Using polarizable POSSIM force field and fuzzy‐border continuum solvent model to calculate pKa shifts of protein residues

Our Fuzzy‐Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second‐order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was then used to compute pK _a shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. The average unsigned errors in the acid and base pK _a values were 0.37 and 0.4 pH units, respectively, versus 0.58 and 0.7 pH units as calculated with a previous version of polarizable protein force field and Poisson Boltzmann continuum solvent. This POSSIM/FB result is produced with explicit refitting of the hydration parameters to the pK _a values of the carboxylic and basic residues of the OMTKY3 protein; thus, the values of the acidity constants can be viewed as additional fitting target data. In addition to calculating pK _a shifts for the OMTKY3 residues, we have studied aspartic acid residues of Rnase Sa. This was done without any further refitting of the parameters and agreement with the experimental pK _a values is within an average unsigned error of 0.65 pH units. This result included the Asp79 residue that is buried and thus has a high experimental pK _a value of 7.37 units. Thus, the presented model is capable or reproducing pK _a results for residues in an environment that is significantly different from the solvated protein surface used in the fitting. Therefore, the POSSIM force field and the FB continuum solvent parameters have been demonstrated to be sufficiently robust and transferable. © 2016 Wiley Periodicals, Inc.     

Three‐body expansion of the fragment molecular orbital method combined with density‐functional tight‐binding

The three‐body fragment molecular orbital (FMO3) method is formulated for density‐functional tight‐binding (DFTB). The energy, analytic gradient, and Hessian are derived in the gas phase, and the energy and analytic gradient are also derived for polarizable continuum model. The accuracy of FMO3‐DFTB is evaluated for five proteins, sodium cation in explicit solvent, and three isomers of polyalanine. It is shown that FMO3‐DFTB is considerably more accurate than FMO2‐DFTB. Molecular dynamics simulations for sodium cation in water are performed for 100 ps, yielding radial distribution functions and coordination numbers. © 2017 Wiley Periodicals, Inc.     

Perturbations in the Spectra of the Rydberg Series of a Silver Atom

The main series of a silver atom with n = 5–70 are investigated. Perturbations of the np ² P _1/2,3/2 states with n = 10 and 17 caused by interaction with the selfionization 4d5s5p ⁴ P _1/2,3/2 states are detected. Energies of the selfionization states are determined.     

Liquid–Vapor Phase Transitions for Systems with Finite-Range Interactions

We consider particles in ^d , d2, interacting via attractive pair and repulsive four-body potentials of the Kac type. Perturbing about mean-field theory, valid when the interaction range becomes infinite, we prove rigorously the existence of a liquid–gas phase transition when the interaction range is finite but long compared to the interparticle spacing for a range of temperature.     

Rules and reals

A ``-rule" is a sequence of pairwise disjoint sets , each of cardinality and subsets . A subset (a ``real') follows a rule if for infinitely many , .

Two obvious cardinal invariants arise from this definition: the least number of reals needed to follow all -rules, , and the least number of -rules with no real that follows all of them, .

Call a bounded rule if is a -rule for some . Let be the least cardinality of a set of bounded rules with no real following all rules in the set.

We prove the following: and for all . However, in the Laver model, .

An application of is in Section 3: we show that below one can find proper extensions of dense independent families which preserve a pre-assigned group of automorphisms. The original motivation for discovering rules was an attempt to construct a maximal homogeneous family over . The consistency of such a family is still open.

     

Localized defects in classical one-dimensional models

Several aspects of localized defects in the Frenkel-Kontorova, classicalXY chain and analogous models with a finite range of interactions are discussed from a general point of view. Precise definitions are given for defect phase shifts (charges) and for creation, pinning, and interaction energies. Corresponding definitions are also provided for interfaces (localized regions separating two phases). For the nearest-neighbor Frenkel-Kontorova model, the various defect energies are related to areas enclosed by contours joining heteroclinic points of the area-preserving map generated by the conditions of mechanical equilibrium.     

Structure of positive solutions for quasilinear elliptic systems—degenerate ecological models

We study the degenerate ecological models where are positive numbers. The structure of positive solutions of the models is discussed via bifurcation theory and monotone techniques. Copyright © 2004 John Wiley & Sons, Ltd.     

Consistent values and the core in continuum market games with two types of players

The consistent value is an extension of the Shapley value to the class of games with non-transferable utility.? In this paper, the consistent value will be characterized for market games with a continuum of players of two types. We will show that for such games the consistent value need not belong to the core, and provide conditions under which there is equivalence between the two concepts. Received: October 1998 RID="*" ID="*"  This thesis was completed under the supervision of Professor Sergiu Hart, The Center for Rationality and Interactive Decision Theory, Department of Mathematics, Department of Economics, The Hebrew University of Jerusalem. I would like to thank Professor Hart for introducing me to this area of research, for his help and guidance, and, especially, for all his patience.? I would also like to thank Michael Borns for improving the style, and an anonymous referee for helpful comments.     

基于碳化硅衬底的宽禁带半导体外延

宽禁带半导体具备禁带宽度大、电子饱和飘移速度高、击穿场强大等优势,是制备高功率密度、高频率、低损耗电子器件的理想材料。碳化硅(SiC)材料具有热导率高、化学稳定性好、耐高温等优点,在SiC衬底上外延宽禁带半导体材料,对充分发挥宽禁带半导体材料的优势,并提升宽禁带半导体电子器件的性能具有重要意义。得益于SiC衬底质量持续提升及成本不断降低,基于SiC衬底的宽禁带半导体电子市场占比呈现逐年增加的态势。在SiC衬底上外延生长高质量的宽禁带半导体材料是提高宽禁带半导体电子器件性能及可靠性的关键瓶颈。本文综述了近年来国内外研究者们在SiC衬底上外延SiC、氮化镓(GaN)、氧化镓(Ga₂O₃)所取得的研究进展,并展望了SiC衬底上宽禁带半导体外延的发展及应用前景。