Temperature-Induced Unfolding Pathway of Staphylococcal Enterotoxin B:Insights from Circular Dichroism and Molecular Dynamics Simulation

In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the relationship between the experimental and simulation results were explored.Our computational findings on the secondary structure of SEB showed that at room temperature,the CD spectroscopic results were highly consistent with the MD results.Moreover,under heating conditions,the changing trends of helix,sheet and random coil obtained by CD spectral fitting were highly consistent with those obtained by MD.In order to gain a deeper understanding of the thermal stability mechanism of SEB,the MD trajectories were analyzed in terms of root mean square deviation(RMSD),secondary structure assignment(SSA),radius of gyration(R_(g)),free energy surfaces(FES),solvent-accessible surface area(SASA),hydrogen bonds and salt bridges.The results showed that at low heating temperature,domain Ⅰ without loops(omitting the mobile loop region)mainly relied on hydrophobic interaction to maintain its thermal stability,whereas the thermal stability of domain Ⅱ was mainly controlled by salt bridges and hydrogen bonds.Under high heating temperature conditions,the hydrophobic interactions in domain Ⅰ without loops were destroyed and the secondary structure was almost completely lost,while domain Ⅱ could still rely on salt bridges as molecular staples to barely maintain the stability of the secondary structure.These results help us to understand the thermodynamic and kinetic mechanisms that maintain the thermal stability of SEB at the molecular level,and provide a direction for establishing safer and more effective food sterilization processes.

论Folding/Unfolding程序转换的能力

本文讨论Burstall与Darlington提出的folding/unfolding系统的程序转换能力,即讨论从一个给定的程序可以推导出什么样的程序。因此,这是正确性与完备性问题的推广。本文证明了可推导性的一个必要条件,并由此得到了该系统提高程序效率的一个界限。该系统的部分正确性和不完备性也均是该条件的推论。

Unfolding算法实现的高速并行CRC电路的VLSI设计

文章通过分析Unfolding算法和被广泛应用的串行CRC校验电路,提出了一种新的高速并行CRC电路,给出了推导过程,并对它的优缺点进行了讨论。

Improvement of Artificial Foldable Wing Models by Mimicking the Unfolding/Folding Mechanism of a Beetle Hind Wing

In an attempt to realize a flapping wing micro-air vehicle with morphing wings, we report on improvements to our previousfoldable artificial hind wing.Multiple hinges, which were implemented to mimic the bending zone of a beetle hind wing, weremade of small composite hinge plates and tiny aluminum rivets.The buck-tails of rivets were flared after the hinge plates wereassembled with the rivets so that the folding/unfolding motions could be completed in less time, and the straight shape of theartificial hind wing could be maintained after fabrication.Folding and unfolding actions were triggered by electrically-activatedShape Memory Alloy (SMA) wires.For wing folding, the actuation characteristics of the SMA wire actuator were modifiedthrough heat treatment.Through a series of flapping tests, we confirmed that the artificial wings did not fold back and arbitrarilyfluctuate during the flapping motion.

Unfolding neutron spectra from water-pumping-injection multilayered concentric sphere neutron spectrometer using self-adaptive differential evolution algorithm

A self-adaptive differential evolution neutron spectrum unfolding algorithm(SDENUA)is established in this study to unfold the neutron spectra obtained from a water-pumping-injection multilayered concentric sphere neutron spectrometer(WMNS).Specifically,the neutron fluence bounds are estimated to accelerate the algorithm convergence,and the minimum error between the optimal solution and input neutron counts with relative uncertainties is limited to 10^(-6)to avoid unnecessary calculations.Furthermore,the crossover probability and scaling factor are self-adaptively controlled.FLUKA Monte Carlo is used to simulate the readings of the WMNS under(1)a spectrum of Cf-252 and(2)its spectrum after being moderated,(3)a spectrum used for boron neutron capture therapy,and(4)a reactor spectrum.Subsequently,the measured neutron counts are unfolded using the SDENUA.The uncertainties of the measured neutron count and the response matrix are considered in the SDENUA,which does not require complex parameter tuning or an a priori default spectrum.The results indicate that the solutions of the SDENUA agree better with the IAEA spectra than those of MAXED and GRAVEL in UMG 3.1,and the errors of the final results calculated using the SDENUA are less than 12%.The established SDENUA can be used to unfold spectra from the WMNS.

TAR~*:an improved process similarity measure based on unfolding of Petri nets

Determining the similarity degree between process models was very important for their management,reuse,and analysis.Current approaches either focused on process model's structural aspect,or had inefficiency or imprecision in behavioral similarity.Aiming at these problems,a novel similarity measure which extended an existing method named Transition Adjacent Relation(TAR) with improved precision and efficiency named TAR * was proposed.The ability of measuring similarity was extended by eliminating the duplicate tasks without impacting the behaviors.For precision,TARs was classified into repeatable and unrepeatable ones to identify whether a TAR was involved in a loop.Two new kinds of TARs were added,one related to the invisible tasks after the source place and before sink place,and the other representing implicit dependencies.For efficiency,all TARs based on unfolding instead of its reach ability graph of a labeled Petri net were calculated to avoid state space explosion.Experiments on artificial and real-world process models showed the effectiveness and efficiency of the proposed method.

Calibration and Unfolding of the Pulse Height Spectra of Liquid Scintillator-Based Neutron Detectors Using Photon Sources

An accurate energy calibration of a 5＂× 2＂ BC501A liquid scintillator-based neutron detector by means of photon sources and the unfolding of pulse height spectra are described. The photon responses were measured with 22Na, 137Cs and 54Mn photon sources and simulated using the GRESP code, which was developed at the Physiknlisch Technische Bundesanstalt in Germany. Pulse height spectra produced by three different photon sources were employed to investigate the effects of the unfolding techniques. It was found that the four unfolding codes of the HEPRO and UMG3.3 packages, including GRAVEL, UNFANA, MIEKE and MAXED, performed well with the test spectra and produced generally consistent results. They could therefore be used to obtain neutron energy spectra in toknmak experiments.

Equilibrium folding and unfolding dynamics to reveal detailed free energy landscape of src SH3 protein by magnetic tweezers

Src SH3 protein domain is a typical two-state protein which has been confirmed by research of denaturant-induced unfolding dynamics.Force spectroscopy experiments by optical tweezers and atomic force microscopy have measured the force-dependent unfolding rates with different kinds of pulling geometry.However,the equilibrium folding and unfolding dynamics at constant forces has not been reported.Here,using stable magnetic tweezers,we performed equilibrium folding and unfolding dynamic measurement and force-jump measurement of src SH3 domain with tethering points at its N-and C-termini.From the obtained force-dependent transition rates,a detailed two-state free energy landscape of src SH3 protein is constructed with quantitative information of folding free energy,transition state barrier height and position,which exemplifies the capability of magnetic tweezers to study protein folding and unfolding dynamics.

(r, s)-STABILITY OF UNFOLDING OF г-EQUIVARIANT BIFURCATION PROBLEM

In this paper,the (?)-equivariant (s, t)-equivalence relation and (?)-equivariant infinitesimally (r, s)-stability of (?)-equivariant bifurcation problem are defined. The criterion for (?)-equivariant infinitesimally (r, s)-stability is proven when (?) is a compact finite Lie group .Transversality condition is used to characterize the stability.

VERSAL UNFOLDING OF EQUIVARIANT BIFURCATION PROBLEMS IN MORE GENERAL CASE UNDER TWO EQUIVALENT GROUPS

For the unfolding of equivariant bifurcation problems with two types of state variables in the presence of parameter symmetry,the versal unfolding theorem with respect to left-right equivalence is obtained by using the related methods and techniques in the singularity theory of smooth map-germs.The corresponding results in[4,9]can be considered as its special cases.A relationship between the versal unfolding w.r.t.left-right equivalence and the versal deformation w.r.t.contact equivalence is established.

Manufacturing of ultra-large plate forgings by unfolding and flattening of thick cylinders

Ultra-large plate forgings are foundation of heavy machinery,but many parts of the type cannot be made by conventional technologies due to the characters of extreme manufacturing in terms of size and quality requirements.This paper introduced a systematically method called cylinder unfolding method(CUM)for producing large plate forgings,by using a serial of operations including“splitting”,“unfolding”,and“flattening”of a thick cylinder obtained from saddle forging.The technological route of CUM was presented in detail with an example of plate forging with the horizontal sizes of 6100 mm and thickness of 300 mm.The deformation features of saddle forging for fabricating transitional cylinders were analyzed,and then the subsequent handling steps including splitting,unfolding and flattening of the cylinder,as well as the auxiliary processing,were addressed.The practice proved that CUM can provide an efficient way for manufacturing ultra-large plate forgings and meet the strict requirements in geometry and mechanical performance,without highly increasing the investments of forming equipment and tooling.

The study of a neutron spectrum unfolding method based on particle swarm optimization combined with maximum likelihood expectation maximization

The neutron spectrum unfolding by Bonner sphere spectrometer(BSS) is considered a complex multidimensional model,which requires complex mathematical methods to solve the first kind of Fredholm integral equation. In order to solve the problem of the maximum likelihood expectation maximization(MLEM) algorithm which is easy to suffer the pitfalls of local optima and the particle swarm optimization(PSO) algorithm which is easy to get unreasonable flight direction and step length of particles, which leads to the invalid iteration and affect efficiency and accuracy, an improved PSO-MLEM algorithm, combined of PSO and MLEM algorithm, is proposed for neutron spectrum unfolding. The dynamic acceleration factor is used to balance the ability of global and local search, and improves the convergence speed and accuracy of the algorithm. Firstly, the Monte Carlo method was used to simulated the BSS to obtain the response function and count rates of BSS. In the simulation of count rate, four reference spectra from the IAEA Technical Report Series No. 403 were used as input parameters of the Monte Carlo method. The PSO-MLEM algorithm was used to unfold the neutron spectrum of the simulated data and was verified by the difference of the unfolded spectrum to the reference spectrum. Finally, the 252Cf neutron source was measured by BSS, and the PSO-MLEM algorithm was used to unfold the experimental neutron spectrum.Compared with maximum entropy deconvolution(MAXED), PSO and MLEM algorithm, the PSO-MLEM algorithm has fewer parameters and automatically adjusts the dynamic acceleration factor to solve the problem of local optima. The convergence speed of the PSO-MLEM algorithm is 1.4 times and 3.1 times that of the MLEM and PSO algorithms. Compared with PSO, MLEM and MAXED, the correlation coefficients of PSO-MLEM algorithm are increased by 33.1%, 33.5% and 1.9%, and the relative mean errors are decreased by 98.2%, 97.8% and 67.4%.

Deep Unfolding for Cooperative Rate Splitting Multiple Access in Hybrid Satellite Terrestrial Networks

Rate splitting multiple access(RSMA)has shown great potentials for the next generation communication systems.In this work,we consider a two-user system in hybrid satellite terrestrial network(HSTN)where one of them is heavily shadowed and the other uses cooperative RSMA to improve the transmission quality.The non-convex weighted sum rate(WSR)problem formulated based on this model is usually optimized by computational burdened weighted minimum mean square error(WMMSE)algorithm.We propose to apply deep unfolding to solve the optimization problem,which maps WMMSE iterations into a layer-wise network and could achieve better performance within limited iterations.We also incorporate momentum accelerated projection gradient descent(PGD)algorithm to circumvent the complicated operations in WMMSE that are not amenable for unfolding and mapping.The momentum and step size in deep unfolding network are selected as trainable parameters for training.As shown in the simulation results,deep unfolding scheme has WSR and convergence speed advantages over original WMMSE algorithm.

Graded Stable Unfoldings in Bifurcation Problems

We introduced stability of arbitrary degree number for unfordings of bifurcation problems and established the equivalence of three stabilities. Thom's transversality theory is used to character the new stability.

UNFOLDING OF MULTIPARAMETER EQUIVARIANT BIFURCATION PROBLEMS WITH TWO GROUPS OF STATE VARIABLES UNDER LEFT-RIGHT EQUIVALENT GROUP

Based on the left_right equivalent relation of smooth map_germs in singularity theory, the unfoldings of multiparameter equivariant bifurcation problems with respect to left_right equivalence are discussed. The state variables of such an equivariant bifurcation problem were divided into two groups, in which the first can vary independently, while the others depend on the first in the varying process. By applying related methods and techniques in the unfolding theory of smooth map_germs, the necessary and sufficient condition for an unfolding of a multiparameter equivariant bifurcation problem with two groups of state variables to be versal is obtained.

基于Fast Unfolding算法的情感词典扩展方法研究

随着互联网技术的发展,越来越多的互联网产品出现了,极大地改变了人们的生活方式。越来越多的人选择在网络上发表自己的观点,分享自己的生活。这些行为带来了大量的数据,其中蕴含着丰富的商业和社会价值。对这些数据进行情感分析就是挖掘其背后隐藏价值的过程。论文在SO-PMI算法的基础上,提出将Fast Unfolding算法与PMI相结合,设计并实现FU-PMI算法,并使用准确率、召回率及F1值对算法的有效性进行评判。对比实验表明,论文提出的算法构建的情感词典相比于SO-PMI算法构建的情感词典效果更好,验证了FU-PMI算法的有效性。

Time-resolved ESI-MS Investigation on Reduction and Alkylation in Unfolding Process of Lysozyme

The kinetic procedure of the unfolding of lysozyme induced by the reduction of disulfide was monitored by the time-resolved ESI-MS with a sheath liquid assistant electrospray interface. It was found that the reduction process for the eight disulfides had a less difference in the reaction time after denatured treatment. In addition, the alkylation of the reduced free thiols was much slower than the reduction procedure. An artifact peak produced by the CID fragmentation in the mass spectra was identified and the possible mechanism of the Hofmann elimination reaction was proposed.

Isoentropic and Isoenthalpic Temperatures of Protein Unfolding in Hydrophobic Interaction Chromatography

The thermal behaviors of five proteins in hydrophobic interaction chromatography （HIC） were investigated in the temperature range from 0 to 50℃. The thermodynamic parameters （△H°,△S°, △Cp°and △G°） of these proteins in the process of retention and unfolding were determined. The existence of enthalpy and entropy convergence with temperature was confirmed. The differences of the isoentropic and isoenthalpic temperatures for protein unfolding in HIC system from the traditional solution were elucidated.

Stability of equivariant bifurcation problems with two types of state variables and their unfoldings in presence of parameter symmetry

Based on the contact equivalent relation of smooth map-germs in singularity theory, the stability of equivariant bifurcation problems with two types of state variables and their unfoldings in the presence of parameter symmetry is discussed. Some basic results are obtained. Transversality condition is used to characterize the stability of equavariant bifurcation problems.

A network of conformational transitions in an unfolding process of HP-35 revealed by high-temperature MD simulation and a Markov state model

An understanding of protein folding/unfolding processes has important implications for all biological processes, in- eluding protein degradation, protein translocation, aging, and diseases. All-atom molecular dynamics （MD） simulations are uniquely suitable for it because of their atomic level resolution and accuracy. However, limited by computational ca- pabilities, nowadays even for small and fast-folding proteins, all-atom MD simulations of protein folding still presents a great challenge. An alternative way is to study unfolding process using MD simulations at high temperature. High temper- ature provides more energy to overcome energetic barriers to unfolding, and information obtained from studying unfolding can shed light on the mechanism of folding. In the present study, a 1000-ns MD simulation at high temperature （500 K） was performed to investigate the unfolding process of a small protein, chicken villin headpiece （HP-35）. To infer the folding mechanism, a Markov state model was also built from our simulation, which maps out six macrostates during the folding/unfolding process as well as critical transitions between them, revealing the folding mechanism unambiguously.