Structure and dynamics of the GH loop of the foot-and-mouth disease virus capsid

The GH loop of VP1 of the foot-and-mouth disease virus capsid is important because it is a major antigenic site and an integrin recognition site. The GH loop is disordered in all X-ray structures of the capsid except for serotype O under reduced conditions in which the loop lies on the capsid surface. Although the structure of the capsid–integrin complex has not yet been determined, the GH loop is known to protrude from the capsid surface when the capsid is bound with an antigen-binding fragment (Fab). To clarify the structure and dynamics of the GH loop under natural unreduced conditions before binding to integrins or Fab fragments, we performed molecular dynamics simulation of 16.3 ns long under rotational symmetry boundary conditions for the capsid of serotype O using the X-ray structure of the reduced capsid for the initial coordinates. When the disulfide bond at the base of the GH loop was formed by the molecular mutation method, the loop protruded into the surrounding water, as reported for Fab–capsid complexes, and fluctuated like a tentacle. After equilibration, the GH loop overlapped the surface of the capsid but continued to fluctuate, being directed toward a 2-fold axis. The conformational change of the GH loop after formation of the disulfide bond was explained by a model of elastic tube. The side chains of arginine and aspartic acid of the integrin recognition residues (RGD tripeptide) extended in opposite directions, and the residues on the C-terminal side of the RGD tripeptide formed a hydrophobic cluster in close proximity of the arginine residue of the tripeptide.     

Structure and dynamics of acyclic networks

Acyclic networks are dynamical systems whose dependency graph (or wiring diagram) is an acyclic graph. It is known that such systems will have a unique steady state and that it will be globally asymptotically stable. Such result is independent of the mathematical framework used. More precisely, this result is true for discrete-time finite-space, discrete-time discrete-space, discrete-time continuous-space and continuous-time continuous-space dynamical systems; however, the proof of this result is dependent on the framework used. In this paper we present a novel and simple argument that works for all of these frameworks. Our arguments support the importance of the connection between structure and dynamics.     

大鼠基因组中硒蛋白的信息学研究

UGA码具有双重功能。通常情况下是蛋白质合成的终止码,当mRNA下游链上出现硒代半胱氨酸插入元件时(SE-CIS),UGA码就可能成为指导硒代半胱氨酸(Sec)直接进入蛋白质的密码子。SECIS是mRNA链上的一种特殊的二级结构,在原核生物和真菌中出现在紧邻UGA码的下游,而在真核生物中它则是出现在UGA码所在阅读框后面的3’-非翻译区(3’-UTR)。根据SECIS特征序列中3个腺嘌呤位置不同可以将其分为Ⅰ型和Ⅱ型。用Genetool、SECISearch、RNADraw以及Dnassist等计算机软件可以对已测序的生物物种基因组进行处理从中找出和发现硒蛋白基因。     

Pure bigraphs: Structure and dynamics

Bigraphs are graphs whose nodes may be nested, representing locality, independently of the edges connecting them. They may be equipped with reaction rules, forming a bigraphical reactive system (Brs) in which bigraphs can reconfigure themselves. Following an earlier paper describing link graphs, a constituent of bigraphs, this paper is a devoted to pure bigraphs, which in turn underlie various more refined forms. Elsewhere it is shown that behavioural analysis for Petri nets, π-calculus and mobile ambients can all be recovered in the uniform framework of bigraphs. The paper first develops the dynamic theory of an abstract structure, a wide reactive system (Wrs), of which a Brs is an instance. In this context, labelled transitions are defined in such a way that the induced bisimilarity is a congruence. This work is then specialised to Brss, whose graphical structure allows many refinements of the theory. The latter part of the paper emphasizes bigraphical theory that is relevant to the treatment of dynamics via labelled transitions. As a running example, the theory is applied to finite pure CCS, whose resulting transition system and bisimilarity are analysed in detail. The paper also mentions briefly the use of bigraphs to model pervasive computing and biological systems.     

Global stability of a discrete virus dynamics model with diffusion and general infection function

ABSTRACT

We investigate a discrete virus dynamics model with diffusion and general infection function. For this model, we derive the basic reproduction number and show the global stability of the equilibria. Example and numerical simulation are performed to illustrate the theoretical results.     

Structure and dynamics of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase

Folates are essential for life. Unlike mammals, most microorganisms must synthesize folates de novo. 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP), the first reaction in folate pathway, and therefore, is an ideal target for developing novel antimicrobial agents. Because of its small size and high thermal stability, E. coli HPPK is also an excellent model enzyme for studying the mechanisms of enzymatic pyrophosphoryl transfer. We have determined the crystal structures of HPPK in the unligated form and in complex with HP, two Mg2+ ions, and AMPCPP (an ATP analog that inhibits the enzymatic reaction). Comparison of the two crystal structures reveals dramatic conformational changes of three flexible loops and many side chains and possible roles of the active site residues.     

A novel computer virus propagation model and its dynamics

By taking into account the fact that, in general, a computer immediately possesses infectivity as soon as it is infected, a novel computer virus propagation model, known as the SLBS model, is established. It is proved that the dynamic behaviour of the model is determined by a threshold R ₀. Specifically, the virus-free equilibrium is globally asymptotically stable if R ₀≤1, whereas the virulent equilibrium is globally asymptotically stable if 1<R ₀≤4. It is conjectured that the virulent equilibrium is also globally asymptotically stable if R ₀>4. These results suggest some effective strategies for eradicating computer viruses distributed in the Internet.     

Learning to Predict the Phonological Structure of English Loanwords in Japanese

Loanword formation seems to provide a good test bed for the growing field of computational phonology, since it occurs in a more tightly controlled environment than other language processing tasks. We show how feedforward neural networks and decision trees can be trained to predict the phonological structure of English loanwords in Japanese, and compare the performance of the two paradigms. In each case the system produces a phonemic representation of the Japanese form, after receiving as input the phonological feature matrix of the current and surrounding phonemes. The performance is improved with the inclusion of information about the stress pattern, orthography of reduced vowels and location of word boundaries.     

Design of backpropagated neurocomputing paradigm for Stuxnet virus dynamics in control infrastructure

Neural Computing and Applications - In the present study, a novel application of backpropagated neurocomputing heuristics (BNCH) is presented for epidemic virus model that portrays the Stuxnet...     

利用Weibull分布描述日本落叶松的直径结构

利用W e ibu ll分布对日本落叶松直径结构进行研究。根据检验结果表明:拟合效果良好,并据此建立起了a、b、c参数的预测模型。提出了日本落叶松人工林林分结构合理分布的理论参数,为合理经营日本落叶松人工林提供了科学的理论依据。     

Structure and dynamics of small protonated rare-gas clusters using quantum and classical methods

The possible structures of small He and Ar clusters containing H⁺ as ionic impurity are shown to be amenable to a detailed analysis of their structures and of the dynamical evolution by means of Ab Initio Molecular Dynamics (AIMD) treatments as well as by quantum treatments via Diffusion Monte Carlo (DMC) approaches. The two methods are briefly reviewed and their computational results are analyzed.     

Vertical backscatter profile of forests predicted by a macroecological plant model

This study describes a new application of a macroecological model to describe the vertical profile of radar backscatter through forest canopy. Given layers of equally sized cylindrical scatterers, the model predicts that one layer within the forest canopy dominates the backscatter profile. This prediction is based on first-order theoretical approximations, in addition to results from a radiative transfer model parameterized by the macroecological model. This model is used to pre-empt specific backscatter trends with results predicting that Rayleigh and Optical backscatter follow negative and positive exponential trends respectively when plotted with respect to backscattering coefficient and branching level through the canopy. A maximum value is predicted by the model associated with the branching level located at the transitional zone between Rayleigh and Optical scattering. This finding follows directly from the size density distribution within a forest combined with dramatic reductions in cross-sectional trends exhibited through the transition. It is a result unrelated to resonant scattering or the effects of penetration depth. The feasibility of describing radar interactions using geometric optics is explored when limits are imposed on the physical optics scattering solution.

The findings offer a significantly new way of understanding the distribution of scattering from differently sized elements in a canopy, and challenge the widely held assumption that backscatter–biomass relationships saturate due to increased opacity of the canopy.     

Evaluating sociotechnical dynamics in a simulated remotely-piloted aircraft system: a layered dynamics approach

As coordination mechanisms change and technology failures occur, a sociotechnical system must reorganise itself across human and technological layers to maintain effectiveness. We present a study examining reorganisation across communication, controls and vehicle layers of a remotely-piloted aircraft system (RPAS) using a layered dynamics approach. Team members (pilot; navigator; photographer) performed 5 simulated RPAS missions using different operator configurations, including all-human and human-autonomy teams. Reorganization (operationally defined using entropy) time series measured the changing system reorganisation profiles under different operator configurations and following autonomy failures. Correlations between these reorganisation profiles and team effectiveness scores describe the manner in which the system had to be coordinated to maintain effectiveness under these changing conditions. Four unplanned autonomy failures were analysed to visualise system reorganisation following a technology failure. With its objective and real-time modelling and measurement capabilities, layered dynamics complements existing systems thinking tools for understanding sociotechnical complexity and enhancing system effectiveness.

Practitioner summary: A layered dynamics approach for understanding how a sociotechnical system dynamically reorganises itself is presented. The layered dynamics of RPAS were analysed under different operator configurations and following autonomy failures. Layered dynamics complements existing system-thinking tools for modelling sociotechnical system complexity and effectiveness.

Abbreviation: RPAS: remotely-piloted aircraft system; HIS: human-systems integration; EAST: event analysis of systemic teamwork; H1: hypothesis 1; H2: hypothesis 2; H3: hypothesis 3; CERTT-STE: cognitive engineering research on team tasks--synthetic task environment; AVO: air vehicle operator; PLO: payload operator; DEMPC: data exploitation, mission planning, and communications; ACT-R: adaptive control of thought-rational; sec: seconds; ANOVA: analysis of variance     

Negotiation of identity and power in a Japanese online discourse community

The study of electronic discourse in the computers and composition field has thus far focused mostly on the English language while electronic discourse practices in non-European languages have received relatively little attention. This article examines the discursive construction of identity and power in a Japanese online discourse community by focusing on an email list for Japanese professionals in the field of Teaching English to Speakers of Other Languages (TESOL). Through the analysis of Japanese linguistic features—including formal verb endings, address terms, and honorifics—as well as metaphors for characterizing relationships, this study shows how social relations among the list members were transformed as the emphasis shifted from conventional criteria for establishing social relations (age, gender, and social status) to other criteria available online, that is, the amount of knowledge one demonstrated through discourse. Based on this analysis, I argue that online discourse communities do not diminish hierarchical social relations found in offline discourses but may allow the negotiation of criteria for hierarchical relations, thus, providing an alternative site for the negotiation of identity and power.     

Modulation of excitatory synaptic coupling facilitates synchronization and complex dynamics in a biophysical model of neuronal dynamics

In this paper, complex dynamical synchronization in a non-linear model of a neural system is studied, and the computational significance of the behaviours is explored. The local neural dynamics is determined by voltage- and ligand-gated ion channels and feedback between densely interconnected excitatory and inhibitory neurons. A mesoscopic array of local networks is modelled by introducing coupling between the local networks via weak excitatory-to-excitatory connectivity. It is shown that with modulation of this long-range synaptic coupling, the system undergoes a transition from independent oscillations to stable chaotic synchronization. Between these states exists a 'weakly' stable state associated with complex, intermittent behaviour in the temporal domain and clusters of synchronous regions in the spatial domain. The paper concludes with a discussion of the putative relevance of such processes in the brain, including the role of neuromodulatory systems and the mechanisms underlying sensory perception, adaptation, computation and complexity.     

Kinematics and dynamics of a rigid body in nonholonomic coordinates

In this paper we consider dynamic equations of nonholomic systes in terms of pseudo-coordinates which appear in the general theory of rigid body. Especially, the rotator kinematics and dynamics in nonholonomic coordinates is presented. Besides, using the appropriate methods of the differential geometry and theory of Lie groups and Lie algebras a simplification of motion equations in the tangent space is obtained.     

Vorton dynamics: a case study of developing a fluid dynamics model for a vector processor

The raw performance of vector processors such as the CDC CYBER-205 has been well documented. The ability to apply this raw power to ever more complex algebraic algorithms has been reported in [9]. The final step in making computers of this class truly the revolutionary tools they are claimed to be is to develop whole applications that perform at a significant fraction of the raw power. This involves two distinct subclasses of problems. On the one hand, there are those pre-existing applications that must be mapped onto vector processors in such a way that not only is performance maintained, but also a (sometimes vague) set of computational boundary conditions of the user community is satisfied. On the other hand, there are those models which are developed ab initio with machines such as the CYBER-205 in mind. The development of solutions to problems in the former class involves psychology and politics as well as mathematics and computer science. We limit ourselves here to reporting on an example of the latter class, viz. a model to study a particular fluid-dynamic phenomenon, that was specifically designed with the CYBER-205 in mind.