{"title":"A Study on How Conformation Entropy of Attached Macromolecules Drives Polymeric Collapse and Protein Folding","authors":"Ionel Popa","doi":"10.1002/mats.202400004","DOIUrl":"10.1002/mats.202400004","url":null,"abstract":"<p>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 <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mi>k</mi>\u0000 <mi>B</mi>\u0000 </msub>\u0000 <mi>T</mi>\u0000 </mrow>\u0000 <annotation>${{k}_{mathrm{B}}}T$</annotation>\u0000 </semantics></math> 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.</p>","PeriodicalId":18157,"journal":{"name":"Macromolecular Theory and Simulations","volume":"33 4","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140105342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Modeling the Interface Between Phases in Dense Polymer-Carbon Black Nanoparticle Composites by Dielectric Spectroscopy: Where Are We Now and What are the Opportunities?","authors":"Christian Brosseau","doi":"10.1002/mats.202400009","DOIUrl":"10.1002/mats.202400009","url":null,"abstract":"<p>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.</p>","PeriodicalId":18157,"journal":{"name":"Macromolecular Theory and Simulations","volume":"33 3","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mats.202400009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140073843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Improving Mixing by Changing Topology Through Intermeshed Perturbation Rings in A Co-Rotating Non-Twin Screw Channel","authors":"Baiping Xu, Ruifeng Liang, Shuping Xiao, Yanhong Feng, Huiwen Yu","doi":"10.1002/mats.202470003","DOIUrl":"https://doi.org/10.1002/mats.202470003","url":null,"abstract":"<p><b>Front Cover</b>: 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.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":18157,"journal":{"name":"Macromolecular Theory and Simulations","volume":"33 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mats.202470003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140024603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Masthead: Macromol. Theory Simul. 2/2024","authors":"","doi":"10.1002/mats.202470004","DOIUrl":"https://doi.org/10.1002/mats.202470004","url":null,"abstract":"","PeriodicalId":18157,"journal":{"name":"Macromolecular Theory and Simulations","volume":"33 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mats.202470004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140024604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The z-Average of Cross-Linked Polymers","authors":"Rolf Bachmann","doi":"10.1002/mats.202300065","DOIUrl":"10.1002/mats.202300065","url":null,"abstract":"<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>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>D</mi>\u0000 <msub>\u0000 <mi>P</mi>\u0000 <mi>z</mi>\u0000 </msub>\u0000 </mrow>\u0000 <annotation>$DP_z$</annotation>\u0000 </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>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>D</mi>\u0000 <msub>\u0000 <mi>P</mi>\u0000 <mi>z</mi>\u0000 </msub>\u0000 <mo>=</mo>\u0000 <mfrac>\u0000 <mrow>\u0000 <msub>\u0000 <mi>λ</mi>\u0000 <mi>z</mi>\u0000 </msub>\u0000 <msup>\u0000 <mrow>\u0000 <mo>(</mo>\u0000 <mn>1</mn>\u0000 <mo>+</mo>\u0000 <mi>α</mi>\u0000 <mo>)</mo>\u0000 </mrow>\u0000 <mn>3</mn>\u0000 </msup>\u0000 <mo>−</mo>\u0000 <msubsup>\u0000 <mi>λ</mi>\u0000 <mi>w</mi>\u0000 <mn>2</mn>\u0000 </msubsup>\u0000 <msup>\u0000 <mi>α</mi>\u0000 <mn>2</mn>\u0000 </msup>\u0000 <mrow>\u0000 <mo>(</mo>\u0000 <mn>3</mn>\u0000 <mo>+</mo>\u0000 <mi>α</mi>\u0000 <mo>)</mo>\u0000 </mrow>\u0000 </mrow>\u0000 <mrow>\u0000 <msup>\u0000 <mrow>\u0000 <mo>(</mo>\u0000 <mn>1</mn>\u0000 <mo>−</mo>\u0000 <mi>α</mi>\u0000 <mrow>\u0000 <mo>(</mo>\u0000 <msub>\u0000 <mi>λ</mi>\u0000 <mi>w</mi>\u0000 </msub>\u0000 <mo>−</mo>\u0000 <mn>1</mn>\u0000 <mo>)</mo>\u0000 </mrow>\u0000 <mo>)</mo>\u0000 </mrow>\u0000 <mn>2</mn>\u0000 </msup>\u0000 <mrow>\u0000 <mo>(</mo>\u0000 ","PeriodicalId":18157,"journal":{"name":"Macromolecular Theory and Simulations","volume":"33 3","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139788346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Poovendran Karuppiah, Ramanujam Nambi Ramachary, Joseph Wilson Kulandai Samy, Prasanna Venkatesh Vadivel Murugan
{"title":"A Theoretical Investigation of the Electrical and Dielectric Properties of PDMS-CNT","authors":"Poovendran Karuppiah, Ramanujam Nambi Ramachary, Joseph Wilson Kulandai Samy, Prasanna Venkatesh Vadivel Murugan","doi":"10.1002/mats.202300062","DOIUrl":"10.1002/mats.202300062","url":null,"abstract":"<p>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.</p>","PeriodicalId":18157,"journal":{"name":"Macromolecular Theory and Simulations","volume":"33 3","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139753167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Masthead: Macromol. Theory Simul. 1/2024","authors":"","doi":"10.1002/mats.202470002","DOIUrl":"https://doi.org/10.1002/mats.202470002","url":null,"abstract":"","PeriodicalId":18157,"journal":{"name":"Macromolecular Theory and Simulations","volume":"33 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mats.202470002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139488403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Potential of Mean Force of Short-Chain Surface Adsorption using Non-Uniform Sampling Windows for Optimal Computational Efficiency","authors":"Naveen Kumar Vasudevan, Dongyang Li, Li Xi","doi":"10.1002/mats.202470001","DOIUrl":"https://doi.org/10.1002/mats.202470001","url":null,"abstract":"<p><b>Front Cover</b>: 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.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":18157,"journal":{"name":"Macromolecular Theory and Simulations","volume":"33 1","pages":""},"PeriodicalIF":1.4,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mats.202470001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139488404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Single-Step Kinetic Predictions Based on a Constructed Isoconversional State Diagram","authors":"Qi Tao, Thomas Krivec, Wolfgang Kern","doi":"10.1002/mats.202300066","DOIUrl":"10.1002/mats.202300066","url":null,"abstract":"<p>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/<i>T</i> and <i>ln</i>β, where <i>T</i> is the temperature and β is the heating rate. The slope of the linear equation is controlled by the activation energy <i>E</i><sub>α</sub> and its intercept contains the inherent information of the kinetic triplet, i.e., the pre-exponential factor <i>A</i><sub>α</sub>, the activation energy <i>E</i><sub>α</sub> and the reaction model <i>f</i>(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 α<sub>i</sub> to α<sub>i+1</sub> at isothermal temperature <i>T</i><sub>iso</sub> is equal to the time to heat from <i>T</i><sub>iso</sub> to <span></span><math>\u0000 <semantics>\u0000 <msub>\u0000 <mi>T</mi>\u0000 <mrow>\u0000 <msub>\u0000 <mi>α</mi>\u0000 <mi>i</mi>\u0000 </msub>\u0000 <mo>+</mo>\u0000 <mn>1</mn>\u0000 </mrow>\u0000 </msub>\u0000 <annotation>${T}_{{alpha }_i + 1}$</annotation>\u0000 </semantics></math> under heating rate <span></span><math>\u0000 <semantics>\u0000 <msub>\u0000 <mi>β</mi>\u0000 <msub>\u0000 <mi>α</mi>\u0000 <mi>i</mi>\u0000 </msub>\u0000 </msub>\u0000 <annotation>${{{beta}}}_{{{{alpha}}}_i}$</annotation>\u0000 </semantics></math>, where <i>T</i><sub>iso</sub>, <span></span><math>\u0000 <semantics>\u0000 <msub>\u0000 <mi>T</mi>\u0000 <mrow>\u0000 <msub>\u0000 <mi>α</mi>\u0000 <mi>i</mi>\u0000 </msub>\u0000 <mo>+</mo>\u0000 <mn>1</mn>\u0000 </mrow>\u0000 </msub>\u0000 <annotation>${T}_{{alpha }_i + 1}$</annotation>\u0000 </semantics></math> and <span></span><math>\u0000 <semantics>\u0000 <msub>\u0000 <mi>β</mi>\u0000 <msub>\u0000 <mi>α</mi>\u0000 <mi>i</mi>\u0000 </msub>\u0000 </msub>\u0000 <annotation>${{{beta}}}_{{{{alpha}}}_i}$</annotation>\u0000 </semantics></math>must be determined from the isoconversional state diagram.</p>","PeriodicalId":18157,"journal":{"name":"Macromolecular Theory and Simulations","volume":"33 3","pages":""},"PeriodicalIF":1.4,"publicationDate":"2023-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139053747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Ligand-Mediated Interaction of Nanoparticles with Lipid Membranes","authors":"Sandeep Mathew, Mohamed Laradji, P.B. Sunil Kumar","doi":"10.1002/mats.202300058","DOIUrl":"10.1002/mats.202300058","url":null,"abstract":"<p>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.</p>","PeriodicalId":18157,"journal":{"name":"Macromolecular Theory and Simulations","volume":"33 2","pages":""},"PeriodicalIF":1.4,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138525023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}