Stability analysis for binary sII hydrogen–promoter hydrates by molecular dynamics simulation

Molecular dynamics simulation was applied for the binary sII hydrogen–promoter hydrates to search the potential promoters to stabilise the hydrogen hydrates. The simulations were performed at 10.1 MPa. The simulation temperature was maintained at 260 K for 100 ps, and then it was increased at the rate of 0.1 TK/s. The cell volumes of the hydrates slowly increased with increasing temperature, and then the cell volumes rapidly increased. The temperature at which the cell volumes rapidly increased is identified as the simulated collapse temperature. The promoter which gives high simulated collapse temperature is judged to stabilise the hydrates. The simulated collapse temperature of the hydrate filled with cyclobutane is the highest among the promoters studied in this work.     

Multiscale simulation for thermo-hydrodynamic lubrication of a polymeric liquid between parallel plates

Thermo-hydrodynamic lubrication of a polymeric liquid composed of short chains between parallel plates is analysed by a multi-scale simulation, i.e. the synchronised molecular dynamics simulation via macroscopic heat and momentum transfer, which has been recently developed by us. The rheological properties and conformation of polymer chains coupled with the temperature rise caused by local viscous heating are investigated with a non-dimensional parameter, i.e. the Nahme–Griffith number, which is defined by the ratio of the viscous heating to the thermal conduction at the characteristic temperature required to sufficiently change the viscosity. The present simulation demonstrates that strong shear thinning and transitional behaviour of the conformation of the polymer chains occurs with a rapid temperature rise when the Nahme–Griffith number exceeds unity.     

Structural Transformations of Ice at High Pressures Via Molecular Dynamics Simulations

Abstract

A simple classical model is used for the study of the structural transformations of ice under high pressures, such as ice VIII to VII and X, via classical molecular dynamics (MD) simulation. In the present MD simulation, pair potentials of a simple form between pair of atoms and a thee-body potential representing the H-O-H angle dependence, originally developed by Kawamura et al., were used. Starting with a stable ice VIII at low pressure and low temperature, we have carried out two different MD runs, one with increasing pressure keeping the temperature constant (simulation I) and the other with increasing temperature under constant pressure (simulation II). From these MD simulations we have obtained the structural transformations from ice VIII to VII for both simulations; the former was finally transformed into ice X for the simulation I. The present results are compatible with recent experiments on high pressure ices.     

Effect of nanostructure on heat transfer between fluid and copper plate: a molecular dynamics simulation study

A molecular simulation is developed to study the effect of surface nanostructures on nanoscale flows. Based on this method, particles equation of motion is solved through the Verlet algorithm. Meanwhile, a physically sound method is applied to control the momentum and temperature of the simulation box. By adding an external force on the top copper plate according to the velocity difference between on-the-fly and desired velocities, simulations on convection of argon flows between two solid walls are performed. The top wall, which holds a higher temperature, moves at a constant velocity relative to bottom one along with the streamwise direction. These simulation results show that the nanostructures particularly affect fluid density oscillations adjacent to solid wall and nanostructures. In addition, these nanostructures also have significant effects on temperature and velocity distributions in simulation system.     

Neuro-genetic optimization of temperature control for a continuous flow polymerase chain reaction microdevice

In this study, a hybridized neuro-genetic optimization methodology realized by embedding finite element analysis (FEA) trained artificial neural networks (ANN) into genetic algorithms (GA), is used to optimize temperature control in a ceramic based continuous flow polymerase chain reaction (CPCR) device. The CPCR device requires three thermally isolated reaction zones of 94 degrees C, 65 degrees C, and 72 degrees C for the denaturing, annealing, and extension processes, respectively, to complete a cycle of polymerase chain reaction. The most important aspect of temperature control in the CPCR is to maintain temperature distribution at each reaction zone with a precision of +/-1 degree C or better, irrespective of changing ambient conditions. Results obtained from the FEA simulation shows good comparison with published experimental work for the temperature control in each reaction zone of the microfluidic channels. The simulation data are then used to train the ANN to predict the temperature distribution of the microfluidic channel for various heater input power and fluid flow rate. Once trained, the ANN analysis is able to predict the temperature distribution in the microchannel in less than 20 min, whereas the FEA simulation takes approximately 7 h to do so. The final optimization of temperature control in the CPCR device is achieved by embedding the trained ANN results as a fitness function into GA. Finally, the GA optimized results are used to build a new FEA model for numerical simulation analysis. The simulation results for the neuro-genetic optimized CPCR model and the initial CPCR model are then compared. The neuro-genetic optimized model shows a significant improvement from the initial model, establishing the optimization method's superiority.     

基于序贯高斯模拟的日最低气温空间不确定性评估

明确日最低气温对于评估低温对作物的危害、指导人们及时采取补救措施、保障粮食安全具有重要意义.克里格是近地面温度场插值的主流方法,但其平滑效应会导致低值区域被过高估计而高值区域被过低估计.对2011年12月12日冷空气影响下的海南岛日最低气温,采用交叉验证法评估了普通克里格和带漂移的克里格两种插值法的预测精度;并对克里格插值法和序贯高斯模拟法产生的当日海南岛最低气温的空间分布进行对比分析.结果表明：带漂移克里格法的预测精度（r=0.86）并不显著优于普通克里格法（r=0.86）;序贯高斯模拟能产生多个等概率的符合数据整体分布和方差函数的模拟结果,模拟结果克服了克里格插值的平滑效应,能够比克里格插值更加真实地反映当日最低气温的空间分布;在低温区域,气温变化小,序贯高斯模拟结果的条件方差小于普通克里格方差;潜在寒害区的空间不确定性能够通过多个序贯高斯模拟实现并加以量化.序贯高斯模拟在低温导致农业气象灾害的评估中具有较高的应用价值.
     

A physiological systems approach to modeling and resetting of mouse thermoregulation under heat stress

Heat stroke (HS) is a serious civilian and military health issue. Due to the limited amount of experimental data available in humans, this study was conducted on a mouse mathematical model fitted on experimental data collected from mice under HS conditions, with the assumption there is good agreement among mammals. Core temperature (T(c)) recovery responses in a mouse model consist of hypothermia and delayed fever during 24 h of recovery that represent potential biomarkers of HS severity. The objective of this study was to develop a simulation model of mouse T(c) responses and identify optimal treatment windows for HS recovery using a three-dimensional predictive heat transfer simulation model. Several bioenergetic simulation variables, including nonlinear metabolic heat production (W/m3), temperature-dependent convective heat transfer through blood mass perfusion (W/m3), and activity-related changes in circadian T(c) were used for model simulation. The simulation results predicted the experimental data with few disparities. Using this simulation model, we tested a series of ambient temperature treatment strategies to minimize hypothermia and delayed fever to accelerate HS recovery. Using a genetic algorithm, we identified eight time segments (ambient temperature = 27, 30, 31, 29, 28, 28, 27, 26°C) of 110 min total duration that optimized HS recovery in our model simulation.     

Molecular simulation of methane adsorption and its effect on kaolinite swelling as functions of pressure and temperature

Molecular simulation was used to study methane adsorption and its effect on kaolinite swelling. The effects of temperature and pressure were also analysed. The comparisons which validate the force field and model in our paper were made between simulation and experiment. Simulation results demonstrate that adsorption behaviour of methane exhibit Langmuir adsorption behaviour. The temperature has a negative effect on gas adsorption, the adsorption amounts will decrease with increasing temperature at a given pressure. A quantitative relationship between the methane adsorption and the kaolinite swelling was provided. The kaolinite–methane interaction dominates and the methane–methane interaction contributes less than 20% to the total interaction energy. The first peak in the RDFs increases with the increasing pressure, illustrating that the system becomes less structured at higher pressure. Compared with the higher temperature, the first peaks at lower temperature increase as a higher amount of methane adsorbed indicating that the interaction between the kaolinite and methane increase with decreasing temperature. Methane is strongly adsorbed on the sites of the hydrogen and oxygen atoms in kaolinite molecules.     

Protein flexibility: multiple molecular dynamics simulations of insulin chain B

Multiple molecular dynamics simulations totaling more than 100 ns were performed on chain B of insulin in explicit solvent at 300 K and 400 K. Despite some individual variations, a comparison of the protein dynamics of each simulation showed similar trends and most structures were consistent with NMR experimental values, even at the elevated temperature. The importance of packing interactions in determining the conformational transitions of the protein was observed, sometimes resulting in conformations induced by localized hydrophobic interactions. The high temperature simulation generated a more diverse range of structures with similar elements of secondary structure and populated conformations to the simulations at room temperature. A broad sampling of the conformational space of insulin chain B illustrated a wide range of conformational states with many transitions at room temperature in addition to the conformational states observed experimentally. The T-state conformation associated with insulin activity was consistently present and a possible mechanism of behavior was suggested.     

激光照射猪肝组织的温度场研究

研究了激光照射下猪肝组织传热过程温度场空间分布的动态规律。采用有限元分析法,利用激光分布公式获得猪肝组织的温度场空间分布,并采用K型热电偶和热电偶放大器来测量猪肝组织表面和内部温度,实验测量结果和模拟结果基本吻合,同时得出血液灌注率和猪肝组织温度的关系。研究结果对于激光临床应用中激光参数的合理选择有一定的指导意义。     

Simulated annealing coupled replica exchange molecular dynamics—An efficient conformational sampling method

Molecular dynamics simulated annealing (SA-MD) simulations are frequently used for refinement and optimization of peptide and protein structures. Depending on the simulation conditions and simulation length SA-MD simulations can be trapped in locally stable conformations far from the global optimum. As an alternative replica exchange molecular dynamics (RexMD) simulations can be used which allow exchanges between high and low simulation temperatures at all stages of the simulation. A significant drawback of RexMD simulations is, however, the rapid increase of the replica number with increasing system size to cover a desired temperature range. A combined SA-MD and RexMD approach termed SA-RexMD is suggested that employs a small number of replicas (4) and starts initially with a set of high simulation temperatures followed by gradual cooling of the set of temperatures until a target temperature has been reached. The protocol has been applied for the folding of several peptide systems and for the refinement of protein model structures. In all the cases, the SA-RexMD method turned out to be significantly more efficient in reaching low energy structures and also structures close to experiment compared to continuous MD simulations at the target temperature and to SA-MD simulations at the same computational demand. The approach is well suited for applications in structure refinement and for systematic force field improvement.     

Investigation of moisture diffusion in cross-linked epoxy moulding compound by molecular dynamics simulation

Molecular dynamics (MD) simulation was carried out to study the moisture diffusion in cross-linked epoxy resin, with the influence of temperature, water concentration and polymer conversion taken into account. The simulation results showed that the moisture diffusion coefficients increased with the increase in temperature. And generally, with the increased moisture concentration or decreased polymer conversion, the moisture diffusion coefficients reduced. However, the moisture diffusion was strongly inhibited when the number of epoxy groups in completely reacted epoxy resins was equal to the number of water molecules.     

土地利用/覆盖变化对中国不同季节气温的影响

近几十年中国地区土地利用/覆盖变化(LUCC)较大,在区域气候模拟中尤其需要使用更加准确的土地利用/覆盖数据。基于模式原有的USGS和新开发的LUC90两种土地利用/覆盖资料,利用区域环境集成模拟系统(RIEMS2.0)分别进行连续10a模拟,分析LUCC对中国不同季节气温的影响。结果表明:1)采用LUC90资料后,中国及东北、华北、华南夏季平均气温增加,但只有东北模拟与观测值的偏差减小,且通过显著性检验(P0.01)。中国及东北、华南冬季平均气温增加,并且模拟与观测值的偏差减少。中国及华北和华南对冬季气温年际变率的模拟改善好于夏季。2)土地利用/覆盖变化通过影响潜热通量的变化和净吸收辐射通量的变化来影响不同季节气温的变化。冬季净辐射通量变化对气温变化的贡献较夏季大,而夏季潜热通量变化对气温变化的贡献较冬季大。雨养农田转变森林、草地、灌溉农田过程造成通量变化,其对气温变化的影响也存在不同分区季节的差异。     

The self-diffusion and hydrogen bond interaction in neat liquid alkanols: a molecular dynamic simulation study

Self-diffusion of methanol, ethanol, 1-propanol and 2-propanol has been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 478 K at pressures up to 300 MPa. The simulation results on self-diffusion of methanol, ethanol and 2-propanol (for 2-propanol, at high temperatures) agree well with experiment, which suggests that the simulation method is a powerful tool to obtain self-diffusion coefficients over wide range of temperature and pressure, under which it is rather difficult for experiments. The local structures of methanol, ethanol and 2-propanol are investigated by calculating the radial distribution functions, H-bond numbers, coordination numbers and the ratios of H-bond number divided by coordination number. The correlation between self-diffusion and structural properties, and the influence of temperature and pressure on them are discussed. The degree of forming H-bond space network in methanol, ethanol and water is higher than that in 2-propanol, and they are all higher than those in ammonia and methylamine. The simulation results demonstrate that the effect of hydrogen bonding on the translational dynamics in methanol and ethanol is more pronounced than that in 2-propanol.     

Structure of Sphingomyelin Bilayers: A Simulation Study

We have carried out a molecular dynamics simulation of a hydrated 18:0 sphingomyelin lipid bilayer. The bilayer contained 1600 sphingomyelin (SM) molecules, and 50,592 water molecules. After construction and initial equilibration, the simulation was run for 3.8 ns at a constant temperature of 50°C and a constant pressure of 1 atm. We present properties of the bilayer calculated from the simulation, and compare with experimental data and with properties of dipalmitoyl phosphatidylcholine (DPPC) bilayers. The SM bilayers are significantly more ordered and compact than DPPC bilayers at the same temperature. SM bilayers also exhibit significant intramolecular hydrogen bonding between phosphate ester oxygen and hydroxyl hydrogen atoms. This results in a decreased hydration in the polar region of the SM bilayer compared with DPPC. Since our simulation system is very large we have calculated the power spectrum of bilayer undulation and peristaltic modes, and we compare these data with similar calculations for DPPC bilayers. We find that the SM bilayer has significantly larger bending modulus and area compressibility compared to DPPC.     

2株耐低温微生物处理污水模拟试验初报

从下水管道的污泥中分离筛选到耐冷细菌H6和耐冷酵母菌J1,采用此2菌株进行模拟污水低温(8℃)处理试验。H6和J1菌株对模拟污水COD的去除率分别为66.6%和72.2%;H6、J1菌株对有机氮去除率分别为76.9%和64.5%;H6、J1菌株对总磷去除率分别为53.9%和14.0%。说明低温微生物在低温环境的污水处理具有广阔的应用前景。     

Modeling temperature variations in a pilot plant thermophilic anaerobic digester

A model that predicts temperature changes in a pilot plant thermophilic anaerobic digester was developed based on fundamental thermodynamic laws. The methodology utilized two simulation strategies. In the first, model equations were solved through a searching routine based on a minimal square optimization criterion, from which the overall heat transfer coefficient values, for both biodigester and heat exchanger, were determined. In the second, the simulation was performed with variable values of these overall coefficients. The prediction with both strategies allowed reproducing experimental data within 5% of the temperature span permitted in the equipment by the system control, which validated the model. The temperature variation was affected by the heterogeneity of the feeding and extraction processes, by the heterogeneity of the digestate recirculation through the heating system and by the lack of a perfect mixing inside the biodigester tank. The use of variable overall heat transfer coefficients improved the temperature change prediction and reduced the effect of a non-ideal performance of the pilot plant modeled.     

Numerical analysis of dynamic temperature in response to different levels of reactive hyperaemia in a three-dimensional image-based hand model

Vascular reactivity (VR) is considered as an effective index to predict the risk of cardiovascular events. A cost-effective alternative technique used to evaluate VR called digital thermal monitoring (DTM) is based on the response of finger temperature to vessel occlusion and reperfusion. In this work, a simulation has been developed to investigate hand temperature in response to vessel occlusion and perfusion. The simulation consists of image-based mesh generation and finite element analysis of blood flow and heat transfer in tissues. In order to reconstruct a real geometric model of human hand, a computer programme including automatic image processing for sequential MR data and mesh generation based on the transfinite interpolation method is developed. In the finite element analysis part, blood flow perfused in solid tissues is considered as fluid phase through porous media. Heat transfer in tissues is described by Pennes bioheat equation and blood perfusion rate is obtained from Darcy velocities. Capillary pressure, blood perfusion and temperature distribution of hand are obtained. The results reveal that fingertip temperature is strongly dependent on larger arterial pressure. This simulation is of potential to quantify the indices used for evaluating the VR in DTM test if it is integrated with the haemodynamic model of blood circulation in upper limb.     

植物表面温度模拟研究进展

本文主要综述60年代以来国内外有关植物表面温度研究的各种模拟模型,其中包括植物局部表面的一元和多元回归的经验模型;稳定和非稳定状态的单叶面和植被表面的微气象模型。此外,还讨论了模拟模型中存在的问题,并提出了未来植物表面温度模拟研究的主要方面。     

Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a Gō model

We study the folding thermodynamics and kinetics of the Pin1 WW domain, a three-stranded beta-sheet protein, by using all-atom (except nonpolar hydrogens) discontinuous molecular dynamics simulations at various temperatures with a Gō model. The protein exhibits a two-state folding kinetics near the folding transition temperature. A good agreement between our simulations and the experimental measurements by the Gruebele group has been found, and the simulation sheds new insights into the structure of transition state, which is hard to be straightforwardly captured in experiments. The simulation also reveals that the folding pathways at approximately the transition temperature and at low temperatures are much different, and an intermediate state at a low temperature is predicted. The transition state of this small beta-protein at its folding transition temperature has a well-established hairpin 1 made of beta1 and beta2 strands while its low-temperature kinetic intermediate has a formed hairpin 2 composed of beta2 and beta3 strands. Theoretical results are compared with other simulation results as well as available experimental data. This study confirms that specific side-chain packing in an all-atom Gō model can yield a reasonable prediction of specific folding kinetics for a given protein. Different folding behaviors at different temperatures are interpreted in terms of the interplay of entropy and enthalpy in folding process.