Chaperone-assisted translocation of flexible polymers in three dimensions

Polymer translocation through a nanometer-scale pore assisted by chaperones binding to the polymer is a process encountered in vivo for proteins. Studying the relevant models by computer simulations is computationally demanding. Accordingly, previous studies are either for stiff polymers in three dimensions or flexible polymers in two dimensions. Here, we study chaperone-assisted translocation of flexible polymers in three dimensions using Langevin dynamics. We show that differences in binding mechanisms, more specifically, whether a chaperone can bind to a single or multiple sites on the polymer, lead to substantial differences in translocation dynamics in three dimensions. We show that the single-binding mode leads to dynamics that is very much like that in the constant-force driven translocation and accordingly mainly determined by tension propagation on the cis side. We obtain $\beta \approx 1.26$ for the exponent for the scaling of the translocation time with polymer length. This fairly low value can be explained by the additional friction due to binding particles. The multiple-site binding leads to translocation whose dynamics is mainly determined by the trans side. For this process we obtain $\beta \approx 1.36$. This value can be explained by our derivation of $\beta = 4/3$ for constant-bias translocation, where translocated polymer segments form a globule on the trans side. Our results pave the way for understanding and utilizing chaperone-assisted translocation where variations in microscopic details lead to rich variations in the emerging dynamics.Comment: 10 pages, 12 figure

Critical evaluation of the computational methods used in the forced polymer translocation

In forced polymer translocation, the average translocation time, $\tau$, scales with respect to pore force, $f$, and polymer length, $N$, as $\tau \sim f^{-1} N^{\beta}$. We demonstrate that an artifact in Metropolis Monte Carlo method resulting in breakage of the force scaling with large $f$ may be responsible for some of the controversies between different computationally obtained results and also between computational and experimental results. Using Langevin dynamics simulations we show that the scaling exponent $\beta \le 1 + \nu$ is not universal, but depends on $f$. Moreover, we show that forced translocation can be described by a relatively simple force balance argument and $\beta$ to arise solely from the initial polymer configuration

Dynamics of polymer ejection from capsid

Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes place within the drift-dominated region there is a very high probability for the ejection process not to be completed. Introducing a small aligning force at the pore entrance enhances ejection dramatically. Such a pore asymmetry is a candidate for a mechanism by which a viral ejection is completed. By detailed high-resolution simulations we show that such capsid ejection is an out-of-equilibrium process that shares many common features with the much studied driven polymer translocation through a pore in a wall or a membrane. We find that the escape times scale with polymer length, $\tau \sim N^\alpha$. We show that for the pore without the asymmetry the previous predictions corroborated by Monte Carlo simulations do not hold. For the pore with the asymmetry the scaling exponent varies with the initial monomer density (monomers per capsid volume) $\rho$ inside the capsid. For very low densities $\rho \le 0.002$ the polymer is only weakly confined by the capsid, and we measure $\alpha = 1.33$, which is close to $\alpha = 1.4$ obtained for polymer translocation. At intermediate densities the scaling exponents $\alpha = 1.25$ and $1.21$ for $\rho = 0.01$ and $0.02$, respectively. These scalings are in accord with a crude derivation for the lower limit $\alpha = 1.2$. For the asymmetrical pore precise scaling breaks down, when the density exceeds the value for complete confinement by the capsid, $\rho \gtrapprox 0.25$. The high-resolution data show that the capsid ejection for both pores, analogously to polymer translocation, can be characterized as a multiplicative stochastic process that is dominated by small-scale transitions.Comment: 10 pages, 6 figure

Organisational downsizing, sickness absence, and mortality: 10-town prospective cohort study

Objective To examine whether downsizing, the reduction of personnel in organisations, is a predictor of increased sickness absence and mortality among employees.Design Prospective cohort study over 7.5 years of employees grouped into categories on the basis of reductions of personnel in their occupation and workplace: no downsizing ( 18%).Setting Four towns in Finland.Participants 5909 male and 16 521 female municipal employees, aged 19-62 years, who kept their jobs.Main outcome measures Annual sickness absence rate based on employers' records before and after downsizing by employment contract; all cause and cause specific mortality obtained from the national mortality register.Results Major downsizing was associated with an increase in sickness absence (P for trend < 0.001) in permanent employees but not in temporary employees. The extent of downsizing was also associated with cardiovascular deaths (P for trend < 0.01) but not with deaths from other causes. Cardiovascular mortality was 2.0 (95% confidence interval 1.0 to 3.9) times higher after major downsizing than after no downsizing. Splitting the follow up period into two halves showed a 5.1 (1.4 to 19.3) times increase in cardiovascular mortality for major downsizing during the first four years after downsizing. The corresponding hazard ratio was 1.4 (0.6 to 3.1) during the second half of follow up.Conclusion Organisational downsizing may increase sickness absence and the risk of death from cardiovascular disease in employees who keep their jobs

Analisa Quality Of Service (QoS) Trafik Multimedia pada Pemodelan Jaringan Multiprotocol Label Switching (MPLS) Menggunakan Router Mikrotik

Quality of Service (QoS) is a performance indicator on many communication systems. The Multiprotocol Label Switching (MPLS) is a part of the communication system. One of approach to find out QoS performance indicator for MPLS is using of a Mikrotik router. The network testing scenario using bus topology, where different types of traffic is delivered audio and video streaming that has a variety of different file sizes. The first scenario involving 1 client to send and the other scenario involving 2 client to send. The result show that MPLS network meets ITU-T G.114 standards where the average accepted delay for packet data transmission is less than 150 ms, in the simulation results indicates that the delay value is below of 150 ms in both scenarios. The value of packet loss based on ITU-T G.1010 standard is less than 1% where the simulation results indicate that packet loss value is below 1% in both scenarios. Overall, the MPLS network is proven to serve a heavy multimedia traffic

Optimasi Perencanaan Jaringan LTE FDD 1800 MHz di Kota Pekanbaru

LTE is a cellular technology developed by 3GPP which has improved from the previous mobile technologies. The implementation of LTE in Indonesia is still not evenly distributed and only for big cities. Hence, it takes some planning and a deeper study for the area that will be implemented by LTE network. Planning and network optimization is necessary in order to meet consumer needs of the LTE network. There are different ways of optimization methods can be used, in previous studies used a joint base station technique, optimization in other research done by changing basic parameters such as replacing the feeder cable and the addition site. In this study optimization techniques used by changing the type of modulation thus affecting the utilization values of SNR. The simulation results based on two scenarios i.e the number of sites for scenario 1in the total of 479 sites, while for scenario 2 indicates number of sites . in the mean time for a signal level coverage for scenario 1 and scenario 2 show -90 dBm and -95 dBm, respectively

Analisa Penerapan Kinerja Frame Relay pada Pemodelan Jaringan

The development of the internet today has given us so many benefits for the user as well as for industries that use it as a communication medium that is cheap, effective, and efficient. With the development of Internet and various technologies that go with it then it is also directly proportional to the need for the use of the internet is more reliable and reasonable. In the use ofthe internet there are several technologies that can be used, one of which is Frame Relay. Frame Relay network is a network share (shared services) by utilizing the Permanent Virtual Circuit(PVC) so as to ensure minimum access level CIR (Committed Information Rate) specific. Frame Relay is designed to reduce the processing on each node by reducing the format and proceduresused. In this research, frame relay network modeling and analysis of network performance using software GNS3, frame relay network performance will be determined by the parameters of delay,throughput and packet loss. With this study will be obtained performance of some frame relay network model that can be used as a reference in designing the new network

Luokanopettajan kokemuksia tuen piirissä olevien oppilaiden opettamisesta yleisopetuksen ryhmässä

Tiivistelmä. Tämän tutkielman tarkoitus on selvittää millaisena aloittelevat opettajat kokevat tehostetun ja erityisen tuen piirissä olevien oppilaiden opettamisen yleisopetuksen ryhmässä sekä millaisia kokemuksia aloittelevilla opettajilla on opettajankoulutuksen tarjoamista lähtökohdista liittyen tuen piirissä olevien oppilaiden opettamiseen. Tutkimus toteutettiin laadullisena haastattelututkimuksena ja analyysitavaksi valikoitui sisällönanalyysi. Tutkimuksen aineisto kerättiin teemahaastatteluna, johon osallistui neljä työuransa aloittanutta luokanopettajaa. Luokanopettajat toimivat eri puolilla Suomea yleisopetuksen ryhmissä ja heillä oli opetusryhmässään tuen piirissä olevia oppilaita. Haastateltavat olivat haastatteluhetkellä toimineet luokanopettajina 1–2 vuotta. Tutkimuksen teoreettinen viitekehys avaa inkluusion historiaa ja inkluusiota käsitteenä, luokanopettajakoulutusta, kolmiportaisen tuen mallia sekä luokanopettajan työssään kohtaamaa moniammatillista yhteistyötä. Tutkimustuloksista käy ilmi, että yhteiskunnallisesti olisi merkittävää, että opettajankoulutus muuttuisi riittävän nopeassa tahdissa, jotta kouluihin saadaan ammattilaisia, jotka kykenevät heti ensimmäisten työvuosien aikana vastaamaan työn asettamiin haasteisiin oppilasaineksen jatkuvasti moninaistuessa. Luokanopettajan työ koetaan kuormittavana ensimmäisten työvuosien aikana. Luokanopettajakoulutukseen halutaan sisällyttää erityispedagogista osaamista sekä opintosisältöjä ja käytännönkokemusta muun muassa tukitoimien järjestämisestä, dokumentoinnista, opettajan käyttämistä sähköisistä työkaluista ja pedagogisten asiakirjojen täyttämisestä sekä moniammatillisesta yhteistyöstä