Johnrob Bantang | University of the Philippines Diliman (original) (raw)

Papers by Johnrob Bantang

We formulate a way of having a granular thermometer using cellular automata simulation of the int... more We formulate a way of having a granular thermometer using cellular automata simulation of the interaction of two different granular materials through an elastic boundary. The packing fraction and pressure of the unknown granular material can be measured from its interaction with a granular material of a known packing fraction, pressure, and kinetic energy. A calibration curve of the movement of the elastic boundary was obtained for a totally elastic system with no driving. The curve was from the final boundary location representing a change in the volume of one of the systems. The final location of the boundary was found to go towards the direction of the system with a smaller packing fraction. This result could be used to identify the packing fraction of an unknown granular system given the packing fraction of a known system and the steady state volume of the known system after interaction. The volume of the system is equal on average when the packing fraction is equal on both side...

International Journal of Modern Physics C

We present a fragmentation model that generates almost any inverse power-law size distribution, i... more We present a fragmentation model that generates almost any inverse power-law size distribution, including dual-scaled versions, consistent with the underlying dynamics of systems with earthquake-like behavior. We apply the model to explain the dual-scaled power-law statistics observed in an Internet access dataset that covers more than 32 million requests. The non-Poissonian statistics of the requested data sizes [Formula: see text] and the amount of time [Formula: see text] needed for complete processing are consistent with the Gutenberg–Richter–law. Inter-event times [Formula: see text] between subsequent requests are also shown to exhibit power-law distributions consistent with the generalized Omori law. Thus, the dataset is similar to the earthquake data except that two power-law regimes are observed. Using the proposed model, we are able to identify underlying dynamics responsible in generating the observed dual power-law distributions. The model is universal enough for its app...

International Journal of Modern Physics C, 2011

Using in silico experiments, we isolate the effects of geometry on the efficiency of passive diff... more Using in silico experiments, we isolate the effects of geometry on the efficiency of passive diffusion transport, PS, of viral cargos to the nuclear region. We model the cell as an elliptical 2D structure (eccentricity e) containing a circular nucleus with radii R (semi-minor) and r, respectively. The cargos move in isotropic random walk inside the cell. PS is estimated as the ratio of the number of cargos that reach the nuclear region and of cargos released. We show that PS decreases with the total distance traveled but increases with r/R. Shifting the nuclear position inside circular cells (e = 0) produce probability distribution functions of total distance traveled that shifts to shorter modes as one side becomes closer to the cell membrane. On the contrary, cargos in more elongated cells (e = 0) have preserved PS-values even for longer distances of travel inside the cell. Finally, an optimum r/R exists due to a trade-off between increased efficiency of transport to the nucleus a...

International Journal of Modern Physics C, 2015

We utilize the original Hodgkin–Huxley (HH) model to consider the effects of defective ion channe... more We utilize the original Hodgkin–Huxley (HH) model to consider the effects of defective ion channels to the temporal response of neurons. Statistics of firing rate and inter-spike interval (ISI) reveal that production of action potentials (APs) in neurons is not sensitive to changes in membrane conductance for sodium and potassium ions, as well as to the reversal potential for sodium ions, as long as the relevant parameters do not exceed 13% from their normal levels. We also found that blockage of a critical fraction of either sodium or potassium channels (dependent on constant input current) respectively limits the firing activity or increases spontaneous spiking activity of neurons. Our model may be used to guide experiment designs related to ion channel control drug development.

International Journal of Modern Physics C, 2012

We study the synchronization of Hodgkin–Huxley (HH) neurons connected in a directed lattice netwo... more We study the synchronization of Hodgkin–Huxley (HH) neurons connected in a directed lattice network under the influence of varying coupling strength (g) and random link malfunctions in the form of probabilistic deletion (probability q) and link direction flipping (p). We quantify the extent of synchronization of the neurons in the network by averaging the fraction of firing neurons that produce action potentials (exceeding a threshold potential of V th ) across the entire observation time. By extensively scanning over the values of g, synchronization of this network type can be enhanced by increasing g until it reaches a threshold value wherein synchronization will deteriorate abruptly due to suppression of neural firings. We also extensively probe the interplay of p and q and show that there are certain combinations for which the synchronization will improve, defying negative notions of how we perceive random malfunctions.

$Research paper thumbnail of Diffraction effects in light propagation through a highly scattering medium$

Lecture Notes in Computer Science, 2009

We modify and extend Cardelli’s Brane Calculus and Danos and Pradalier’s Projective Brane Calculu... more We modify and extend Cardelli’s Brane Calculus and Danos and Pradalier’s Projective Brane Calculus (PBC) to improve consistency with biological characteristics of membrane reactions. We propose a Projective Activate-Bud-Mate (PABM) calculus as an alternative to the Phago-Exo-Pino (PEP) basic calculus of L. Cardelli. PABM uses a generalized formalism for Action activation with receptor-ligand type channel construction that incorporates multiple association

Physical Review E, 2002

High-resolution segregation is demonstrated for elastic granular materials of the same mass and s... more High-resolution segregation is demonstrated for elastic granular materials of the same mass and size. Each grain starts at a randomly selected position in the entrance facet of a cylinder, accelerates downwards due to gravity, and then bounces against a massive obstacle with a collision cross section that is proportional to the facet size. Bounce dynamics of the falling grain is a function of its relative elasticity with the obstacle. Subsequent collisions of the grain with the wall are assumed to be perfectly elastic. In the absence of interparticle collisions, grain focusing occurs at points along the cylinder axis. In the absence of rotation, focusing occurs regardless of the initial locations and (downward) velocities of the grains at the entrance facet. The focus location depends only on the coefficient of restitution of the falling particle and the obstacle size. Grains arrive at the focus in temporally localized bursts even if released simultaneously from the facet. Efficient segregation is, therefore, achieved without additional mechanical work (e.g., shaking, spinning) on the system configuration.

Physical Review A, 2003

Via the Richards-Wolf vector diffraction theory, we analyze the three-dimensional intensity distr... more Via the Richards-Wolf vector diffraction theory, we analyze the three-dimensional intensity distribution of the focal volume that is produced by a strongly focused 750-nm beam of ultrafast, Gaussian-shaped optical pulses (10 Ϫ9 sу pulse width у1 fsϭ10 Ϫ15 s). Knowledge of the three-dimensional distribution near focus is essential in determining the diffraction-limited resolution of an optical microscope. The optical spectrum of a short pulse is characterized by side frequencies about the carrier frequency. The effect of spectral broadening on the focused intensity distribution is evaluated via the Linfoot's criteria of fidelity, structural content, and correlation quality and with reference to a 750-nm cw focused beam. Different values are considered for and numerical aperture of the focusing lens (0.1рX NA р1.2). At X NA ϭ0.8, rapid deterioration of the focused intensity distribution is observed at ϭ1.2 fs. This happens because a 750-nm optical pulse with ϭ1.2 fs has an associated coherence length of 359.7 nm which is less than the Nyquist sampling interval of 375 nm that is required to sample 750 nm sinusoid without loss of information. The ill-effects of spectral broadening is weaker in two-photon excitation microscope than in its single-photon counterpart for the same focusing lens and light source.

Physica A: Statistical Mechanics and its Applications, 2009

... Kinks, logarithmic tails, and super-stability in bi-disperse granular media. Rene Batac a , M... more ... Kinks, logarithmic tails, and super-stability in bi-disperse granular media. Rene Batac a , Marissa Pastor a , Marko Arciaga a , Johnrob Bantang a and Christopher Monterola Corresponding Author Contact Information , a , E-mail The Corresponding Author. ...

Molecular BioSystems, 2011

Conflicting reports in leading journals have indicated the minimum number of influenza hemaggluti... more Conflicting reports in leading journals have indicated the minimum number of influenza hemagglutinin (HA) trimers required for fusion to be between one and eight. Interestingly, the data in these reports are either almost identical, or can be transformed to be directly comparable. Different statistical or phenomenological models, however, were used to analyze these data, resulting in the varied interpretations. In an attempt to resolve this contradiction, we use PABM, a brane calculus we recently introduced, enabling an algorithmic systems biology approach that allows the problem to be modeled in a manner following a biological logic. Since a scalable PABM executor is still under development, we sufficiently simplified the fusion model and analyzed it using the model checker, PRISM. We validated the model against older HA-expressing cell-to-cell fusion data using the same parameters with the exception of three, namely HA and sialic acid (SA) surface densities and the aggregation rate, which were expected to be different as a result of the difference in the experimental setup. Results are consistent with the interpretation that a minimum aggregate size of six HA trimers, of which three undergo a conformational change to become fusogenic, is required for fusion. Of these three, two are free, while one is bound. Finally, we determined the effects of varying the SA surface density and showed that only a limited range of densities permit fusion. Our results demonstrate the potential of modeling in providing more precise interpretations of data.

Journal of Statistical Mechanics: Theory and Experiment, 2009

We report the existence of enhanced heap stability as a result of the mixing of granular material... more We report the existence of enhanced heap stability as a result of the mixing of granular materials. Our setup consists of a rectangular container, filled with a binary mixture of granular matter up to some height h, that is rapidly opened at one wall to allow repose angle (thetac) formation. We develop an empirical model for thetac based on the

Complexity, 2006

We show that non-Poisson and Poisson processes can coexist in ordered parallel multilane pedestri... more We show that non-Poisson and Poisson processes can coexist in ordered parallel multilane pedestrian traffic, in the presence of lane switching which asymmetrically benefits the switchers and nonswitchers. Pedestrians join at the tail end of a queue and transact at the opposite front end. Their aim is to complete a transaction within the shortest possible time, and they can transfer to a shorter queue with probability p s. Traffic is described by the utilization parameter U ϭ ͗t s ͘/N, where is the average rate of pedestrians entering the system, ͗t s ͘ is the average transaction time, and N is the number of lanes. Using an agent-based model, we investigate the dependence of the average completion time ͗t c ͘ with variable K ϭ 1 ϩ (1 Ϫ U) Ϫ1 for different N and ͗t s ͘ values. In the absence of switching (p s ϭ 0), we found that ͗t c ͘ ϰ K , where Ϸ 1 regardless of N and ͗t s ͘. Lane switching (p s ϭ 1) reduces ͗t c ͘ for a given K, but its characteristic dependence with K differs for nonswitchers and switchers in the same traffic system. For the nonswitchers, ͗t c ͘ ϰ K , where Ͻ 1. At low K values, switchers have a larger ͗t c ͘ that also increases more rapidly with K. At large K, the increase rates become equal for both. For nonswitchers, the possible t c values obey an exponentially decaying probability density function p(t c). The switchers on the other hand, are described by a fat-tailed p(t c) implying that a few are penalized with t c values that are considerably longer than any of those experienced by nonswitchers.

Arxiv preprint physics/ …, 2003

We show that time-dependent fluctuations {∆x} in foreign exchange rates are accurately described ... more We show that time-dependent fluctuations {∆x} in foreign exchange rates are accurately described by a random walk in a complex plane that is demarcated into the gain (+) and loss (−) sectors. ∆x is the outcome of N random steps from the origin and |∆x| is the square of the Euclidean distance of the final N-th step position. Sign of ∆x(t) is set by the N-th step location in the plane. The model explains not only the exponential statistics of the probability density of {∆x} for G7 markets but also its observed asymmetry, and power-law dependent broadening with increasing time delay.

h i g h l i g h t s • Single Hodgkin-Huxley (HH) neurons exhibit stochastic resonance behavior. •... more h i g h l i g h t s • Single Hodgkin-Huxley (HH) neurons exhibit stochastic resonance behavior. • We extend the original HH neuron model for a directed lattice network. • Interplay of link direction flipping and noise influences network synchronization. • Our neural network produced a stochastic resonance signature similar to real neurons. • Minimum noise is needed to obtain optimal synchronization for highly random networks.

Physical review. E, Statistical, nonlinear, and soft matter physics, 2002