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1.

Xin Feng Kelin Xia Zhan Chen Yiying Tong Guo‐Wei Wei 《Journal of computational chemistry》2013,34(24):2100-2120

Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics, and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X‐ray, NMR, and cryo‐electron microscopy, and theoretical/mathematical models, such as molecular dynamics, the Poisson–Boltzmann equation, and the Nernst–Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger's functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent–solute interaction, and ion channel dynamics, whereas our coarse resolution representations highlight the compatibility of protein‐ligand bindings and possibility of protein–protein interactions. © 2013 Wiley Periodicals, Inc. 相似文献

2.

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc. 相似文献

3.

Yanliang Ren Bo Chi Osama Melhem Ke Wei Lingling Feng Yongjian Li Xinya Han Ding Li Ying Zhang Jian Wan Xin Xu Minghui Yang 《Journal of computational chemistry》2013,34(12):1005-1012

In the present study, the electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria C‐phycocyanin (C‐PC) were investigated in term of the Förster theory. The corresponding excited states and transition dipole moments of phycocyanobilins (PCBs) located into C‐PC were examined by model chemistry in gas phase at time‐dependent density functional theory (TDDFT), configuration interaction‐singles (CIS), and Zerner's intermediate neglect of differential overlap (ZINDO) levels, respectively. Then, the long‐range pigment‐protein interactions were approximately taken into account by using polarizable continuum model (PCM) at TDDFT level to estimate the influence of protein environment on the preceding calculated physical quantities. The influence of the short‐range interaction caused by aspartate residue nearby PCBs was examined as well. Only when the protonation of PCBs and its long‐ and short‐range interactions were properly taken into account, the calculated energy transfer rates (1/

*K*) in the framework of Förster model at TDDFT/B3LYP/6‐31+G* level were in good agreement with the experimental results of C‐PC monomer and trimer. Furthermore, the present calculated results suggested that the energy transfer pathway in C‐PC monomer is predominant from β‐155 to β‐84 (1/*K*= 13.4 ps), however, from α‐84 of one monomer to β‐84 (1/*K*= 0.3–0.4 ps) in a neighbor monomer in C‐PC trimer. In C‐PC hexamer, an additional energy flow was predicted to be from β‐155 (or α‐84) in top trimer to adjacent β‐155 (or α‐84) (1/*K*= 0.5–2.7 ps) in bottom trimer. © 2013 Wiley Periodicals, Inc. 相似文献4.

In this paper, we demonstrate how to apply recently discovered ferromagnetic nematic liquid crystal for visualisation of magnetic fields. The material exhibits strong optical response to both external electric and magnetic fields, which gives us an opportunity to use it for the detection of an area of magnetic vector field in a way that both, the magnitude and the direction of a given field can be simultaneously measured. We discuss the physical model that describes the behaviour of ferromagnetic liquid crystal placed in a liquid crystal cell and demonstrate the method of extracting the information about an arbitrary magnetic field from the combination of magneto-optic and electro-optic response of the sample placed in that field. We have applied the principle to a special case, where magnetic field was visualised on a 2D area near a cylindrical permanent magnet. 相似文献

5.

Recently it has been shown experimentally by the authors that a highly twisted thin nematic cell at low temperatures can separate into a smectic A region in the middle of the cell surrounded by twisted nematic layers at the boundaries. In this case the twist is expelled into the nematic layers and the nematic–smectic A transition temperature is strongly depressed. We present a thermodynamic theory of such a phase transition in a twisted nematic cell, taking into account that the smectic A slab inside the nematic cell can be stable only if the decrease of free energy in the smectic region overcomes the increase in distortion energy of the twist deformation in the nematic layers plus the energy of the nematic–smectic A interface. In such a system the equilibrium thickness of the smectic A slab corresponds to the minimum of the total free energy of the whole cell, which includes all the bulk and surface contributions. Existing experimental data are at least qualitatively explained by the results of the present theory. This opens a unique possibility to study the properties of the nematic–smectic interface which is perpendicular to the smectic layers. 相似文献

6.

It is shown that the orientational structure of intermediate smectic phases can be determined using the symmetry properties of the general free energy with arbitrary orientational coupling between smectic layers, without addressing a particular model. The structure of three‐ and four‐layer intermediate phases, obtained in this way, corresponds to experimental data. The same method enables one to predict the structure of intermediate phases with periodicity of five and six layers, which have not been observed experimentally so far. The resonant X‐ray spectra of the five‐ and six‐layer intermediate phases with predicted structure have also been calculated. These spectra are characterized by a number of features which enable one to distinguish five‐layer and six‐layer intermediate phases from phases with smaller periods. 相似文献

7.

《印度化学会志》2023,100(3):100935

The educational value of nanofluids in several industrial and biological sectors, particularly in fluid movement systems known as peristalsis, has piqued researchers' interest in studying the peristaltic movement of nanofluids. Additionally, nanoparticles have crucial roles in many engineering and manufacturing processes, including those involving heat exchangers, cooling systems, boilers, MEMS, chemical engineering, laser diode arrays, and cool automotive engines. Various studies have been conducted on this subject. This is done by looking at how migratory gyrotactic microorganisms migrate through an artery that is anisotropically narrowing in a blood-based nanofluid that is non-Newtonian. To comprehend, the Powell-Eyring fluid model is used how the blood's rheology differs from that of a Newtonian fluid. Both Newtonian fluid characteristics and non-Newtonian traits can be seen in this fluid pattern. Equations for continuity, temperature, motile microbes, momentum, and concentration are used to create the mathematical formulation. The series solutions, which are produced using perturbation theory solutions are discussed using graphs for all dominant parameters. Discussion also includes the distribution of temperature, velocity, and swimming microorganisms. Additionally, the effects of wall shear stress, the Nusselt and Sherwood numbers, as well as the phenomena of trapping, are all examined in detail and shown in the graphs. Entropy generation analyses have also been undertaken. The investigation also reveals a crucial behaviour in the use of the heart-lung engine for extracorporeal blood circulation in medicine that may have an impact on the damage of red blood cells as a result of the large fluctuation in wall shear stress. When liquids are transported using arthro pumps and roller pumps in living organs, the results are likewise of significant use. The results are very helpful for executing particle movements in cardiac surgery and may be applicable to the fluid peristaltic pump used in haemodialysis. 相似文献

8.

《印度化学会志》2023,100(3):100937

Main core part of the research is to develop a novel mathematical model of MHD-Maxwell nanofluid over a stretching and shrinking surface. The stretching ratio, velocity slip and convective boundary conditions are also incorporated. The PDE's with associative boundary conditions are deduced into coupled highly non-linear ODE's by utilizing suitable transformations. The deduced dimensionless sets of Ordinary differential equations are solved by Optimal-Homotopy Analysis Method (OHAM). Behavior of pertinent parameters on the velocity, temperature and concentration fields as well as important aspects skin friction, Nusselt number and Sherwood number are recorded in Table 2. Outcomes declared that role of stretching ratio plays a prominent role in stretching surfaces its clearly recorded in Table 1(a & b). 相似文献

9.

《印度化学会志》2023,100(2):100913

Owing to contribution of thermo-diffusion phenomenon in various engineering and industrial frame works, scientists have presented some exclusive investigations on this topic. In current research, the thermos-diffusion prospective of second grade material accounted by a moving cylinder have been predicted. The applications of Soret and Dufour effects based on the thermos-diffusion phenomenon is evaluated. The magnetic force and viscous dissipation effects are presented for the current flow model. Additionally, the improvement in thermal transport of viscoelastic fluid is suggested with radiative phenomenon. The convective boundary constraints are used to report the thermos-diffusion phenomenon. The system based on dimensionless form is obtained with interaction of new variables. The shooting technique is used for numerical observations by using MATLAB software. The physical impact of phenomenon in view of parameters is graphically attributed. It has been noted that increasing velocity profile is results due to curvature parameter and viscoelastic parameter. The enhancement in thermal profile is noted due to Dufour number and Eckert number. 相似文献

10.