基于接触数引导的迭代多组独立分子动力学模拟实现配体-蛋白质结合与解离过程

配体的结合与解离过程在蛋白质实现其生物学功能方面非常关键,因此对这些高度动态过程的研究变得非常重要. 尽管已有实验方法可以确定蛋白质-配体复合物的三维结构,但一般仅可获得静态图片. 随着计算机算力的快速提高以及算法的优化,分子动力学模拟在探索配体的结合与解离过程方面具有诸多优势. 然而,当系统变得足够大时,分子动力学模拟的时间和空间尺度成为了巨大的挑战. 本工作提出了一种研究配体-蛋白质结合与解离的增强采样工具,它基于配体和蛋白质之间形成的接触数来引导迭代多组独立分子动力学模拟. 在腺苷酸激酶的模拟结果中,观测到配体的结合和解离过程,而使用传统分子动力学模拟在同一时间尺度下则无法实现这一过程.     

The formation of biaxial nematic phases in binary mixtures of thermotropic liquid-crystals composed of uniaxial molecules

ABSTRACT

Monte Carlo simulations in the isothermal-isobaric ensemble are used to investigate the formation of an ordered, biaxial nematic phase in a binary mixture of thermotropic liquid crystals. The orientational dependence of the interaction between molecules of each pure component is the same as in the well-known Maier-Saupe model; each pure component of the mixture is therefore capable of forming a uniaxial nematic phase. For the interaction between molecules of different components, we use the same Maier-Saupe model but change the sign of the coupling constant. As a consequence a T-shaped arrangement of these molecules is energetically favoured. The formation of the biaxial phase occurs in two steps. At higher temperatures T, one of the components forms a uniaxial nematic phase whereas the other is in a quasi two-dimensional restricted isotropic liquid state. We develop a simple theoretical model to understand the high degree of (ostensible) nematic order in the latter. At lower T, the second component becomes nematic and then the entire mixture of the two compounds has biaxial symmetry. The biaxial nematic phase does not demix into domains rich in molecules of one or the other species.     

Predicting Low-Pressure O2 Adsorption in Nanoporous Framework Materials for Sensing Applications

A set of 98 nanoporous framework material (NFM) structures was investigated by classical Grand canonical Monte Carlo simulations for low-pressure O₂ adsorption properties (Henry’s constant and isosteric heat of adsorption). The set of materials includes those that have shown high O₂ uptake experimentally as well as a subset of more than 2000 structures previously screened for noble-gas uptake. While use of the general force field UFF is fruitful for noble-gas adsorption studies, its use is shown to be limited for the case of O₂ adsorption—one distinct limitation is a lack of sufficient O₂–metal interactions to be able to describe O₂ interaction with open metal sites. Nonetheless, those structures without open metal sites that have very small pores (<2.5 Å) show increased O₂/N₂ selectivity. Additionally, O₂/N₂ mixture simulations show that in some cases, H₂O or N₂ can hinder O₂ uptake for NFMs with small pores due to competitive adsorption.     

Comparison of phantom materials for use in quality assurance of microbeam radiation therapy

Microbeam radiation therapy (MRT) is a promising radiotherapy modality that uses arrays of spatially fractionated micrometre‐sized beams of synchrotron radiation to irradiate tumours. Routine dosimetry quality assurance (QA) prior to treatment is necessary to identify any changes in beam condition from the treatment plan, and is undertaken using solid homogeneous phantoms. Solid phantoms are designed for, and routinely used in, megavoltage X‐ray beam radiation therapy. These solid phantoms are not necessarily designed to be water‐equivalent at low X‐ray energies, and therefore may not be suitable for MRT QA. This work quantitatively determines the most appropriate solid phantom to use in dosimetric MRT QA. Simulated dose profiles of various phantom materials were compared with those calculated in water under the same conditions. The phantoms under consideration were RMI457 Solid Water (Gammex‐RMI, Middleton, WI, USA), Plastic Water (CIRS, Norfolk, VA, USA), Plastic Water DT (CIRS, Norfolk, VA, USA), PAGAT (CIRS, Norfolk, VA, USA), RW3 Solid Phantom (PTW Freiburg, Freiburg, Germany), PMMA, Virtual Water (Med‐Cal, Verona, WI, USA) and Perspex. RMI457 Solid Water and Virtual Water were found to be the best approximations for water in MRT dosimetry (within ±3% deviation in peak and 6% in valley). RW3 and Plastic Water DT approximate the relative dose distribution in water (within ±3% deviation in the peak and 5% in the valley). PAGAT, PMMA, Perspex and Plastic Water are not recommended to be used as phantoms for MRT QA, due to dosimetric discrepancies greater than 5%.     

Multivariate Normal Slice Sampling

By introducing auxiliary variables, the traditional Markov chain Monte Carlo method can be improved in certain cases by implementing a “slice sampler.” In the current literature, this sampling technique is used to sample from multivariate distributions with both single and multiple auxiliary variables. When the latter is employed, it generally updates one component at a time.

In this article, we propose two variations of a new multivariate normal slice sampling method that uses multiple auxiliary variables to perform multivariate updating. These methods are flexible enough to allow for truncation to a rectangular region and/or exclusion of any n-dimensional hyper-quadrant. We present results of our methods and existing state-of-the-art slice samplers by comparing efficiency and accuracy. We find that we can generate approximately iid samples at a rate that is more efficient than other methods that update all dimensions at once. Supplemental materials are available online.     

The aliasing‐phenomenon in visual terms

In a recent paper it was shown that the aliasing phenomenon, which leads to a severe identification problem in the estimation of stochastic differential equations, can be overcome by using a polygonal (or higher) approximation for the time paths of the exogenous variables. This work attempts to visualize the problem and presents several simulated trajectories of a continuous time AR(2)‐process (Ornstein‐Uhlenbeck‐process) together with the observationally equivalent structures. Furthermore it is shown that aliasing can even change the analytical properties of the time paths of the system: whereas the first component of the Ornstein‐Uhlenbeck‐process is differentiable, the trajectories of the aliasing structures are continuous, but not differentiable any more.