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}
}