Thermodynamic Control of Domain Swapping by Modulating the Helical Propensity in the Hinge Region of Myoglobin

Domain swapping is an exception to Anfinsen's dogma, and more than one structure can be produced from the same amino acid sequence by domain swapping. We have previously shown that myoglobin (Mb) can form a domain‐swapped dimer in which the hinge region is converted to a helical structure. In this study, we showed that domain‐swapped dimerization of Mb was achieved by a single Ala mutation of Gly at position 80. Multiple Ala mutations at positions 81 and 82 in addition to position 80 facilitated dimerization of Mb by stabilization of the dimeric states. Domain swapping tendencies correlated well with the helical propensity of the mutated residue in a series of Mb mutants with amino acids introduced to the hinge region. These findings demonstrate that a single mutation in the hinge loop to modify helical propensity can control oligomer formation, providing new ideas to create high‐order protein oligomers using domain swapping.     

Full spin and spatial symmetry adapted technique for correlated electronic hamiltonians: Application to an icosahedral cluster

One of the long standing problems in quantum chemistry had been the inability to exploit full spatial and spin symmetry of an electronic Hamiltonian belonging to a non‐Abelian point group. Here, we present a general technique which can utilize all the symmetries of an electronic (magnetic) Hamiltonian to obtain its full eigenvalue spectrum. This is a hybrid method based on Valence Bond basis and the basis of constant z‐component of the total spin. This technique is applicable to systems with any point group symmetry and is easy to implement on a computer. We illustrate the power of the method by applying it to a model icosahedral half‐filled electronic system. This model spans a huge Hilbert space (dimension 1,778,966) and in the largest non‐Abelian point group. The C₆₀ molecule has this symmetry and hence our calculation throw light on the higher energy excited states of the bucky ball. This method can also be utilized to study finite temperature properties of strongly correlated systems within an exact diagonalization approach. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

A cell functional minimization scheme for parabolic problem

We are interested in a robust and accurate finite volume scheme for 2-D parabolic problems derived from the cell functional minimization approach. The scheme has a local stencil, is locally conservative, treats discontinuity rigorously and leads to a symmetric positive definite linear system. Since the scheme has both cell centered unknowns and cell edge unknowns, the computational cost is an issue and a parallel algorithm is then suggested based on nonoverlapping domain decomposition approach. The interface condition is of the Dirichlet–Robin type and has a parameter λ. By choosing this parameter properly, the convergence of the iteration process could be sped up. Numerical results for linear and nonlinear problems demonstrate the good performance of the cell functional minimization scheme and its parallel version on distorted meshes.     

MORPHOLOGY OF POLYURETHANES REVISITED BY COMPLEMENTARY AFM AND TEM

Cast, segmented polyetherurethanes with 30 and 50% hard-segment content (HSC), respectively, were studied by transmission electron microscopy (TEM) and atomic force microscopy (AFM). Multi-phase segregation was observed in both samples on two levels (micro and nano) of structural organization. Spherulites with a prominent radial structure, built of branched fibrils and globules, were captured on the micrometer level. The use of AFM enabled us to investigate the nanostructure in the polyurethanes studied here. In the sample with low (30%) HSC, nano-scale phase separation was observed by AFM in areas outside the crystalline aggregates. The morphology in these domains exhibited short, rodlike hard domains embedded in the matrix of the soft segments. The other sample (50% HSC) contained four identifiable morphological features. These included spherulites, globules, bundles of lamellae, and nanophase-separated, rodlike hard domains, embedded in the soft-segment matrix.

The globules did not have any internal structure visible by AFM down to the nanometer scale. We speculate that the globules form as a result of macro-phase segregation, due to incompatibility of the reactants, during synthesis and may thus be identified as pockets of free hard segments. The AFM phase imaging has been very useful to observe the bundles of lamellae and the nanoscale phase-separated structures, which were not captured by TEM, due to large differences in AFM phase signal contrast between the hard and the soft domains.     

Dynamic Models of Simple Judgments: I. Properties of a Self-Regulating Accumulator Module

This is the first of two papers comparing connectionist and traditional stochastic latency mechanisms with respect to their ability to account for simple judgments. In this paper, we show how the need to account for additional features of judgment has led to the formulation of progressively more sophisticated models. One of these, a self-regulating, generalized accumulator process, is treated in detail, and its simulated performance across a sample of tasks is described. Since an adaptive decision module of this kind possesses all the ingredients of intelligent behavior, it is eminently suited as a basic computing element in more complex networks.     

Order Environments of Topological Spaces

In this paper it is proved that a space may be realized as the set of the maximal elements in a continuous poset if and only if it is Tychonoff.     

Variations of Constrained Domain Functionals Associated with Boundary-Value Problems

We study variational formulas for maximizers for domain functionalsF(x0, u(x0)), x0, and F(x,u(x))dxover all Lipschitz domains satisfying the constraintg(x) dx=1. Here, u is the solution ofa diffusion equation in . Functional variations arecomputed using domain variations which preserve the constraint exactly. Weshow that any maximizer solves a moving boundary problem for the diffusionequation. Further, we show that, for problems with symmetry, the optimaldomains are balls.     

Cosmic Strings and Domain Walls in a Scale-Covariant Theory of Gravitation

Axially symmetric space-time is considered in the presence of cosmic string source and thick domain walls in the frame work of a scale-covariant theory of gravitation. A relation between metric potential is assumed to get a determinate solution of the field equations of this theory. In this particular case, it is observed that the geometric (Nambu) string p-string (Takabayasi string) and Reddy string do not survive. It is also seen that the stiff (self-gravitating) domain walls do not exist in this theory.     

Surface antiferromagnetic domain structures of NiO (0 0 1) studied using UV photoemission electron microscope

Direct observation of the antiferro (AF) magnetic domain structures of a NiO (0 0 1) surface is found to be possible using a spectroscopy photoelectron low-energy electron microscope (SPELEEM) and a commercial UV Hg excitation light source without using any polarizers. The principle is based on the magnetic linear dichroism (MLD) effect, where different domain contrasts are produced according to the relative angle between the antiferromagnetic axis and the linearly polarized light. The observed AF magnetic domain structures are strongly affected by both bulk AF magnetic domain structures and the stresses induced during the sample cleaving process. Moreover, the AF magnetic domain structures are found to be irreversible when the sample is heated to over its Néel temperature and then cooled. The possibility of imaging AF magnetic domain structures without using synchrotron radiation or a polarizer is attractive.     

Analytical and numerical study of coupled atomistic-continuum methods for fluids

The stability and convergence rate of coupled atomistic-continuum methods are studied analytically and numerically. These methods couple a continuum model with molecular dynamics through the exchange of boundary conditions in the continuum-particle overlapping region. Different coupling schemes, including velocity–velocity, flux–velocity, velocity–flux and flux–flux, are studied. It is found that the velocity–velocity and flux–velocity schemes are stable. The flux–flux scheme is weakly unstable. The stability of the velocity–flux scheme depends on the parameter T_c which is the length of the time interval between successive exchange of boundary conditions. It is stable when T_c is small and unstable when T_c is large. For steady-state problems, the flux–velocity scheme converges faster than the other coupling schemes.