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  Current Research Projects

Spiral Wave Modeling
Effects of Randomization on Stability of Spiral Waves
Spiral waves are self-repeating waves that can form in excitable media, propagating outward from their center in a spiral pattern. Spiral waves have been observed in different natural phenomena and have been linked to medical conditions such as epilepsy and atrial fibrillation.

In this project we are interested in developing 2-dimensional siumlations of spiral waves in different situations. We first developed a Python code to simulate spiral waves in neuronal networks and studied the effects of randomization of the characteristic times in the stability of these waves. The randomization of the active (𝜏A) and refractory (𝜏A) periods of a neuron is able to explain the breakdown of the "Human Spiral Wave" created at Georgia Tech University.

We have also developed a code to study Predator-Prey-Vegetation interactions and determined under what conditions spiral patterns form and their effects on local biodiversity. This model can be easily extended to interactions of multiple populations.

Studens Involved in the Project
Summer of 2018
Karm-Amjal Ali
Minhyeok Kwon
Vincent Vangelista

Summer of 2019
Erica Albrigo
Genghis Husameddin
Brenda Muñoz

Summer of 2020
Jason Izui
Phillip Noffz (in memorian)
Recent Publications in this Project

V. Vangelista, K. Amjad-Ali, M. Kwon, and P. H. Acioli , "Effects of randomization of characteristic times on spiral wave generation in a discrete excitable medium" , submitted to AIP Advances


We would like to thank funding from Northeastern Illinois University Student Center for Science Engagement (SCSE) and the U.S. Department of Education (USDOE) Title III Award # P031C160209.4-6

and 𝜏R=2-5

and 𝜏R=4-6

Viral Diffusion
The enf of 2019 and begining of 2020 were marked by the appearance of the novel corona virus COVID-19. The spread of this disease to the point of a pandemic disrupted the lives of the world population. The modelling of the exponential growth of the rate of infection is a great teachable moment in STEM disciplines, and have been used to teach the logarithmic scale and how to fit data and show the seriousness of this infection.

In the present work we present a simple dynamical model of the spread of viral infections. This model can show a visualization of the spread of the infection in addition to predicting the number of infections. It uses the diffusion equation in 2D

where D is known as the diffusion constant. This equation represented the motion of Brownian particle. The method allows for the diffusion of individuals in a population, represented by spherical particles. The main ingredients of the method are the population density ρ the number of habitants (particles in the simulation cell) Npop>, the diffusion constant D, the number of simulation steps Nstep, the time step dt, the incubation period (tinc), the transmission radius, and the probability of transmission from an infected to a healthy individual (prob).
All of these variables are set at the beginning of the simulation. The algorithm is described below:
  1. Input Npop, Nstep, D, dt, tinc, prob, rtransm

  2. Calculate the size of the square cell as L = (Npop/ρ)1/2

  3. Initialize the initial population

  4. Choose a fraction of the initial population to be infected, and set timer for the sickness (tsick)

  5. Loop over Nstep

  6. Move all individuals according to the Gaussian distribution .

  7. Compute the distance between each healthy and infected individuals

       If the distance is less than rtransm, the healthy individual
       becomes sick with probability prob

  8. Subtract the sickness timer by dt

  9. If tsick < 0 the sick individual gets cured

This model is meant to be used in introductory computational physics codes to qualitatively and semi-quantitatively describe the spread of viral infections. It has been first implemented in the PHYS 309 - Computation for Scientists course at NEIU in Spring 2020. A manuscript describing the method has been submitted to the American Journal of Physics and a preprint can be found at . Some of the results in the manuscript are displayed to the right. We were able to show that the infection rate in the city of Chicago is lower than in NYC if we consider the same mobility (diffusion constant), probability of infection, and incubation period. In a simulation with a larger population we were able to quantitatively reproduce the initial rate of infection in the city of Chicago. The manuscript describes modifications to the model to more realistic situations such as quarantine, social distancing, spread of the disease to different regions just to name a few. The python code can be found in the link below. Please, cite this work in any publication that results from the use of this code or its modifications.

Recent Publications in this Project

Paulo H. Acioli "Diffusion as a First Model of Spread of Viral Infection", Am. J. Phys. 88, 600 (2020).

Python Code for Viral Diffusion

Number of Corona Virus Cases in CHI and NYC

Simulation of Viral Infection with

Logarithmic Scale Graph of the Total Number of Infections

Simulation of Viral Infection with

Logarithmic Scale Graph of the Total Number of Infections

Snapshots of a typical simulation cell
Susceptible (white), Sick (red), Recovered (white)

STEM Education Research
Example of a computer simulation of asteroid collisions in a University Physics I project.
Student engagement has been demonstraded an effective strategy for long term concept retention in physics and STEM education. At NEIU we are engaging students through the infusion f mini-research projects in the introductory STEM courses Programing I and II, General Chemistry I and II, Physical Geology, Calculus II and Computational Statistics, and University Physics I and II. This implementation is facilitated by Peer Leaders that help students through the projects by working mostly as a sounding board, but also as someone that has gone through the process and is able to aid the students find their own answers to the question raised in their projects. This work is a result of an NSF-IUSE funded project name Peer Enhanced Experiential research in STEM (PEERS). An integral portion of the implementation in the physics courses is the use of computer simulations. We have studied how computer simulations can help understand classical mechanics as well as the elusive concept of energy. Our latest contribution was proposing a diffusion model to simulate the spread of viral infection.

Current collaborators

Elisabet Head - Earth Science (NEIU)

Joseph Hibdon Jr. - Mathematics (NEIU)

Ken Nicholson - Chemistry (NEIU)

Rachel Trana - Computer Science (NEIU)

Sudha Srinivas - Physics (NEIU)

Recent Publications in this Project

Paulo H. Acioli "Diffusion as a First Model of Spread of Viral Infection", submited to the Am. J. Phys. (2020).

Paulo H. Acioli "An example of computer modeling to teach energy conservation concepts", Am. J. Phys. 87, 543 (2019).

Paulo H. Acioli, and Sudha Srinivas, "Experiential Learning of Classical Mechanics Through Molecular Dynamics", in Proceedings of the World Conference in Physics Education 2012, Istanbul, Turkey, 2014, pp. 379-390.


This work is supported by a Improving Undergraduate Education in STEM (IUSE) grant #1431839 from the Division of Undergraduate Education (DUE) of the National Science Foundation (NSF).

Initial Condition

Final result

Energy exchanges

Computational Photoelectron Spectroscopy
Evolution of the PES Spectrum of Al12- into Al13- and NiAl12-
Experimental photoelectron spectroscopy (PES) is a very powerfull technique to probe the electronic structure of a molecular system. It has been widely used in negatively charged clusters of metal elements to probe a transition to metallicity and half-metallicity in finite systems. PES are obtaining by shining light (laser) into the molecular system and removing electrons from it. The difference in the kinetic energy of the electron and the incident laser energy is the electron binding energy. Although a powerful techinique, PES cannot provide information about the structure and other properties of the system. It is then of fundamental importance to perfomr high accuracy computations to bridge this gap.

We have developed a technique to extract electron binding energies from the Kohn-Sham single particle eigenenergies that can be used in any combination of exchange-correlation functionals. This technique has been successfuly applied to: explain the PES and transition to metallicity of magnesium clustersi and the PES and transition to half-metallicity in manganese clusters.

More recently we developed a new strategy to explain the role of size, composition, structure and symmetry in mixed-metal clusters. We applied this methodology to disintangle the effects in Al12-, Al13-, and NiAl12-.

Current collaborators

Julius Jellinek

Kit H. Bowen Jr.ek

Recent Publications in this Project

Paulo H Acioli, "Predicting the Photoelectron Spectrum of Al6Mo-, submitted to Int. J. Quant. Chem.

Paulo H. Acioli, Xinxing Zhang, Kit H. Bowen Jr., and Julius Jellinek, "Electron Binding Energy Spectra of AlnMo- Clusters: Measu rements, Calculations, and Theoretical Analysis", J. Phys. Chem. C (2018).

P. H. Acioli and J. Jellinek, "Theoretical Analysis of Photoelectron Spectra of Pure and Mixed Metal Clusters: Disentangling Size, Structure and Composition Effects", J. Chem. Phys. C 121, 16665-16672 (2017).


This work was supported by the Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, U.S. Department of Energy, under Contract DE-AC02-06CH11357.

Possible pathways of Al12- into Al13- and NiAl12-

Computation Simulations of Organic Conductors
Exciton diffusivity D (cm2/s) as a function of temperature T (K).
Organic conductors have palyed a remarkable role in the recent years. The use of polymers have reduced the cost of electronic devices, while being very versatile. For example the modern solar panels are not only inexpensive as they are flexible and can be manipulated in many different shapes. It is then importatn to understand the dynamics of charge transport in organic materials.

In our recent work we have made major contributions in the field. We have established the limit of exciton mobility in highly ordered π-conjugated systems. We studied the thermoelectric effects in organic polymers and we determined the different conduction modes in armchair graphene nanoribbons. Graphene is one of the hottest materials in terms of electronic and magnetic properties and is the driving force in the development of 2D materials.

These contributions are of high interest in the green energy technology as they are used either in organic photovotalic devices, transforming light into electricity or vice and versa, or using a temperature gradient to create a an electric current and vice and versa.

We are currently interested in study of vacancies in graphene nanoribbons as as the structural and magnetic proerties of Mobius graphene nanorribons.

Current collaborators

Prof. Demetrio da Silva Filho
Universidade de Brasilia - Brazil

Prof. Geraldo Magela e Silva
Universidade de Brasilia - Brazil

Prof. Luiz Fernando Roncaratti
Universidade de Brasilia - Brazil

Prof. Pedro Henrique de Oliveira Neto
Universidade de Brasilia - Brazil

Prof. Ricardo Gargano
Universidade de Brasilia - Brazil

Prof. William Ferreira da Cunha
Universidade de Brasilia - Brazil

Recent Publications in this Project

P. H. Oliveira Neto, D. A. Silva Filho, L. F. Roncaratti, P. H. Acioli, and G. M. e Silva Low-Temperature Seebeck Coefficients for Polaron-Driven Thermoelectric Effect in Organic Polymers, J. Phys. Chem. A 120(27), 4923-4927 (2016)

W. F. Cunha, P. H. Acioli, P. H. Oliveira Neto, R. Gargano, and G. M. e Silva Polaron Properties in Armchair Graphene Nanoribbons, J. Phys. Chem. A 120(27), 4893-4900 (2016)

P. H. Oliveira Neto, Demétrio A. da Silva Filho, W. F. Cunha, P. H. Acioli, and G. M. E Silva, The Limit of Exciton Diffusion in Highly Ordered π-Conjugated Systems , J. Phys. Chem. C 119,19654 (2015)


I thank the Universidade de Brasilia for the visinting professorship that allowed part of this work to be developed.

Thermoelectric current (left) and Seebeck coefficient (right) as a function of the temperature.

Polaron dynamics for 6x200 Armchair Graphene Nanorribon (AGNR)
subjected to 1.5 mV/Å electric field.

Interaction of DNA Nucleobases with Noble Metals Two possible structures of the Ag-adenine-thymine complex
The underlying mechanisms behind the double helix structure of the DNA are the formation of hydrogen bonds between complementary base pairs and the relative orientations of successive base pairs along two polynucleotide strands. These nucleotides carry the cellular information for replication and synthesis, thus playing a critical role in metabolism, cellular signaling and enzymatic activity. Drug therapies, particularly those that seek to enhance or inhibit the cellular activities facilitated by these nucleotides, work by the binding of site-targeted drugs to specific nucleotides to achieve this end. For example, atoms of heavy metals such as platinum and ruthenium play a key role in anti-cancer drugs that act as intercalating agents and preferentially bind the drug molecule to a nucleotide in DNA, thereby interfering with the process of normal synthesis and transcription of DNA. It is now well established that the platinum-based anti-cancer drug cisplatin (Cl2H6N2Pt), works by the binding of platinum to two 7N guanine sites, thereby causing intrastrand and interstrand cross-links, the basis of the drugs efficacy in fighting cancer by inhibiting further uncontrolled growth of the tumorous cells. In this project we are interested in investigating, using ab ibitio computations, alternatives to cisplatin. Systems of interest are small neutral and charged clusters of silver and gold.

Current collaborators

Sudha Srinivas - Faculty

Recent Publications in this Project

Paulo H. Acioli and Sudha Srinivas, "Silver- and gold-mediated nucleobase bonding", J. Mol. Model. 20(8), 2391 (2014).


We acknowledge the financial support provided by an Extramural Associate Research Development Award (EARDA) Type G11 grant (5G11HD049644-03) from the National Institutes of Health and administered by Northeastern Illinois University, Chicago, IL.

Two possible structures of the Ag-guanine-cytosine complex

Stable structures of gas phase a) guanine-Ag-guanine; b) guanine-Au-guanine; and c) guanine-Pt-guanine complexes

Small Clusters and Ligand Interactions Lowest Energy Structures of AgN, N=1,4
Metals and noble metals have an important role in catalytic processes such as those in the pharmaceutical, automobile and petroleum indistries. Catalysts have been used in the chemical industry for a long time, however an atomic level understanding of catalysis is still lacking and therefore catalysts have traditionally been developed on a trial and error basis. This picture has been changing recently, thanks to development of faster and more powerfull computers and quantum chemistry computational methods. These developments are allowing the computational modeling of metal and metal-ligand interactions and their role in heterogenous catalysis at reasonable costs.

We are currently interested in understanding the nature of bonding of ligands such as oxygen (O2), carbon monoxide (CO) and carbon dioxide (CO2) to small clusters of noble metals and its implications on catalys. We use density functional theory calculations to model the interactions between the clusters and the molecules, the structural and electronic properties of the cluster-molecule system. The long-term goal of this project is to understand how clusters of noble metals like silver interact with small ligand molecules to gain an insight into the catalytic properties of similar metals at a microscopic level.

Current collaborators

Sudha Srinivas - Faculty

Students Involved in the Project

Cesar Bustos
David Capotaq
John Gonzales
Biguun S. Woods

Greg Freimark
Steve Burkland
Indira Bambur
Michael Cline
Narin Ratanavade

Recent Publications in this Project

Paulo H. Acioli, Steve Burkland, and Sudha Srinivas, "An exploration of the potential energy surface of the seven atom silver cluster and a carbon monoxide ligand", Eur. Phys. J. D, 66 215 (2012).

This articles was featured on the cover of the August 2012 Issue of the European Physics Journal D.

Paulo H. Acioli, N. Ratanavade, M. R. Cline, and Sudha Srinivas, "Density functional Theory study of Ag-Cluster/CO Interactions", in ICCS 2009, Part II, Lecture Notes in Computer Science 5545, G. Allen et al., Eds., Springer-Verlag, Berlin-Heildelberg, 2009, pp. 203-210.


This work was partially supported by a NEIU - COR grant (2007-2008) and a NEIU-SCSE grant (Summer 2009).

Lowest Energy Structures of Ag(CO)X, X=1,3

Lowest Energy Structures of Ag2(CO)X, X=1,6

Lowest Energy Structures of Ag3(CO)X, X=1,6

Lowest Energy Structures of Ag4(CO)X, X=1,8

Computational Vibrational Spectroscopy C2v global minimum of the PES of H5+.
Vibrational spectroscopy can provide insight about the structure and reactivity of gas phase molecules. In particular, I am interested in studying the effects of impurities in the excited state spectra of helium clusters and in the general properties of the ground and excited states of H5+. In the case of He clusters, these systems have being studied in the past, but most of the studies were restricted to the ground state. I am interested in studying their excited states. The main goal is to understand the difference between the spectra of the pure He clusters and the spectra as an impurity is added. This study will focus in the energies of the excited states and in their pair density functions. The understanding of these differences at the molecular level is of great importance to shed light in such a fascinating systems, which display exotic properties such as superfluidity in bulk quantities. The main challenge to carry out such study is to solve the multidimensional integrals that appear in the eigenvalue problems defined by the time-independent Shrödinger equation. One can overcome such challenge with the use of correlation function quantum Monte Carlo (CFQMC), a technique that we have shown to be effective in treating the vibrational spectrum, beyond the harmonic approximation, of systems with more than four atoms. Quantum Monte Carlo techniques can be also utilized to study H5+. This molecule is of particular interest in the physics and chemistry of interstellar medium. It is a weakly bound complex important in reactions involving H3+ and H2. One of the questions is to decide if the complex, in its ground state is symmetric or if it resembles H2 bound to H3+. Another important aspect is to study the isotope effects when H atoms are replaced by deuterium.

Current collaborators

Prof. Joel M. Bowman
Emory University

Prof. Geraldo Magela e Silva
Universidade de Brasilia - Brazil

Prof. Ricardo Gargano
Universidade de Brasilia - Brazil

Dr. Angelo Marconi Maniero
Universidade Federal da Bahia - Brazil

Recent Publications in this Project

Angelo M. Maniero, Paulo H. Acioli, Geraldo Magela e Silva, Ricardo Gargano, "Theoretical calculations of a new potential energy surface for the H + Li2 reaction", Chem. Phys. Lett. 490(4-6), 123 (2010).

G. M. e Silva, R. Gargano, W. B. da Silva, L. F. Roncaratti, and Paulo H. Acioli, "Quantum Monte Carlo and Genetic Algorithm Study of the Potential Energy Surface of the H5+ Molecule", Int. J. Quant. Chem. 108 (13), 2318 (2008).

Paulo H. Acioli, Z. Xie, B. J. Braams, and J. M. Bowman, "Vibrational Ground State properties of H5+ and its Isotopomers from Diffusion Monte Carlo Calculations", J. Chem. Phys. 128, 104318 (2008).

A. M. Maniero and P. H. Acioli , "Potential energy curves of Li2 and LiH from a full configuration interaction pseudopotential procedure". Int. J. Quant. Chem. 103 , 711 (2005).


This work was partially supported by the National Science Foundation through Research Opportunity Award as Supplemental Funding to CHE-0446527 (JM Bowman - PI).

D2d saddle point of the PES of H5+.

HH pair distribution function of the H5+. The vertical sticks represent the bond lengths at the C2v global minimum (solid) and at the lowest D2d (dashed) saddle point of the PES.

Energy landscape of the reactants, intermediate complexes, and products for scattering reactions of H3+ and H2 and isotopomers.

Wind Power Generation A Wind Turbine Made of Recycled Materials
The ever growing development of new technologies demands a continuous growth in energy production. Traditional energy production relies heavily on fossil fuels. At the current production rate the known deposits of coal, oil, and natural gas are expected to last for 148, 43, and 61 years, respectively. In addition, fossil fuels have a harmful impact in our environment. For instance, it is estimated that 90% of the greenhouse effect emissions in the US come from the burning of fossil fuels. Hidroelectric power plants are cleaner but they have a huge impact in the environment. The impact can be physical or biological. These effects start during the construction of the dam and they can change river itself as well as the surrounding ecosystem. The blocking of the flow of water have also a huge impact as the land that gets flooded could be home of many endangered species, could have been used for residence or even agriculture. Nuclear power plants are somewhat clean during the production stage. However, there is a big risk of nuclear accidents such as the Chernobyl disaster in 1987 and the Fukushima I nuclear accident in 2011. To address the ever growing energy demand and to reduce the negative environmental impacts there is a push for cleaner and renewable sources of energy. Ethanol is a cleaner alternative to oil. However, large scale alcohol production for energy production does create other issues such as the use of land for non food producing agriculture. Solar and wind producing generators are a greener alternative. Although wind and solar farming also have negative environmental impact and the cost and efficiency are still far from ideal many governments are still promoting the construction of vast wind "farms," and encouraging private companies with subsidies and regulatory support. The goals of this project are: 1) to study the viability of the use of wind and solar generators around NEIU neighborhood; 2) To research the basic physics of electric power generation in general, and wind power generation in particular; 3) Design and build a wind power generator that would be adequate for low power applications in a urban environment; 4) Write a wind generation booklet to be distribute in local mid and high schools to aid students that are interested in developing renewable energy science projects.

Students Involved in the Project
Sergio Guerrero
Max Hansen
Thomas McLaughlin
Esosa Ogbomo
Steve Roothaan
Caroline Williams

Recent Presentations in this Project
Esosa Ogbomo, Thomas McLaughlin, Max Hansen, and Paulo Acioli, "Building a Wind Turbine from Recycled Components", Poster presented at the Annual SACNAS meeting, Seattle, Oct. 2012.

Steven Roothaan, Caroline Williams, Sergio Guerrero, and Paulo Acioli, "Optimization of H-Darrieus Vertical Axis Wind Turbine Design for Application in Urban Areas", Poster presented at the Annual SACNAS meeting, Seattle, Oct. 2012.

This work supported by a USDA-CREEAR grant.

Response of a Vertical Axis Wind Turbine in Turbulent Air

Last Updated: 4/01/2009 .
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