Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides

Molecular dynamics (MD) simulation using the reference potential spatial warping algorithm (REPSWA) is a promising method for computing the conformational equilibrium of a system with a rugged energy surface. Its effectiveness has previously been demonstrated using only a simplified model system of a hydrocarbon chain omitting nonbonded interaction terms from the potential energy function. To evaluate the applicability of REPSWA MD simulation to more realistic problems, we applied it to small peptide systems in an aqueous environment. Difficulties were encountered, however, forcing us to devise several modifications. We investigated their effectiveness in comparison to conventional constant-temperature and multicanonical MD simulations. We found that the sampling efficiency of the modified REPSWA MD after a careful optimization of its parameters was better than that of the constant-temperature MD and comparable to that of the multicanonical MD in several cases.     

Predictive power of molecular dynamics receptor structures in virtual screening

Molecular dynamics (MD) simulation is a well-established method for understanding protein dynamics. Conformations from unrestrained MD simulations have yet to be assessed for blind virtual screening (VS) by docking. This study presents a critical analysis of the predictive power of MD snapshots to this regard, evaluating two well-characterized systems of varying flexibility in ligand-bound and unbound configurations. Results from such VS predictions are discussed with respect to experimentally determined structures. In all cases, MD simulations provide snapshots that improve VS predictive power over known crystal structures, possibly due to sampling more relevant receptor conformations. Additionally, MD can move conformations previously not amenable to docking into the predictive range.     

Membranes and theoretical modeling of membrane distillation: a review

Membrane distillation (MD) is one of the non-isothermal membrane separation processes used in various applications such desalination, environmental/waste cleanup, food, etc. It is known since 1963 and is still being developed at laboratory stage for different purposes and not fully implemented in industry. An abrupt increase in the number of papers on MD membrane engineering (i.e. design, fabrication and testing in MD) is seen since only 6 years ago. The present paper offers a comprehensive MD state-of-the-art review covering a wide range of commercial membranes, MD membrane engineering, their MD performance, transport mechanisms, experimental and theoretical modeling of different MD configurations as well as recent developments in MD. Improved MD membranes with specific morphology, micro- and nano-structures are highly demanded. Membranes with different pore sizes, porosities, thicknesses and materials as well as novel structures are required in order to carry out systematic MD studies for better understanding mass transport in different MD configurations, thereby improving the MD performance and looking for MD industrialization.     

Dynamics Studies on Molecular Diffusion in Zeolites

1 INTRODUCTION Zeolites have attracted much attention in both scientific and industrial areas for their special characteristics and multiple uses. Zeolites are composed of TO4 (T = Si, Al, Ga, P, etc.) tetrahedra which are connected with each other by sharing oxygen atoms to produce a complex and repetitive three-dimensional atom network with regular molecular dimension cavities joined by channels. Shape selectivity is the most important property of zeolites. Combined with the possib…     

计算机辅助药物设计中的多维定量构效关系模型化方法

多维定量构效关系(MD QSAR)在计算机辅助药物设计中得到了广泛而成功的应用,结合本研究组的工作,本文系统综述了建立各种MD QSAR模型的方法和策略,对近年来有关的MD QSAR应用研究进展进行了回顾,并对其在新世纪药物设计中应用前景做了展望。     

MD2 blockade prevents modified LDL-induced retinal injury in diabetes by suppressing NADPH oxidase-4 interaction with Toll-like receptor-4

Modified LDL-induced inflammation and oxidative stress are involved in the pathogenesis of diabetic retinopathy. Recent studies have also shown that modified LDL activates Toll-like receptor 4 (TLR4) to mediate retinal injury. However, the mechanism by which modified LDL activates TLR4 and the potential role of the TLR4 coreceptor myeloid differentiation protein 2 (MD2) are not known. In this study, we inhibited MD2 with the chalcone derivatives L2H17 and L6H21 and showed that MD2 blockade protected retinal Müller cells against highly oxidized glycated-LDL (HOG-LDL)-induced oxidative stress, inflammation, and apoptosis. MD2 inhibition reduced oxidative stress by suppressing NADPH oxidase-4 (NOX4). Importantly, HOG-LDL activated TLR4 and increased the interaction between NOX4 and TLR4. MD2 was required for the activation of these pathways, as inhibiting MD2 prevented the association of NOX4 with TLR4 and reduced NOX4-mediated reactive oxygen species production and TLR4-mediated inflammatory factor production. Furthermore, treatment of diabetic mice with L2H17 significantly reduced LDL extravasation in the retina and prevented retinal dysfunction and apoptosis by suppressing the TLR4/MD2 pathway. Our findings provide evidence that MD2 plays a critical role in mediating modified LDL-induced cell injury in the retina and suggest that targeting MD2 may be a potential therapeutic strategy.Subject terms: Obesity, Type 2 diabetes     

Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent

Replica exchange methods (REMs) are increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. However, despite having been shown to be very effective on model systems, the application of REM in complex systems such as for the simulation of protein and peptide folding in explicit solvent has not been objectively tested in detail. Here we present a comparison of conventional MD and temperature replica exchange MD (T-REMD) simulations of a beta-heptapeptide in explicit solvent. This system has previously been shown to undergo reversible folding on the time scales accessible to MD simulation and thus allows a direct one-to-one comparison of efficiency. The primary properties compared are the free energy of folding and the relative populations of different conformers as a function of temperature. It is found that to achieve a similar degree of precision T-REMD simulations starting from a random set of initial configurations were approximately an order of magnitude more computationally efficient than a single 800 ns conventional MD simulation for this system at the lowest temperature investigated (275 K). However, whereas it was found that T-REMD simulations are more than four times more efficient than multiple independent MD simulations at one temperature (300 K) the actual increase in conformation sampling was only twofold. The overall gain in efficiency using REMD resulted primarily from the ordering of different conformational states over temperature, as opposed to a large increase of conformational sampling. It is also shown that in this system exchanges are accepted primarily based on (random) fluctuations within the solvent and are not strongly correlated with the instantaneous peptide conformation raising questions in regard to the efficiency of T-REMD in larger systems.     

Recent advances in clinical microdialysis

Clinical microdialysis (MD) is a minimally invasive sampling technique that offers selective in-vivo measurement of free, active drug or biomolecule concentrations in human tissues and organs. From a regulatory perspective, MD can thus be seen as a suitable scientific tool that meets regulatory requirements for the study of tissue distribution or bioequivalence during drug development. From a clinical perspective, the use of MD in different applications has shown the potential to rationalize drug-dosing regimens and to influence clinical decision-making, although validation and correlation of MD-derived results with clinical response are required to promote routine clinical use of the technique. From an analytical perspective, highly sensitive analytical systems have increasingly become available for MD-sample analysis, and these have further improved the quality and the power of MD-derived information. Given the constant development in recent years, MD data might become an important part of new drug submissions and clinical treatment algorithms, and might positively influence patient benefit in the future.     

Self-consistency in frozen-density embedding theory based calculations

The bi-functional for the non-electrostatic part of the exact embedding potential of frozen-density embedding theory (FDET) depends on whether the embedded part is described by means of a real interacting many-electron system or the reference system of non-interacting electrons (see [Wesolowski, Phys. Rev. A. 77, 11444 (2008)]). The difference δΔF(MD)[ρ(A)]/δρ(A)(r), where ΔF(MD)[ρ(A)] is the functional bound from below by the correlation functional E(c)[ρ(A)] and from above by zero. Taking into account ΔF(MD)[ρ(A)] in both the embedding potential and in energy is indispensable for assuring that all calculated quantities are self-consistent and that FDET leads to the exact energy and density in the limit of exact functionals. Since not much is known about good approximations for ΔF(MD)[ρ(A)], we examine numerically the adequacy of neglecting ΔF(MD)[ρ(A)] entirely. To this end, we analyze the significance of δΔF(MD)[ρ(A)]/δρ(A)(r) in the case where the magnitude of ΔF(MD)[ρ(A)] is the largest, i.e., for Hartree-Fock wavefunction. In hydrogen bonded model systems, neglecting δΔF(MD)[ρ(A)]/δρ(A)(r) in the embedding potential marginally affects the total energy (less than 5% change in the interaction energy) but results in qualitative changes in the calculated hydrogen-bonding induced shifts of the orbital energies. Based on this estimation, we conclude that neglecting δΔF(MD)[ρ(A)]/δρ(A)(r) may represent a good approximation for multi-reference variational methods using adequate choice for the active space. Doing the same for single-reference perturbative methods is not recommended. Not only it leads to violation of self-consistency but might result in large effect on orbital energies. It is shown also that the errors in total energy due to neglecting δΔF(MD)[ρ(A)]/δρ(A)(r) do not cancel but rather add up to the errors due to approximation for the bi-functional of the non-additive kinetic potential.     

Shielding of ionic interactions by sulfur dioxide in an ionic liquid

The effect of adding SO2 on the structure and dynamics of 1-butyl-3-methylimidazolium bromide (BMIBr) was investigated by low-frequency Raman spectroscopy and molecular dynamics (MD) simulations. The MD simulations indicate that the long-range structure of neat BMIBr is disrupted resulting in a liquid with relatively low viscosity and high conductivity, but strong correlation of ionic motion persists in the BMIBr-SO2 mixture due to ionic pairing. Raman spectra within the 5相似文献   

NiO-Fe2O3/MD催化剂的制备及其在城市生活垃圾气化中的应用

以改性白云石(Modified Dolomite, MD)为载体,利用沉积沉淀法制备了负载型NiO-Fe₂O₃/MD催化剂,并利用XRD、SEM、TEM、BET等手段对催化剂进行了表征和分析.同时,利用双固定床反应器对NiO-Fe₂O₃/MD催化剂在城市生活垃圾气化中的催化活性和使用寿命进行了评价,并与NiO/MD催化剂进行了比较.实验结果表明,NiO-Fe₂O₃/MD催化剂为核壳式涂层结构,表面活性颗粒粒径约为37 nm,比表面积62.48 m²/g.催化剂活性测试显示,NiO-Fe₂O₃/MD催化剂用于城市生活垃圾气化具有极高的催化活性,能够显著提高产品燃气品质及燃气中的H₂含量,减少焦油的产生;相对于NiO/MD催化剂,其抗失活能力强,使用寿命长.     

Evaluation of sulfated maltodextrin as a novel anionic chiral selector for the enantioseparation of basic chiral drugs by capillary electrophoresis

Introducing a new class of chiral selectors is an interesting work and this issue is still one of the hot topics in separation science and chirality. In this study, for the first time, sulfated maltodextrin (MD) was synthesized as a new anionic chiral selector and then it was successfully applied for the enantioseparation of five basic drugs (amlodipine, hydroxyzine, fluoxetine, tolterodine, and tramadol) as model chiral compounds using CE. This chiral selector has two recognition sites: a helical structure and a sulfated group which contribute to three corresponding driving forces; inclusion complexation, electrostatic interaction, and hydrogen binding. Under the optimized condition (buffer solution: 50 mM phosphate (pH 3.0) and 2% w/v sulfated MD; applied voltage: 18 kV; temperature: 20°C), baseline enantioseparation was observed for all mentioned chiral drugs. When instead of sulfated MD neutral MD was used under the same condition, no enantioseparation was observed which means the resolution power of sulfated MD is higher than neutral MD due to the electrostatic interaction between sulfated groups and protonated chiral drugs. Also, the countercurrent mobility of negatively charged MD (sulfated MD) allows more interactions between the chiral selector and chiral drugs and this in turn results in a successful resolution for the enantiomers. Furthermore, a higher concentration of neutral MD (approximately five times) is necessary to achieve the equivalent resolution compared with the negatively charged MD.     

3,4-二羟基苯甲酸在自组装结构中的电化学行为

电极与有确定取向的电活性基团之间的电子传递是电化学领域的研究热点．利用二维有序薄膜固定电活性官能团是一个成熟的方法［１］,主要包括ＬＢ技术和自组装技术,这两者都存在着样品合成困难的问题．近年来,通过表面逐层反应来固定电活性官能团已有研究,但是反应过程...     

Implementation of pi-pi interactions in molecular dynamics simulation

No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation.     

High-performance liquid chromatographic determination of L-3-(3,4-dihydroxyphenyl)-2-methylalanine (alpha-methyldopa) in human urine and plasma

A procedure is described for the determination of alpha-methyldopa (MD) [L-3-(3,4-dihydroxyphenyl)-2-methylalanine], its metabolite and catecholamines in the urine and plasma of patients undergoing MD therapy, by high-performance liquid chromatography with dual working electrode coulometric detection. An efficient sample preparation procedure is presented for the isolation of endogenous MD, its metabolite and catecholamines from plasma or urine. After deproteinization of a plasma sample with methanol containing 2% of 0.5 M perchloric acid and dilution of a urine sample (1:200), MD, dihydroxyphenylacetic acid (DOPAC), 3-O-methylmethyldopa (3-OMMD) and homovanillic acid (HVA) were separated with a Supelcosil LC-18 column. Catecholamines were extracted from the supernatant of deproteinized plasma or from urine by ion exchange on a Sephadex CM-25 column and subsequent adsorption on alumina. The use of the same mobile phase for the concurrent assay of MD, its metabolite and catecholamines increased considerably the efficiency of sample separation. Recoveries were close to 100% for MD, DOPAC, 3-OMMD and HVA and 70% for catecholamines. The effects of various experimental parameters related to mobile phase composition on chromatographic performance are reported. The purity of the eluted compounds was tested by recording both the first detector response (oxidation current) and the second detector response (reduction current). The ratio of the detector responses yielded a chemical reversibility ratio for the detected compound. A number of applications such as monitoring data from patients under MD therapy are presented.     

Structures and Hydrogen Bonding Interactions in Urea-water System Studied by All-atom MD Simulation and Chemical Shifts in NMR Spectrum

The interactions and structures of the urea-water system are studied by an all-atom molecular dynamics （MD） simulation. The hydrogen-bonding network and the radial distribution functions are adopted in MD simulations. The structures of urea-water mixtures can be classified into different regions from the analysis of the hydrogen-bonding network. The urea molecule shows the certain tendency to the self-aggregate with the mole fraction of urea increasing. Moreover, the results of the MD simulations are also compare with the chemical shifts and viscosities of the urea aqueous solutions, and the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data such as chemical shifts of the hydrogen atom and viscosity.     

Charge separation reaction in clusters of polar molecules: MD simulations

Rate constant of intermolecular electron transfer (ET) in a photoexcited donor-acceptor model system solvated by a cluster of polar molecules has been expressed in terms of the statistical distribution of the electrostatic potential energy difference between the reacting sites. This distribution has been calculated for a particular case of acetonitrile clusters a ≈120 K by MD computer simulation. The MD values of the cluster reorganization energy and the ET rate constant have been compared with the corresponding MD results for the donor-acceptor pair solvated in bulk acetonitrile and with theoretical predictions based on the continuum model.     

Drag on a nanotube in uniform liquid argon flow

In this work, nonequilibrium molecular dynamics (MD) simulations were performed to investigate uniform liquid argon flow past a carbon nanotube. In the simulation, nanotubes were modeled as rigid cylinders of carbon atoms. Both argon-argon and argon-carbon interactions were calculated based on Lennard-Jones potential. Simulated drag coefficients were compared with (i) published empirical equation which was based on experiments conducted with macroscale cylinders and (ii) finite element (FE) analyses based on Navier-Stokes equation for flow past a circular cylinder using the same dimensionless parameters used in MD simulations. Results show that classical continuum mechanics cannot be used to calculate drag on a nanotube. In slow flows, the drag coefficients on a single-walled nanotube calculated from MD simulations were larger than those from the empirical equation or FE analysis. The difference increased as the flow velocity decreased. For higher velocity flows, slippage on the surface of the nanotube was identified which resulted in lower drag coefficient from MD simulation. This explains why the drag coefficient from MD dropped faster than those from the empirical equation or FE simulation as the flow velocity increased. It was also found that the drag forces are almost equal for single- and double-walled nanotubes with the same outer diameter, implying that inner tubes do not interact with fluid molecules.     

Hybrid particle‐field molecular dynamics simulations: Parallelization and benchmarks

The parallel implementation of a recently developed hybrid scheme for molecular dynamics (MD) simulations (Milano and Kawakatsu, J Chem Phys 2009, 130, 214106) where self‐consistent field theory (SCF) and particle models are combined is described. Because of the peculiar formulation of the hybrid method, considering single particles interacting with density fields, the most computationally expensive part of the hybrid particle‐field MD simulation can be efficiently parallelized using a straightforward particle decomposition algorithm. Benchmarks of simulations, including comparisons of serial MD and MD‐SCF program profiles, serial MD‐SCF and parallel MD‐SCF program profiles, and parallel benchmarks compared with efficient MD program GROMACS 4.5.4 are tested and reported. The results of benchmarks indicate that the proposed parallelization scheme is very efficient and opens the way to molecular simulations of large scale systems with reasonable computational costs. © 2012 Wiley Periodicals, Inc.     

HTMoL: full-stack solution for remote access,visualization, and analysis of molecular dynamics trajectory data

Research on biology has seen significant advances with the use of molecular dynamics (MD) simulations. The MD methodology enables explanation and discovery of molecular mechanisms in a wide range of natural processes and biological systems. The need to readily share the ever-increasing amount of MD data has been hindered by the lack of specialized bioinformatic tools. The difficulty lies in the efficient management of the data, i.e., in sending and processing 3D information for its visualization. In this work, we present HTMoL, a plug-in-free, secure GPU-accelerated web application specifically designed to stream and visualize MD trajectory data on a web browser. Now, individual research labs can publish MD data on the Internet, or use HTMoL to profoundly improve scientific reports by including supplemental MD data in a journal publication. HTMoL can also be used as a visualization interface to access MD trajectories generated on a high-performance computer center directly. Furthermore, the HTMoL architecture can be leveraged with educational efforts to improve learning in the fields of biology, chemistry, and physics.