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  • 1
    Electronic Resource
    Electronic Resource
    The effective field approximation for Ising spin glasses on simply connected lattices (1991)
    College Park, Md. : American Institute of Physics (AIP)
    Journal of Mathematical Physics 32 (1991), S. 2561-2562 
    Details
    ISSN: 1089-7658
    Source: AIP Digital Archive
    Topics: Mathematics , Physics
    Notes: A spin glass on a one-dimensional Ising lattice is considered. The entropy at fixed nonuniform bond and field energies is written down as a functional of singlet and pair spin expectations, in terms of which bond and field energies are then expressed. The solution is reformulated in terms of effective fields which, in a spin-glass ensemble, are distributed as in a Markov chain. This result, and the corresponding free energy, shows that the effective field approximation previously used is exact for such systems, an assertion which extends to Cayley trees.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.529150
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  • 2
    Electronic Resource
    Electronic Resource
    Magnetic properties of antiferromagnetic superlattices : 38th Annual Conference on Magnetism and Magnetic Materials (1994)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 75 (1994), S. 6685-6687 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The temperature dependence of the magnetic properties of magnetic superlattices by using the Bethe approximation to the inhomogeneous Ising model is studied. A self-consistent equation which determines the variation of the magnetic moment for any layer thicknesses is derived. In particular, the crossover from bulk-dominated behavior for large thicknesses of layers to interface-dominated behavior for small thicknesses is discussed. The results both qualitatively and quantitatively differ from mean-field theory; the experimental observation for FeF2/CoF2 and CoO/NiO superlattices is explained.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.356895
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  • 3
    Electronic Resource
    Electronic Resource
    The Langevin/implicit-Euler/normal-mode scheme for molecular dynamics at large time steps (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 4995-5012 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: As molecular dynamics simulations continue to provide important insights into biomolecular structure and function, a growing demand for increasing the time span of the simulations is emerging. Our focus here is developing a new algorithm, LIN (Langevin/implicit-Euler/normal mode), that combines normal-mode and implicit-integration techniques, for large time step biomolecular applications. In the normal-mode phase of LIN, we solve an approximate linearized Langevin formulation to resolve the rapidly varying components of the motion. In the implicit phase, we resolve the remaining components of the motion by numerical integration with the implicit-Euler scheme. Developments of the normal-mode phase of LIN are discussed in this paper. Specifically, we solve two crucial issues of the method. The first involves how to choose and how often to update the Hessian approximation for the linearized Langevin equation. This approximation must be computationally feasible and physically reasonable to capture the motion in the higher end of the vibrational spectrum. Three such general Hessian approximations are discussed. The related issue—the frequency of the Hessian update—is analyzed by projecting the motion onto the different vibrational modes. This analysis demonstrates that a one-picosecond interval is reasonable for updating the Hessian in the model system examined here.In this connection, we illustrate that the high-frequency motions are highly localized while the low-frequency motions are delocalized. We also show rigorously that the mode amplitudes are inversely proportional to the frequency (consistent with the equipartition theorem), with 90% of the displacement fluctuations coming from a very small group of low-frequency modes. Anharmonic effects essentially influence the low-frequency modes. The second issue involves how to solve the linearized Langevin equation at large timesteps correctly, where the usual discretized formulation of the random force is invalid. This is accomplished by using analytic expressions for the distributions associated with positions and velocities of the individual oscillators as a function of frequency, obtained as the solution of the corresponding Fokker–Planck equation. We apply LIN with these developments to the nucleic acid component deoxycytidine with timesteps ranging from 100 to 1000 fs. We demonstrate that LIN is stable in these simulations, with energies fluctuating about the same values—and possessing overall similar dynamical features—in comparison to 1 fs explicit simulations, though the fluctuations are significantly larger at larger timesteps. Moreover, continuous dynamics is maintained, and pathway information can be obtained. Computational performance is competitive only at very large time steps: a gain factor of 3–4 is obtained for runs with 1000 fs time steps. Larger gains may be achieved for biomolecules, where sparsity and parallelization can be exploited significantly.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.467422
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  • 4
    Electronic Resource
    Electronic Resource
    A truncated Newton minimizer adapted for CHARMM and biomolecular applications (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 532-552 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report the adaptation of the truncated Newton minimization package TNPACK for CHARMM and biomolecular energy minimization. TNPACK is based on the preconditioned linear conjugate-gradient technique for solving the Newton equations. The structure of the problem - sparsity of the Hessian - is exploited for preconditioning. Experience with the new version of TNPACK is presented on a series of molecular systems of biological and numerical interest: alanine dipeptide (N-methyl-alanyl-acetamide), a dimer of N-methyl-acetamide, deca-alanine, mellitin (26 residues), avian pancreatic polypeptide (36 residues), rubredoxin (52 residues), bovine pancreatic trypsin inhibitor (58 residues), a dimer of insulin (99 residues), and lysozyme (130 residues). Detailed comparisons among the minimization algorithms available in CHARMM, particularly those used for large-scale problems, are presented along with new mathematical developments in TNPACK. The new TNPACK version performs significantly better than ABNR, the most competitive minimizer in CHARMM, for all systems tested in terms of CPU time when curvature information (Hessian/vector product) is calculated by a finite-difference of gradients (the numeric option of TNPACK). The remaining derivative quantities are, however, evaluated analytically in TNPACK. The CPU gain is 50% or more (speedup factors of 1.5 to 2.5) for the largest molecular systems tested and even greater for smaller systems (CPU factors of 1 to 4 for small systems and 1 to 5 for medium systems). TNPACK uses curvature information to escape from undesired configurational regions and to ensure the identification of true local minima. It converges rapidly once a convex region is reached and achieves very low final gradient norms, such as of order 10-8, with little additional work. Even greater overall CPU gains are expected for large-scale minimization problems by making the architectures of CHARMM and TNPACK more compatible with respect to the second-derivative calculations. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150506
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  • 5
    Electronic Resource
    Electronic Resource
    LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1212-1233 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A central goal in molecular dynamics simulations is increasing the integration time-step to allow the capturing of biomolecular motion on biochemically interesting time frames. We previously made a step in that direction by developing the Langevin/implicit-Euler scheme. Here, we present a modified Langevin/implicit-Euler formulation for molecular dynamics. The new method still maintains the major advantage of the original scheme, namely, stability over a wide range of time-steps. However, it substantially reduces the damping effect of the high-frequency modes inherent in the original implicit scheme. The new formulation involves separation of the solution into two components, one of which is solved exactly using normal-mode techniques, the other of which is solved by implicit numerical integration. In this way, the high-frequency and fast-varying components are well resolved in the analytic solution component, while the remaining components of the motion are obtained by a large time-step integration phase. Full details of the new scheme are presented, accompanied by illustrative examples for a simple pendulum system. An application to liquid butane demonstrates stability of the simulations at time-steps up to 50 fs, still with activation of the high-frequency modes. © John Wiley & Sons, Inc.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540141011
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  • 6
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    IJGI, Vol. 8, Pages 291: Evaluating the Suitability of Urban Expansion Based on the Logic Minimum Cumulative Resistance Model: A Case Study from Leshan, China (2019)
    MDPI
    Details
    Publication Date: 2019
    Description: This paper focuses on the suitability of urban expansion in mountain areas against the background of accelerated urban development. Urbanization is accompanied by conflict and intense transformations of various landscapes, and is accompanied by social, economic, and ecological impacts. Evaluating the suitability of urban expansion (UE) and determining an appropriate scale is vital to solving urban environmental issues and realizing sustainable urban development. In mountain areas, the natural and social environments are different from those in the plains; the former is characterized by fragile ecology and proneness to geological disasters. Therefore, when evaluating the expansion of a mountain city, more factors need to be considered. Moreover, we need to follow the principle of harmony between nature and society according to the characteristics of mountain cities. Thus, when we evaluate the expansion of a mountain city, the key procedure is to establish a scientific evaluation system and explore the relationship between each evaluation factor and the urban expansion process. Taking Leshan (LS), China—a typical mountain city in the upper Yangtze River which has undergone rapid growth—as a case study, the logic minimum cumulative resistance (LMCR) model was applied to evaluate the suitability of UE and to simulate its direction and scale. The results revealed that: An evaluation system of resistance factors (ESRFs) was established according to the principle of natural and social harmony; the logic resistance surface (LRS) scientifically integrated multiple resistance factors based on the ESRF and a logic regression analysis. LRS objectively and effectively reflected the contribution and impact of each resistance factor to urban expansion. We found that landscape, geological hazards and GDP have had a great impact on urban expansion in LS. The expansion space of the mountain city is limited; the area of suitable expansion is only 23.5%, while the area which is unsuitable for expansion is 39.3%. In addition, it was found that setting up ecological barriers is an effective way to control unreasonable urban expansion in mountain cities. There is an obvious scale (grid size) effect in the evaluation of urban expansion in mountain cities; an evaluation of the suitable scale yielded the result of 90 m × 90 m. On this scale, taking the central district as the center, the urban expansion process will extend to the neighboring towns of Mianzhu, Suji, Juzi and Mouzi. Urban expansion should be controlled in terms of scale, especially in mountain cities. The most suitable urban size of LS is 132 km2.This would allow for high connectivity of urban-rural areas with the occupation of relatively few green spaces.
    Electronic ISSN: 2220-9964
    Topics: Architecture, Civil Engineering, Surveying , Geosciences
    Published by MDPI on behalf of International Society for Photogrammetry and Remote Sensing (ISPRS).
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  • 7
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    Influences of watershed landscape composition and configuration on lake water quality in the Yangtze River basin of China (2011)
    Wiley
    Details
    Publication Date: 2011-04-28
    Description: Lake water quality is highly dependent on the landscape characteristics in its respective watershed. In this study, we investigated the relationships between lake water quality and landscape composition and configuration within the watershed in the Yangtze River basin of China. Water quality variables, including pH, electrical conductivity (EC), dissolved oxygen (DO), Secchi depth (SD), NO 2 – , NO 3 – , NH 4 + , TN, TP, chemical oxygen demand (COD Mn ), chlorophyll-a (Chl- a ), and trophic state index (TSI) were collected from 16 lakes during the period of 2001–2003. Landscape composition (i.e., the percentage of vegetation, agriculture, water, urban, and bare-land) and landscape configuration metrics, including number of patches (NP), patch density (PD), largest patch index (LPI), edge density (ED), mean patch area (MPA), mean shape index (MSI), contagion (CONTAG), patch cohesion index (COHESION), shannon's diversity index (SHDI), and aggregation index (AI), were calculated for each lake's watershed. Results revealed that percentage of agriculture was negatively related to NO 2 – , TN, TP, Chl- a concentrations, and TSI, while percentage of urban was significantly correlated with EC, NH 4 + , and COD Mn concentrations. Among landscape-level configuration metrics, only ED showed significant relationships with TN, TP concentrations and TSI. However, at the class level, the PD, LPI, ED, and AI of agriculture and urban land uses were significantly correlated with two or more water quality variables. This study suggests that, for a given total area, large and clustered agricultural or urban patches in watershed may have a greater impact on lake water quality than small and scattered ones. Copyright © 2011 John Wiley & Sons, Ltd.
    Print ISSN: 0885-6087
    Electronic ISSN: 1099-1085
    Topics: Architecture, Civil Engineering, Surveying , Geography
    Published by Wiley
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  • 8
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    Silver-catalysed direct amination of unactivated C–H bonds of functionalized molecules (2014)
    Springer Nature
    Details
    Publication Date: 2014-08-22
    Description: Article Functionalizing unactivated carbon–hydrogen bonds is a powerful and atom efficient method to introduce functionality into a molecule. Here, the authors show activation and intramolecular amination of primary C–H bonds using a silver catalyst. Nature Communications doi: 10.1038/ncomms5707 Authors: Mingyu Yang, Bo Su, Yang Wang, Kang Chen, Xingyu Jiang, Yun-Fei Zhang, Xi-Sha Zhang, Guihua Chen, Ye Cheng, Zhichao Cao, Qing-Yun Guo, Lushun Wang, Zhang-Jie Shi
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 9
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    Agronomy, Vol. 8, Pages 210: Effects of TaPHS1 and TaMKK3-A Genes on Wheat Pre-Harvest Sprouting Resistance (2018)
    MDPI
    In: Agronomy
    Details
    Publication Date: 2018
    Description: Pre-harvest sprouting (PHS) constrains wheat production worldwide by reducing both wheat grain yield and end-use quality. TaPHS1 on wheat chromosome 3AS and TaMKK3-A on chromosome 4AL are two cloned genes with major effects on PHS resistance and they are independent from grain color (GC). In this study, we used marker-assisted backcrossing (MAB) to introgress TaPHS1 and TaMKK3-A from two PHS resistant sources—‘Tutoumai A’ and ‘AUS1408′—into a sprouting-susceptible white wheat line, NW97S186. Progeny were tested in four environments to investigate individual and combined effects of those two genes. TaPHS1 significantly reduced PHS and its effect on PHS varied with environments and gene sources. In contrast, the TaMKK3-A gene also significantly reduced PHS but its effectiveness was influenced by environments. The two genes had additive effects on PHS resistance, indicating pyramiding those two quantitative trait lici (QTLs) could increase PHS resistance. The additive effects were greater in a mild environment, such as a greenhouse, than in a dry and hot environment during maturation.
    Electronic ISSN: 2073-4395
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by MDPI
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  • 10
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    Entropy, Vol. 18, Pages 163: Quantum Private Query Protocol Based on Two Non-Orthogonal States (2016)
    MDPI Publishing
    In: Entropy
    Details
    Publication Date: 2016-05-04
    Description: We propose a loss tolerant quantum private query (QPQ) protocol based on two non-orthogonal states and unambiguous state discrimination (USD) measurement. By analyzing a two-point attack by a third party, we find that our protocol has a stronger ability to resist external attacks than G-protocol and Y-protocol. Our protocol requires a smaller number of compressions than that in G-protocol (Gao et al., Opt. Exp. 2012, 20, 17411–17420) and Y-protocol (Yan et al. Quant. Inf. Process. 2014, 13, 805–813), which means less post-processing. Our protocol shows better database security and user privacy compared with G-protocol.
    Electronic ISSN: 1099-4300
    Topics: Chemistry and Pharmacology , Physics
    Published by MDPI Publishing
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