Polymer ejection from strong spherical confinement

We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an individual monomer to eject grows exponentially with the number of ejected monomers. By measurements of the force at the pore we show this dependence to be a consequence of the excess free energy of the polymer due to confinement growing exponentially with the number of monomers initially inside the capsid. This growth relates closely to the divergence of mixing energy in the Flory-Huggins theory at large concentration. We show that the pressure inside the capsid driving the ejection dominates the process that is characterized by the ejection time growing linearly with the lengths of different polymers. Waiting time profiles would indicate that the superlinear dependence obtained for polymers amenable to computer simulations results from a finite-size effect due to the final retraction of polymers' tails from capsids.Comment: 6 pages, 9 figures, accepted for publication in Phys. Rev. E, increased readability from previous versio

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

LAPORAN PRAKTIK PENGALAMAN LAPANGAN (PPL) PERIODE 10 AGUSTUS-10 SEPTEMBER 2015 SMA N 1 WONOSARI

Pelaksanaan Praktik Pengalaman Lapangan (PPL) merupakan salah satu mata kuliah yang wajib ditempuh oleh mahasiswa sebagai salah satu syarat dalam menyelesaikan gelar sebagai sarjana pendidikan selain tugas akhir skripsi di Universitas Negeri Yogyakarta. Visi dari Praktik Pengalaman Lapangan adalah wadah pembentukan calon guru atau tenaga kependidikan yang profesional. Praktik Pengalaman Lapangan (PPL) dilaksanakan di SMA N 1 Wonosari, Gunungkidul tepatnya di Jalan Brigjen Katamso Nomor 04 Wonosari Gunungkidul. Kegiatan ini dimulai secara efektif pada tanggal 10 Agustus dan diakhiri pada tanggal 10 September 2015. Praktik Pengalaman Lapangan merupakan kegiatan pembelajaran di sekolah. Dalam kegiatan pembelajaran perlu melakukan persiapan, diantaranya pembuatan RPP, administrasi pendidik, serta media pembelajaran yang diperlukan. Selama kegiatan PPL mahasiswa diberi kepercayaan untuk mengampu kelas XI MIA 3, XI MIA 4, XI IIS 1, dan XI IIS 2 dibawah bimbingan Bapak Tri Widodo, S.Pd Evaluasi terhadap peserta didik dilakukan melalui Ujian Praktik Pranatacara dan Ulangan Harian. Secara kesuluruhan PPL berjalan dengan baik dan lancar. Keberhasilan pelaksanaan PPL ini hendaknya disikapi oleh pihak Universitas Negeri Yogyakarta dengan mempertahankan dan meningkatkan jalinan komunikasi dan kerjasama dengan SMA N 1 Wonosari

Thermal conduction and interface effects in nanoscale Fermi-Pasta-Ulam conductors

We perform classical non-equilibrium molecular dynamics simulations to calculate heat flow through a microscopic junction connecting two larger reservoirs. In contrast to earlier works, we also include the reservoirs in the simulated region to study the effect of the bulk-nanostructure interfaces and the bulk conductance. The scalar Fermi--Pasta--Ulam (FPU) model is used to describe the effects of anharmonic interactions in a simple manner. The temperature profile close to the junction in the low temperature limit is shown to exhibit strong directional features that fade out when temperature increases. Simulating both the FPU chain and the two bulk regions is also shown to eliminate the non-monotous temperature variations found for simpler geometries and models. We show that with sufficiently large reservoirs, the temperature profile in the chain does not depend on the details of thermalization used at the boundaries.Comment: 9 pages, 7 figures, minor modifications to the previous versio

Journal Staff

Background: Internet-based cognitive behavioral therapy (ICBT) is a form of guided self-help that has been found to be effective for addressing several problems. The target for this type of therapy is usually restricted to one specific disorder. Tailoring the treatment widens the scope of ICBT in that it can address comorbid conditions directly. Objectives: The working, or therapeutic, alliance has been found to predict outcome in studies of face-to-face therapy. The extent to which these findings apply to ICBT is largely unknown. We therefore decided to find out whether the working alliance could predict outcome in tailored ICBT for anxiety disorders. Methods: Data were obtained from the treatment group (n=27) in a randomized controlled trial aiming to test the effects of tailored ICBT for anxiety disorders. The forthcoming study was designed to test the hypothesis that the working alliance measured both pre-treatment and early in treatment (week 3) can predict treatment outcome as measured by the Clinical Outcomes in Routine Evaluation–Outcome Measure (CORE-OM) in a heterogeneous group of patients with anxiety disorders (n=27). Results: Working alliance measured at week 3 into the treatment correlated significantly with the residual gain scores on the primary outcome measure (r=-.47, P=.019, n=25), while expected working alliance pre-treatment did not (r=-.17, P=.42, n=27). Conclusions: These results raise questions about the importance of working alliance in ICBT treatments, and suggest that the working alliance could be important in ICBT.Funding Agencies|Swedish Council for Working Life and Social Research|2008-1145|</p

EKSPERIMENTASI PEMBELAJARAN DENGAN MENGGUNAKAN METODE PEMBELAJARAN KOOPERATIF TIPE TEAM ASSISTED INDIVIDUALIZA TION (TAI)MELALUI PEMANFAATAN LKS TERHADAP PEMAHAMAN KONSEP SISWA POKOK BAHASAN BANGUN RUANG SISI DATAR KUBUS DAN BALOK PADA SISWA KELAS VIII SEMESTER 2 SMP NEGERI 1 GIRIMARTO TAHUN AJARAN 2009/2010

Penelitian ini bertujuan:1. Perbedaan pemahaman konsep Bangun Ruang Sisi Datar Kubus dan Balok antara siswa yang diberi pembelajaran dengan metode pembelajaran kooperatif tipe TAI (Team Assisted Individualization) dan siswa yang diberi pembelajaran dengan metode konvensional. 2. Pemahaman konsep siswa yang diberi pembelajaran dengan metode kooperatif tipe TAI (Team Assisted Individualization) dengan media LKS (Lembar Kerja Siswa) lebih baik dari pada siswa yang diberi pembelajaran dengan metode konvensional. Metode pengumpulan data yang digunakan dalam penelitian ini adalah metode tes dan dokumentasi. Teknik analisis data yang digunakan adalah dengan menggunakan rumus T-tesyang sebelumnya dilakukan uji prasyarat analisis yaitu uji normalitas dan uji homogenitas. Berdasarkan hasil analisis data, diperoleh nilai thitung sebesar 2,251; dan dengan nilai df= 50 maka diperoleh ttabel sebesar 2,009. Oleh karena nilai ttabel < thtung (2,009 < 2,251) maka H0 ditolak, sehingga terdapat perbedaan pemahaman konsep Bangun Ruang Sisi Datar Kubus dan Balok antara siswa yang diberi pembelajaran dengan metode pembelajaran kooperatif tipe Team Assisted Individualization (TAI) dan siswa yang diberi pembelajaran dengan metode konvensional.Hasil perhitungan juga diketahui bahwa untuk kelas eksperimen diperoleh nilai rata-rata sebesar 7,62 dan untuk kelas kontrol diperoleh nilai rata- rata sebesar 6,62; sehingga pemahaman konsep siswa yang diberi pembelajaran dengan metode kooperatif tipe TAI (Team Assisted Individualization) dengan media LKS (Lembar Kerja Siswa) lebih baik dari pada siswa yang diberi pembelajaran dengan metode konvensional

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

Influences of Body Composition, Multimorbidity and Polypharmacy on Physical Mobility of Older Adults

Background and Purpose: The prevalence of falls, and the resulting injuries and complications reflect a key concern in the older adult population. An increased risk of falls is highly correlated with decreases in physical mobility and related functions. The Timed Up-and-Go test (TUG) has an established reliability and validity in assessing physical function and the risk of falling in the older adult population. With age, a person typically has an increased number of health morbidities, which may be reflected in changing body composition and the number of medications associated with diseases. However, the influence of these factors on physical mobility in the older adult population has not been quantified. The purpose of this study was to investigate how common indicators of health, including body mass index (BMI), presence of multimorbidity and polypharmacy influence the TUG performance in the older adult population. Methods: A total of 222 individuals ≥ 65 years of age were recruited (68 men and 154 women, mean age = 75.1 yrs). Additional subjects (28 men and 54 women, mean age = 72.7 yrs) from previous research were included in the analysis of BMI on TUG performance with a total of 304 subjects (96 men and 208 women, mean age= 74.4 yrs). Height and weight were obtained in conjunction with a medical history survey. Subjects completed 3 trials of the TUG test at 3 and 9 m walking distances. Comparison was made between 3 participant groups according to their BMI (underweight: BMI \u3c 24 kg/m2, normal weight: BMI 24-30 kg/m2, overweight: BMI \u3e 30 kg/m2). Multimorbidity was categorized into 2 groups (multimorbidity: ≥ 2 morbidities, non-multimorbidity: 0-1 morbidity). Polypharmacy was categorized into 2 groups (polypharmacy: ≥ 5 medications, non-polypharmacy: 0-4 medications). Non-parametric tests were run for all 3 variables (BMI, multimorbidity, and polypharmacy). Results: The underweight BMI group exhibited a trend of slower performance than normal weight BMI group for the 3 m (underweight = 8.8±5.3s, normal weight = 8.5±3.3s, p = 0.055) and the 9 m TUG distances (underweight = 17.3±8.9s, normal weight = 17.0±6.1s, p = 0.071). There was a trend toward the overweight BMI group having slower performance than the normal weight BMI group on the 9 m distance (normal weight = 17.0±6.1s, overweight = 18.0±5.5s, p = 0.069). The group with ≥ 2 morbidities had slower performance on the 3 m (multimorbidity = 9.2±3.9s, non-multimorbidity = 7.7±2.1s, p \u3c 0.001) and 9 m TUG distances (multimorbidity = 18.3±6.8s, non-multimorbidity = 15.6±4.0s, p \u3c 0.001). The polypharmacy group had slower performance on the 3 m (polypharmacy = 9.6±3.3s, non-polypharmacy = 8.3±3.4s, p = 0.001) and 9 m TUG distances (polypharmacy = 19.1 ± 5.9s, non-polypharmacy = 16.7±6.0s, p = 0.001). Discussion: Being underweight and overweight were shown to impact a person’s walking ability. We expected overweight individuals to have a slower performance on the TUG but underweight individuals did as well. This could be due to frail older adults having decreased muscle mass and strength. Polypharmacy and multimorbidity were shown to also have a significant impact on mobility performance. Limitations: The examined older adult population was relatively healthy as they are community dwelling individuals who are active in the retirement community. Conclusion: This study provided quantitative information regarding the effects of common health indicators (BMI, status of multimorbidity and polypharmacy) on mobility. Understanding the impact of BMI, multimorbidity, and polypharmacy on TUG performance will assist in identifying patients at risk of decrease physical mobility and falls. Wellness interventions might include reducing/altering medications used or adopting a healthier BMI to improve mobility