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All Journal FLYWHEEL : Jurnal Teknik Mesin Untirta Jurnal Fisika FLUX Spektra: Jurnal Fisika dan Aplikasinya PENDIPA Journal of Science Education Jurnal Teori dan Aplikasi Fisika Makara Journal of Science
Efta Yudiarsah, Efta
Departemen Fisika Fakultas Matematika Dan Ilmu Pengetahuan Alam Universitas Indonesia
Aerospace Engineering Automotive Engineering Chemical Engineering, Chemistry & Bioengineering Chemistry Control & Systems Engineering Earth & Planetary Sciences Education Electrical & Electronics Engineering Energy Engineering Industrial & Manufacturing Engineering Materials Science & Nanotechnology Mathematics Mechanical Engineering Physics Transportation

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Perubahan Panjang Lokalisasi dan Kerapatan Keadaan Elektron pada Molekul DNA Poli(dA)-Poli(dT) Karena Medan Magnet Efta Yudiarsah; Andi Muhammad Risqi
Jurnal Fisika FLUX Vol 15, No 2 (2018): Jurnal Fisika Flux: Jurnal Ilmiah Fisika FMIPA Universitas Lambung Mangkurat
Publisher : Lambung Mangkurat University Press

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1375.496 KB) | DOI: 10.20527/flux.v15i2.4929

Abstract

The localization length and the Density Of State (DOS) of electron in a Poly(dA)-Poly(dT) DNA molecule at two temperatures have been calculated for several values of magnetic field. The calculation are carried out on a DNA molecule model that consists of adenine (A) and Thymine (T) nucleobases and sugar-phosphate backbone. The DNA molecule is modeled in tight binding Hamiltonian approachwith semi empirical Slater-Koster theory and Peierls phase factor for introducing the effect of temperature and magnetic field, respectively. In the model, electron is allowed to move between nucleobase sites, backbode sites, and between backbone site and nucleobase site. The localization length is obtained from the smallest Lyapunov exponent which is calculated using transfer matrix method along with Gram-Schmidtorthonormalization procedure. The DOS is calculated using Green’s function methodby taking into account the presence of metallic electrode at both ends of the DNA molecule. The localization length and the DOS change as a result of the change in electron wave phase due to magnetic field. The change is observed at both temperature used in the study, but the change at lower temperature is larger than the one at higher temperature. Thermally agitated vibrational twisting motion perturbs electron motion in the DNA molecule such that the influence of magnetic field on the localization length and the DOS of electron at higher temperature becomes smaller.
Studi probabilitas transmisi dan karakteristik IV pada molekul DNA G4 Refpo Rahman; Efta Yudiarsah
PendIPA Journal of Science Education Vol 4, No 2 (2020): MARCH - JUNE
Publisher : University of Bengkulu

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (450.028 KB) | DOI: 10.33369/pendipa.4.2.51-57

Abstract

[The study of transmission probability and IV chracteristics of a G4 molecule] In this era, there have been many theoretical and experimental studies conducted to enhance technological development. The development of technology continues to grow rapidly with electronic components that are getting smaller towards nano. Nanotechnology is becoming increasingly interesting because it can be created through DNA that is found in either the human body or other living things. This research was conducted to study DNA transport properties by calculating transmission probabilities and I-V characteristics. The DNA studied is DNA that has been modified consisting of 4 guanine bases arranged stacked to form a square called G4-DNA. G4-DNA is composed by having 32 base pairs and connected by electrodes at the end. The transport properties of G4-DNA were studied using the Hamiltonian tight binding approach. Transmission probability is calculated using the method of the Green Function Hamiltonian to determine the possibility of electrons flowing along the DNA pathway. This transmission probability is used in determining the I-V Characteristics based on the Landauer Büttiker formula. The results are obtained that the electron transport process along the G4-DNA molecule is an increase in current to high voltage. The effects of I-V characteristics are seen by affecting the twisting motion frequency up to 5.12 meV which is a significant increase in current. The results of this study can provide information about the characteristics of DNA that can be applied in the future in manufacture of nanotechnology device.
Effect of Backbone, Sequence, and Positional Disorders on Electrical Transport in Modified Poly(dA)–Poly(dT) DNA Wire Suhendro, Daniel Kurnia; Yudiarsah, Efta; Saleh, Rosari
Makara Journal of Science Vol. 23, No. 1
Publisher : UI Scholars Hub

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Abstract

The effect of medium and thermal fluctuations on charge transport in two types of modified poly(dA)–poly(dT) DNA was studied by calculating the transmission probability and current–voltage (I–V) characteristics of a model DNA wire sandwiched between two metal electrodes. Modification was performed by randomly replacing several A–T base pairs with C–G or G–C base pairs along the DNA chain. The medium–DNA interaction was modeled as the backbone onsite energy disorder in the DNA tight-binding Hamiltonian. The helicity of the molecule was considered by incorporating twist-angle-dependent intrastrand hopping amplitude in the model. Thermal fluctuation was modeled by varying the twist angles of each base in the DNA wire. Twist-angle disorder was influenced by temperature and frequency. The I–V results obtained by modeling the backbone disorder effect showed that the current decreased and the threshold voltage generally increased as disorder strength increased to a critical value. The current increased and the threshold voltage decreased as the disorder strength exceeded this critical value. However, certain values of the backbone disorder reduced the threshold voltage before the critical value was reached because the transmission bands shifted toward the Fermi energy. The results of thermal fluctuation modeling indicated that increasing thermal fluctuation (increasing temperature and decreasing frequency) degraded the electrical properties of the DNA modified with C–G base pairs but enhanced those of the DNA modified by G–C base pairs. This trend, however, did not always hold for all frequency values for the latter DNA type.
MAGNETIC FIELD-DEPENDENT ELECTRIC CURRENT ON A PERIODIC POLY(DA)-POLY(DT) DNA MOLECULE STRUCTURE Efta Yudiarsah
Spektra: Jurnal Fisika dan Aplikasinya Vol 7 No 3 (2022): SPEKTRA: Jurnal Fisika dan Aplikasinya, Volume 7 Issue 3, December 2022
Publisher : Program Studi Fisika Universitas Negeri Jakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21009/SPEKTRA.073.05

Abstract

An electric current flowing on the Poly(dA)-poly(dT) DNA molecule structure has been calculated. The current was calculated from transmission probabilities by employing Landauer-Buttiker formalism. Green’s function technique has been used for obtaining the transmission probabilities. The DNA molecule structure was modeled within the tight-binding Hamiltonian model approach. The model takes into account electron hopping parameters which are dependent on the magnetic field as well as the electric field. The presence of a magnetic field causes the Peierls phase factor on the electron hopping parameters. The calculation results at low electric voltages show that after decreasing, the electric current oscillates with the magnetic field. However, at higher electric voltages, the electric current is increasing and oscillates with the magnetic field.
Dynamic Viscosity Measurement Method Based on the Stokes Drag of Prolate Ellipsoidal Mass Arifrahman Yustika Putra; Efta Yudiarsah; Arief Sudarmaji
Jurnal Teori dan Aplikasi Fisika Vol 12, No 1 (2024): Jurnal Teori dan Aplikasi Fisika
Publisher : Universitas Lampung

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23960/jtaf.v12i1.14205

Abstract

Viscometer plays an important role in the field of tribology. One way to measure viscosity is to use the Stokes drag principle in the underdamped harmonic oscillation phenomenon. This paper proposes a dynamic viscosity measurement method based on the related physical laws. Our experimental model involves a prolate ellipsoidal mass that experiences underdamped harmonic oscillation within viscous liquid samples. We observed the oscillations of the prolate ellipsoid to obtain the viscous damping coefficient of each sample and substituted it to the theoretical formula of dynamic viscosity. Experimental data suggest that the mathematical model has failed to predict the viscosity values of the samples. In addition, the regression curve of the reference viscosity and the measured viscous damping coefficient shows that the two quantities have an exponential relation instead of linear relation as explained in the theoretical model. We considered the regression formula as the empirical measurement transfer function and used it to measure the viscosity of an ISO VG 150 industrial oil sample. This measurement resulted in a 2.40 % of relative error percentage. Lastly, this measurement method is only valid for measuring samples with viscosities ranging from 0.0400 Pa s to 0.256 Pa s.
Viscous Damping Coefficient Measurement System Using Incremental Optical Encoder Sudarmaji, Arief; Putra, Arifrahman Yustika; Yudiarsah, Efta
FLYWHEEL : Jurnal Teknik Mesin Untirta Volume 9, Issue 1, April 2023
Publisher : Universitas Sultan Ageng Tirtayasa

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36055/fwl.v0i0.19525

Abstract

We built a viscous damping coefficient measurement system that applies the principles of underdamped harmonic oscillation within viscous liquid. The scientific novelty of this paper lies on the type of sensor used to capture the oscillation. An incremental optical encoder is chosen as a motion detector due to its ability to convert angular position as well as rotation direction into a pair of square wave signals. The harmonic oscillator system consists of a spring with the spring constant value of 82.8 N/m, a 1.50 kg cylindrical mass and a 95.0 g prolate ellipsoidal mass. The data acquisition system converts the encoder output pulses into counts which represent the displacements of the oscillating mass under viscous liquid. We used a Proportional Integral Derivative (PID) temperature control system to maintain the sample temperature at a constant value. Experimental data suggests that the air resistance and the total friction of the mechanical components give good contribution to the damping effect of the mass’ harmonic oscillation. The repeatability test of the viscous damping coefficient measurement resulted 1.26975744 % of relative standard deviation
Co-Authors Al Rasyid Andi Muhammad Risqi Arief Sudarmaji Arifrahman Yustika Putra Daniel Kurnia Suhendro Ina S Timan, Ina S Jan S Purba, Jan S Jusuf Misbach Lugyanti Sukrisman Muchtaruddin Mansyur Putra, Arifrahman Yustika Refpo Rahman Rosari Saleh Sudarmaji, Arief Suhendro, Daniel Kurnia Suroto Suroto