European Physical Journal-special Topics最新文献

{"title":"Efficiently determining membrane-bound conformations of peripheral membrane proteins using replica exchange with hybrid tempering: Orientation of PMP on lipid bilayer using replica exchange.","authors":"Chandramouli Natarajan, Anand Srivastava","doi":"10.1140/epjs/s11734-024-01386-x","DOIUrl":"10.1140/epjs/s11734-024-01386-x","url":null,"abstract":"<p><p>Accurately sampling the membrane-bound conformations of peripheral membrane proteins (PMP) using classical all-atom molecular dynamics simulations (AAMD) is a formidable enterprise due to the wide rugged free energy landscape of the protein-membrane system. In general, AAMD-based extraction of binding geometry requires simulations of multiple systems with different initial user-defined binding poses that may not be exhaustive. As an alternative, advanced sampling methods are also applied to elucidate the membrane-binding mechanism of PMPs. But these techniques are generally computationally expensive and often depend on the choice of the collective variables (CV). In this work, we showcase the utility of CV-free replica exchange with the hybrid tempering (REHT) method in capturing the membrane-bound conformations of PMPs by testing it on the Osh4 amphipathic lipid-packing sensor (ALPS) motif, a 27 amino-acid membrane-binding peptide. We show that REHT samples all the membrane-bound conformations of the Osh4 ALPS peptide observed in AAMD simulations and does it in a highly efficient manner. We clearly show that, out of the two significant conformations, the peptide prefers horizontal conformations over vertical ones. In both the conformations, REHT captures all the vital residue-wise membrane contacts. The transition between the two configurations is not uncommon as our calculations reveal a ~1 kT free energy difference between the two conformations. Interestingly, from our simulations, we also find that the transition from vertical to horizontal conformation involves limited unfolding of the main helix's last turn. From our findings, we conclude that REHT samples the membrane-bound conformations of Osh4 ALPS peptide very efficiently and also provides additional insights and information that are often not available with regular piece-wise AAMD simulations. The method can be used as an efficient tool to explore the membrane-binding mechanisms of PMPs.</p>","PeriodicalId":12221,"journal":{"name":"European Physical Journal-special Topics","volume":"233 21-22","pages":"3039-3051"},"PeriodicalIF":2.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7617745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144247202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Is a higher frequency of esophageal dilations more effective in treating benign esophageal strictures? Retrospective, multicenter study.","authors":"Christiana Graf, Monika Reden, Tobias Blasberg, Mate Knabe, Andrea May, Christian Ell, Edris Wedi, Nils Wetzstein, Florian Michael, Stefan Zeuzem, Jörg Bojunga, Mireen Friedrich-Rust","doi":"10.1055/a-2117-8197","DOIUrl":"10.1055/a-2117-8197","url":null,"abstract":"<p><p><b>Background and study aims</b> There is still a lack of evidence-based recommendations concerning endoscopic bougienage in benign esophageal strictures. Our study aimed to assess the relevance of the time interval between endoscopic dilation (ED) sessions with regard to endoscopic and clinical response. <b>Patients and methods</b> We performed a retrospective study including patients treated with endoscopic bougienage for a benign esophageal stricture in two German centers. Primary endpoint was the number of ED until freedom from dysphagia was achieved. Secondary endpoints were analyses on reaching a diameter of 15 mm and on achieving clinical freedom from symptoms. <b>Results</b> Between April 2014 and March 2020, bougienage was used as the primary treatment for benign esophageal strictures in 238 patients (194 patients in Center 1; 44 patients in Center 2). Both centers differed in their endoscopic bougienage regime: Center 1 was characterized by a higher frequency of interventions compared to Center 2 (median: 2 days [range 1-28] vs. 10 days [range 1-41]; <i>P</i> <0.001). Clinical response was achieved significantly earlier using the high-frequency regimen in all patients except for those with post-radiogen strictures, who clinically benefited from a low-frequency ED program. Accordingly, patients receiving higher-frequency ED reached a significantly larger post-dilation diameter and considerably larger diameter differences. <b>Conclusions</b> The results of our study demonstrate that a treatment concept consisting of higher-frequency bougienages seems to be more effective in treating most types of esophageal stricture. Radiogenic strictures were the only types of stenoses that benefited from a lower frequency ED program.</p>","PeriodicalId":12221,"journal":{"name":"European Physical Journal-special Topics","volume":"186 1","pages":"E78-E89"},"PeriodicalIF":2.2,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10781580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85843714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Continuous percolation in a Hilbert space for a large system of qubits","authors":"Shohei Watabe, Michael Zach Serikow, Shiro Kawabata, Alexandre Zagoskin","doi":"10.1140/epjs/s11734-023-01008-y","DOIUrl":"https://doi.org/10.1140/epjs/s11734-023-01008-y","url":null,"abstract":"Abstract The development of percolation theory was historically shaped by its numerous applications in various branches of science, in particular in statistical physics, and was mainly constrained to the case of Euclidean spaces. One of its central concepts, the percolation transition, is defined through the appearance of the infinite cluster, and therefore cannot be used in compact spaces, such as the Hilbert space of an N -qubit system. Here, we propose its generalization for the case of a random space covering by hyperspheres, introducing the concept of a “maximal cluster”. Our numerical calculations reproduce the standard power-law relation between the hypersphere radius and the cover density, but show that as the number of qubits increases, the exponent quickly vanishes (i.e., the exponentially increasing dimensionality of the Hilbert space makes its covering by finite-size hyperspheres inefficient). Therefore the percolation transition is not an efficient model for the behavior of multiqubit systems, compared to the random walk model in the Hilbert space. However, our approach to the percolation transition in compact metric spaces may prove useful for its rigorous treatment in other contexts.","PeriodicalId":12221,"journal":{"name":"European Physical Journal-special Topics","volume":"54 11","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134902638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analytic continuations of the Horn $$H_1$$ and $$H_5$$ functions","authors":"Souvik Bera, Tanay Pathak","doi":"10.1140/epjs/s11734-023-00990-7","DOIUrl":"https://doi.org/10.1140/epjs/s11734-023-00990-7","url":null,"abstract":"","PeriodicalId":12221,"journal":{"name":"European Physical Journal-special Topics","volume":"27 25","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136282406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Utility coupling promotes cooperation in multiplayer snowdrift games on interdependent simplicial networks","authors":"Juan Wang, Shiqiang Guo, Chengyi Xia, Matjaž Perc","doi":"10.1140/epjs/s11734-023-01003-3","DOIUrl":"https://doi.org/10.1140/epjs/s11734-023-01003-3","url":null,"abstract":"","PeriodicalId":12221,"journal":{"name":"European Physical Journal-special Topics","volume":"112 27","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135137459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prediction of various observables for $$B_s^0 rightarrow D_s^{(*)-}ell ^+nu _ell$$ within covariant confined quark model","authors":"J. N. Pandya, P. Santorelli, N. R. Soni","doi":"10.1140/epjs/s11734-023-01006-0","DOIUrl":"https://doi.org/10.1140/epjs/s11734-023-01006-0","url":null,"abstract":"","PeriodicalId":12221,"journal":{"name":"European Physical Journal-special Topics","volume":"46 8","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135933901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent advancement of fractional calculus and its applications in physical systems","authors":"Salah Boulaaras, Rashid Jan, Viet-Thanh Pham","doi":"10.1140/epjs/s11734-023-01002-4","DOIUrl":"https://doi.org/10.1140/epjs/s11734-023-01002-4","url":null,"abstract":"","PeriodicalId":12221,"journal":{"name":"European Physical Journal-special Topics","volume":"634 ","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136067796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-stability analysis and energy control for 4D hyperchaotic system with hidden attractors","authors":"Shaojuan Ma, Meibo Wang, Xiaoyan Ma, Hufei Li","doi":"10.1140/epjs/s11734-023-00997-0","DOIUrl":"https://doi.org/10.1140/epjs/s11734-023-00997-0","url":null,"abstract":"","PeriodicalId":12221,"journal":{"name":"European Physical Journal-special Topics","volume":"16 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135368650","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The smeared-horizon observer of a black hole","authors":"Theodorus Maria Nieuwenhuizen","doi":"10.1140/epjs/s11734-023-01001-5","DOIUrl":"https://doi.org/10.1140/epjs/s11734-023-01001-5","url":null,"abstract":"Abstract A class of observers is introduced that interpolate smoothly between the Schwarzschild observer, stable at spatial infinity, and the Kerr–Schild observer, who falls into a black hole. For these observers, the passing of the event and inner horizon takes a finite time, which diverges logarithmically when the interpolation parameter $$sigma $$ <mml:math xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"> <mml:mi>σ</mml:mi> </mml:math> goes to zero. In the field theoretic approach to gravitation, the behavior at the horizons becomes regular, making the mass of the metric well defined.","PeriodicalId":12221,"journal":{"name":"European Physical Journal-special Topics","volume":"24 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135366481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Control of particle transport driven by active noise: strategy of amplification via a periodic potential","authors":"Karol Białas, Jerzy Łuczka, Jakub Spiechowicz","doi":"10.1140/epjs/s11734-023-01004-2","DOIUrl":"https://doi.org/10.1140/epjs/s11734-023-01004-2","url":null,"abstract":"Abstract We extend our previous studies on a counter-intuitive effect in which a directed transport of a free Brownian particle induced by active fluctuations can be significantly enhanced when the particle is placed in a periodic potential. It is in clear contrast to a common situation when the velocity of the Brownian particle is notably reduced if the periodic potential is switched on. As a model of active fluctuations, we employ white Poissonian shot noise. We reconsider the case of the skew-normal amplitude distribution of shot noise and focus on the impact of statistical characteristics of its amplitude like mean, variance, and skewness on the magnitude of free particle transport enhancement. In particular, we detect intriguing oscillations of the rescaled velocity of the particle as a function of the variance. Our findings can be corroborated experimentally in both biological and artificial microscopic systems.","PeriodicalId":12221,"journal":{"name":"European Physical Journal-special Topics","volume":"182 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135728879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}