满足其渐近无偏性和有效性的大样本特性。     

大兴安岭林区针叶林的生长方程及火灾林木死亡率

本文用随机模拟的方法建立了北方针叶林的生长方程及其受到火灾侵害后的林木死亡率,定量地研究了火灾对这种林分变动的影响．