Biomedical simulation of heat transfer in a human heart

Theory and practical experiences from numerical simulations of heat transfer in the field of medicine are presented in this paper. The cooling of a human heart during surgery was taken as an illustrative example. All phases of the simulation process are described starting with the construction of an irregularly shaped 3-dimensional model. The mathematical model is based on diffusion and Navier-Stokes equations. The system of partial differential equations is solved by finite difference approximation using an explicit time-stepping scheme to obtain the time evolution of the solution for the complete simulated interval, which is typically 1 h. A typical domain is composed of several million voxels; therefore, the program was parallelized to speed up the simulation. A speed-up of 8.2 was obtained on 16 processors in a Linux cluster.     

Chromenone-based GSK-3β inhibitors as potential therapeutic targets for cardiovascular diseases: In silico study,molecular dynamics,and ADMET profiles

Glycogen synthase kinase-3 beta (GSK-3β) regulates glycogen metabolism and many different cellulars, including apoptosis, signaling, and neural. It is a crucial therapeutic receptor in heart disease, type 2 diabetes, and Alzheimer's. In this study, using computational methods, flavonoid compounds were investigated for potential inhibitors against GSK-3β. Virtual screening was utilized to investigate flavonoid compounds obtained from the PubChem database. Structure of human heart mitochondria of GSK-3β receptor constructed by homology modeling. Best binding poses were discovered via in silico molecular docking simulation. We surveyed noncovalent interactions among amino acid residues involved in the active site of the modeled Protein and compounds via molecular docking and molecular dynamics (MD).Moreover, ADMET characteristics of best docking conformers have been investigated. The obtained results revealed that compound 1 containing chromenone moiety with binding energy H-bond ?11.4 kcal/mol inhibited effectively binding pocket of the GSK-3β receptor. Moreover, MD simulation analysis (RMSD and radius of gyration indicated complex of the compound and GSK-3β receptor remained stable throughout 100 ns MD simulation, and also analysis of ADMET profiles revealed that selected compounds had good drug-likeness and pharmacokinetic properties. Hence, it was suggested that compounds with chromenone scaffold could potentially inhibit GSK-3β. Structural modification of the chromenone derivatives may result in the discovery of promising candidates for identifying novel drugs as GSK-3β inhibitors.     

A new approach to the ferritin iron core growth: influence of the H/L ratio on the core shape

An electron microscopy study, in combination with modeling and image simulation, of four different reconstituted ferritin samples: recombinant human H and L homopolymers, and H and L heteropolymers of native L-subunit-rich horse spleen and H-subunit-rich human heart ferritins, points out the existence of a correlation between iron core shape and protein shell.     

Epicardial development in the rat: a new perspective.

Development of the epicardium is critical to proper heart formation. It provides all of the precursor cells that form the coronary system and supplies signals that stimulate cardiac myocyte proliferation. The epicardium forms from mesothelial cells associated with the septum transversum and is referred to as the proepicardium (PE). Two different methods by which these PE cells colonize the developing heart have been described. In avians, PE cells form a bridge to the heart over which PE cells migrate onto the heart. In fish and mammals, PE cells form vesicles of cells that detach from the mesothelium, float through the pericardial cavity, and attach to the heart. A previous study of rat PE development investigated this process at the histological level. Protein markers have been developed since this study. Thus, we investigated this important developmental process coupled with these new markers using other visualization techniques such as scanning electron microscopy (SEM) and confocal microscopy. Finally, a novel, three-dimensional (3-D) culture system was used to confirm the identity of the PE cells. In this study, we found convincing evidence that the rat PE cells directly attach to the heart in a manner similar to that observed in avians.     

Preprogramming Complex Hydrogel Responses using Enzymatic Reaction Networks

The creation of adaptive matter is heavily inspired by biological systems. However, it remains challenging to design complex material responses that are governed by reaction networks, which lie at the heart of cellular complexity. The main reason for this slow progress is the lack of a general strategy to integrate reaction networks with materials. Herein we use a systematic approach to preprogram the response of a hydrogel to a trigger, in this case the enzyme trypsin, which activates a reaction network embedded within the hydrogel. A full characterization of all the kinetic rate constants in the system enabled the construction of a computational model, which predicted different hydrogel responses depending on the input concentration of the trigger. The results of the simulation are in good agreement with experimental findings. Our methodology can be used to design new, adaptive materials of which the properties are governed by reaction networks of arbitrary complexity.     

分子动力学模拟在聚合物热解中的应用

分子动力学模拟作为分子模拟的重要分支已经在化学、化工、材料、生物等领域受到了广泛的关注。介绍了分子动力学模拟的基本原理,阐述了分子动力学模拟在高分子聚合物热解反应机理研究中的应用。实例表明:在研究物质化学反应机理方面,分子动力学模拟是一种有效的研究手段。     

Ion trajectory simulation of inductively coupled plasma mass spectrometry based on plasma-interface behavior

An ion trajectory simulation study of inductively coupled plasma mass spectrometry (ICP-MS) was conducted based on a newly proposed plasma interface model. The model is based on the formation of a plasma boundary by interaction between plasma behind the skimmer cone and the electric field of the extraction lens system. An estimated plasma boundary position, or charge separation position is used to determine the initial conditions of the simulation study. Two regions of conditions, in terms of radio frequency (RF) power for the ICP and first extraction lens voltage showing characteristic sensitivity, were reasonably explained by this simulation. This paper suggests that the location and shape of the plasma boundary are key factors that affect the focusing properties and transmission of the ion lens.     

离子液体的分子模拟与量化计算

分子模拟方法是研究离子液体结构与性质关系非常有效的方法,可以从分子间相互作用出发研究离子液体的微观结构、热力学和动力学性质;量子化学计算则在分子、电子水平上对离子液体的结构、性能及催化机理进行理论研究。本文综述了分子模拟方法应用于离子液体体系的研究进展,重点介绍了利用分子动力学模拟和量子化学计算方法对不同离子液体进行研究,获得离子液体的结构性质、光谱性质(红外光谱、拉曼光谱)及离子液体催化反应机理等,为探讨离子液体结构-性质的关系、离子对的作用方式、催化反应活性中心、反应途径、反应活化能、振动模式和频率以及设计功能性离子液体提供理论导向。     

The protective effects of silymarin against doxorubicin-induced cardiotoxicity and hepatotoxicity in rats

Silymarin is a complex of five major compounds, and silibinin is the most biologically active component of the complex. The aim of this study was to investigate, evaluate and confirm the potential cardioprotective and hepatoprotective effects of administration of silymarin, rich in silibinin, at a dose of 60 mg/kg orally for a time-span of 12 days on doxorubicin induced toxicity in male Wistar rats. The in vivo model was used to explore whether silymarin could prevent damage of liver and heart tissue induced by doxorubicin administered every other day at dose of 1.66 mg/kg intraperitoneally for twelve days. In the study the change of body weight, ECG changes, biochemical parameters of oxidative stress, serum activity of alanine and aspartate transaminase, lactate dehydrogenase, creatine kinase and histological preparations of heart and liver samples of treated animals were examined. According to physiological, pharmacological, microscopic and biochemical results, we confirmed that at the examined dose, silymarin exhibits a protective influence on the heart and liver tissue against toxicity induced by doxorubicin.     

Heritability and linkage study on heart rates in a Mongolian population

Elevated heart rate has been proposed as an independent risk factor for cardiovascular diseases, but their interrelationships are not well understood. In this study, we performed a genome-wide linkage scan in 1,026 individuals (mean age 30.6 years, 54.5% women) from 73 extended families of Mongolia and determined quantitative trait loci that influence heart rate. The DNA samples were genotyped using deCODE 1,039 microsatellite markers for 3 cM density genome-wide linkage scan. Correlation analysis was carried out to evaluate the correlation of the covariates and the heart rate. T-tests of the heart rate were also performed on sex, smoking and alcohol intake. Consequently, this model was used in a nonparametric genome-wide linkage analysis using variance component model to create a multipoint logarithm of odds (LOD) score and a corresponding P value. In the adjusted model, the heritability of heart rate was estimated as 0.32 (P<.0001) and a maximum multipoint LOD score of 2.03 was observed in 77 cM region at chromosome 18. The second largest LOD score of 1.52 was seen on chromosome 5 at 216 cM. Genes located on the specified locations in chromosomes 5 and 18 may be involved in the regulation of heart rate.     

心脏胶原蛋白中交联氨基酸的质谱分析

心脏衰竭可能与心脏胶原蛋白交联异常有关,因为交联过程对心脏胶原蛋白的机械强度起决定作用.研究表明,某些交联氨基酸的含量可以用作对应胶原蛋白交联异常的分子标记,但心脏胶原蛋白交联异常的分子标记尚不清楚.本研究建立了串联质谱的分析方法可以高选择性的检测水解胶原蛋白质中两种重要的交联氨基酸-吡啶诺林(PYD)和去氧吡啶诺林(DPD).在小鼠心室胶原蛋白酸性水解产物中检测到DPD,未检测到PYD,说明PYD与心脏胶原蛋白的交联过程无关,而DPD在心脏胶原蛋白交联中起更重要的作用,有可能成为与心脏衰竭相关的分子标记.本研究提供了一种基于质谱的研究心脏胶原蛋白交联产物的方法,也可用于其它胶原蛋白的分析.     

两相聚合物熔体中相区粗化过程的格子Boltzmann研究

在自由能格子Boltzmann方法的基础上, 采用附加的作用力项描述非理想流体作用, 得到了改进自由能形式的格子Boltzmann模型. 对于高分子共混体系, 采用了Flory-Huggins自由能函数形式, 对两相聚合物熔体中的相区粗化过程进行了模拟. 首先通过格子Boltzmann方法计算得到了聚合物共混物的相分离曲线, 该曲线与两相共存曲线的解析值吻合得较好. 应用此模型, 研究了聚合物共混体系不稳分相机理的相区粗化过程. 在此基础上, 探讨了分相后期相区尺寸随时间的增长指数与高分子链长和Flory-Huggins相互作用参数的关系. 模拟结果表明, 相区的后期增长机理与高分子链长和Flory-Huggins相互作用参数关系不大, 而流体的粘度决定了相区的后期增长机理, 是影响相区后期增长指数的重要因素.     

Analysis and design of photobioreactors for microalgae production I: method and parameters for radiation field simulation

Having capabilities for the simulation of the radiation field in suspensions of microalgae constitutes a great asset for the analysis, optimization and scaling-up of photobioreactors. In this study, a combined experimental and computational procedure is presented, specifically devised for the assessment of the coefficients of absorption and scattering, needed for the simulation of such fields. The experimental procedure consists in measuring the radiant energy transmitted through samples of suspensions of microalgae of different biomass concentrations, as well as the forward and backward scattered light. At a microscopic level, suspensions of microalgae are complex heterogeneous media and due to this complexity, in this study they are modeled as a pseudocontinuum, with centers of absorption and scattering randomly distributed throughout its volume. This model was tested on suspensions of two algal species of dissimilar cell shapes: Chlorella sp. and Scenedesmus quadricauda. The Monte Carlo simulation algorithm developed in this study, when used as a supporting subroutine of a main optimization program based on a genetic algorithm, permits the assessment of the physical parameters of the radiation field model. The Monte Carlo algorithm simulates the experiments, reproducing the events that photons can undergo while they propagate through culture samples or at its physical boundaries.     

Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length

Molecular dynamics (MD) simulations in conjunction with thermodynamic perturbation approach was used to calculate relative solvation free energies of five pairs of small molecules, namely; (1) methanol to ethane, (2) acetone to acetamide, (3) phenol to benzene, (4) 1,1,1 trichloroethane to ethane, and (5) phenylalanine to isoleucine. Two studies were performed to evaluate the dependence of the convergence of these calculations on MD simulation length and starting configuration. In the first study, each transformation started from the same well-equilibrated configuration and the simulation length was varied from 230 to 2,540 ps. The results indicated that for transformations involving small structural changes, a simulation length of 860 ps is sufficient to obtain satisfactory convergence. In contrast, transformations involving relatively large structural changes, such as phenylalanine to isoleucine, require a significantly longer simulation length (>2,540 ps) to obtain satisfactory convergence. In the second study, the transformation was completed starting from three different configurations and using in each case 860 ps of MD simulation. The results from this study suggest that performing one long simulation may be better than averaging results from three different simulations using a shorter simulation length and three different starting configurations.     

Thermodynamically Motivated Criterion of Hydrogen Bonds in Water Simulations

A computer simulation study of a system containing 33666 SPC/E water molecules at the atmospheric pressure and room temperature is carried out. A thermodynamically motivated geometric criterion of the hydrogen bond is developed based on statistical regularities of joint distributions of oxygen-oxygen, oxygen-hydrogen distances, and the interaction energies of molecular pairs corresponding to these distances. Using this criterion makes it possible to substantially increase the selectivity of the algorithms for identifying hydrogen bonds during computer simulation.     

计算机模拟技术在表面活性剂研究中的应用

根据表面活性剂溶液行为的模拟所需的时间和空间尺度,介绍了三种主要的计算机模拟方法:原子模拟、粗粒模拟和介观模拟.综述了这些模拟方法在表面活性剂单体、缔合体系及与聚合物相互作用等研究中的应用.指出了用计算机模拟方法研究表面活性剂体系的发展前景.     

Domain growth dynamics and Freedericksz transitions of liquid crystals: Brownian dynamics simulations on lattices

A Brownian dynamics simulation using the Lebwohl-Lasher (LL) nematogen model is developed to investigate liquid crystals (LCs) on two-dimensional lattices. According to the examination of defect annihilation and domain growth, this methodology appears to be a successful approach in studying the LC dynamics, its main advantage being that the time evolution in the simulation mimics the physical time, in contrast to related modellings published recently. In addition, the Freedericksz transition of an LC under static magnetic fields is reproduced. Further analysis of the simulation outputs and the associated continuum theory of LC elasticity reveals that the LL potential can, by analogy, be obtained from the Frank energy. As a result, the methodology of the combination of Brownian dynamics simulation with the LL model is proven valid and can be extended to study the director dynamics of LCs subjected to external fields.     

Dynamics of liquid–liquid demixing: mesoscopic simulations of polymer solutions

In this article, the mesoscopic simulation method dissipative particle dynamics (DPD) is applied to study the dynamics of polymer–solvent liquid–liquid phase separation. It will be shown that the degree of branching has a pronounced effect on the radius of gyration and the centre of mass diffusion of the polymer. Based on the simulation results it can be concluded that the difference in chemical potential between the mixed and the demixed state is the main driving force behind the centre of mass diffusion (and thus phase separation), rather than the reduced radius of gyration due to to polymer chain collapse.