Transferable neural networks for enhanced sampling of protein dynamics

Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a collective variable for enhanced sampling, and present a simple modification that allows us to rapidly perform sampling in multiple related systems. We first demonstrate our method is able to describe the effects of force field changes in capped alanine dipeptide after learning a model using AMBER99. We further provide a simple extension to variational dynamics encoders that allows the model to be trained in a more efficient manner on larger systems by encoding the outputs of a linear transformation using time-structure based independent component analysis (tICA). Using this technique, we show how such a model trained for one protein, the WW domain, can efficiently be transferred to perform enhanced sampling on a related mutant protein, the GTT mutation. This method shows promise for its ability to rapidly sample related systems using a single transferable collective variable and is generally applicable to sets of related simulations, enabling us to probe the effects of variation in increasingly large systems of biophysical interest.Comment: 20 pages, 10 figure

Folded waveguide resonator filter for communication and radar systems

In this thesis, a primary investigation into developing a compact and low-loss bandpass filter, using novel folded waveguide resonators with a footprint reduction, has been addressed. A slot coupling between adjacent resonators is introduced, which is characterized by using full-wave EM simulations and verified experimentally. Two designs of 2-pole folded waveguide resonator filters of this type have been considered, fabricated and tested. In this thesis, an even more compact FWG resonator filter using a novel slot technique is reported. The attainable size reduction is about 50%, and the filter design is based on theoretical and full-wave electromagnetic (EM) simulations. Based on FWG structure, two types of folded waveguide resonators have been studied and considered the half-wavelength resonator and the quarter-wavelength resonator. Moreover, both structures for the realization of microwave cavities with high-Q, with the result of a high spurious free range and reduced footprint, have been evaluated. Furthermore, a novel folded waveguide resonator with about a 75 % reduction of the volume from the conventional size has been described. For comparison, two types of folded waveguide resonators have been studied, i.e. the quarter-wavelength resonator of square shape and the newly proposed triangular shape. In addition, a demonstration of a filter application for miniature triangular folded waveguide resonators has been designed and simulated using an EM simulator. In addition, numbers of experiments have been conducted to develop cavity FWG and Substrate Integrated folded waveguide SIFW resonator filters using a folded structure, which is the main aim of this thesis. Furthermore, this thesis deals with the simulation and implementation for many designs and topologies of FWG and SIFW resonator filters and their frequency response. Simulation and experimental results were presented to validate the design and to show the advantages of these types of filters. In addition, a new type of filter with a compact multi-layer structure and low loss is attractive for implementation with advanced device technologies, such as micromachining, LTCC and LCP technologies

Increase in germination and plating efficiency of Neurospora crassa microconidia by amino acid supplementation

A major difficulty that has limited the use of uninucleate microconidia in genetic research is their low and erratic germination. We found that the supplementation of sorbose plating medium by amino acids, notably aspartic acid and methionine, markedly improved germination and plating efficiency of microconidia of mcm and pe fl genotypes of N. crassa. The plating efficiency of mcm microconidia in amino acid supplemented medium was comparable to macroconidia

Determination Of Aerosol Optical Thickness From Spectral Sky Transmittance.

The objective of this study is to test the feasibility of the proposed technique for retrieving spectral aerosol optical thickness (AOT) from the spectral transmittance measurements. The measurements have been acquired around Penang Island, Malaysia. Ground-based measurements were made with a handheld spectroradiometer. The measured spectral transmittance data were then converted to AOT values 6 spectral bands between 400 and 900 nm. Spectral AOT maps were generated using Kriging interpolation method for the 6 spectral bands. Air quality map was produced using this technique

HUBUNGAN HASIL BELAJAR KEWIRAUSAHAAN DAN PRAKTIK KERJA INDUSTRI TERHADAP KESIAPAN KERJA PESERTA DIDIK SMK KOMPETENSI KEAHLIAN PENGELASAN

Tujuan penelitian ini yaitu ingin memperoleh data tentang hubungan hasil belajar kewirausahaan dan praktik kerja industri terhadap kesiapan kerja peserta didik SMK kompetensi keahlian pengelasan. Penelitian ini menggunakan metode penelitian ex post pacto, penelitian dilakukan di dua sekolah yaitu SMK Negeri 1 Makassar dan SMK Negeri 5 makassar.  Subjek penelitian adalah kelas XII SMKN 1 Makassar keahlian teknik pengelasan dan kelas XII SMKN 5 Makassar keahlian teknik pengelasan. Teknik pengumpulan data menggunakan angket (kusioner) dan dokumentasi. Hasil penelitian menunjukkan bahwa hasil belajar kewirausahaan dan praktik kerja industri memberikan pengaruh terhadap kesiapan kerja peseta didik, koefisien determinasi sebesar 83,1%, artinya kontribusi hasil belajar kewirausahaan dan praktik kerja industri terhadap kesiapan kerja sebesar 83,1%. Hubungan hasil belajar kewirausahaan dan praktik kerja industri terhadap kesiapan kerja sangat signifikan

PEMETAAN POTENSI DAERAH UNTUK PENGEMBANGAN SMK MASA DEPAN

Tujuan penelitian ini adalah (i) untuk mengetahui seberapa besar relevansi keberadaan SMK dengan potensi daerah yang ada. (ii) Untuk mengetahui sumber daya alam dan sumber daya manusia yang ada di daerah tersebut. (iii) untuk mengetahui prospek pengembangan SMK masa depan yang berbasis potensi lokal di kabupaten Bone. Jenis penelitian ini adalah penelitian deskriptif dengan menggunakan metode survei dalam mengumpulkan data untuk mengungkap fenomena tentang relevansi SMK terhadap potensi daerah serta menggambarkan potensi daerah yang ada di wilayah tersebut dan sebagai prospek pengembangan SMK masa depan yang berbasis potensi daerah. Teknik pengumpulan data yang digunakan adalah observasi, penyebaran angket, wawancara dan data dokumentasi yang dibutuhkan. Hasil penelitian ini menunjukkan bahwa (i) keberadaan SMK saat ini masih belum relevan dengan potensi daerah yang ada. (ii) gambaran pemetaan potensi daerah diuraikan dalam setiap kecamatan yang ada di Kabupaten Bone, serta (iii) prospek pengembangan SMK masa depan yang paling besar di Kabupaten Bone adalah SMK pertanian

Remote Sensing Of Turbidity Mapping From Digital Camera Imagery.

A complete set of normal digital camera data and ground-based measurements are used to test an algorithm for retrieval of turbidity distribution in the Prai Estuary, Penang, Malaysia