@inproceedings {710, title = {Comparing genome initializations in the asexual Penna model}, booktitle = {Proceedings of the 43rd Samahang Pisika ng Pilipinas Physics Conference}, year = {2025}, month = {25{\textendash}28 Jun 2025}, pages = {SPP-2025-PC-27}, address = {Quezon City}, abstract = {The asexual Penna model, a Monte Carlo method on biological aging, has been implemented with varying population initialization methods by different authors. These methods implicitly assume that differing initializations lead to equivalent final states. However, considering these initialization methods represent distinct initial conditions, this assumption may not universally hold. This study examines two initialization methods: initialization with purely healthy genomes, and initialization with genomes containing randomly distributed harmful genes. The two initialization methods were compared under two conditions: the semelparous case and the iteroparous case. Penna model simulations were run until a steady state was achieved. The results indicate no significant differences between the initialization methods in the semelparous case. However, a small but consistent difference in genetic diversity was observed in the iteroparous case. More research is needed to assess the impact this small difference has.}, url = {https://proceedings.spp-online.org/article/view/SPP-2025-PC-27}, author = {John Benedick A. Estrada and Ronald S. Banzon} } @inproceedings {674, title = {Genetic diversity in semelparous and iteroparous Penna Model with population reduction for T < R}, booktitle = {Proceedings of the 42nd Samahang Pisika ng Pilipinas Physics Conference}, year = {2024}, month = {3{\textendash}6 Jul 2024}, pages = {SPP-2024-PC-19}, address = {Batangas City}, abstract = {We use a 32-bit string Penna Model of biological aging as a framework for investigating the influence of varying population reduction intensity on the population size and in the conservation of the genetic diversity of both semelparous and iteroparous reproducing species in a population. We limit the implementation to cases where there is a delay in reproduction and the population{\textquoteright}s tolerance to deleterious mutations are lowered (T < R). The genetic diversity of both semelparous and iteroparous cases after reaching a peak decreases towards a nonzero value. However, the decrease for iteroparous is much slower. The presence of selection ensures a T - 1 limit of active bad genes on bits on or before R, resulting to a nonzero diversity even for large t.}, url = {https://proceedings.spp-online.org/article/view/SPP-2024-PC-19}, author = {Jami Joyce T. Carig and Ronald S. Banzon} } @inproceedings {621, title = {Fractal dimension, critical exponents, and weak universality on a modified 2D Ising model}, booktitle = {Proceedings of the 41st Samahang Pisika ng Pilipinas Physics Conference}, year = {2023}, month = {19{\textendash}21 July 2023}, pages = {SPP-2023-PA-07}, address = {Siargao}, abstract = {We investigate the behavior of a 2D square Ising system with central regions without spins, providing insights into its critical behavior and dimensionality. Increasing the density of these regions changes the dimensionality of the finite lattice, and the critical temperature decreases as the blocked region density increases, consistent with a similar percolation study in 2D. The fractal dimension tends towards D = 1 as the density of blocked sites increases, indicating a more one-dimensional lattice system. Results from the analysis of modified Ising system, where the value of β varies with the degree of dilution or the density of blocked region, ρ, supports the weak universality hypothesis.}, url = {https://proceedings.spp-online.org/article/view/SPP-2023-PA-07}, author = {Kryss C. Urbano and Ronald S. Banzon} } @inproceedings {580, title = {Fractal dimension in a modified 2D Ising system with regions without spin}, booktitle = {Proceedings of the 40th Samahang Pisika ng Pilipinas Physics Conference}, year = {2022}, month = {19{\textendash}21 Oct 2022}, pages = {SPP-2022-PB-09}, address = {Legazpi City}, abstract = {We investigate the change in dimensionality of an Ising system by increasing the area of a central region without spin, essentially decreasing the density of sites with spin. We describe this change by analyzing the geometrical phase transition and change in magnetization as the system changes. We estimate the critical temperature for each lattice with blocked region density ρ and found that the critical temperature decreases as the blocked region density increases suggesting that the reduced dimensionality affects the critical behavior for each ρ. Fractal dimension is also measured by determining the cluster size and radius of gyration and using their power-law relation to estimate its value. It is found that general trend of the plot tends towards D = 1 as the density of blocked sites ρ increases, indicating that the dimension is becoming more one-dimensional.}, url = {https://proceedings.spp-online.org/article/view/SPP-2022-PB-09}, author = {Kryss C. Urbano and Ronald S. Banzon} } @article {566, title = {Optimal fixed-point quantum search in an interacting Ising spin system}, journal = {Quantum Inf. Process.}, volume = {20}, year = {2021}, pages = {90}, abstract = {In Grover{\textquoteright}s search algorithm, a priori knowledge of the number of target states is needed to effectively find a solution. This is due to the inherent oscillatory nature of unitary gates in the algorithm. A fixed-point quantum search is introduced in [Phys. Rev. Lett. 113, 210501 (2014)] to mitigate this oscillation even without knowing the size of the target space. This is done by modifying the phase inversion and oracle of the original Grover{\textquoteright}s algorithm so that the phase can assume intermediate values in [-π,π]. Naturally, qubits in a quantum computer are interacting among themselves and this might introduce an error in the phase assignment. In this work, we used the Ising spin chain to simulate the interactions among the qubits and demonstrate how to implement the fixed-point quantum search. By inspecting the state vectors after some finite number of iterations, we found that the error is primarily due to the phase difference of the ideal target state with that of the final state. Further investigation shows that high fidelity between the ideal and real evolution can be achieved by using a low Rabi frequency.}, doi = {10.1007/s11128-021-03023-1}, author = {Neris I. Sombillo and Ronald S. Banzon and Cristine Villagonzalo} } @inproceedings {548, title = {Age-dependent random deaths by Verhulst factor in an iteroparous Penna model}, booktitle = {Proceedings of the 38th Samahang Pisika ng Pilipinas Physics Conference}, year = {2020}, month = {19{\textendash}23 Oct 2020}, pages = {SPP-2020-2A-10}, address = {Presented online}, abstract = {An age-dependent Verhulst death factor was implemented using the Penna bit string model. Adaptation is simulated by decreasing the effect of carrying capacity at certain ages. We have shown that the sudden immunity to environmental effects produces population with greater size, higher diversity index, and extended lifespan. Older individuals are able to adapt to the environment.}, url = {https://paperview.spp-online.org/proceedings/article/view/SPP-2020-2A-10}, author = {Jammy Rey C. Guinid and Ronald S. Banzon} } @inproceedings {547, title = {Characterization and synthesis of classical reversible circuits}, booktitle = {Proceedings of the 38th Samahang Pisika ng Pilipinas Physics Conference}, year = {2020}, month = {19{\textendash}23 Oct 2020}, pages = {SPP-2020-4A-04}, address = {Presented online}, abstract = {Irreversible circuits were transformed into their equivalent reversible circuits. The resulting reversible circuits were optimized using a synthesis method proposed by Miller, Maslov, and Dueck, and a line reduction algorithm proposed by Wille, Soeken, and Drechsler. The application of the line-reduction algorithm reduced the number of circuit lines from 5 to 4. The effect of the line-reduction algorithm on the matrix representation of the original circuit was shown to preserve the reversibility of the function. It was also shown that only the matrix representation of a circuit or cascade of gates is needed to determine the operation of its n successive applications, which may be useful in length reduction of reversible circuits.}, url = {https://paperview.spp-online.org/proceedings/article/view/SPP-2020-4A-04}, author = {Joanne Mae B. Adelino and Ronald S. Banzon} } @inproceedings {546, title = {Cluster behavior in a finite 2D Ising model with central blocked regions}, booktitle = {Proceedings of the 38th Samahang Pisika ng Pilipinas Physics Conference}, year = {2020}, month = {19{\textendash}23 Oct 2020}, pages = {SPP-2020-4G-03}, address = {Presented online}, abstract = {We simulate a 2D ferromagnetic Ising model in a square lattice with non-periodic or finite boundary conditions. We implemented the Monte Carlo Metropolis algorithm to simulate the possible spin configurations of a square lattice with a central region without spins. The resulting magnetic domains of the system were investigated under varying sizes of the blocked region and at different temperature points. It was then observed that higher number of clusters, but of smaller cluster size, occur at high temperatures. Meanwhile, the number of positive and negative spins become almost equal beyond the critical temperature, however, no discernible trend could be observed in the spin up and spin down cluster distribution.}, url = {https://paperview.spp-online.org/proceedings/article/view/SPP-2020-4G-03}, author = {Jersey Dianne T. Ganding and Ronald S. Banzon} } @inproceedings {urbanoSPP2019, title = {2D Ising model with regions without spin}, booktitle = {Proceedings of the 37th Samahang Pisika ng Pilipinas Physics Conference}, year = {2019}, month = {29 May 2019}, pages = {SPP-2019-1G-04}, address = {Tagbilaran City, Philippines}, abstract = {The percolation threshold of 2D Ising lattice with a nonmagnetic region was found to change as the ares of this region increases, effectively changing the region with spins from 2D to 1D. These results are found to be consistent with the effective change in dimensionality of the lattice in a previous study that focuses on the change of the system with a critical temperature (2D) to one without (1D).}, url = {https://paperview.spp-online.org/proceedings/article/view/SPP-2019-1G-04}, author = {Kryss Urbano and Ronald Banzon} } @inproceedings {gomnSPP2019, title = {Determining higher order periods of the Logistic equation using a Chebyshev Transform}, booktitle = {Proceedings of the 37th Samahang Pisika ng Pilipinas Physics Conference}, year = {2019}, month = {29 May 2019}, pages = {SPP-2019-PB-12}, address = {Tagbilaran City, Philippines}, abstract = {The Logistic Equation is an iterative equation which exhibits complicated dynamics when the control parameter r is varied. When r is in between 3 and 3.57, a period doubling phenomena occurs in which periods of 2N is observed, where N∈(1,$\infty$). The Time Series of the Logistic Equation can be interpreted using Power Spectrum analysis method in which one can determine the periods present with a given r value. A popular method in determining the Power Spectrum is the Fast Fourier Transform (FFT). A difficulty encountered by the FFT however is presenting the Power Spectrum of higher order periods since the lower order periods have larger magnitudes, making the higher periods barely visible in the plot. In this paper, we explore the possibility of determining the Power Spectrum of the Logistic Equation using a Chebyshev Transform. The transform was constructed with the help of a package in Matlab called Chebfun in extracting the Chebyshev coefficients. The coefficients together with the scaled frequency bin was used in comparison to the power spectrum of the FFT. It was seen that the Chebyshev Transform had larger peaks compared to that of the FFT and had better numerical accuracy when it comes to determining the periods of the time series.}, url = {https://paperview.spp-online.org/proceedings/article/view/SPP-2019-PB-12}, author = {Michael Nicholas Go and Ronald Banzon} } @inproceedings {guinidSPP2019, title = {Diversity in iteroparous Penna Model with delayed mutations}, booktitle = {Proceedings of the 37th Samahang Pisika ng Pilipinas Physics Conference}, year = {2019}, month = {29 May 2019}, pages = {SPP-2019-PB-23}, address = {Tagbilaran City, Philippines}, abstract = {The Penna bit string model is used as a framework for the genetic diversity investigations of iteroparous population with delayed mutations. We used a Shannon-type measure to quantify genetic diversity. At stable populations, the diversity decreases with increasing mutation delay. Cases with longer mutation delay have higher populations and extended lifespans.}, url = {https://paperview.spp-online.org/proceedings/article/view/SPP-2019-PB-23}, author = {Jammy Rey C. Guinid and Ronald Banzon} } @inproceedings {riveraSPP2019, title = {Floating point representation error propagation analysis in quantum computing from a fixed point example}, booktitle = {Proceedings of the 37th Samahang Pisika ng Pilipinas Physics Conference}, year = {2019}, month = {29 May 2019}, pages = {SPP-2019-PB-25}, address = {Tagbilaran City, Philippines}, abstract = {This study is motivated by the search for a minimum precision benchmark required of a binary computer to simulate a quantum computing algorithm. In using the floating point system, there is an inherent representation error due to limited memory of the computer to express numbers that cannot be perfectly represented in binary. The case of a test function iterated about a fixed point was used to demonstrate a procedure for the accounting for error propagation, where the argument is misrepresented to some other value 1/n + δ. For i iterations, the error, δ was found to grow by (n+1)i and decrease at a rate 2-f to mantissa precision. This procedure was applied in the case of quantum computing, to account for the error propagation of a misrepresented qubit and gate ρ = ρ + Δ ρ and G{\textquoteright} = G + ΔG, which was shown for 1 operation.}, url = {https://paperview.spp-online.org/proceedings/article/view/SPP-2019-PB-25}, author = {Vincent Rivera and Ronald Banzon} } @inproceedings {adelinoSPP2019, title = {Implementation of a quantum algorithm for solving linear equations}, booktitle = {Proceedings of the 37th Samahang Pisika ng Pilipinas Physics Conference}, year = {2019}, month = {29 May 2019}, pages = {SPP-2019-PB-10}, address = {Tagbilaran City, Philippines}, abstract = {A quantum algorithm that solves linear systems of equations were proposed by Harrow, Hassidim and Lloyd (HHL) and was implemented in this study using Cirq which is a library in Python used for implementing quantum circuits. Four cases of the quantum circuit implementation were studied: |b〉 is either |0〉 or |+〉, and the number of controlled rotations is either four or six. It has been observed that for larger number of trials per observable, the variance or the fluctuation of the simulated value from the theoretical one becomes smaller. However, the effects of the number of controlled rotations or circuit size to the measured values were not observed.}, url = {https://paperview.spp-online.org/proceedings/article/view/SPP-2019-PB-10}, author = {Joanne Mae B. Adelino and Ronald Banzon} } @conference {480, title = {Diversity of semelparous populations in a penna model with continuous and periodic mutations}, year = {2018}, month = {18{\textendash}19 June 2018}, pages = {P127}, publisher = {ASTHRDP Graduate Scholars{\textquoteright} Conference}, address = {PICC, Pasay City}, abstract = {The Penna-bit string approach is used as a framework for the genetic diversity investigations of continuous and periodic mutation implementations. We quantify genetic diversity with time in Penna model populations using Shannon diversity index as a measure. The absence of deaths due to mutation accumulation removes selection and results to all populations reaching the same genome. We find that periodic mutation in this case allows the population to reach homogeneity at a much larger time than continuous mutations. On the other hand, the presence of selection results to conservation of diversity. We also know that populations under periodic mutation with selection case tend to be more genetically diverse before reaching steady-state diversity than continuous mutation implementation.}, author = {Jammy Rey C. Guinid and Ronald S. Banzon} } @conference {493, title = {Effect of error tolerance probability to the fidelity of a 4-qubit quantum search simulation}, year = {2018}, month = {5{\textendash}9 Nov 2018}, pages = {P.16}, publisher = {2018 ICTP Asian Network School and Workshop on Complex Condensed Matter Systems}, address = {Suranaree University of Technology, Thailand}, abstract = {We simulate the optimized fixed-point quantum search (OFPQS) algorithm with first- and second-nearest neighbor interactions in a 4-qubit Ising spin system using a nonrefocusing technique. In order to perform a single qubit gate, we utilize the coupling interactions to control the neighboring spins. The phase-marking scheme of the OFPQS is implemented using a single rotation about the transverse axis instead of the usual rotation about the field axis. Furthermore, the state of the ancilla is initialized in a superposition of the basis states to avoid the generation of unwanted states. This procedure gives us a probability of finding the target state within the prescribed bound of the OFPQS. Based on this scheme, we investigate the effect of error tolerance probability of the OFPQS to the fidelity of the nonrefocusing implementation.}, url = {https://indico.cern.ch/event/745791/contributions/3202508/}, author = {Neris Sombillo and Ronald Banzon and Cristine Villagonzalo} } @conference {481, title = {Genetic diversity in asexually reproducing populations of the semelparous Penna model}, year = {2018}, month = {18{\textendash}19 June 2018}, pages = {P129}, publisher = {ASTHRDP Graduate Scholars{\textquoteright} Conference}, address = {PICC, Pasay City}, abstract = {We quantify the diversity of populations simulated using the Penna model with an entropy of genetic diversity measure by Pan et al. When selection is removed by increasing the resistance to disease, populations result to a zero-steady state diversity. While for cases with selection, greater genetic diversity was achieved by delaying reproduction. It was also found that populations with genetic diversity tend to have increased average lifespan and resilience to epidemics.}, author = {Amancio II S. Manceras and Ronald S. Banzon} } @inproceedings {460, title = {Mutation rate and genetic diversity in a Penna Model}, booktitle = {Proceedings of the 36th Samahang Pisika ng Pilipinas Physics Conference}, year = {2018}, month = {6{\textendash}9 June 2018}, pages = {SPP-2018-PC-13}, address = {Puerto Princesa City, Philippines}, abstract = {The Penna bit string model is used as a framework for the genetic diversity investigations of continuous (every time step) and periodic mutation implementations of a semelparous population. We quantify genetic diversity using a Shannon-type measure. The absence of deaths due to mutation accumulation removes selection and results to the entire population reaching the same genome. We find that periodic mutation in this case allows the population to reach homogeneity at a much later time compared to the case of continuous mutations. Our results indicate that periodic mutation with selection has a higher genetic diversity compared to that of continuous mutation.}, url = {https://paperview.spp-online.org/proceedings/article/view/SPP-2018-PC-13}, author = {Jammy Rey C. Guinid and Ronald Banzon} } @inproceedings {471, title = {Two-dimension Ising model simulation via Monte Carlo method with regions without spin}, booktitle = {Proceedings of the 36th Samahang Pisika ng Pilipinas Physics Conference}, year = {2018}, month = {6{\textendash}9 June 2018}, pages = {SPP-2018-PC-32}, address = {Puerto Princesa City, Philippines}, abstract = {We investigate Ising spins in a 2D lattice with a nonmagnetic region. Simulations of increasing regions without spin suggest an effective change in dimensionality: from a system with an effective critical temperature (2D) to one without (1D).}, url = {https://paperview.spp-online.org/proceedings/article/view/SPP-2018-PC-32}, author = {Kryss Urbano and Ronald Banzon} } @conference {manceras2017spc, title = {An advantage of greater diversity}, year = {2017}, month = {24{\textendash}26 May 2017}, pages = {126}, publisher = {12th Siam Physics Congress}, address = {Rayong, Thailand}, abstract = {We find greater genetic diversity in a Penna model when the mutation threshold is less than the reproductive age, for the case of individuals reproducing only once in their lifetime. This greater diversity is obtained at the cost of decreased saturation population. An increased mean lifespan was obtained for the population with greater genetic diversity. We interpret this longer lifespan as a benefit that supports the idea that it is better to have greater genetic diversity.}, url = {https://indico.cern.ch/event/486350/contributions/2493755}, author = {Amancio II S. Manceras and Ronald Banzon} } @inproceedings {sombillo, title = {Amplitude amplification of the marked states in quantum search simulation}, booktitle = {Proceedings of the 35th Samahang Pisika ng Pilipinas Physics Conference}, year = {2017}, month = {7{\textendash}10 June 2017}, pages = {SPP-2017-PB-17}, address = {Cebu City, Philippines}, abstract = {Yoder et al. [1] proposed a quantum search algorithm that prevents the system to move away from the marked states when the number of target states M is unknown. This method uses a recursive approach that makes the target state act as a fixed-point. We simulate the algorithm in an Ising spin chain with first- and second-nearest neighbor interaction. Our method involves a selective phase-shift rotation per iteration to obtain the target state. We find the probability of success for the fixed-point implementation to fluctuate only about a limited range of values within an indicated tolerance as compared to the large oscillations of the same for Grover{\textquoteright}s non-fixed-point algorithm.}, url = {http://paperview.spp-online.org/proceedings/article/view/142}, author = {Neris Sombillo and Ronald Banzon and Cristine Villagonzalo} } @inproceedings {elegado, title = {Avoiding artificial deaths in a Penna model population}, booktitle = {Proceedings of the 35th Samahang Pisika ng Pilipinas Physics Conference}, year = {2017}, month = {7{\textendash}10 June 2017}, pages = {SPP-2017-PB-32}, address = {Cebu City, Philippines}, abstract = {In the Penna model, deaths by old age are known to artificially truncate age demographics. We propose to avoid these deaths by obtaining a parameter space plot (Penna parameters R and T, here constrained to a birth rate B=8) for which these deaths do not occur. For both TR, the genetic diversity and number of species decreased more slowly in populations with old age deaths than those without. This confirms a difference in the genetic evolution of these populations.}, url = {http://paperview.spp-online.org/proceedings/article/view/245}, author = {Christopher Patrick P. Elegado and Ronald Banzon} } @conference {420, title = {Fixed-point quantum search as implemented in an Ising spin system}, year = {2017}, month = {26{\textendash}29 June 2017}, pages = {50}, publisher = {6th Adiabatic Quantum Computing Conference}, address = {Tokyo, Japan}, abstract = {The fixed-point quantum search provides a solution to the oscillation problem in a quantum search algorithm through the variation of oracle and inversion phases at each iteration. We simulate the fixed-point algorithm in an Ising spin system with first- and second-nearest neighbor interactions. Since the oracle and the inversion operator acts on O(2), then the oracle qubit is required to be in a superposition of states at the start of the simulation. This provides a way to implement the rotation required in the variation of phases at each iteration. Results show that the probability of success calculated from the algorithm and obtained from the simulation gives a similar behavior which effectively damps the oscillation. We also investigate the effect of tolerance on the fidelity as we increase the number of iterations.}, url = {http://www.smapip.is.tohoku.ac.jp/~aqc2017/program.html}, author = {Neris I Sombillo and Ronald S. Banzon and Cristine Villagonzalo} } @inproceedings {trinidad, title = {Local periodicity of migrating populations in the Penna model}, booktitle = {Proceedings of the 35th Samahang Pisika ng Pilipinas Physics Conference}, year = {2017}, month = {7{\textendash}10 June 2017}, pages = {SPP-2017-PB-18}, address = {Cebu City, Philippines}, abstract = {Migrating populations are considered under two conditions: migrating threshold based on the population{\textquoteright}s non-migrating steady state population for each value of R, and migrations of newborns to a random nearest neighbor site. We determined that the time series of the migrating populations result to multiple periods on single runs, but single when averaged over 50 runs for all values of R in all sites in the lattice.}, url = {http://paperview.spp-online.org/proceedings/article/view/210}, author = {Jhames Ni{\~n}o T. Trinidad and Ronald Banzon} } @article {377, title = {Measurement-enhanced quantum search}, journal = {AIP Conf. Proc. (8th Jagna International Workshop)}, volume = {1871}, year = {2017}, pages = {020002}, abstract = {The oscillatory nature of the unitary Grover operator makes quantum searching difficult if one has no prior knowledge of the number of target states in the database. In this work, we coupled the database to an external qubit to transfer the target state in a space where the quantum search operation is not applied. This is followed by a measurement of the external and the ancilla qubit which result to a mixed state with a higher probability of finding the target state. The algorithm is simulated in a spin chain having first and second order neighbor interactions. The result shows that the oscillation is suppressed and the probability of success generally increased with iteration number.}, doi = {10.1063/1.4996512}, url = {http://aip.scitation.org/doi/10.1063/1.4996512}, author = {Neris I Sombillo and Ronald Banzon and Cristine Villagonzalo} } @inproceedings {manceras, title = {Resilience in a semelparous Penna model}, booktitle = {Proceedings of the 35th Samahang Pisika ng Pilipinas Physics Conference}, year = {2017}, month = {7{\textendash}10 June 2017}, pages = {SPP-2017-3B-06}, address = {Cebu City, Philippines}, abstract = {We consider the effect of a harsher environment on Penna populations with different genetic diversities. A change in the environment, in the form of an epidemic, is simulated by a lowering of the mutation threshold. Our results suggest that populations with greater genetic diversity have a greater probability of survival during an epidemic.}, url = {http://paperview.spp-online.org/proceedings/article/view/132}, author = {Amancio II S. Manceras and Ronald Banzon} } @inproceedings {334, title = {Genetic diversity in a Penna model}, booktitle = {Proceedings of the 34th Samahang Pisika ng Pilipinas Physics Congress}, year = {2016}, month = {18{\textendash}21 Aug 2016}, pages = {SPP-2016-PA-20}, address = {University of the Philippines Visayas, Iloilo City}, abstract = {We considered genetic diversity within the framework of the Penna model. Using the entropy of genetic diversity as measure, we found genetic diversity to increase with reproductive age R, for the case where the threshold parameter T is less than R. In addition, we found the saturation population to decrease with increasing genetic diversity.}, author = {Amancio II S. Manceras and Ronald Banzon} } @inproceedings {312, title = {Near-resonant approximation in quantum search simulation}, booktitle = {Proceedings of the 34th Samahang Pisika ng Pilipinas Physics Congress}, year = {2016}, month = {18{\textendash}21 Aug 2016}, pages = {SPP-2016-2C-01}, address = {University of the Philippines Visayas, Iloilo City}, abstract = {
The simulation of a quantum search algorithm in an Ising spin chain is equivalent to solving a system of 2^L coupled first order differential equations with L being the number of qubits. The near-resonant approximation can be used to simplify the evolution of the states in the database. In this work, we compare the simulation of a quantum search algorithm using the exact evolution according to Schr{\"o}dinger equation and using the near-resonant approximation. Our results show that the error of the near-resonant approximation is comparable to that of the exact evolution in terms of the fidelity measure. The advantage gained in having this small error at the near-resonant approximation is its faster execution time relative to the exact case.
}, author = {Neris D Ilano and Ronald Banzon and Cristine Villagonzalo} } @inproceedings {315, title = {Threshold carrying capacity for competing populations in a Penna model}, booktitle = {Proceedings of the 34th Samahang Pisika ng Pilipinas Physics Congress}, year = {2016}, month = {18{\textendash}21 Aug 2016}, pages = {SPP-2016-5C-05}, address = {University of the Philippines Visayas, Iloilo City}, abstract = {We consider two types of Penna model populations: VA, where the Verhulst factor is applied to the entire population, and VB, for which Verhulst is applied to newborns only. Resources are shared by summing both populations during coevolution. We determined a relative threshold carrying capacity for VB that still drives VA to extinction.}, author = {Christopher Patrick P. Elegado and Ronald Banzon} } @inproceedings {320, title = {A critically damped quantum search may not necessarily be optimal}, booktitle = {Proceedings of the AQIS Conference 2015}, year = {2015}, month = {24{\textendash}30 Aug 2015}, pages = {147-148}, address = {Korea Institute for Advanced Study, Seoul}, abstract = {We explore the rate at which the target state is obtained in a damped quantum search of an Ising system. As the number of target states is reduced, the damped quantum search gives a higher probability of success than that of the classical search. For any system in general, a new damping parameter was obtained from an optimization of the damped quantum search. Application of the optimum damping parameter per iteration on the damped quantum search shows a significant improvement of the probability of success over the critically damped quantum search.}, url = {http://aqis-conf.org/2015/program/}, author = {Neris D Ilano and Ronald Banzon and Cristine Villagonzalo} } @conference {350, title = {Effect of varying the position of the ancilla qubit and the coupling constants in the simulation of Grover{\textquoteright}s quantum search algorithm}, year = {2015}, month = {7{\textendash}11 Jan 2015}, pages = {P-62}, publisher = {9th International Conference on Computational Physics}, address = {National University of Singapore}, abstract = {We simulate Grover{\textquoteright}s algorithm in an Ising spin chain quantum computer with spatially-dependent coupling constant. The interaction to the nearest and second-nearest neighbor of the spins is considered. The behavior of the fidelity as a function of the number of Grover iteration during the algorithm is determined. For a fixed location of the ancilla qubit, the overall fidelity decreases as we increase the size of the database. Also, as we vary the coupling constant per neighbor, we obtain a high fidelity for a given number of iteration. The simulation of the algorithm using a classical computer system restricts the size of the database that gives a high fidelity result.}, url = {http://www.physics.nus.edu.sg/iccp9/}, author = {Neris D Ilano and Cristine Villagonzalo and Ronald Banzon} } @inproceedings {ilano-spp-2015, title = {Simulation of Grover{\textquoteright}s algorithm with position-variation of the ancilla qubit}, booktitle = {Proceedings of the 33rd Samahang Pisika ng Pilipinas Physics Congress}, year = {2015}, month = {3{\textendash}6 Jun 2015}, pages = {SPP-2015-2B-06}, address = {University of Northern Philippines, Vigan City}, abstract = {
We simulate Grover{\textquoteright}s quantum search algorithm in an Ising spin chain quantum computer with nearest and second-nearest neighbor interactions. We determine the optimum Rabi frequency that satisfies the 2πk method by selecting a high fidelity value in the frequency scan for each database size. Also, we vary the position of the ancilla qubit and investigate the effect on the fidelity for different sizes of the database. The behavior of the fidelity as a function of the number of Grover iterations during the algorithm is considered. For a fixed location of the ancilla qubit, the overall fidelity decreases as we increase the size of the database.
}, author = {Neris D Ilano and Ronald S. Banzon and Cristine Villagonzalo} } @conference {354, title = {Simulation of Grover{\textquoteright}s algorithm with spatially-dependent coupling constant}, year = {2014}, month = {16{\textendash}25 Sep 2014}, pages = {19}, publisher = {Okinawa School in Physics: Coherent Quantum Dynamics}, address = {Okinawa Institute of Science and Technology, Japan}, abstract = {We simulate Grover{\textquoteright}s algorithm in an Ising spin chain quantum computer with spatially-dependent coupling constant. The simulation shows that the tendency of two distinct states to transition from the same initial state is reduced. The fidelity with the ideal result and the probability of finding the target state are also investigated.}, url = {https://groups.oist.jp/cqd/participants-0}, author = {Neris D Ilano and Cristine Villagonzalo and Ronald Banzon} } @inproceedings {ilano-spp-2014, title = {Working precision in a simulation of Grover{\textquoteright}s algorithm in an Ising spin system}, booktitle = {Proceedings of the 32nd Samahang Pisika ng Pilipinas Physics Congress}, year = {2014}, month = {17{\textendash}20 Oct 2014}, pages = {SPP2014-5A-2}, address = {University of the Philippines Diliman, Quezon City}, abstract = {
We consider the simulation of Grover{\textquoteright}s algorithm in an Ising nuclear spin chain computer with first- and second-nearest neighbor interaction. We calculate the fidelity, a measure of the accuracy of the state, as a function of π/2- and π-pulses and investigate the precision of the success probability of the target state. The fidelity is constrained by the set working precision of the computer system, hence we simulate the algorithm using different working precisions. A reduction of precision is also observed as you increase the number of iterations that restricts the size of the database to effectively simulate the algorithm. The amount of decrease is dependent on the decomposition of pulses.
}, author = {Neris D Ilano and Cristine Villagonzalo and Ronald S. Banzon} } @inproceedings {suico-spp-2013, title = {Characteristics of non-spanning clusters in a percolating two-dimensional square lattice}, booktitle = {Proceedings of the 31st Samahang Pisika ng Pilipinas Physics Congress}, year = {2013}, month = {23{\textendash}25 Oct 2013}, pages = {SPP2013-PB-10}, address = {University of San Carlos, Cebu City}, abstract = {
A study of interest in site percolation is to determine the characteristics of other clusters formed that do not span a given space. In this work we simulate on a square lattice of size L x L\ and show the behavior of the mean cluster size and its associated parameters near the percolation threshold. We find that at the percolation threshold the mean cluster size is proportional to L^1.656.
}, author = {Joachim Suico and Ronald S. Banzon and Cristine Villagonzalo} } @inproceedings {capili-spp-2013, title = {Determination of the percolation critical exponent as measure of dimension}, booktitle = {Proceedings of the 31st Samahang Pisika ng Pilipinas Physics Congress}, year = {2013}, month = {23{\textendash}25 Oct 2013}, pages = {SPP2013-4C-6}, address = {University of San Carlos, Cebu City}, abstract = {
The critical exponent\ β\ related to the percolation probability describes the dimensionality of a specific lattice topology. The\ accurate determination of\ β\ will aid in distinguishing different universality classes. This work describes the fine tuning of the\ Sigma method developed previously by the authors in obtaining\ β. The approach uses the log-log plot of the percolation\ probability versus the difference of the occupation probability and the percolation threshold. Considering a symmetric distribution of points about the midpoint of this plot yields the\ β\ with (1) the lowest standard deviation and (2) the\ appropriate asymptotic behavior for both one and two-dimensional lattices.
}, author = {Micielle N Capili and Ronald S. Banzon and Cristine Villagonzalo} } @inproceedings {ilano-spp-2013, title = {The effect of the Hadamard gate decomposition in the simulation of Grover{\textquoteright}s algorithm}, booktitle = {Proceedings of the 31st Samahang Pisika ng Pilipinas Physics Congress}, year = {2013}, month = {23{\textendash}25 Oct 2013}, pages = {SPP2013-5B-2}, address = {University of San Carlos, Cebu City}, abstract = {
Simulation of Grover{\textquoteright}s algorithm in an Ising nuclear spin chain computer with first- and second-nearest neighbor interaction is considered. The most frequently used quantum gate in the algorithm is the Hadamard gate. We investigate the effect of its decomposition into several rotation matrices and numerically calculate the fidelity and probability of success of finding the target state. Using an appropriate decomposition, we obtain a high fidelity for different numbers of iterations. The probability of finding the target state also increased and is much closer to the ideal result.
}, author = {Neris D Ilano and Cristine Villagonzalo and Ronald S. Banzon} } @inproceedings {242, title = {The effect of RF distribution on the implementation of quantum CN gate in an Ising spin chain}, booktitle = {Proceedings of the 30th Samahang Pisika ng Pilipinas Physics Congress}, year = {2012}, month = {22{\textendash}24 Oct 2012}, pages = {SPP-2012-056}, address = {De La Salle Health Sciences Institute, Dasmari{\~n}as, Cavite}, abstract = {
We consider the dynamics of an Ising spin quantum computer with a radio frequency (RF) pulse distribution. The effect of the frequency spread decreases the resonant transition probability and increases thenear-resonant transition probability. Also, we apply the 2πk method to suppress the near-resonant transition. However, it has an unwanted effect on the probability of the resonant transition. It turns out that the desirable result can be obtained if we use the lowest possible value of k.
}, author = {Neris D Ilano and Cristine Villagonzalo and Ronald S. Banzon} } @inproceedings {245, title = {Percolation critical exponent of a constrained lattice}, booktitle = {Proceedings of the 30th Samahang Pisika ng Pilipinas Physics Congress}, year = {2012}, month = {22{\textendash}24 Oct 2012}, pages = {SPP-2012-004}, address = {De La Salle Health Sciences Institute, Dasmari{\~n}as, Cavite}, abstract = {
We implement the Average Occupation Probability method to treat site percolation on a square lattice with banned sites. It was found that the introduction of banned sites increases the value of the percolation probability while reducing the value of the critical exponent\ β. The deviation of\ β\ in site percolation of a constrained lattice from that of a regular system suggests that these\ lattice\ topologies belong to two different universality classes.
}, author = {Micielle N Capili and Cristine Villagonzalo and Ronald S. Banzon} } @article {Pi{\~n}ol2011101, title = {Catastrophic senescence and semelparity in the Penna aging model}, journal = { Theory Biosci.}, volume = {130}, number = {2}, year = {2011}, note = {cited By 2}, pages = {101-106}, abstract = {
The catastrophic senescence of the Pacific salmon is among the initial tests used to validate the Penna aging model. Based on the mutation accumulation theory, the sudden decrease in fitness following reproduction may be solely attributed to the semelparity of the species. In this work, we report other consequences of mutation accumulation. Contrary to earlier findings, such dramatic manifestation of aging depends not only on the choice of breeding strategy but also on the value of the reproduction age, R, and the mutation threshold, T. Senescence is catastrophic when T <= R. As the organism{\textquoteright}s tolerance for harmful genetic mutations increases, the aging process becomes more gradual. We observe senescence that is threshold dependent whenever T \> R. That is, the sudden drop in survival rate occurs at age equal to the mutation threshold value.
}, doi = {10.1007/s12064-010-0115-7}, author = {Chrysline Margus N Pi{\~n}ol and Ronald Banzon} } @inproceedings {248, title = {Determination of the critical exponent β in site percolation using average occupation probability on a square lattice}, booktitle = {Proceedings of the 29th Samahang Pisika ng Pilipinas National Physics Congress}, year = {2011}, month = {24{\textendash}26 Oct 2011}, pages = {SPP2011-5A-3}, address = {University of the Philippines Diliman, Quezon City}, abstract = {
Using the Average Occupation Probability in site percolation, the critical exponent\ β\ for a lattice (L {\texttimes} L) is determined. The results for different lattice\ sizes show that as the lattice becomes larger, the calculated\ β\ agrees better with that obtained from 2D scaling theory. There appears a common\ range of p-pc which can be used for any L to compute for\ β. We estimate that a minimum lattice size of 200 {\texttimes} 200 is necessary for the\ procedure to yield an acceptable value of the critical exponent.
}, url = {https://paperview.spp-online.org/proceedings/article/view/3139}, author = {Micielle N Capili and Cristine Villagonzalo and Ronald S. Banzon} } @inproceedings {ilano-spp-2011, title = {Optimizing the damped quantum search algorithm}, booktitle = {Proceedings of the 29th Samahang Pisika ng Pilipinas National Physics Congress}, year = {2011}, month = {24{\textendash}26 Oct 2011}, pages = {SPP2011-4A-4}, address = {University of the Philippines Diliman, Quezon City}, abstract = {
An optimization of the damped quantum search is introduced by calculating the damping parameter that gives the minimum probability of failure per iteration. The resulting damping parameter is compared with the critical damping. The result shows that the optimized damping is generally not equal to the critical damping if the degeneracy of the target state is not comparable to the size of the database. The probability of failure for the optimized damping and critical damping does not differ significantly for the first two iterations. This difference is relatively large for the third iteration. This suggests that for greater number of iterations, the critically damped search is not optimized.
}, url = {https://paperview.spp-online.org/proceedings/article/view/3135}, author = {Neris D Ilano and Ronald S. Banzon and Cristine Villagonzalo} } @inproceedings {249, title = {Persistence in the zero temperature dynamics of the 1D Ising model with long range interactions}, booktitle = {Proceedings of the 29th Samahang Pisika ng Pilipinas National Physics Congress}, year = {2011}, month = {24{\textendash}26 Oct 2011}, pages = {SPP2011-PB-33}, address = {University of the Philippines Diliman, Quezon City}, abstract = {
We study the zero-temperature dynamics of the 1D Ising Model with long range interactions. In particular, we focus on the persistence behavior as the strength of the long range interaction is varied. Persistence pertains to those spins that did not flip after some time. We observe that whatever the strength of the long range interaction, the system exhibits blocking where some spins do not flip at all. The system size is also varied to see its effect on these properties.
}, url = {https://paperview.spp-online.org/proceedings/article/view/3240}, author = {Hilton Lazo and Ronald Banzon and Cristine Villagonzalo} } @article {Pi{\~n}ol20111295, title = {Stability in a population model without random deaths by the Verhulst factor}, journal = {Physica A}, volume = {390}, number = {7}, year = {2011}, note = {cited By 1}, pages = {1295-1299}, abstract = {
A large amount of population models use the concept of a carrying capacity. Simulated populations are bounded by invoking finite resources through a survival probability, commonly referred to as the Verhulst factor. The fact, however, that resources are not easily accounted for in actual biological systems makes the carrying capacity parameter ill-defined. Henceforth, we deem it essential to consider cases for which the parameter is unnecessary. This work demonstrates the possibility of Verhulst-free steady states using the Penna aging model, with one semelparous birth per adult. Stable populations are obtained by setting a mutation threshold that is higher than the reproduction age.
}, doi = {10.1016/j.physa.2010.11.046}, author = {Chrysline Margus N Pi{\~n}ol and Ronald S. Banzon} } @inproceedings {antoniospp2010, title = {Characterization of an Ising-Like SI model}, booktitle = {Proceedings of the 28th Samahang Pisika ng Pilipinas Physics Congress}, year = {2010}, month = {25{\textendash}27 Oct 2010}, pages = {SPP-2010-003}, address = {Meralco Management and Leadership Development Center, Antipolo City}, abstract = {
An Ising-like system was used to model a computer network through which malware is spreading. The rate of spread of infection was estimated by fitting the infection curves with a standard logistic model and an exponential model. Graphical analysis shows that the exponential decay model fit the infection curves better than the logisitic model. Trends in the residuals suggest that current mathematical models for epidemics are not consistent with the system.
}, author = {Kristine Eia S Antonio and Ronald S. Banzon} } @conference {357, title = {Penna model estimate of improved medical care in the Philippines}, year = {2010}, month = {14{\textendash}16 Jun 2010}, pages = {59}, publisher = {10th Science Council of Asia Conference}, address = {Pasay City}, abstract = {The average life expectancy at birth is one indicator of the overall health of a country. In a Penna model that accounts for enhancements in medical services and welfare, the effect of heritable diseases is diminished. Individuals may live longer with probability equal to the relative increase in health care. Choosing the 1950 data for the Philippine population as baseline, the 44\% rise in average life span of Filipinos from then to 1995 may be attributed to a 20\% improvement in medical care. The 2010 life expectancy estimate follows from a 6\% increase in the quality of medical assistance during the last 15 years.}, url = {http://www.scj.go.jp/en/sca/activities/conferences/conf_10.html}, author = {Chrysline Margus N Pi{\~n}ol and Ronald S. Banzon} } @inproceedings {258, title = {Penna model estimate of medical care improvement}, booktitle = {Proceedings of the 28th Samahang Pisika ng Pilipinas Physics Congress}, year = {2010}, month = {25{\textendash}27 Oct 2010}, pages = {SPP-2010-001}, address = {Meralco Management and Leadership Development Center, Antipolo City}, abstract = {
Quantitative estimates for the quality of care are obtained from a Penna model that incorporates medical care. Enhancements in health services and welfare increase the average lifespan by decreasing the effect of heritable diseases. Feasibility of the approach was demonstrated by fitting simulation results with the Philippine life expectancy data. We find that the relative increase in lifespan is proportional to the improvement in care. The Penna model estimates of life expectancy compare well with the UN projections for the Philippine population.
}, author = {Chrysline Margus Pi{\~n}ol and Ronald S. Banzon} } @inproceedings {ilano-spp-2009, title = {Damped quantum search in an Ising spin system}, booktitle = {Proceedings of the 27th Samahang Pisika ng Pilipinas Physics Congress}, year = {2009}, month = {28{\textendash}30 Oct 2009}, pages = {SPP-2009-006}, address = {Development Academy of the Philippines Convention Center, Tagaytay City}, abstract = {
We seek on 8 and a 12 spins Ising systems at least one of their eigenstates of a certain eigenvalue by applying the damped quantum search. In particular, without the knowledge of the number of degeneracy, it requires 150 queries to find at least one of the characteristic states having an eigenvalue of -11ε in a database of 4096 items with a probability of 99.1\%. The average number of queries are compared with that of the undamped quantum search. It is found that for a small number of target states, the damped quantum search still preserves the quantum results, while for a large number of target states the classical limit is approached. Moreover, the damped quantum search is shown to increase monotonically as the number of iteration is increased.
}, author = {Neris D Ilano and Ronald S. Banzon and Cristine Villagonzalo} } @inproceedings {pinol-spp-2009, title = {Obtaining finite populations in a Verhulst-free 8-bit Penna model with periodic change in reproduction}, booktitle = {Proceedings of the 27th Samahang Pisika ng Pilipinas Physics Congress}, year = {2009}, month = {28{\textendash}30 Oct 2009}, pages = {SPP-2009-033}, address = {Development Academy of the Philippines Convention Center, Tagaytay City}, abstract = {
Periodic changes in reproduction age slow down population growth or decay. The minimum reproductive age in an 8-bit, Verhulst-free Penna model varied repeatedly between two values. It is an invariable characteristic of an individual which is set at birth. A steady state is found when the period for the smaller reproductive age is slightly longer.
}, author = {Chrysline Margus Pi{\~n}ol and Ronald S. Banzon} } @inproceedings {antonio-spp-2009, title = {Selecting a practical successive over relaxation parameter for a particle-in-cell method}, booktitle = {Proceedings of the 27th Samahang Pisika ng Pilipinas Physics Congress}, year = {2009}, month = {28{\textendash}30 Oct 2009}, pages = {SPP-2009-156}, address = {Development Academy of the Philippines Convention Center, Tagaytay City}, abstract = {
The rate of convergence of the Successive Over-Relaxation (SOR) method depends on the choice of SOR Parameter,\ ω. It is shown\ that the SOR method as a Poisson Solver in the Particle-in-Cell (PIC), has a practical SOR parameter,\ ωp, that is independent\ of the number of particles contained by the system. A method that speeds up the selection of this\ ωp\ is proposed.\ For a 16x16 Plasma PIC system, using 7 test points and an increment of s = 0.03215, the\ ωp\ selected by the method is\ 1.71 which is equal to the\ ωp\ determined from a parameter scan.
}, author = {Kristine Eia S Antonio and Ronald S. Banzon} } @inproceedings {lazo-spp-2009, title = {Site percolation of a fixed lattice size with growing regions of disallowed occupancy}, booktitle = {Proceedings of the 27th Samahang Pisika ng Pilipinas Physics Congress}, year = {2009}, month = {28{\textendash}30 Oct 2009}, pages = {SPP-2009-036}, address = {Development Academy of the Philippines Convention Center, Tagaytay City}, abstract = {
We study site percolation in a rectangular lattice with increasing size of two clumped groups of banned sites. The percolation threshold was found to increase as the size of the banned sites is increased. The results were compared to the previously studied lattice with a system with a single group of clumped banned sites with the same number of available sites for occupation. It was observed that the percolation threshold for the dual case is greater than that of the single case. However, the thresholds follow the same trend as the number of available sites is increased.
}, author = {Hilton Lazo and Cristine Villagonzalo and Ronald S. Banzon} } @inproceedings {panganiban-spp-2009, title = {Thresholds of percolating systems with two symmetric forbidden zones having a constant separation}, booktitle = {Proceedings of the 27th Samahang Pisika ng Pilipinas Physics Congress}, year = {2009}, month = {28{\textendash}30 Oct 2009}, pages = {SPP-2009-034}, address = {Development Academy of the Philippines Convention Center, Tagaytay City}, abstract = {
In this paper, we investigate the percolation thresholds for a two-dimensional system with two square banned sites, its topological equivalence with another system with a single square banned site, and the scaling property between their thresholds. An eight-corner check algorithm was implemented to evaluate the percolation of this dual banned sites system. We found that percolation threshold for the dual case follows the same trend as the single case, where the threshold increases as the banned site dimension (X) is increased. Our results suggest that the thresholds for the single and dual case are related by some finite scaling laws.
}, author = {Earl Angelo Panganiban and Cristine Villagonzalo and Ronald S. Banzon} } @inproceedings {uy-spp-2008, title = {Regions of constant earth magnetic fields}, booktitle = {Proceedings of the 26th Samahang Pisika ng Pilipinas Physics Congress}, year = {2008}, month = {22{\textendash}24 Oct 2008}, pages = {SPP-2008-175}, address = {University of the Phlippines Baguio, Baguio City}, abstract = {
Approximating the magnetic field surrounding the Earth to be due to that of a dipole, we determine effective regions of constant field. Each region was identified utilizing as basis the outline of a circular trajectory for a charged particle that travels in the equatorial plane. The trajectories were obtained by indicating the center and radius of the circles. It was found that as the distance of the center of the circular trajectory from the Earth is increased, the radius of the trajectory increases. Increasing the particle{\textquoteright}s initial velocity also increased the radius of the trajectory.
}, author = {Toni Lei Uy and Ronald S. Banzon} } @inproceedings {pi{\~n}ol-spp-2008, title = {Reproduction age and survival of a Verhulst-free 8-bit Penna population}, booktitle = {Proceedings of the 26th Samahang Pisika ng Pilipinas Physics Congress}, year = {2008}, month = {22{\textendash}24 Oct 2008}, pages = {SPP-2008-071}, address = {University of the Phlippines Baguio, Baguio City}, abstract = {
A Verhulst-free Penna model is shown to be equivalent to a Malthusian model. The population is driven to exponentially increase or decrease with time depending on the value of its minimum reproductive age. This demonstration justifies its identification as a critical parameter. Unlike the Malthusian model however, we are able to obtain a relatively persistent population by imposing a distribution for the critical minimum reproductive age values.
}, author = {Chrysline Margus Pi{\~n}ol and Ronald S. Banzon} } @inproceedings {amarra-spp-2008, title = {Simulation of Grover{\textquoteright}s algorithm on a one-dimensional two-level Ising spin system}, booktitle = {Proceedings of the 26th Samahang Pisika ng Pilipinas Physics Congress}, year = {2008}, month = {22{\textendash}24 Oct 2008}, pages = {SPP-2008-004}, address = {University of the Phlippines Baguio, Baguio City}, abstract = {
We present an application of Grover{\textquoteright}s search algorithm for quantum computers to the one-dimensional Ising model. In particular, a linear, open ferromagnetic system of four spins is considered, and the algorithm is used to find the six states having energy -ε. By using the Hamiltonian operator, the action of a phase-flipping oracle is defined. An 84\% probability of success is obtained after one iteration.
}, author = {Anthony Amarra and Cristine Villagonzalo and Ronald S. Banzon} } @inproceedings {hernal-spp-2008, title = {Spanning a space in a quasi-one dimensional lattice vs. two-dimensional lattice with square banned sites}, booktitle = {Proceedings of the 26th Samahang Pisika ng Pilipinas Physics Congress}, year = {2008}, month = {22{\textendash}24 Oct 2008}, pages = {SPP-2008-163}, address = {University of the Phlippines Baguio, Baguio City}, abstract = {
Percolation thresholds in quasi- one and two dimensional systems were compared. In the former, one-way spanning is employed with a spanning cluster defined as an array that extends horizontally from one end of the lattice to the other. A four-corner checking procedure is introduced in this study to measure the percolation threshold in the corresponding two-dimensional systems with square banned sites (2DSBS). The results indicate that the threshold values from the two methods converge suggesting that the quasi-1D system and the 2DSBS are equivalent topologically.
}, author = {Mary Joyce Hernal and Cristine Villagonzalo and Ronald S. Banzon} } @inproceedings {capili-spp-2007, title = {Calculation of the average occupation probability for spanning cluster formation in site percolation}, booktitle = {Proceedings of the 25th Samahang Pisika ng Pilipinas Physics Congress}, year = {2007}, month = {24{\textendash}26 Oct 2007}, pages = {SPP-2007-192}, address = {University of the Phlippines Los Ba{\~n}os, Laguna}, abstract = {
The average occupation probability for spanning cluster formation in square lattice using site percolation was calculated. Starting with an empty lattice, sites were generated using a pseudo-random number generator. A cluster labeling procedure was implemented for the detection of a spanning cluster. Our results show that the average occupation probability decreases linearly with inverse lattice edge length. The average occupation probability{\textquoteright}s extrapolated value of 0.608 as the lattice size approaches infinity is found to be a good estimate of the accepted value for the site percolation threshold in two dimensions equal to 0.598.
}, author = {Micielle N Capili and Cristine Villagonzalo and Ronald S. Banzon} } @inproceedings {rodriguez-spp-2007, title = {Crafting a predictor-corrector method}, booktitle = {Proceedings of the 25th Samahang Pisika ng Pilipinas Physics Congress}, year = {2007}, month = {24{\textendash}26 Oct 2007}, pages = {SPP-2007-068}, address = {University of the Phlippines Los Ba{\~n}os, Laguna}, abstract = {
We aim to tailor a predictor-corrector method for an oscillatory-type of solution. The derived method consists of a fourth order predictor and corrector pair. The corrector was chosen from the so-called stability triangle which ensures the method{\textquoteright}s stability. Methods with small errors were chosen as correctors. These correctors were each paired to the already existing Milne-Simpson{\textquoteright}s predictor. The pair with the least error was selected and examined for a simple harmonic oscillator and a damped driven oscillator. The results clearly illustrate the validity of the method for an oscillatory-type of solution since it has reasonably small errors and it was shown to be comparable to the performance of RK4. Our resulting PC4 method has the advantage of less function evaluations, which translates to less error compared to RK4.
}, author = {Mariel Rodriguez and Ronald Banzon} } @inproceedings {pi{\~n}ol-spp-2007, title = {A finite population without imposing the Verhulst factor}, booktitle = {Proceedings of the 25th Samahang Pisika ng Pilipinas Physics Congress}, year = {2007}, month = {24{\textendash}26 Oct 2007}, pages = {SPP-2007-100}, address = {University of the Phlippines Los Ba{\~n}os, Laguna}, abstract = {
The necessity of imposing the concept of a carrying capacity was investigated within the framework of the Penna Model. We find that the number of deaths in a population approaches a saturation point. The carrying capacity {\textendash} Verhulst factor, is the main contributing factor for deaths, over 70\%, in an 8-bit Penna model. Only 3\% and 20\% of the deaths are caused by old age and mutation accumulation, respectively. However, the effect of the common method of accounting for a carrying capacity is diminished as the bit-string length of the Penna Model is decreased. Furthermore, at bit-string length of 2, the Verhulst factor may be removed while still maintaining a finite population.
}, author = {Chrysline Margus Pi{\~n}ol and Ronald S. Banzon} } @inproceedings {belisario-spp-2007, title = {Molecular dynamics approach to the reaction rate of composite particles}, booktitle = {Proceedings of the 25th Samahang Pisika ng Pilipinas Physics Congress}, year = {2007}, month = {24{\textendash}26 Oct 2007}, pages = {SPP-2007-073}, address = {University of the Phlippines Los Ba{\~n}os, Laguna}, abstract = {
We present an approach for the determination of the reaction rate of composite particles. We demonstrated that the reaction rate of composite particles may be obtained from the reaction rates of its constituent particles. That is, that the composite particle reaction rate is a function of reaction rates of each individual particles. The use of virtual modelling allowed us to investigate the different configurations of the particles and determine its properties. In this study, a molecular dynamics method was utilized to simulate the behavior of 10 particles moving in a one-dimensional ring. This is done by assuming the particles to be hard spheres interacting via the Lennard-Jones potential. Equilibrium is achieved by reducing the kinetic energy of the particles during a particle-particle collision. A pair is considered to have bonded when their separation distance corresponds to a certain fraction of the minimum potential energy. The model shows that as we increase the fractional energy loss between collisions, the time to equilibrium decreases exponentially.
}, author = {Karla V Belisario and Ronald S. Banzon} } @inproceedings {antonio-spp-2007, title = {Parameter estimates for a reaction rate model}, booktitle = {Proceedings of the 25th Samahang Pisika ng Pilipinas Physics Congress}, year = {2007}, month = {24{\textendash}26 Oct 2007}, pages = {SPP-2007-101}, address = {University of the Phlippines Los Ba{\~n}os, Laguna}, abstract = {
A model for chemical reaction rates that relies solely on the depth of any potential-well function and two parameters intrinsic to the model, A and f, was previously proposed. This study aims to show that using that model, the experimental reaction rate constant can be replicated by simply scaling these two parameters and choosing the proper period to calculate the rate constant, k. It was shown that k is best calculated for the period t4-t2 and for A = 0.01 and f = 0.25 where the \% error is 1.38\%.
}, author = {Kristine Eia S Antonio and Ronald S. Banzon} } @inproceedings {mandingiado-spp-2006, title = {Complexity in competitive populations}, booktitle = {Proceedings of the 24th Samahang Pisika ng Pilipinas Physics Congress}, year = {2006}, month = {25{\textendash}27 Oct 2006}, pages = {SPP-2006-61}, address = {Ateneo de Davao University, Davao City}, abstract = {
Our results suggest that a more complex strategy for survival is favored in a competitive environment. The degree of complexity is associated with the estimated embedding dimension for population sets where the birth rate, b, and mutation threshold, th, are independently varied. The embedding dimension for a time series determined by parameters of the Penna model was estimated from a simplex projection method. A deviation was encountered, however, for population sets where the maximum number of offspring in a lifetime, max_off, is varied. It is presumed that this may be due to the coupling of the parameters b and the minimum reproductive age r.
}, author = {Ralph Paolo V Mandingiado and Stephanie B Ibo and Ronald S. Banzon} } @inproceedings {belisario-spp-2006, title = {The molecular dynamics of two particles on a ring}, booktitle = {Proceedings of the 24th Samahang Pisika ng Pilipinas Physics Congress}, year = {2006}, month = {25{\textendash}27 Oct 2006}, pages = {SPP-2006-68}, address = {Ateneo de Davao University, Davao City}, abstract = {
We consider the behavior of two particles on a one-dimensional ring interacting via the Lennard-Jones potential. A collision occurs when the distance between the particles falls within a range corresponding to the minimum potential energy of the system. Equilibrium is achieved when the kinetic energy, which is reduced to an amount proportional to the square of the velocity during particle-particle collision, is less than a fraction of the minimum potential energy. The model shows that as we increase the range in which the Lennard Jones potential is allowed to act on the system, the time needed to achieve equilibrium also increases.
}, author = {Karla V Belisario and Elise Agra and Kristine Eia S Antonio and Ronald S. Banzon} } @inproceedings {antonio-spp-2006, title = {Particle density dependence of molecular dynamics estimated reaction rates}, booktitle = {Proceedings of the 24th Samahang Pisika ng Pilipinas Physics Congress}, year = {2006}, month = {25{\textendash}27 Oct 2006}, pages = {SPP-2006-72}, address = {Ateneo de Davao University, Davao City}, abstract = {
The dependence of the rate of reaction on the particle density of a one-dimensional gaseous system was investigated using molecular dynamics. The particle density in the system was changed by changing the size of the particles, the length of the system, and the number of particles in the system. It was found that, in general, as particle density increased, the rate of the reaction for a system that forms diatomic molecules increased. It was also shown that as the initial kinetic energy of the particles as denoted by the speed was increased, the rate of the reaction increased as well. These findings agree with empirical observations.
}, author = {Kristine Eia S Antonio and Ronald Banzon} } @inproceedings {jaramillo-spp-2005, title = {Constrained percolation in two dimensions}, booktitle = {Proceedings of the 23rd Samahang Pisika ng Pilipinas Physics Congress}, year = {2005}, month = {26{\textendash}28 Oct 2005}, pages = {SPP-2005-130}, address = {Central Philippine University, Iloilo City}, abstract = {
The effect of implanting square lattice sites of zero occupation probability at the center of a finite but large square lattice for site percolation was investigated. The introduction of symmetrical forbidden site lattices of different sizes inside 40x40 and 60x60 lattices yield percolation threshold values increasing with the size of the forbidden lattice. It was shown that topology in two dimensions dictates the value of the percolation threshold.
}, author = {Christian Oliver Jaramillo and Cristine Villagonzalo and Ronald Banzon} } @inproceedings {antonio-spp-2005, title = {A model for molecular reaction rates}, booktitle = {Proceedings of the 23rd Samahang Pisika ng Pilipinas Physics Congress}, year = {2005}, month = {26{\textendash}28 Oct 2005}, pages = {SPP-2005-121}, address = {Central Philippine University, Iloilo City}, abstract = {
We propose a model for the determination of the rate of a chemical reaction using molecular dynamics. This is done by approximating the molecules to be hard spheres interacting via the Lennard-Jones potential. A collision occurs in the event that the particle separation falls within a predetermined collision range. Equilibrium is achieved by reducing the kinetic energy by an amount proportional to the square of the velocity, -Av^2, during particle-particle collision. The model shows that as A\ increases, the time to equilbrium, T, decreases exponentially. On the other hand, it also shows that for increasing particle radius R, T\ increases linearly.
}, author = {Kristine Eia S Antonio and Karla V Belisario and Ronald S. Banzon} } @inproceedings {nicolas-spp-2005, title = {Modelling molecular function via multiple collisions}, booktitle = {Proceedings of the 23rd Samahang Pisika ng Pilipinas Physics Congress}, year = {2005}, month = {26{\textendash}28 Oct 2005}, pages = {SPP-2005-147}, address = {Central Philippine University, Iloilo City}, abstract = {
We propose a molecular dynamics model for molecular formation. We utilize a Lennard-Jones potential for the interaction and introduced an energy loss upon collision to what otherwise would have been completely elastic. Results indicates that the rate of reaction increases as the concentration of the substance increases.
}, author = {Mark Lawrence Nicolas and Ronald S. Banzon} } @inproceedings {beech-spp-2005, title = {Survivability in an 8-bit Penna model}, booktitle = {Proceedings of the 23rd Samahang Pisika ng Pilipinas Physics Congress}, year = {2005}, month = {26{\textendash}28 Oct 2005}, pages = {SPP-2005-111}, address = {Central Philippine University, Iloilo City}, abstract = {
Intraspecific competition was simulated using an 8-bit Penna Model, showing that one would harvest resources, while the other would be driven to extinction. The ability of a population to compete with their coexistent population is largely affected by intrinsic properties that affect the population saturation. Results suggest that it is the high tolerance of mutations and the high maximum number of offspring in a lifetime that describe a more competitive population. Given these parameters to be equal, the population which fluctuates less about the equilibrium population is preferred.
}, author = {Maria Donna N Beech and Ronald S. Banzon} } @inproceedings {marco-spp-2004, title = {Effect of the hopping parameter on the current through a two-atom molecular wire}, booktitle = {Proceedings of the 22nd Samahang Pisika ng Pilipinas Physics Congress}, year = {2004}, month = {25{\textendash}27 Oct 2004}, pages = {27}, address = {Bohol Tropics Resort, Tagbilaran City}, abstract = {
We utilize the Hubbard model approach in analyzing the effect of the hopping parameter in the transport properties of a two-atom molecular device. A root finding method was utilized to implement self-consistent calculations to obtain the transport properties and our results agree with that in the literature. Variation of the hopping parameter shows that its value is proportional to the threshold voltage in the presence of an on-site Coulomb interaction U.
}, author = {Ronaldo Marco Jr and Ronald S. Banzon and Cristine Villagonzalo} } @article {Marco2004, title = {Hopping in a molecular wire}, journal = {Science Diliman}, volume = {16}, year = {2004}, pages = {10-11}, abstract = {
We utilize the Hubbard model approach in analyzing the effect of the hopping parameter in the transport properties of a two-atom molecular device.
}, url = {http://journals.upd.edu.ph/index.php/sciencediliman/article/view/86}, author = {Ronaldo Marco Jr and Ronald Banzon and Cristine Villagonzalo} } @inproceedings {beech-spp-2004, title = {Periodicity in a Penna model}, booktitle = {Proceedings of the 22nd Samahang Pisika ng Pilipinas Physics Congress}, year = {2004}, month = {25{\textendash}27 Oct 2004}, pages = {11}, address = {Bohol Tropics Resort, Tagbilaran City}, abstract = {
A population of an asexually reproducing species is simulated using a suggested 8-bit string length implementation and a modified implementation of the Verhulst factor. The age structure of the population generated by this implementation is found to be non-Gompertzian and time-dependent. The change in age structure is shown to be a result of the periodic behavior of the population of its component ages, with relatively similar period, but different phase.
}, author = {Maria Donna N Beech and Ronald S. Banzon} } @inproceedings {nombres-spp-2004, title = {Random deaths and chaos in a Penna model}, booktitle = {Proceedings of the 22nd Samahang Pisika ng Pilipinas Physics Congress}, year = {2004}, month = {25{\textendash}27 Oct 2004}, pages = {54}, address = {Bohol Tropics Resort, Tagbilaran City}, abstract = {
We utilise an 8-bit Penna bit-string model of biological aging in studying the dynamics of an asexually reproducing, single species and non-migrating population using a modified version of the Verhulst death factor. It was seen that different implementations of the death procedure, one that is applied to all the individuals within the population (VA), and one that is applied only to newborns (VB) exhibited some similar, but mostly different dynamical behaviours. It was shown that the VB population has a higher level of chaos as compared to VA. Aside from an increase in the birth rate, B, chaos also resulted from an increase in the mutation threshold, T.
}, author = {Chris Nombres and Ronald S. Banzon} } @inproceedings {obias-spp-2004, title = {Tempering and annealing in a Verdier-Stockmayer polymer}, booktitle = {Proceedings of the 22nd Samahang Pisika ng Pilipinas Physics Congress}, year = {2004}, month = {25{\textendash}27 Oct 2004}, pages = {32}, address = {Bohol Tropics Resort, Tagbilaran City}, abstract = {
Two Monte Carlo methods, simulated annealing and parallel tempering, were applied to a Verdier-Stockmayer polymer. The efficiency of the two algorithms in exploring the lowest energy state possible for the model polymers was measured by the number of energy degenerate configurations (configurations that have the same energy but are structurally different). Parallel tempering consistently explored more energy degenerate configurations as compared to simulated annealing.
}, author = {Eric Bryan Obias and Ronald S. Banzon} } @article {Obias2004, title = {Tempering and annealing in a Verdier-Stockmayer polymer}, journal = {Science Diliman}, volume = {16}, year = {2004}, pages = {12-16}, abstract = {
Two Monte Carlo methods, simulated annealing and parallel tempering, were applied to a Verdier-Stockmayer polymer. The efficiency of the two algorithms in exploring the lowest energy state possible for the model polymers was measured by the number of energy-degenerate configurations (configurations that have the same energy but are structurally different). Parallel tempering consistently explored more energy-degenerate configurations as compared with simulated annealing.
}, url = {http://journals.upd.edu.ph/index.php/sciencediliman/article/view/87}, author = {Eric R Obias and Ronald S. Banzon} } @inproceedings {sandagon-spp-2004, title = {Variational Monte Carlo of a 2D quantum well system}, booktitle = {Proceedings of the 22nd Samahang Pisika ng Pilipinas Physics Congress}, year = {2004}, month = {25{\textendash}27 Oct 2004}, pages = {153}, address = {Bohol Tropics Resort, Tagbilaran City}, abstract = {
The convergence of a Variational Monte Carlo method with Gaussian importance sampling (VMC-GIS), as applied to a two-dimensional time-independent quantum well, was improved by optimizing the standard deviation σ of the Gaussian probability distribution. The fastest convergence in attaining the ground state is obtained by using VMC-GIS with σ=0.6 .
}, author = {Ryan Sandagon and Ronald S. Banzon and Cristine Villagonzalo} }