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A Study on How Conformation Entropy of Attached Macromolecules Drives Polymeric Collapse and Protein Folding 关于附着大分子的构象熵如何驱动聚合物坍缩和蛋白质折叠的研究
IF 1.8 4区 工程技术 Q3 POLYMER SCIENCE Pub Date : 2024-03-11 DOI: 10.1002/mats.202400004
Ionel Popa

The conformation of macromolecules attached to a surface is influenced by both their excluded volume and steric forces. Here, self-avoiding random walk simulations are used to evaluate the occurrence of various conformations as a function of the number of monomeric units to estimate the effect of conformational entropy of a tethered chain. Then, a more realistic scenario is assessed, which can more accurately reproduce the shape of a tethered macromolecule. The simulations presented here confirm that it is more likely for a polymer to undergo a collapse conformation rather than a stretched one, as a collapse conformation can be realized in more different ways. Also, they confirm the “mushroom” shape of polymers close to a surface. From this simple approach, the conformation entropy of a model 100-unit polymer close to a surface is estimated to contribute with over 129 kBT${{k}_{mathrm{B}}}T$ toward its collapse. This conformation entropy is higher than that of typical hydrogen bonds and even barriers that keep proteins folded. As such, entropic collapse of macromolecules plays an important role in realizing the mushroom shape of attached polymers and can be the driving force in protein folding, while the polypeptide chain emerges from the ribosome.

附着在表面上的大分子的构象受其外排体积和立体力的影响。在这里,我利用自避让随机游走模拟来评估各种构象的出现与单体单元数量的函数关系,从而估计系链构象熵的影响。然后,评估了一种更现实的情况,它能更准确地再现系链大分子的形状。本文介绍的模拟证实,聚合物更有可能发生塌缩构象,而不是拉伸构象,因为塌缩构象可以通过更多不同的方式实现。此外,模拟还证实了聚合物接近表面时的 "蘑菇 "形状。通过这种简单的方法,我们可以估算出构象熵随分子大小的变化情况。这些结果预测,对于接近表面的 100 单位模型聚合物,构象熵对其坍缩的贡献超过 129 kBT${{k}_B}T$。这一构象熵高于典型的氢键,甚至高于保持蛋白质折叠的屏障。因此,当多肽链从核糖体中出现时,大分子的熵塌缩在实现附着聚合物的蘑菇形状方面起着重要作用,并可能成为蛋白质折叠的驱动力。
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引用次数: 0
Modeling the Interface Between Phases in Dense Polymer-Carbon Black Nanoparticle Composites by Dielectric Spectroscopy: Where Are We Now and What are the Opportunities? 通过介电光谱学模拟致密聚合物-碳黑纳米粒子复合材料中的相间界面:我们的现状和机遇是什么?
IF 1.4 4区 工程技术 Q3 POLYMER SCIENCE Pub Date : 2024-03-07 DOI: 10.1002/mats.202400009
Christian Brosseau

The macroscopic properties of polymer nanocomposites (PNC) rely largely on the interphase between the polymer chains and the filler particles. One significant difficulty to solve this issue is to quantitatively model the structure-property correlations due to the interfacial region in these complex materials. While dielectric spectroscopy (DS) measurements are routinely used to characterize the effective permittivity of filled polymers, fitting standard effective medium models and mixing equations to these data remains notoriously difficult to interpret. This is due to the absence of explicit reference to internal length scales characterizing the interfaces in the PNC. As an illustrative example, a two-level homogenization framework is proposed which enables the extraction of useful information on the impact of a thin interphase confined on a nanometer length scale based on broadband DS data. This model leads to new ways of tuning the interphase so as to optimize the material's response to electric field, a situation relevant for electromagnetic shielding. This approach provides guidance on how to observe directly and experimentally the actual properties of the interface between the phases (as opposed to model-based inference). Aside from its secure physical foundation in the theory of effective medium, a significant advantage of this approach is that a genetic algorithm (GA) technique applied to this physics-based model enables the uniqueness of the fit parameters to be considered, as the GA method is robust in terms of finding globally optimum solutions, therefore placing confidence in non-universal values of the percolation exponents. Recent work in physics-informed machine learning indicates that the effective dielectric properties of PNC with many degrees of freedom due to their complex morphology can be described by considering only a few degrees of freedom describing the interface features between the phases in these composites.

聚合物纳米复合材料(PNC)的宏观特性在很大程度上取决于聚合物链与填料颗粒之间的相位。解决这一问题的一个重大难题是对这些复杂材料的界面区所产生的结构-性能相关性进行定量建模。虽然介电光谱(DS)测量通常用于表征填充聚合物的有效介电常数,但将标准有效介质模型和混合方程拟合到这些数据上仍然难以解释。这是因为没有明确参考表征 PNC 界面的内部长度尺度。作为一个示例,我们提出了一个两级均质化框架,它可以根据宽带 DS 数据提取纳米长度尺度上限制的薄相间影响的有用信息。该模型带来了调整相间物的新方法,从而优化材料对电场的响应,这种情况与电磁屏蔽有关。这种方法为如何通过实验直接观察相间界面的实际特性(而不是基于模型的推断)提供了指导。除了有效介质理论中可靠的物理基础之外,这种方法的一个重要优势是,将遗传算法(GA)技术应用于这种基于物理的模型,可以考虑拟合参数的唯一性,因为 GA 方法在寻找全局最优解方面非常稳健,因此可以对渗流指数的非普遍值抱有信心。物理信息机器学习的最新研究表明,由于 PNC 的形态复杂,其有效介电性能具有很多自由度,只需考虑描述这些复合材料中各相间界面特征的几个自由度即可。
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引用次数: 0
Improving Mixing by Changing Topology Through Intermeshed Perturbation Rings in A Co-Rotating Non-Twin Screw Channel 在同向非双螺旋通道中通过间隙扰动环改变拓扑结构改善混合效果
IF 1.4 4区 工程技术 Q3 POLYMER SCIENCE Pub Date : 2024-03-03 DOI: 10.1002/mats.202470003
Baiping Xu, Ruifeng Liang, Shuping Xiao, Yanhong Feng, Huiwen Yu

Front Cover: A repetitive topology of splitting and recombination is introduced into the flow channel of a dual-speed non-twin screws with the speed ratio of 2. A new kind of perturbation ring elements is proposed to achieve the above purpose. The mixing is numerically characterized in terms of evolution of tracer particles, mixing variance index and residence time distribution. This is reported by Baiping Xu, Ruifeng Liang, Shuping Xiao, Yanhong Feng, and Huiwen Yu in article number 2300048.

封面:在转速比为 2 的双速非双螺杆流道中引入分裂和重组的重复拓扑结构。从示踪粒子的演变、混合方差指数和停留时间分布等方面对混合进行了数值表征。徐百平、梁瑞峰、肖淑萍、冯艳红和于慧文在文章编号 2300048 中对此进行了报道。
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引用次数: 0
Masthead: Macromol. Theory Simul. 2/2024 刊头:Macromol.2/2024
IF 1.4 4区 工程技术 Q3 POLYMER SCIENCE Pub Date : 2024-03-03 DOI: 10.1002/mats.202470004
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引用次数: 0
The z-Average of Cross-Linked Polymers 交联聚合物的 z 平均值
IF 1.4 4区 工程技术 Q3 POLYMER SCIENCE Pub Date : 2024-02-09 DOI: 10.1002/mats.202300065
Rolf Bachmann
<p>Stockmayer's formula for the weight average of cross-linked primary chains is extended to the <i>z</i>-average degree of polymerization <span></span><math> <semantics> <mrow> <mi>D</mi> <msub> <mi>P</mi> <mi>z</mi> </msub> </mrow> <annotation>$DP_z$</annotation> </semantics></math>. This average is a function of the weight- and <i>z</i>-average degree of polymerization λ<sub><i>w</i></sub> and λ<sub><i>z</i></sub> of the primary chain distribution and the branching density α: <span></span><math> <semantics> <mrow> <mi>D</mi> <msub> <mi>P</mi> <mi>z</mi> </msub> <mo>=</mo> <mfrac> <mrow> <msub> <mi>λ</mi> <mi>z</mi> </msub> <msup> <mrow> <mo>(</mo> <mn>1</mn> <mo>+</mo> <mi>α</mi> <mo>)</mo> </mrow> <mn>3</mn> </msup> <mo>−</mo> <msubsup> <mi>λ</mi> <mi>w</mi> <mn>2</mn> </msubsup> <msup> <mi>α</mi> <mn>2</mn> </msup> <mrow> <mo>(</mo> <mn>3</mn> <mo>+</mo> <mi>α</mi> <mo>)</mo> </mrow> </mrow> <mrow> <msup> <mrow> <mo>(</mo> <mn>1</mn> <mo>−</mo> <mi>α</mi> <mrow> <mo>(</mo> <msub> <mi>λ</mi> <mi>w</mi> </msub> <mo>−</mo> <mn>1</mn> <mo>)</mo> </mrow> <mo>)</mo> </mrow> <mn>2</mn> </msup> <mrow> <mo>(</mo>
斯托克迈尔的交联主链重量平均值公式被扩展到 z 平均聚合度 DPz。该平均值是主链分布的重量平均聚合度 λw 和 z 平均聚合度 λz 以及支化密度 α 的函数:本文受版权保护。本文受版权保护。
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引用次数: 0
A Theoretical Investigation of the Electrical and Dielectric Properties of PDMS-CNT PDMS-CNT 的电学和介电特性理论研究
IF 1.4 4区 工程技术 Q3 POLYMER SCIENCE Pub Date : 2024-02-08 DOI: 10.1002/mats.202300062
Poovendran Karuppiah, Ramanujam Nambi Ramachary, Joseph Wilson Kulandai Samy, Prasanna Venkatesh Vadivel Murugan

In the present study, the dielectric and electrical properties of the carbon nanotube/polydimethylsiloxane (CNT/PDMS) composite are theoretically analyzed for various doping concentrations. For both single-walled and multiwalled CNTs (SCNTs and MCNTs), the work is done between 75 and 750 THz. The behavior of the dielectric constant, loss factor, and conductivity are analyzed as functions of frequency. It is observed that there is no appreciable change in the real part of the dielectric constant at high frequencies in single-walled CNT. The loss tangent is high at lower frequencies, and the loss peak is observed at a particular frequency. The Cole–Cole plot is used to interpret the static- and high-frequency dielectric constants and relaxation time of the composite. With increasing concentrations of SCNT and MCNT, the conductivity at the obtained peak maximum shifts to a lower frequency.

本研究从理论上分析了不同掺杂浓度的碳纳米管/聚二甲基硅氧烷(CNT/PDMS)复合材料的介电性能和电气性能。研究分析了介电常数、损耗因子和电导率随频率变化的情况。据观察,单壁 CNT 在高频率下介电常数的实部没有明显变化。损耗正切在较低频率下较高,在特定频率下会出现损耗峰值。Cole-Cole 图用于解释复合材料的静态和高频介电常数以及弛豫时间。随着 SCNT 和 MCNT 浓度的增加,峰值最大值处的电导率会向较低频率移动。
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引用次数: 0
Masthead: Macromol. Theory Simul. 1/2024 刊头:Macromol.理论模拟1/2024
IF 1.4 4区 工程技术 Q3 POLYMER SCIENCE Pub Date : 2024-01-17 DOI: 10.1002/mats.202470002
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引用次数: 0
Potential of Mean Force of Short-Chain Surface Adsorption using Non-Uniform Sampling Windows for Optimal Computational Efficiency 利用非均匀采样窗口优化计算效率的短链表面吸附平均力潜力
IF 1.4 4区 工程技术 Q3 POLYMER SCIENCE Pub Date : 2024-01-17 DOI: 10.1002/mats.202470001
Naveen Kumar Vasudevan, Dongyang Li, Li Xi

Front Cover: Free energy of polymer adsorption is sampled in a series of windows – each constrains the system with a harmonic bias potential. Efficiency of this umbrella sampling technique can be significantly improved by allowing the sampling windows to vary along the reaction coordinate. This is reported by Naveen Kumar Vasudevan, Dongyang Li, and Li Xi in article number 2300057.

封面:聚合物吸附的自由能在一系列窗口中取样--每个窗口用谐波偏置电势对系统进行约束。通过允许采样窗口沿反应坐标变化,可以显著提高这种伞状采样技术的效率。Naveen Kumar Vasudevan、Dongyang Li 和 Li Xi 在文章编号 2300057 中对此进行了报道。
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引用次数: 0
Single-Step Kinetic Predictions Based on a Constructed Isoconversional State Diagram 基于构建的等转化状态图的单步动力学预测
IF 1.4 4区 工程技术 Q3 POLYMER SCIENCE Pub Date : 2023-12-22 DOI: 10.1002/mats.202300066
Qi Tao, Thomas Krivec, Wolfgang Kern

A new concept called isoconversional state diagram, which can be used to predict the kinetics of single-step condensed phase reactions, is introduced. A state represents a certain extent of conversion degree α in a reaction. The construction of the isoconversional state diagram is based on the isoconversional state equation, which is a piecewise linear equation about 1/T and lnβ, where T is the temperature and β is the heating rate. The slope of the linear equation is controlled by the activation energy Eα and its intercept contains the inherent information of the kinetic triplet, i.e., the pre-exponential factor Aα, the activation energy Eα and the reaction model f(α). Consequently, the geometric methods for nonisothermal and isothermal kinetic predictions are derived. The latter reflects the physical meaning of the relationship between reactions under isothermal and nonisothermal conditions, i.e., the time to advance from αi to αi+1 at isothermal temperature Tiso is equal to the time to heat from Tiso to Tαi+1${T}_{{alpha }_i + 1}$ under heating rate βαi${{{beta}}}_{{{{alpha}}}_i}$, where Tiso, Tαi+1${T}_{{alpha }_i + 1}$ and βαi${{{beta}}}_{{{{alpha}}}_i}$must be determined from the isoconversional state diagram.

我们提出了一个新概念,即等转化状态图,它可用于预测单步凝聚相反应的动力学。一个状态代表反应中一定程度的转化率 α。等转化状态图的构建基于等转化状态方程,这是一个关于 1/T 和 lnβ 的片断线性方程,其中 T 是温度,β 是加热速率。线性方程的斜率由活化能 Eα 控制,其截距包含动力学三元组的固有信息,即预指数因子 Aα、活化能 Eα 和反应模型 f(α)。因此,得出了非等温和等温动力学预测的几何方法。后者反映了等温和非等温条件下反应之间关系的物理意义,即在等温温度 Tiso 下,从 αi 进入 αi+1 的时间等于从 Tiso 加热到 Tαi+1 的时间${T_{{α_i}}$。+ 1}}$在加热速率 βαi${{rm{beta }}_{{{rm{alpha }}_i}}}$ 下,其中 Tiso、Tαi+1${T_{{alpha _i}+ 1}}$ 和 βαi${{rm{beta }}_{{{rm{alpha }}_i}}$ 必须从等转换状态图中确定。
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引用次数: 0
Ligand-Mediated Interaction of Nanoparticles with Lipid Membranes 配体介导的纳米颗粒与脂质膜的相互作用
IF 1.4 4区 工程技术 Q3 POLYMER SCIENCE Pub Date : 2023-11-28 DOI: 10.1002/mats.202300058
Sandeep Mathew, Mohamed Laradji, P.B. Sunil Kumar

While many studies are performed on the effect of ligands on the adhesion and endocytosis of NPs, the effects of ligand length and surface density on the NPs' interaction with lipid membranes are poorly investigated. Here, a computational investigation is presented, based on molecular dynamics of a coarse-grained implicit-solvent model, of the interaction between ligand-decorated spherical NPs and lipid membranes. Specifically,the case is considered where the ligands interact attractively with lipid membranes only through their ends. In particular, the effects of ligand grafting density, ligand length, and strength of ligand-lipid interaction is investigated on the degree of wrapping of the NP by the membrane and on the morphology of the membrane close to the NP. Whereas the degree of wrapping is found to increase with increasing the grafting density for a given interaction strength and ligand length, it decreases with ligand length for a given grafting density and interaction strength. For moderate values of the adhesion strength and long ligands, it is found that the end ligands form long linear clusters, which lead to an anisotropic conformation of the membrane around the NP. For short ligands, the wrapping of the membrane around the NP is almost complete, with the wrapped NP showing a regular faceted structure for high adhesion strength.

虽然许多研究已经对配体对NPs的粘附和内吞作用的影响进行了研究,但对配体长度和表面密度对NPs与脂质膜相互作用的影响的研究很少。在这里,我们提出了一个基于粗粒度隐式溶剂模型的分子动力学的计算研究,研究配体修饰的球形NPs和脂质膜之间的相互作用。我们特别考虑配体仅通过其末端与脂质膜相互作用的情况。我们特别研究了配体接枝密度、配体长度和配体-脂质相互作用强度对NP被膜包裹的程度和靠近NP的膜形态的影响。在一定的相互作用强度和配体长度下,包裹度随接枝密度的增加而增加,而在一定的接枝密度和相互作用强度下,包裹度随配体长度的增加而减小。对于中等黏附强度和长配体,我们发现末端配体形成长线性簇,导致NP周围的膜呈各向异性构象。对于短配体,膜在NP周围的包裹几乎完全,包裹的NP呈现出规则的面形结构,具有较高的粘附强度。
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引用次数: 0
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Macromolecular Theory and Simulations
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