检索结果-内蒙古大学图书馆

Parameter effects on binding chemistry in crowded media using a two-dimensional stochastic off-lattice model

Physical Review E 2009年第4期80卷 041918-041918页

作者： Byoungkoo Lee Philip R. LeDuc Russell Schwartz 654 Mellon Institute Carnegie Mellon/University of Pittsburgh Joint Program in Computational Biology 4400 Fifth Avenue Pittsburgh Pennsylvania 15213 USA 420 Scaife Hall Department of Mechanical Engineering Carnegie Mellon University 5000 Forbes Avenue Pittsburgh Pennsylvania 15213 USA 654 Mellon Institute Department of Biological Sciences Carnegie Mellon University 4400 Fifth Avenue Pittsburgh Pennsylvania 15213 USA

The intracellular environment imposes a variety of constraints on biochemical reaction systems that can substantially change reaction rates and equilibria relative to an ideal solution-based environment. One of the most notable features of the intracellular environment is its dense macromolecular crowding, which, among many other effects, tends to strongly enhance binding and assembly reactions. Despite extensive study of biochemistry in crowded media, it remains extremely difficult to predict how crowding will quantitatively affect any given reaction system due to the dependence of the crowding effect on numerous assumptions about the reactants and crowding agents involved. We previously developed a two dimensional stochastic off-lattice model of binding reactions based on the Green’s function reaction dynamics method in order to create a versatile simulation environment in which one can explore interactions among many parameters of a crowded assembly system. In the present work, we examine interactions among several critical parameters for a model dimerization system: the total concentration of reactants and inert particles, the binding probability upon a collision between two reactant monomers, the mean time of dissociation reactions, and the diffusion coefficient of the system. Applying regression models to equilibrium constants across parameter ranges shows that the effect of the total concentration is approximately captured by a low-order nonlinear polynomial model, while the other three parameter effects are each accurately captured by a linear model. Furthermore, validation on tests with multi-parameter variations reveals that the effects of these parameters are separable from one another over a broad range of variation in all four parameters. The simulation work suggests that predictive models of crowding effects can accommodate a wider variety of parameter variations than prior theoretical models have so far achieved.

关键词： Equilibrium constants

来源：评论

学校读者我要写书评

暂无评论

Optimal packings of superballs

引用

Physical Review E 2009年第4期79卷 041309-041309页

作者： Y. Jiao F. H. Stillinger S. Torquato Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08540 USA

Dense hard-particle packings are intimately related to the structure of low-temperature phases of matter and are useful models of heterogeneous materials and granular media. Most studies of the densest packings in three dimensions have considered spherical shapes, and it is only more recently that nonspherical shapes (e.g., ellipsoids) have been investigated. Superballs (whose shapes are defined by |x1|2p+|x2|2p+|x3|2p≤1) provide a versatile family of convex particles (p≥0.5) with both cubic-like and octahedral-like shapes as well as concave particles (0

关键词： Temperature

来源：评论

学校读者我要写书评

暂无评论

Interactions leading to disordered ground states and unusual low-temperature behavior

引用

Physical Review E 2009年第3期80卷 031105-031105页

作者： Robert D. Batten Frank H. Stillinger Salvatore Torquato Department of Chemical Engineering Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Materials Institute Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08544 USA

We have shown that any pair potential function v(r) possessing a Fourier transform V(k) that is positive and has compact support at some finite wave number K yields classical disordered ground states for a broad density range [R. D. Batten, F. H. Stillinger, and S. Torquato, J. Appl. Phys. 104, 033504 (2008)]. By tuning a constraint parameter χ (defined in the text), the ground states can traverse varying degrees of local order from fully disordered to crystalline ground states. Here, we show that in two dimensions, the “k-space overlap potential,” where V(k) is proportional to the intersection area between two disks of diameter K whose centers are separated by k, yields anomalous low-temperature behavior, which we attribute to the topography of the underlying energy landscape. At T=0, for the range of densities considered, we show that there is continuous energy degeneracy among Bravais-lattice configurations. The shear elastic constant of ground-state Bravais-lattice configurations vanishes. In the harmonic regime, a significant fraction of the normal modes for both amorphous and Bravais-lattice ground states have vanishing frequencies, indicating the lack of an internal restoring force. Using molecular-dynamics simulations, we observe negative thermal-expansion behavior at low temperatures, where upon heating at constant pressure, the system goes through a density maximum. For all temperatures, isothermal compression reduces the local structure of the system unlike typical single-component systems.

关键词： Ground state

来源：评论

学校读者我要写书评

暂无评论

Dense packings of polyhedra: Platonic and Archimedean solids

引用

Physical Review E 2009年第4期80卷 041104-041104页

作者： S. Torquato Y. Jiao Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08540 USA Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey 08544 USA

Understanding the nature of dense particle packings is a subject of intense research in the physical, mathematical, and biological sciences. The preponderance of previous work has focused on spherical particles and very little is known about dense polyhedral packings. We formulate the problem of generating dense packings of nonoverlapping, nontiling polyhedra within an adaptive fundamental cell subject to periodic boundary conditions as an optimization problem, which we call the adaptive shrinking cell (ASC) scheme. This optimization problem is solved here (using a variety of multiparticle initial configurations) to find the dense packings of each of the Platonic solids in three-dimensional Euclidean space R3, except for the cube, which is the only Platonic solid that tiles space. We find the densest known packings of tetrahedra, icosahedra, dodecahedra, and octahedra with densities 0.823…, 0.836…, 0.904…, and 0.947…, respectively. It is noteworthy that the densest tetrahedral packing possesses no long-range order. Unlike the densest tetrahedral packing, which must not be a Bravais lattice packing, the densest packings of the other nontiling Platonic solids that we obtain are their previously known optimal (Bravais) lattice packings. We also derive a simple upper bound on the maximal density of packings of congruent nonspherical particles and apply it to Platonic solids, Archimedean solids, superballs, and ellipsoids. Provided that what we term the “asphericity” (ratio of the circumradius to inradius) is sufficiently small, the upper bounds are relatively tight and thus close to the corresponding densities of the optimal lattice packings of the centrally symmetric Platonic and Archimedean solids. Our simulation results, rigorous upper bounds, and other theoretical arguments lead us to the conjecture that the densest packings of Platonic and Archimedean solids with central symmetry are given by their corresponding densest lattice packings. This can be regarded to be

关键词： Optimization

来源：评论

学校读者我要写书评

暂无评论

Analysis of a modified wien bridge using maple

Analysis of a modified wien bridge using maple

引用

2008 International Conference on Scientific Computing, CSC 2008

作者： Correa, Valentina Londoño Logic and Computational Group Program of Physical Engineering School of Sciences and Humanities EAFIT University Medellín Colombia

ISBN: (纸本)1601320590

This paper describes the problem of the modification of Wien Bridge Oscillator. It was realized using Maple. The constructed equations were obtained using the Lagrange method. The results of this modification have more precision and coherence than the Classic Wien Bridge. The Analysis of a Modified Wien Bridge was done using a computer program to perform symbolic calculus, algebraic and computational algebra. Therefore based on this program did this paper since its tools are quite useful in carrying out the equations later this played.

关键词： Calculations

来源：评论

学校读者我要写书评

暂无评论

Midwest Structural sciences Center A University‐Government Partnership

引用

AIP Conference Proceedings 2008年第1期973卷 377-382页

作者： William A. Dick Executive Director Midwest Structural Sciences Center Computational Science and Engineering Program University of Illinois at Urbana‐Champaign 2270 Digital Computer Laboratory 1304 West Springfield Avenue Urbana Illinois 61801 USA

Strategic partnerships among universities, industry and government have been a trademark of the research environment in the United States for more than two decades. Each member of this research triad brings a set of unique perspectives and strengths to the table, as well as being hampered with an often equally daunting set of weaknesses. It is clear that given appropriate opportunities in specific technologies, university‐industry‐government collaboration is a “big winner.” Our observation, however, is that some federally‐funded research programs have failed to achieve the synergistic result envisioned by the funding agency, the host university, or collaborating industries. This paper introduces the relationships and highlights a new research program at the University of Illinois focused on the structural sciences necessary for next‐generation air vehicles. Keys to successful programs are realistic expectations on all sides, a clear focus on appropriate science and engineering technologies, flexibility on the part of the federal funding agency, and a strong university management team.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Green’s function reaction dynamics

引用

Physical Review E 2008年第3期78卷 031911-031911页

作者： Byoungkoo Lee Philip R. LeDuc Russell Schwartz Joint Program in Computational Biology Carnegie Mellon University and University of Pittsburgh 654 Mellon Institute 4400 Fifth Avenue Pittsburgh Pennsylvania 15213 USA Department of Mechanical Engineering Carnegie Mellon University 415 Scaife Hall 5000 Forbes Avenue Pittsburgh Pennsylvania 15213 USA Department of Biological Sciences Carnegie Mellon University 654 Mellon Institute 440 Fifth Avenue Pittsburgh Pennsylvania 15213 USA

The environment inside a living cell is dramatically different from that found in in vitro models, presenting a problem for computational models of biochemistry that are only beginning to capture these differences. This deviation between idealized in vitro models and more realistic intracellular conditions is particularly problematic for models of molecular self-assembly, but also specifically hard to address because the large sizes and long assembly times of biological self-assembly systems force the use of highly simplified models. We have developed a prototype of a molecular self-assembly simulator based on the Green’s function reaction dynamics (GFRD) model to achieve more realistic models of assembly in the crowded conditions of the cell without unduly sacrificing tractability. We tested the model on a simple representation of dimer assembly in a two-dimensional space. Our simulations verify that the model is computationally efficient, provides a realistic quantitative model of reaction kinetics in uncrowded conditions, and exhibits expected excluded volume effects under conditions of high crowding. This work confirms the effectiveness of the GFRD technique for more realistic coarse-grained modeling of self-assembly in crowded conditions and helps lay the groundwork for exploring the effects of in vivo crowding on more complex assembly systems.

关键词： Assembly

来源：评论

学校读者我要写书评

暂无评论

Optimal Packings of Superdisks and the Role of Symmetry

引用

Physical Review Letters 2008年第24期100卷 245504-245504页

作者： Y. Jiao F. H. Stillinger S. Torquato Department of Mechanical and Aerospace Engineering Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA School of Natural Sciences Institute for Advanced Study Princeton New Jersey 08540 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA

Almost all studies of the densest particle packings consider convex particles. Here, we provide exact constructions for the densest known two-dimensional packings of superdisks whose shapes are defined by |x1|2p+|x2|2... 详细信息

关键词： Condensed matter physics

来源：评论

学校读者我要写书评

暂无评论

The location of Ti atom in sodium alanate: An ab initio spin-polarised study

The location of Ti atom in sodium alanate: An ab initio spin...

引用

作者： Du, A.J. Smith, Sean C. Lu, G.Q. Centre for Computational Molecular Science ARC Centre for Functional Nanomaterial University of Queensland Brisbane QLD 4072 Australia University of Queensland Australia Hydrogen Storage Systems Australia Department of Computational Molecular Science University of Queensland Australia Centre for Computational Molecular Science UQ Australia Computational Nanotecnnology Program ARC Centre for Functional Nanomaterials Australia Department of Chemical Engineering in Nanotechnology University of Queensland Australia ARC Centre for Functional Nanomaterials Australia Australian Academy of Technological Sciences and Engineering Australia

In this work, ab initio spin-polarised Density Functional Theory (DFT) calculations are performed to study the interaction of a Ti atom with a NaAlH4(001) surface. We confirm that an interstitially located Ti atom in the NaAlH4 subsurface is the most energetically favoured configuration as recently reported (Chem. Comm. (17) 2006, 1822). On the NaAlH4(001) surface, the Ti atom is most stable when adsorbed between two sodium atoms with an AlH4 unit beneath. A Ti atom on top of an Al atom is also found to be an important structure at low temperatures. The diffusion of Ti from the Al-top site to the Na-bridging site has a low activation barrier of 0.20 eV and may be activated at the experimental temperatures (∼323 K). The diffusion of a Ti atom into the energetically favoured subsurface interstitial site occurs via the Na-bridging surface site and is essentially barrierless. Copyright © 2007 Inderscience Enterprises Ltd.

关键词： Titanium

来源：评论

学校读者我要写书评

暂无评论

Decision fusion of circulating markers for breast cancer detection in premenopausal women

Decision fusion of circulating markers for breast cancer det...

引用

7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Jesneck, Jonathan L. Mukherjee, Sayan Nolte, Loren W. Lokshin, Anna E. Marks, Jeffrey R. Lo, Joseph Department of Biomedical Engineering Department of Statistical Science Computational Biology and Bioinformatics Program Duke Advanced Imaging Labs. Institute for Genome Sciences and Policy Department of Computer Science Duke University Department of Electrical and Computer Engineering Division of Hematology/Oncology University of Pittsburgh School of Medicine University of Pittsburgh Cancer Institute Pittsburgh PA 15213 United States Department of Experimental Surgery Duke University Medical Center Medical Physics Graduate Program Duke University Durham NC 27708 United States

ISBN: (纸本)1424415098

Current mammographic screeningfor breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Because the data set was very noisy and contained only weak features, we used a classifier designed for noisy data: decision fusion. Decision fusion outperformed both a support vector machine (SVM) and linear regression with forward stepwise feature selection on all three two-class classification tasks: normal tissue vs. cancer, normal tissue vs. benign lesions, and benign lesions vs. cancer. Decision fusion detected cancer moderately well (AUC=0.84 on normal vs. cancer), demonstrating promise as a screening tool. Decision fusion also detected benign lesions similarly well (AUC=0.83 on normal vs. benign lesions) and was the only classifier to achieve any success in separating benign from malignant lesions (AUC=0.64 on benign vs. cancer). The classification results suggest that the assayed proteins are more indicative of a secondary effect, such as immune response, rather than specific for breast cancer. In conclusion, the decision fusion classifier demonstrated some promise in detecting breast lesions and outperformed other classifiers, especially for the very noisy classification problem of distinguishing benign from malignant lesions. ©2007 IEEE.

关键词： Tissue

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：