In silico design of small RNA switches

The discovery of natural RNA sensors that respond to a change in the environment by a conformational switch can be utilized for various biotechnological and nanobiotechnological advances. One class of RNA sensors is the riboswitch: an RNA genetic control element that is capable of sensing small molecules, responding to a deviation in ligand concentration with a structural change. Riboswitches are modularly built from smaller components. Computational methods can potentially be utilized in assembling these building block components and offering improvements in the biochemical design process. We describe a computational procedure to design RNA switches from building blocks with favorable properties. To achieve maximal throughput for genetic control purposes, future designer RNA switches can be assembled based on a computerized preprocessing buildup of the constituent domains, namely the aptamer and the expression platform in the case of a synthetic riboswitch. Conformational switching is enabled by the RNA versatility to possess two highly stable states that are energetically close to each other but topologically distinct, separated by an energy barrier between them. Initially, computer simulations can produce a list of short sequences that switch between two conformers when trigerred by point mutations or temperature. The short sequences should possess an additional desirable property; when these selected small RNA switch segments are attached to various aptamers, the ligand binding mechanism should replace the aforementioned event triggers, which will no longer be effective for crossing the energy barrier. In the assembled RNA sequence, energy minimization folding predictions should then show no difference between the folded structure of the entire sequence relative to the folded structure of each of its constituents. Moreover, energy minimization methods applied on the entire sequence could aid at this preprocessing stage by exhibiting high mutational robustness to capture the stability of the formed hairpin in the expression platform. The above computer-assisted assembly procedure together with application specific considerations may further be tailored for therapeutic gene regulation. Index Terms-Design of RNA switches, energy minimization methods, RNA folding predictions.     

High‐TC Interfacial Ferromagnetism in SrMnO3/LaMnO3 Superlattices

Heterostructures of strongly correlated oxides demonstrate various intriguing and potentially useful interfacial phenomena. LaMnO₃/SrMnO₃ superlattices are presented showcasing a new high‐temperature ferromagnetic phase with Curie temperature, T_C ≈360 K, caused by electron transfer from the surface of the LaMnO₃ donor layer into the neighboring SrMnO₃ acceptor layer. As a result, the SrMnO₃ (top)/LaMnO₃ (bottom) interface shows an enhancement of the magnetization as depth‐profiled by polarized neutron reflectometry. The length scale of charge transfer, λ_TF ≈2 unit cells, is obtained from in situ growth monitoring by optical ellipsometry, supported by optical simulations, and further confirmed by high resolution electron microscopy and spectroscopy. A model of the inhomogeneous distribution of electron density in LaMnO₃/SrMnO₃ layers along the growth direction is concluded to account for a complex interplay between ferromagnetic and antiferromagnetic layers in superlattices.     

Earliest Deadline First Scheduling with Active Buffer Management for Real-Time Traffic in the Internet

We studied the problem of QoS guarantee for differentiated services. A two-level hierarchical scheduling framework was deployed to separate QoS metrics. Due to its desirable property of minimizing the maximum packet lateness, the Earliest Deadline First (EDF) scheduling was adopted to provide the in-class scheduling for the time-sensitive traffic. We employed an EDF scheduler combined with an active buffer management scheme (CHOKe) to improve the fairness of resource allocation and to maintain a good delay performance for real-time applications. Simulation results showed that the proposed scheme can achieve a better delay performance and make a more fair bandwidth allocation between the real-time TCP and UDP connections than the First Come First Served (FCFS) scheduling with the drop-tail buffer management which is commonly deployed in traditional IP routers.     

Co‐optimization of SnS absorber and Zn(O,S) buffer materials for improved solar cells

Thin‐film solar cells consisting of earth‐abundant and non‐toxic materials were made from pulsed chemical vapor deposition (pulsed‐CVD) of SnS as the p‐type absorber layer and atomic layer deposition (ALD) of Zn(O,S) as the n‐type buffer layer. The effects of deposition temperature and annealing conditions of the SnS absorber layer were studied for solar cells with a structure of Mo/SnS/Zn(O,S)/ZnO/ITO. Solar cells were further optimized by varying the stoichiometry of Zn(O,S) and the annealing conditions of SnS. Post‐deposition annealing in pure hydrogen sulfide improved crystallinity and increased the carrier mobility by one order of magnitude, and a power conversion efficiency up to 2.9% was achieved. Copyright © 2014 John Wiley & Sons, Ltd.     

Joint Rate-and-Power Allocation for Multi-channel Spectrum Sharing Networks with Balanced QoS Provisioning and Power Saving

In this paper we study the joint rate-and-power allocation for multi-channel spectrum sharing networks with balanced QoS provisioning and power saving. We formulate this cross-layer optimization problem as a non-cooperative game G _JRPA in which each user has a coupled two-tuple strategy, i.e., simultaneous rate and multi-channel power allocations. A multi-objective cost function is proposed to represent user’s awareness of both QoS provisioning and power saving. We analyze the properties of Nash equilibrium (N.E.) for our G _JRPA , including its existence, and properties of QoS provisioning and power saving. Furthermore, we derive a layered structure by applying the Lagrangian dual decomposition to G _JRPA and design a distributed algorithm to find the N.E.. Simulation results are presented to show the validity of our game theoretic formulation and the performance of our proposed algorithm. Detailed studies on the performance tradeoff between QoS provisioning and power saving are also carried out.

Sensitivity of trigate MOSFETs to random dopant induced threshold voltage fluctuations

In this paper, we investigate random doping fluctuation effects in trigate SOI MOSFETs by solving the three-dimensional (3D) Poisson, drift-diffusion and continuity equations numerically. A single doping impurity atom is introduced in the undoped channel region of the device and the resulting shift of threshold voltage is measured from the simulated I–V characteristics. This enables the derivation of the threshold voltage shift (ΔV_TH) for any arbitrary location of the doping atom in the transistor. Based on an analysis of a sub-20 nm trigate MOSFET device, we find that the typical variation of V_TH per doping atom is a few tens of mV. Inversion-mode (IM) trigate devices are more sensitive to the doping fluctuation effects than accumulation-mode (AM) devices. The threshold voltage shift arising from doping fluctuations is maximum when the doping atom is near the center of the channel region, which means the original SOI film doping, the random contamination effects or any other impurity doping in the channel region is more important than atoms introduced in the channel by the S/D implantation process for sub-20 nm transistors.     

Completeness in Two-Party Secure Computation: A Computational View

A Secure Function Evaluation (SFE) of a two-variable function f(·,·) is a protocol that allows two parties with inputs x and y to evaluate f(x,y) in a manner where neither party learns "more than is necessary". A rich body of work deals with the study of completeness for secure two-party computation. A function f is complete for SFE if a protocol for securely evaluating f allows the secure evaluation of all (efficiently computable) functions. The questions investigated are which functions are complete for SFE, which functions have SFE protocols unconditionally and whether there are functions that are neither complete nor have efficient SFE protocols. The previous study of these questions was mainly conducted from an information theoretic point of view and provided strong answers in the form of combinatorial properties. However, we show that there are major differences between the information theoretic and computational settings. In particular, we show functions that are considered as having SFE unconditionally by the combinatorial criteria but are actually complete in the computational setting. We initiate the fully computational study of these fundamental questions. Somewhat surprisingly, we manage to provide an almost full characterization of the complete functions in this model as well. More precisely, we present a computational criterion (called computational row non-transitivity) for a function f to be complete for the asymmetric case. Furthermore, we show a matching criterion called computational row transitivity for f to have a simple SFE (based on no additional assumptions). This criterion is close to the negation of the computational row non-transitivity and thus we essentially characterize all "nice" functions as either complete or having SFE unconditionally.     

Catalyst Design by NH4OH Treatment of USY Zeolite

Hierarchical zeolites are a class of superior catalysts which couples the intrinsic zeolitic properties to enhanced accessibility and intracrystalline mass transport to and from the active sites. The design of hierarchical USY (Ultra‐Stable Y) catalysts is achieved using a sustainable postsynthetic room temperature treatment with mildly alkaline NH₄OH (0.02 m ) solutions. Starting from a commercial dealuminated USY zeolite (Si/Al = 47), a hierarchical material is obtained by selective and tuneable creation of interconnected and accessible small mesopores (2–6 nm). In addition, the treatment immediately yields the NH₄⁺ form without the need for additional ion exchange. After NH₄OH modification, the crystal morphology is retained, whereas the microporosity and relative crystallinity are decreased. The gradual formation of dense amorphous phases throughout the crystal without significant framework atom leaching rationalizes the very high material yields (>90%). The superior catalytic performance of the developed hierarchical zeolites is demonstrated in the acid‐catalyzed isomerization of α‐pinene and the metal‐catalyzed conjugation of safflower oil. Significant improvements in activity and selectivity are attained, as well as a lowered susceptibility to deactivation. The catalytic performance is intimately related to the introduced mesopores, hence enhanced mass transport capacity, and the retained intrinsic zeolitic properties.