首页 | 本学科首页   官方微博 | 高级检索  
相似文献
 共查询到20条相似文献,搜索用时 31 毫秒
1.
Abstract

Equilibrium NPT molecular dynamics computer simulations have been used to determine the chemical potential, partial enthalpy and partial volume of model Ar-Kr mixtures using newly devised non-intrusive particle insertion and particle swap techniques [P. Sindzingre et al. Chemical Physics, 129 (1989) 213]. In this report we examine, for the first time, in some detail the relative convergence statistics of the particle swap and particle insertion methods for these properties for binary Lennard-Jones (LJ) mixtures. Both species are represented by single-site Lennard-Jones pair potentials with Lorentz-Berthelot rules for the cross-species interactions. We show that, over the whole phase diagram and especially in the vicinity of the fluid-solid coexistence line, the particle swap method gives significantly better statistics than the particle insertion method for the difference in chemical potential of the two species, partial enthalpy and partial volume of each species. Also, we find that, using the particle swap method, the difference in the chemical potential converges more rapidly than the differences in the partial enthalpy and volume.  相似文献   

2.
The interfacial mechanical properties of carbon nanotube (CNT)-reinforced silicon nanocomposites are investigated by using molecular dynamics simulation method. The hybrid potential that includes Tersoff_2 potential for Si–Si in the silicon matrix, AIREBO potential for C–C in the CNTs and the Lennard-Jones (LJ) potential for Si–C in the interface is used in the nanocomposite system. The effects of such parameters as the CNT chirality, the CNT diameter and the CNT embedded length, the defects (Vacancy defects, Stone–Wales defects), the size of model, the temperature, the bonding strength and the cut-off distance of the interfacial LJ potential of nanocomposites on the pull force and the average interfacial shear strength (ISS) are investigated and discussed. The results show that the toughness and the maximum tensile strength have been increased significantly by adding the CNTs into the Si matrix. Also by increasing the LJ bonding strength and the cut-off distance of the LJ potential, the pull force and the ISS are increased significantly. The CNT chirality, the CNT diameter and the CNT embedded length have a great influence on the pull force and the ISS, while the effects of temperature, the defects and the size of model are very slight.  相似文献   

3.
Huang SY  Zou X 《Proteins》2008,72(2):557-579
Using an efficient iterative method, we have developed a distance-dependent knowledge-based scoring function to predict protein-protein interactions. The function, referred to as ITScore-PP, was derived using the crystal structures of a training set of 851 protein-protein dimeric complexes containing true biological interfaces. The key idea of the iterative method for deriving ITScore-PP is to improve the interatomic pair potentials by iteration, until the pair potentials can distinguish true binding modes from decoy modes for the protein-protein complexes in the training set. The iterative method circumvents the challenging reference state problem in deriving knowledge-based potentials. The derived scoring function was used to evaluate the ligand orientations generated by ZDOCK 2.1 and the native ligand structures on a diverse set of 91 protein-protein complexes. For the bound test cases, ITScore-PP yielded a success rate of 98.9% if the top 10 ranked orientations were considered. For the more realistic unbound test cases, the corresponding success rate was 40.7%. Furthermore, for faster orientational sampling purpose, several residue-level knowledge-based scoring functions were also derived following the similar iterative procedure. Among them, the scoring function that uses the side-chain center of mass (SCM) to represent a residue, referred to as ITScore-PP(SCM), showed the best performance and yielded success rates of 71.4% and 30.8% for the bound and unbound cases, respectively, when the top 10 orientations were considered. ITScore-PP was further tested using two other published protein-protein docking decoy sets, the ZDOCK decoy set and the RosettaDock decoy set. In addition to binding mode prediction, the binding scores predicted by ITScore-PP also correlated well with the experimentally determined binding affinities, yielding a correlation coefficient of R = 0.71 on a test set of 74 protein-protein complexes with known affinities. ITScore-PP is computationally efficient. The average run time for ITScore-PP was about 0.03 second per orientation (including optimization) on a personal computer with 3.2 GHz Pentium IV CPU and 3.0 GB RAM. The computational speed of ITScore-PP(SCM) is about an order of magnitude faster than that of ITScore-PP. ITScore-PP and/or ITScore-PP(SCM) can be combined with efficient protein docking software to study protein-protein recognition.  相似文献   

4.
目的:探讨以问题为基础的教学方式结合临床路径教学模式在肿瘤教学中的应用效果。方法:以2015年12月-2017年11月于我院肿瘤科实习的临床本科实习生88例为研究对象。将其按照随机数字表法分成研究组(n=44)和对照组(n=44)。对照组接受传统教学方式进行学习,研究组接受以问题为基础的教学方式结合临床路径教学模式进行学习。带教结束后对两组实习生各项考核成绩、实习生对教学方式过程中各项问题的认可度以及对教学方式的满意度情况进行分析。结果:研究组理论考试、实践操作、病例分析与总成绩均高于对照组,差异有统计学意义(P0.05)。研究组实习生对问题1-问题7的认可人数占比均高于对照组,差异有统计学意义(P0.05)。研究组实习生对教学方式满意度高于对照组,差异有统计学意义(P0.05)。结论:以问题为基础的教学方式结合临床路径教学模式应用于肿瘤教学中效果明显,可显著提高实习生各项考核成绩,增加其对教学方式的认可度以及满意度。  相似文献   

5.
Abstract

Chemical potentials of a homogeneous and an inhomogeneous Lennard-Jones fluid have been determined by molecular dynamics simulations on the vector computer CYBER 205 by applying essentially the fictitious test particle method of Widom. For the homogeneous fluid we find, contrary to the previous result of Guillot and Guissani, that the simulated chemical potential is independent of the particle number. The crucial point, however, is a sufficiently large cut-off radius in the evaluation of the Boltzmann factor. Comparing with our WCA-type perturbation theory, we get agreement in the chemical potentials within 0.1 kT up to the density n[sgrave]3 = 0.80 and a difference of 0.2 kT at n[sgrave]3 = 0.85. For the inhomogeneous case we consider a fluid in a cylindrical pore and integrate Widom's equation over a certain probe volume as suggested earlier by us. Chemical potentials are then calculated independently in five different probe volumes, which are cylindrical shells. The results agree well from the second to the fourth shell. Inaccuracies in the innermost cylinder can be easily explained by bad statistics. In the shell close to the wall the extremely high local density is responsible for the inaccuracies. Extending the probe volume over all cylindrical shells besides the one closest to the wall is thought to yield rather reliable results for the chemical potential. As a by-product of the simulations we also obtained diffusion coefficients, which are given in an appendix.  相似文献   

6.
Abstract

We have performed molecular dynamics simulations for liquid n-butane in order to understand liquid structures in terms of both inter- and intra-molecular interactions. Each n-butane molecule consists of four sites interacting with LJ potential and only a dihedral angle is taken into account as the internal degree of freedom. The population of gauche conformations with respect to the ideal gas state is found to increase in the liquid state. To investigate how the intermolecular interaction affects the dihedral angle distribution, we also adopt the repulsive LJ potential (RLJ) model. It is found that the nearest neighbor packing of the methyl and/or methylene groups can be approximately represented by using only the repulsive interaction. From the dihedral angle distribution, however, the rate of the shift of RLJ model to gauche is larger than that of LJ model and the attractive force also plays a significant role in the conformational equilibrium.  相似文献   

7.
Abstract

This paper describes techniques for calculating the forces and torques for molecular simulations that use anisotropic site-site potentials. The general techniques are illustrated for pairs of linear and tetrahedral molecules. A technique for combining anisotropic site-site potentials with constraint dynamics is described. These ideas are tested by simulating an anisotropic site-site potential model for the non-bonded interactions in liquid butane. This model is as accurate as the all-atom Williams potential from which it is derived but can be simulated using approximately half the computer time of the all-atom potential. Anisotropic site-site potentials offer a flexible and cost-effective method of simulating a range of hydrocarbon systems.  相似文献   

8.
摘要 目的:探究长程运动诱发试验(exercise test, ET)的两种方法在诊断低钾性周期性麻痹患者的价值比较。方法:选择2018年2月~2020年3月我院住院和门诊的72例低钾性周期性麻痹患者,根据ET检测的方法分为观察组和对照组,对比两组ET检测在运动后即刻、运动后的10、20、30、40、50、60 min的双侧尺神经进行复合肌肉动作电位(compound muscle action potential,cMAP)波幅和ET阳性率;以临床诊断结果为金指标,分析两组ET诊断价值。结果:两组的ET检测的阳性发生率对比无显著性差异(P>0.05)。两组波幅降低百分比在运动后即刻以及运动后的10、20、30、40、50、60 min对比无差异(P>0.05),在20 min后观察组波幅降低百分比趋势稍比对照组慢。临床诊断结果阳性68例,阳性率为94.44 %。观察组ET检测的特异性为50.0 %,灵敏度为88.23 %,对照组ET检测的特异性为25.0 %,灵敏度为80.88 %,观察组的特异性和灵敏度均优于对照组。结论:长程运动诱发试验是低钾型周期性麻痹诊断中重要的辅助诊断方法之一,且运动持续50 s,休息10 s,只做1个循环的方法,简单、快捷,可供临床诊断时优先选择。  相似文献   

9.
Nucleoside triphosphate diphosphohydrolase (NTPDase) activity was recently characterized in Leishmania (Viannia) braziliensis promastigotes (Lb), and an antigenic conserved domain (r82–121) from the specific NTPDase 1 isoform was identified. In this work, mouse polyclonal antibodies produced against two synthetic peptides derived from this domain (LbB1LJ, r82–103; LbB2LJ, r102–121) were used. The anti-LbB1LJ or anti-LbB2LJ antibodies were immobilized on protein A-sepharose and immunoprecipitated the NTPDase 1 of 48 kDa and depleted approximately 40% of the phosphohydrolytic activity from detergent-homogenized Lb preparation. Ultrastructural immunocytochemical microscopy identified the NTPDase 1 on the parasite surface and in its subcellular cytoplasmic vesicles, mitochondria, kinetoplast and nucleus. The ATPase and ADPase activities of detergent-homogenized Lb preparation were partially inhibited by anti-LbB1LJ antibody (43–79%), which was more effective than that inhibition (18–47%) by anti-LbB2LJ antibody. In addition, the immune serum anti-LbB1LJ (67%) or anti-LbB2LJ (33%) was cytotoxic, significantly reducing the promastigotes growth in vitro. The results appoint the conserved domain from the L. braziliensis NTPDase as an important target for inhibitor design and the potential application of these biomolecules in experimental protocols of disease control.  相似文献   

10.
Placental abnormalities are the main factor in the high incidence of somatic cell clone abnormalities. The expression of several trophoblast cell-specific molecules is enhanced during gestational days 7 to 14. To determine the possible genes whose expression patterns might reflect calf normality, we first compared the gene expression profiles on day 15 between in vitro-fertilized (IVF) embryos and two types of somatic cell nuclear-transferred embryos with either a high (FNT) or low (CNT) incidence of neonatal abnormalities using a cDNA microarray containing 16 of 21 placenta-specific genes developed from tissues collected across gestation. To identify significant genes from the screening of day 15 embryos, genes with a less than two-fold difference in expression between IVF and CNT embryos, and those with a greater than two-fold difference between IVF and FNT and between CNT and FNT were considered to contribute to clone abnormalities. These two comparisons revealed 18 down-regulated and 18 upregulated genes of the 1722 genes examined. We then examined the expression levels of 10 genes with known functions in eight-cell and blastocyst-stage embryos by real-time PCR. The mRNA expression pattern of interferon (IFN)-tau, a trophectoderm-related gene, differed between IVF, CNT, and FNT eight-cell embryos; few or none of the IVF or CNT eight-cell embryos expressed IFN-tau mRNA, but all eight-cell FNT embryos expressed IFN-tau. IFN-tau mRNA expression was significantly higher in IVF blastocysts, however, than in nuclear-transferred blastocysts. Average IFN-tau mRNA expression in FNT blastocysts was not different from that in CNT blastocysts, due to one CNT blastocyst with high expression. The precise relation between early expression of IFN-tau mRNA and inferior developmental potential in cloned embryos should be examined further.  相似文献   

11.
Enterovirus 71 (EV71) is the predominant pathogen for severe hand, foot, and mouth disease (HFMD) in children younger than 5 years, and currently no effective drugs are available for EV71. Thus, there is an urgent need to develop new drugs for the control of EV71 infection. In this study, LJ04 was extracted from Laminaria japonica using diethylaminoethyl cellulose-52 with 0.4 mol/l NaCl as the eluent, and its virucidal activity was evaluated based on its cytopathic effects on a microplate. LJ04 is composed of fucose, galactose, and mannose and mainly showed good virucidal activity against EV71. The antiviral mechanisms of LJ04 were the direct inactivation of the virus, the blockage of virus binding, disruptions to viral entry, and weak inhibitory activity against the nonstructural protein 3C. The two most important findings from this study were that LJ04 inhibited EV71 proliferation in HM1900 cells, which are a human microglia cell line, and that LJ04 can directly inactivate EV71 within 2 hr at 37°C. This study demonstrates for the first time the ability of a polysaccharide from L. japonica to inhibit viral and 3C activity; importantly, the inhibition of 3C might have a minor effect on the antiviral effect of LJ04. Consequently, our results identify LJ04 as a potential drug candidate for the control of severe EV71 infection in clinical settings.  相似文献   

12.
Summary A simple method for the determination of asymmetric surface potentials in lipid bilayers is described. The method is based on the dependence of bilayer capacitance on transmembrane voltage. The capacitance is measured by rectifying the 90° component of an applied alternating current signal. A superimposed slow triangular wave results in a hysteresis-like time course of capacitance. The center of the hysteresis figure is shifted along the voltage axis by an amount equal to the difference of the dipole plus surfacecharge potentials on the two sides of the bilayer (capacitance minimization potential).Alternatively, such bilayer asymmetry was studied by using the current-voltage characteristics in the presence of nonactin as a carrier. This analysis was based on the integrated Nernst-Planck equation, assuming a trapezoidal energy barrier and equilibrium of the surface reactions.The two methods gave consistent results for the surface potentials of phosphatidyl serine membranes asymmetrically shielded with calcium. In addition, the current analysis yields the positions of the corners of the barrier, found to be set in 13% for this lipid.  相似文献   

13.
BackgroundNatural killer (NK) cells play important roles in immune responses and have been wildly used in immunotherapy. Nevertheless, some limitations remain. It is urgent to explore novel and safe strategies to enhance NK cell activity.PurposeThe aim of this study was to investigate the immuno-stimulatory effects and to reveal the molecular mechanism of LJ101019C, a derivative of a natural small-molecule compounds cajanine, on NK cells.MethodsCell proliferation was examined by CCK8 assay, then we used the cytotoxicity detection kit to detect the cytotoxicity of NK cells. The change of cell cycle, intracellular reactive oxygen species (ROS) level and mitochondrial mass were evaluated by FACS and Operetta high-content image analysis, respectively. Furthermore, the IFN-γ secretion of NK cells were measured by ELISA. The Kv1.3 protein expression and function were detected by western blot and patch-clamp technique, respectively. The role of Kv1.3 in AKT/mTOR pathway activation was determined by western blot.ResultsThe results showed that LJ101019C at relatively low concentrations (0.05–0.1 µM) significantly increased the proliferation of NK cells. And 1 µM LJ101019C could elevate the proportion of NK cells in the S-phase of the cell cycle (*p < 0.1). Furthermore, the cytotoxic effects of NK cells targeting MIA PaCa-2 cells were significantly enhanced by 0.1 and 1 µM LJ101019C, and were associated with the enhanced secretion of IFN-γ by NK cells (*p < 0.1; **p < 0.05). 0.1 and 1 µM LJ101019C increased intracellular levels of ROS (**p < 0.05), and 0.1 µM LJ101019C elevated mitochondrial mass (*p < 0.1). Electrophysiological recordings indicated that LJ101019C led to a remarkably increase the Kv1.3 current density. Moreover, western blot results indicated that LJ101019C elevated Kv1.3 protein expression and activated AKT/mTOR signaling via increasing the expression of Kv1.3 in NK cells.ConclusionLJ101019C increases the proliferation and the cytotoxicity of NK cells at relatively low concentrations. The mechanism is the activation of AKT/mTOR signaling pathway driven by up-regulation of Kv1.3 in NK cells. These suggest LJ101019C is a promising candidate for improving the efficacy of NK cell-based immunotherapies.  相似文献   

14.
F. Luo  Y. Su 《Molecular simulation》2013,39(5):391-399
Grand canonical Monte Carlo simulation is used to study the density profiles of Lennard–Jones (LJ) fluid next to a large hard sphere (mimicking a colloidal particle) of various sizes. The LJ fluid in the inhomogeneous system thus maintains equilibrium with the bulk LJ fluid. The chosen density and potential parameters for the bulk fluid correspond to the conditions situated at “dangerous” regions of the phase diagram, i.e. near the critical temperature or close to the gas–liquid coexistence curve. The aim of present extensive simulations is to provide exact data for the broad range of the bulk parameters against which the “universality” of adjustable parameter associated with a perturbation density functional approximation (DFA) can be tested. Here the term “universality” means independence of this parameter on the particular external field responsible for the generation of a non-uniform density profile of the fluid. It is shown that the “universality” of this parameter associated with a third order+second order perturbation DFA holds also in the present case of a large spherical particle as a source of external potential, similarly as established in previous studies dealing with other interaction potential and other external fields [J. Chem. Phys., 122, 064503 (2005); J. Chem. Phys., 123 124708 (2005)]. This DFA can be used as input into a recently proposed framework for the calculation of interparticle potential of mean force (PMF).  相似文献   

15.
The goal of a Brain-Computer Interface (BCI) is to control a computer by pure brain activity. Recently, BCIs based on code-modulated visual evoked potentials (c-VEPs) have shown great potential to establish high-performance communication. In this paper we present a c-VEP BCI that uses online adaptation of the classifier to reduce calibration time and increase performance. We compare two different approaches for online adaptation of the system: an unsupervised method and a method that uses the detection of error-related potentials. Both approaches were tested in an online study, in which an average accuracy of 96% was achieved with adaptation based on error-related potentials. This accuracy corresponds to an average information transfer rate of 144 bit/min, which is the highest bitrate reported so far for a non-invasive BCI. In a free-spelling mode, the subjects were able to write with an average of 21.3 error-free letters per minute, which shows the feasibility of the BCI system in a normal-use scenario. In addition we show that a calibration of the BCI system solely based on the detection of error-related potentials is possible, without knowing the true class labels.  相似文献   

16.
A ligase chain reaction (LCR) DNA amplification method for the molecular diagnosis of Mycobacterium tuberculosis complex (Abbott LCx MTB) was evaluated in comparison with solid (Lowenstein Jensen), liquid (7H12, Bactec 460 system) phase culture and microscopic examination (ME) on 86 tissue samples collected from 86 intradermal tuberculin positive cattle and one pool from 4 guinea pigs experimentally infected with M. bovis. Overall, 48 samples (58.81%) were culturally positive for mycobacteria, and on the basis of biochemical characters, all the isolates were identified as M. bovis. Sensitivity was 83.92% for LCx, 53.57% for LJ, 85.71% for Bactec and 41.07% for ME. In 3 out of 25 "no visible lesion" tissue samples, M. bovis was detected only by LCx and Bactec but not by LJ and ME. The concordance in the determination of positives and negatives among the methods observed in pairs was calculated according to Cohen's K concordance coefficient and showed 81.1% of concordance of LCx vs Bactec, 68.8% LCx vs LJ, 72.2% LCx vs ME, 80.0% Bactec vs LJ, 66.7% Bactec vs ME, 85.5% LJ vs ME. Despite a certain variability in concordance rates, both Cohen's K concordance coefficients or standardized (Zk) values were statistically significant. Both LCx and Bactec appear not alternative but subsidiary to the other methods traditionally applied for direct diagnosis of bovine tuberculosis on tissue samples from cattle reacting to intradermal tuberculin test.  相似文献   

17.
In two trials, pigs were given lucerne juice (LJ) as the only protein supplement from 20–90 kg liveweight. The effects of reducing the mineral supplementation of the meal given with LJ and of increasing water intake were studied.In Trial 1, a total of 45 pigs were given either control diets with 7% white-fish meal to 54 kg liveweight and 3.5% thereafter, or diets in which the fish meal provided by the control diets was replaced with LJ. The meal mixture given with LJ was either supplemented or unsupplemented with limestone flour, dicalcium phosphate and salt. In the former case, as in previous studies, the Ca, P and Na content of LJ was not taken into account in formulating the meal mixture; in the latter treatment, taking these into account eliminated the need for supplements.In Trial 2, 18 pigs received LJ at a similar level to that given in Trial 1, together with a meal mixture without the mineral supplements. The water intake of half the pigs was restricted to 2.5 l/kg meal, including the water in LJ. The remaining pigs had, in addition, a supply of water ad libitum.The pigs given LJ in Trial 1 had much lower growth rates and feed: gain ratios than the controls given white-fish meal. A significant, but relatively small, improvement in performance was achieved by giving LJ with the unsupplemented meal rather than with meal supplemented with minerals. In Trial 2, supplying additional water ad libitum significantly increased feed intake. There was a tendency for this to increase daily gain, although the difference was not significant.Despite the improvements due to adjustments of mineral and water intake, the performance of the pigs given LJ as the only protein supplement was unsatisfactory. This may be due to the very high level of potassium in LJ. This cannot be taken into account in formulating a practical basal meal mixture.  相似文献   

18.
Abstract

A multilayer film of argon adsorbed on the basal plane of graphite at 103 K was simulated using isokinetic molecular dynamics. The local chemical potentials in the film were evaluated using three algorithms suggested in the literature: test particle insertion, real particle calculation and the ratio method, which relies on calculations of the local energy distribution functions for test and real particles. Although none of these was suitable for calculations involving the partially solidified first adsorbed layer, the test particle and the ratio method produced useful results for regions in the film corresponding to second and higher layers. The ratio method is shown to be the most realistic, giving constant local chemical potentials of reasonably high precision for all points other than in the first layer.  相似文献   

19.
AimThe aim of this work is to present a method of beam weight and wedge angle optimization for patients with prostate cancer.Background3D-CRT is usually realized with forward planning based on a trial and error method. Several authors have published a few methods of beam weight optimization applicable to the 3D-CRT. Still, none on these methods is in common use.Materials and methodsOptimization is based on the assumption that the best plan is achieved if dose gradient at ICRU point is equal to zero. Our optimization algorithm requires beam quality index, depth of maximum dose, profiles of wedged fields and maximum dose to femoral heads. The method was tested for 10 patients with prostate cancer, treated with the 3-field technique. Optimized plans were compared with plans prepared by 12 experienced planners. Dose standard deviation in target volume, and minimum and maximum doses were analyzed.ResultsThe quality of plans obtained with the proposed optimization algorithms was comparable to that prepared by experienced planners. Mean difference in target dose standard deviation was 0.1% in favor of the plans prepared by planners for optimization of beam weights and wedge angles. Introducing a correction factor for patient body outline for dose gradient at ICRU point improved dose distribution homogeneity. On average, a 0.1% lower standard deviation was achieved with the optimization algorithm. No significant difference in mean dose–volume histogram for the rectum was observed.ConclusionsOptimization shortens very much time planning. The average planning time was 5 min and less than a minute for forward and computer optimization, respectively.  相似文献   

20.
The effects of human body model resolution on computed electric fields induced by 60 Hz uniform magnetic fields are investigated. A recently-developed scalar potential finite difference code for low-frequency electromagnetic computations is used to model induction in two anatomically realistic human body models. The first model consists of 204 290 cubic voxels with 7.2-mm edges, while the second comprises 1 639 146 cubic voxels with 3.6-mm edges. Calculations on the lower-resolution model using, for example, the finite difference time domain or impedance methods, push the capabilities of workstations. The scalar method, in contrast, can handle the higher-resolution model using comparable resources. The results are given in terms of average and maximum electric field intensities and current density magnitudes in selected tissues and organs. Although the lower-resolution model provides generally acceptable results, there are important differences that make the added computational burden of the higher-resolution calculations worthwhile. In particular, the higher-resolution modelling generally predicts peak electric fields intensities and current density magnitudes that are slightly higher than those computed using the lower-resolution modelling. The differences can be quite large for small organs such as glands. Bioelectromagnetics 18:478–490, 1997. © 1997 Wiley-Liss, Inc.  相似文献   

设为首页 | 免责声明 | 关于勤云 | 加入收藏

Copyright©北京勤云科技发展有限公司  京ICP备09084417号