Investigating the Disordered and Membrane-Active Peptide A-Cage-C Using Conformational Ensembles

The driving forces and conformational pathways leading to amphitropic protein-membrane binding and in some cases also to protein misfolding and aggregation is the subject of intensive research. In this study, a chimeric polypeptide, A-Cage-C, derived from α-Lactalbumin is investigated with the aim of elucidating conformational changes promoting interaction with bilayers. From previous studies, it is known that A-Cage-C causes membrane leakages associated with the sporadic formation of amorphous aggregates on solid-supported bilayers. Here we express and purify double-labelled A-Cage-C and prepare partially deuterated bicelles as a membrane mimicking system. We investigate A-Cage-C in the presence and absence of these bicelles at non-binding (pH 7.0) and binding (pH 4.5) conditions. Using in silico analyses, NMR, conformational clustering, and Molecular Dynamics, we provide tentative insights into the conformations of bound and unbound A-Cage-C. The conformation of each state is dynamic and samples a large amount of overlapping conformational space. We identify one of the clusters as likely representing the binding conformation and conclude tentatively that the unfolding around the central W23 segment and its reorientation may be necessary for full intercalation at binding conditions (pH 4.5). We also see evidence for an overall elongation of A-Cage-C in the presence of model bilayers.     

Bound state solutions of D‐dimensional schrödinger equation with exponential‐type potentials

In this article, using an exactly‐solvable multiparameter exponential‐type potential we propose a unified treatment of the analytical bound—state solutions of the Schrödinger equation for exponential‐type potentials in D‐dimensions. Our proposal accepts different approximations to the centrifugal term; however, its usefulness is exemplified in the frame of the Green and Aldrich approach. This fact enables us to compare our results with specific potentials found in the literature and that are obtained here as particular cases of our proposal. That is, instead of solving a specific exponential‐type potential, by resorting each time to a specialized method, the energy spectra and wavefunctions are derived straightforward from the proposed approach. Furthermore, our proposal can be used as an alternative way in the search of solutions to new exponential‐type potentials besides that one can study different approximations to the term . © 2014 Wiley Periodicals, Inc.     

Energy elastic effects and the concept of temperature in flowing polymeric liquids

The incorporation of energy elastic effects in the modeling of flowing polymeric liquids is discussed. Since conformational energetic effects are determined by structural features much smaller than the end-to-end vector of the polymer chains, commonly employed single conformation tensor models are insufficient to describe energy elastic effects. The need for a local structural variable is substantiated by studying a microscopic toy model with energetic effects in the setting of a generalized canonical ensemble. In order to examine the dynamics of flowing polymeric liquids with energy elastic effects, a thermodynamically admissible set of evolution equations is presented that accounts for the evolution of the microstructure in terms of a slow tensor, as well as a fast, local scalar variable. It is demonstrated that the temperature used in the definition of the heat flux is directly related to the Lagrange multiplier of the microscopic energy in the generalized canonical partition function. The temperature equation is discussed with respect to, first, the dependence of the heat capacity on the polymer conformation and, second, the possibility to measure experimentally the effects of the conformational energy.

Modeling of isothermal processes in porous materials on the basis of the concept of an ensemble of pores

A class of models of porous media based on the concept of an ensemble of pores with a certain distribution of the main geometric parameters (for example, the pore size) is considered. The cases of pores saturated with single-and two-phase multicomponent liquid mixtures are investigated. The properties of equilibrium states of the mixture are derived from the minimum free energy condition and the transfer laws from the decreasing free energy condition. The hydrodynamic connectivity of the pores is described by two types of kernels: one describes the spatial connectivity and the other the connectivity in an elementary macrovolume. Analytically and numerically, the one-dimensional problems of establishment of a steady-state regime, propagation of a passive admixture, and two-phase flow (an analog of the Buckley-Leverett problem) are investigated. A relationship between the models in question and relaxational filtration models is demonstrated. A simple model of capillary hysteresis related with the non-monotonicity of the pore area to volume ratio function is proposed.     

Sommerfeld-type integrals for discrete diffraction problems

Three problems for a discrete analog of the Helmholtz equation are studied analytically using the plane wave decomposition and the Sommerfeld integral approach. They are: (1) the problem with a point source on an entire plane; (2) the problem of diffraction by a Dirichlet half-line; (3) the problem of diffraction by a Dirichlet right angle. It is shown that the total field can be represented as an integral of an algebraic function over a contour drawn on some manifold. The latter is a torus. As a result, explicit solutions are obtained in terms of recursive relations (for the Green’s function), algebraic functions (for the half-line problem), or elliptic functions (for the right angle problem).     

NOON State Generation with Phonons in Acoustic Wave Resonators Assisted by a Nitrogen‐Vacancy‐Center Ensemble

Since the quality factor of an acoustic wave resonator (AWR) reached 10¹¹, AWRs have been regarded as a good carrier of quantum information. In this paper, a scheme to construct a NOON state with two AWRs assisted by a nitrogen‐vacancy‐center ensemble (NVE) is proposed. The two AWRs cross each other vertically, and the NVE is located at the center of the crossing. By considering the decoherence of the system and using resonant interactions between the AWRs and the NVE, and the single‐qubit operation of the NVE, a NOON state can be achieved with a fidelity higher than 98.8% when the number of phonons in the AWR is $N\le 3$.     

Belief functions contextual discounting and canonical decompositions

In this article, the contextual discounting of a belief function, a classical discounting generalization, is extended and its particular link with the canonical disjunctive decomposition is highlighted. A general family of correction mechanisms allowing one to weaken the information provided by a source is then introduced, as well as the dual of this family allowing one to strengthen a belief function.     

On the limitation of the van der Waals-Platteeuw-based thermodynamic models for hydrates with multiple occupancy of cavities

Thermodynamic models based on the van der Waals–Platteeuw statistical theory (Adv. Chem. Phys. 2, 1 (1959)) can be very accurate in describing hydrate equilibrium conditions, even for some occasions when multiple cavity occupancy occurs. These are cases outside the range of assumptions used for the development of the original statistical theory. However, during multiple cavity occupancy such models can perform poorly when calculating the cavity occupancies. This paper reports novel Grand Canonical Monte Carlo molecular simulations for the case of pure structure II N₂ hydrate and compares the calculated cavity occupancies with experimental data and observe reasonable agreement. Also examined are the van der Waals–Platteeuw-based modifications that retained the single-occupancy assumption of the original theory and how they perform when predicting cavity occupancies and hydrate equilibrium pressures.     

冷原子介质中基于相干诱导高反射带和高透射带的全光路由控制

以相干诱导光子带隙结构为工作基础,提出了一种可对两个弱光信号的传播路径同时进行动态调控的新型全光路由控制方案。利用描述光波在空间周期介质中相干散射的传输矩阵理论,结合描述单频激光与多能级原子共振相互作用的密度矩阵方程,计算了作为控制媒介的相干驱动超冷原子系综的稳态反射光谱和稳态透射光谱。结果表明,通过改变两个较强相干激光的空间模式、强度和频率等参数,可在探测跃迁共振频率附近建立反射率约为95%或者透射率约为95%的两个特殊频带。对这样的相干诱导高反射带和高透射带进行了实时动态调控,可根据需要引导两个不同频率的弱光信号进入指定的网络通道。该方案很好地满足了在量子信息处理领域对弱光信号进行全光路由控制时的低损耗和低形变要求。