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Defect Annihilation Pathways in Directed Assembly of Lamellar Block Copolymer Thin Films

ACS NANO 2018年第10期12卷 9974-9981页

作者： Hur, Su-Mi Thapar, Vikram Ramirez-Hernandez, Abelardo Nealey, Paul F. de Pablo, Juan J. Chonnam Natl Univ Sch Polymer Sci & Engn Gwangju 500757 South Korea Univ Chicago Inst Mol Engn Chicago IL 60637 USA Argonne Natl Lab Div Mat Sci 9700 South Cass Ave Argonne IL 60439 USA Univ Texas San Antonio Dept Biomed Engn Chem Engn Program San Antonio TX 78249 USA

Defects in highly ordered self-assembled block copolymers represent an important roadblock toward the adoption of these materials in a wide range of applications. This work examines the pathways for annihilation of defects in symmetric diblock copolymers in the context of directed assembly using patterned substrates. Past theoretical and computational studies of such systems have predicted minimum free energy pathways that are characteristic of an activated process. However, they have been limited to adjacent dislocations with opposite Burgers vectors. By relying on a combination of advanced sampling techniques and particle-based simulations, this work considers the long-range interaction between dislocation pairs, both on homogeneous and nanopatterned substrates. As illustrated here, these interactions are central to understanding the defect structures that are most commonly found in applications and in experimental studies of directed self-assembly. More specifically, it is shown that, for dislocation dipoles separated by several lamellae, multiple consecutive free energy barriers lead to effective kinetic barriers that are an order of magnitude larger than those originally reported in the literature for tightly bound dislocation pairs. It is also shown that annihilation pathways depend strongly on both the separation between dislocations and their relative position with respect to the substrate guiding stripes used to direct the assembly.

关键词： block copolymer directed assembly defect annihilation string method minimum free energy path

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A Continuum-on-Atomistic Framework with Bi-Stable Elements for the Computation of Minimum Free Energy Paths

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MECHANICS OF SOLIDS 2019年第6期54卷 975-994页

作者： Ulz, M. H. Graz Univ Technol Inst Strength Mat Kopernikusgasse 24-1 A-8010 Graz Austria

The exploration of non-convex energy landscapes, as arising in phase transitions, is an important task in solid state mechanics. An often employed system in the literature for the study of phase transitions in deformable solids denotes the elastic bar with a non-monotone stress-strain curve. This setting is chosen and modelled by a continuum-on-atomistic model (molecular dynamics coupled with the finite element method). The rod's material denotes a copper single crystal and undergoes a model phase transition. The resulting non-convex energy landscape is explored by the string method in collective variables. The string method allows for the computation of energy barriers between local minima and to identify minimum free energy paths. The novelty of the present work is the combination of a continuum-on-atomistic method with the string method applied to a problem in mechanics. Numerical examples demonstrate the performance of the numerical model.

关键词： heterogeneous multiscale method continuum-on-atomistic coupling homogenisation string method rare events phase transition

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Conformational Transitions and Alternating-Access Mechanism in the Sarcoplasmic Reticulum Calcium Pump

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JOURNAL OF MOLECULAR BIOLOGY 2017年第5期429卷 647-666页

作者： Das, Avisek Rui, Huan Nakamoto, Robert Roux, Benoit Univ Chicago Dept Biochem & Mol Biol 929 East 57th St Chicago IL 60637 USA Univ Virginia Sch Med Dept Mol Physiol & Biol Phys POB 800886480Ray C Hunt Dr Charlottesville VA 22908 USA

Ion pumps are integral membrane proteins responsible for transporting ions against concentration gradients across biological membranes. Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA), a member of the P-type ATPases family, transports two calcium ions per hydrolyzed ATP molecule via an "alternating-access" mechanism. High-resolution crystallographic structures provide invaluable insight on the structural mechanism of the ion pumping process. However, to understand the molecular details of how ATP hydrolysis is coupled to calcium transport, it is necessary to gain knowledge about the conformational transition pathways connecting the crystallographically resolved conformations. Large-scale transitions in SERCA occur at time scales beyond the current reach of unbiased molecular dynamics simulations. Here, we overcome this challenge by employing the string method, which represents a transition pathway as a chainofstates linking two conformational endpoints. Using a multiscale methodology, we have determined all-atom transition pathways for three main conformational transitions responsible for the alternating-access mechanism. The present pathways provide a clear chronology and ordering of the key events underlying the active transport of calcium ions by SERCA. Important conclusions are that the conformational transition that leads to occlusion with bound ATP and calcium is highly concerted and cooperative, the phosphorylation of Asp351 causes areorganization of the cytoplasmic domains that subsequently drives the opening of the luminal gate, and thereclosing of luminal gate induces a shift in the cytoplasmic domains that subsequently enables the dephosphorylation of Asp351-P. Formation of transient residue residue contacts along the conformational transitions predicted by the computations provide an experimental route to test the general validity of the computational pathways. (C) 2017 Elsevier Ltd. All rights reserved.

关键词： SERCA ion pumps conformational transition molecular dynamics simulation string method

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Molecular pathways for defect annihilation in directed self-assembly

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2015年第46期112卷 14144-14149页

作者： Hur, Su-Mi Thapar, Vikram Ramirez-Hernandez, Abelardo Khaira, Gurdaman Segal-Peretz, Tamar Rincon-Delgadillo, Paulina A. Li, Weihua Mueller, Marcus Nealey, Paul F. de Pablo, Juan J. Argonne Natl Lab Div Mat Sci Lemont IL 60439 USA Univ Chicago Inst Mol Engn Chicago IL 60637 USA Chonnam Natl Univ Sch Polymer Sci & Engn Kwangju 500757 South Korea Cornell Univ Sch Chem & Biomol Engn Ithaca NY 14853 USA Univ Gottingen Inst Theoret Phys D-37077 Gottingen Germany Fudan Univ Dept Macromol Sci Shanghai 200433 Peoples R China

Over the last few years, the directed self-assembly of block copolymers by surface patterns has transitioned from academic curiosity to viable contender for commercial fabrication of next-generation nanocircuits by lithography. Recently, it has become apparent that kinetics, and not only thermodynamics, plays a key role for the ability of a polymeric material to self-assemble into a perfect, defect-free ordered state. Perfection, in this context, implies not more than one defect, with characteristic dimensions on the order of 5 nm, over a sample area as large as 100 cm(2). In this work, we identify the key pathways and the corresponding free energy barriers for eliminating defects, and we demonstrate that an extraordinarily large thermodynamic driving force is not necessarily sufficient for their removal. By adopting a concerted computational and experimental approach, we explain the molecular origins of these barriers and how they depend on material characteristics, and we propose strategies designed to overcome them. The validity of our conclusions for industrially relevant patterning processes is established by relying on instruments and assembly lines that are only available at state-of-the-art fabrication facilities, and, through this confluence of fundamental and applied research, we are able to discern the evolution of morphology at the smallest relevant length scales-a handful of nanometers-and present a view of defect annihilation in directed self-assembly at an unprecedented level of detail.

关键词： directed self-assembly copolymer defect minimum free energy path string method

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Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2019年第30期116卷 14989-14994页

作者： Zhou, Shenggao Weiss, R. Gregor Cheng, Li-Tien Dzubiella, Joachim McCammon, J. Andrew Li, Bo Soochow Univ Dept Math Suzhou 215006 Jiangsu Peoples R China Soochow Univ Math Ctr Interdiscipline Res Suzhou 215006 Jiangsu Peoples R China Swiss Fed Inst Technol Lab Phys Chem CH-8093 Zurich Switzerland Humboldt Univ Inst Phys D-12489 Berlin Germany Univ Calif San Diego Dept Math La Jolla CA 92093 USA Albert Ludwigs Univ Freiburg Phys Inst D-79104 Freiburg Germany Helmholtz Zentrum Berlin Res Grp Simulat Energy Mat D-14109 Berlin Germany Univ Calif San Diego Dept Pharmacol Dept Chem & Biochem La Jolla CA 92093 USA

Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge theoretical descriptions. Here, we devise a holistic, implicit-solvent, multimethod approach to predict the (un)binding kinetics for a generic ligand-pocket model. We use the variational implicit-solvent model (VISM) to calculate the solute-solvent interfacial structures and the corresponding free energies, and combine the VISM with the string method to obtain the minimum energy paths and transition states between the various metastable ("dry" and "wet") hydration states. The resulting dry-wet transition rates are then used in a spatially dependent multistate continuous-time Markov chain Brownian dynamics simulation and the related FokkerPlanck equation calculations of the ligand stochastic motion, providing the mean first-passage times for binding and unbinding. We find the hydration transitions to significantly slow down the binding process, in semiquantitative agreement with existing explicit-water simulations, but significantly accelerate the unbinding process. Moreover, our methods allow the characterization of nonequilibrium hydration states of pocket and ligand during the ligand movement, for which we find substantial memory and hysteresis effects for binding vs. unbinding. Our study thus provides a significant step forward toward efficient, physics-based interpretation and predictions of the complex kinetics in realistic ligand-receptor systems.

关键词： ligand-receptor binding/unbinding kinetics dry-wet transitions variational implicit-solvent model level-set method string method

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Wetting hysteresis induced by nanodefects

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2016年第3期113卷 E262-E271页

作者： Giacomello, Alberto Schimmele, Lothar Dietrich, Siegfried Max Planck Inst Intelligente Syst D-70569 Stuttgart Germany Univ Roma La Sapienza Dipartimento Ingn Meccan & Aerosp I-00184 Rome Italy Univ Stuttgart Inst Theoret Phys 4 D-70569 Stuttgart Germany

Wetting of actual surfaces involves diverse hysteretic phenomena stemming from ever-present imperfections. Here, we clarify the origin of wetting hysteresis for a liquid front advancing or receding across an isolated defect of nanometric size. Various kinds of chemical and topographical nanodefects, which represent salient features of actual heterogeneous surfaces, are investigated. The most probable wetting path across surface heterogeneities is identified by combining, within an innovative approach, microscopic classical density functional theory and the string method devised for the study of rare events. The computed rugged free-energy landscape demonstrates that hysteresis emerges as a consequence of metastable pinning of the liquid front at the defects;the barriers for thermally activated defect crossing, the pinning force, and hysteresis are quantified and related to the geometry and chemistry of the defects allowing for the occurrence of nanoscopic effects. The main result of our calculations is that even weak nanoscale defects, which are difficult to characterize in generic microfluidic experiments, can be the source of a plethora of hysteretical phenomena, including the pinning of nanobubbles.

关键词： contact angle hysteresis pinning nanoscale wetting string method

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Pore opening and closing of a pentameric ligand-gated ion channel

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2010年第46期107卷 19814-19819页

作者： Zhu, Fangqiang Hummer, Gerhard NIDDKD Chem Phys Lab NIH Bethesda MD 20892 USA

Nerve signaling in humans and chemical sensing in bacteria both rely on the controlled opening and closing of the ion-conducting pore in pentameric ligand-gated ion channels. With the help of a multiscale simulation approach that combines mixed elastic network model calculations with molecular dynamics simulations, we study the opening and closing of the pore in Gloeobacter violaceus channel GLIC at atomic resolution. In our simulations of the GLIC transmembrane domain, we first verify that the two endpoints of the transition are open and closed to sodium ion conduction, respectively. We then show that a two-stage tilting of the pore-lining helices induces cooperative drying and iris-like closing of the channel pore. From the free energy profile of the gating transition and from unrestrained simulations, we conclude that the pore of the isolated GLIC transmembrane domain closes spontaneously. The mechanical work of opening the pore is performed primarily on the M2-M3 loop. Strong interactions of this short and conserved loop with the extracellular domain are therefore crucial to couple ligand binding to channel opening.

关键词： ELIC nicotinic acetylcholine receptor hydrophobic gate conformational change string method

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All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element

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PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2013年第6期81卷 1017-1030页

作者： Vashisth, Harish Abrams, Cameron F. Univ Michigan Dept Chem Ann Arbor MI 48109 USA Univ Michigan Biophys Program Ann Arbor MI 48109 USA Drexel Univ Dept Chem & Biol Engn Philadelphia PA 19104 USA

Insulin regulates blood glucose levels in higher organisms by binding to and activating insulin receptor (IR), a constitutively homodimeric glycoprotein of the receptor tyrosine kinase (RTK) superfamily. Therapeutic efforts in treating diabetes have been significantly impeded by the absence of structural information on the activated form of the insulin/IR complex. Mutagenesis and photo-crosslinking experiments and structural information on insulin and apo-IR strongly suggest that the dual-chain insulin molecule, unlike the related single-chain insulin-like growth factors, binds to IR in a very different conformation than what is displayed in storage forms of the hormone. In particular, hydrophobic residues buried in the core of the folded insulin molecule engage the receptor. There is also the possibility of plasticity in the receptor structure based on these data, which may in part be due to rearrangement of the so-called CT-peptide, a tandem hormone-binding element of IR. These possibilities provide opportunity for large-scale molecular modeling to contribute to our understanding of this system. Using various atomistic simulation approaches, we have constructed all-atom structural models of hormone/receptor complexes in the presence of CT in its crystallographic position and a thermodynamically favorable displaced position. In the displaced-CT complex, many more insulinreceptor contacts suggested by experiments are satisfied, and our simulations also suggest that R-insulin potentially represents the receptor-bound form of hormone. The results presented in this work have further implications for the design of receptor-specific agonists/antagonists. Proteins 2013;(c) 2012 Wiley Periodicals, Inc.

关键词： insulin receptor diabetes temperature-accelerated molecular dynamics string method Monte-Carlo docking hormone recognition

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On-the-Path Random Walk Sampling for Efficient Optimization of Minimum Free-Energy Path

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JOURNAL OF COMPUTATIONAL CHEMISTRY 2009年第11期30卷 1649-1653页

作者： Chen, Mengen Yang, Wei Florida State Univ Inst Mol Biophys Tallahassee FL 32306 USA Florida State Univ Dept Chem & Biochem Tallahassee FL 32306 USA Nankai Univ Coll Life Sci Tianjin 300071 Peoples R China

A sampling method is proposed for the efficient acquisition of minimum free-energy path (MFEP). Here, the MFEP optimization is realized based on the sampling via single on-the-path random walk simulation. The present strategy naturally ensures the on-the-path structural continuity so that the MFEP optimization can be simplified and its efficiency can be improved as well. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 1649-1653, 2009

关键词： minimum free-energy path string method generalized ensemble simulation conformational sampling

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A minimization principle for transition paths of maximum flux for collective variables

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THEORETICAL CHEMISTRY ACCOUNTS 2016年第1期136卷 14,2-12-14,2-12页

作者： Skeel, Robert D. Zhao, Ruijun Post, Carol Beth Purdue Univ Dept Comp Sci W Lafayette IN 47906 USA Minnesota State Univ Dept Math & Stat Mankato MN 56001 USA Purdue Univ Dept Med Chem & Mol Pharmacol W Lafayette IN 47906 USA

Considered is the construction of transition paths of conformational changes for proteins and other macromolecules, using methods that do not require the generation of dynamics trajectories. Special attention is given to the use of a reduced set of collective variables for describing such paths. A favored way to define transition paths is to seek channels through the transition state having cross sections with a high reactive flux (density of last hitting points of reactive trajectories). Given here is a formula for reactive flux that is independent of the parameterization of "collective variable space." This formula is needed for the principal curve of the reactive flux (as in the revised finite temperature string method) and for the maximum flux transition (MaxFlux) path. Additionally, a resistance functional is derived for narrow tubes, which when minimized yields a MaxFlux path. A strategy for minimization is outlined in the spirit of the string method. Finally, alternative approaches based on determining trajectories of high probability are considered, and it is observed that they yield paths that depend on the parameterization of collective variable space, except in the case of zero temperature, where such a path coincides with a MaxFlux path.

关键词： Reaction path Minimum energy path string method

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