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Stochastic simulation of HIV population dynamics through complex network modelling

P. M.A. Sloot, S. V. Ivanov, A. V. Boukhanovsky, D. A.M.C. van de Vijver, C. A.B. Boucher
2008 International Journal of Computer Mathematics  
Acknowledgements The authors would like to acknowledge the financial support of the European Union through the ViroLab project (www.virolab.org), EU project number: IST-027446.  ...  We thank Breanndán Ó Nualláin (University of Amsterdam) and Alex Vespignani (Indiana University) for proofreading the manuscript.  ...  The various routes of infection and the inhomogeneity of the involved population pose additional problems [27] . Many mathematical models have been suggested to simulate HIV population dynamics.  ... 
doi:10.1080/00207160701750583 fatcat:rfzhpkkamrcqxiixaxc5nzgovi

Optimizing Protein Expression Levels as a Function of Network Topology Minimizes Nonfunctional Complex Formation

David O. Holland, Margaret E. Johnson
2015 Biophysical Journal  
We simulate the complex switching dynamics between the multiattractor states in these systems through direct sampling using continuous stochastic approaches Langevin dynamics and Fokker Plank equation  ...  The stochastic trajectories obtained through numerical simulations not only unveil the complex dynamics leading to multi-stability, they also help explore rigorously the variations, if any, in the dynamics  ... 
doi:10.1016/j.bpj.2014.11.1706 fatcat:l5ftkchjxvfjzmozweoq5ogriy

Designing Stem-Cell Based Anti-HIV Therapies using Molecular-Detailed Multiscale Models

Iraj Hosseini, Feilim Mac Gabhann
2015 Biophysical Journal  
We simulate the complex switching dynamics between the multiattractor states in these systems through direct sampling using continuous stochastic approaches Langevin dynamics and Fokker Plank equation  ...  The stochastic trajectories obtained through numerical simulations not only unveil the complex dynamics leading to multi-stability, they also help explore rigorously the variations, if any, in the dynamics  ... 
doi:10.1016/j.bpj.2014.11.1707 fatcat:gnba3on2rrc7ffx2scmjq7i7le

DNA Fluorescence Parameters and Methylation Levels of Gut Commensal Escherichia coli from Crohn's Disease Patients

Astghik Pepoyan, Marine Balayan, Anahit Manvelyan, Seda Marutyan, Lia Minasbekyan, Karlen Hovnanyan, Vardan Tsaturyan
2015 Biophysical Journal  
We simulate the complex switching dynamics between the multiattractor states in these systems through direct sampling using continuous stochastic approaches Langevin dynamics and Fokker Plank equation  ...  The stochastic trajectories obtained through numerical simulations not only unveil the complex dynamics leading to multi-stability, they also help explore rigorously the variations, if any, in the dynamics  ... 
doi:10.1016/j.bpj.2014.11.1708 fatcat:lc5xfwrsmnadtirqun4v42ydiy

Structural sensitivity in HIV modeling: A case study of vaccination

Cora L. Bernard, Margaret L. Brandeau
2017 Infectious Disease Modelling  
We illustrate the value of inference robustness assessment through a case study of the effects of a hypothetical HIV vaccine in multiple population subgroups over eight related transmission models, which  ...  Parameter complexity does not appear to play a consistent role in differentiating the projections of network models.  ...  Increasing our understanding of the link between macro-network assumptions, population size, and thresholds for aggregated compartmental models through simulation can help to inform modelers as to when  ... 
doi:10.1016/j.idm.2017.08.002 pmid:29532039 pmcid:PMC5844493 fatcat:7ia2uydngnhhrp5yhgih7rx6ty

P1-S4.19 Stochastic network models

P. A. Noel, A. Allard, L. Hebert-Dufresne, V. Marceau, L. J. Dube
2011 Sexually Transmitted Infections  
The model and an analysis of national data have been recently published in BMJ.  ...  Method We will give a live demonstration of our spreadsheet model using the example from our recent study.  ...  Methods We represent the interaction structure of the population with complex network models.  ... 
doi:10.1136/sextrans-2011-050108.163 fatcat:wlawt3kkafhslgawhim6iehqpu

NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model-Free Framework and Markov State Simulations

Junchao Xia, Nan-jie Deng, Ronald M. Levy
2013 Journal of Physical Chemistry B  
Using simulations of HIV-1 Protease as an example, we show how the populations of slowly exchanging conformational states as well as order parameters for the different states can be determined from the  ...  Calculating NMR relaxation effects for proteins with dynamics on multiple timescales generally requires very long trajectories based on conventional molecular dynamics simulations.  ...  MD simulations were carried out on the Gyges cluster at Rutgers supported by NIH shared instrumentation grants No. S10-RR022375 and S10-RR027444.  ... 
doi:10.1021/jp400797y pmid:23638941 pmcid:PMC3727231 fatcat:gtdo4vxbp5gpxh4kqzka6fiig4

Isolation, Fragmentation and the Detection of Listeria DNA from Ground Beef

Tonya M. Santaus
2015 Biophysical Journal  
We simulate the complex switching dynamics between the multiattractor states in these systems through direct sampling using continuous stochastic approaches Langevin dynamics and Fokker Plank equation  ...  The stochastic trajectories obtained through numerical simulations not only unveil the complex dynamics leading to multi-stability, they also help explore rigorously the variations, if any, in the dynamics  ... 
doi:10.1016/j.bpj.2014.11.1709 fatcat:7tlubbcs5jbrjmgq2xp4d4em2y

Noise Treatment in Models of Genetic Switches

Mahua Roy, Elizabeth L. Read
2015 Biophysical Journal  
We simulate the complex switching dynamics between the multiattractor states in these systems through direct sampling using continuous stochastic approaches Langevin dynamics and Fokker Plank equation  ...  The stochastic trajectories obtained through numerical simulations not only unveil the complex dynamics leading to multi-stability, they also help explore rigorously the variations, if any, in the dynamics  ... 
doi:10.1016/j.bpj.2014.11.1705 fatcat:lmcbiuycjrctncckngu4cmipja

A Complex Systems Approach to Evaluate HIV Prevention in Metropolitan Areas: Preliminary Implications for Combination Intervention Strategies

Brandon D. L. Marshall, Magdalena M. Paczkowski, Lars Seemann, Barbara Tempalski, Enrique R. Pouget, Sandro Galea, Samuel R. Friedman, Edward White
2012 PLoS ONE  
Conclusions/Significance: Complex systems models of adaptive HIV transmission dynamics can be used to identify potential collective benefits of hypothetical combination prevention interventions.  ...  Agents also interact with simulated HIV prevention interventions (e.g., syringe exchange programs, substance abuse treatment, HIV testing) and initiate antiretroviral treatment (ART) in a stochastic manner  ...  We hypothesize that the simulated interventions will decrease HIV prevalence, HIV incidence, and AIDS incidence in the agent population through the following pathways of action: 1.  ... 
doi:10.1371/journal.pone.0044833 pmid:23028637 pmcid:PMC3441492 fatcat:44p6n2pj25hf7dcemgddj5avmi

Stochastic effects are important in intrahost HIV evolution even when viral loads are high

E. L. Read, A. A. Tovo-Dwyer, A. K. Chakraborty
2012 Proceedings of the National Academy of Sciences of the United States of America  
.), Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard (A.K.C.), and a National Institutes of Health Director's Pioneer award (to A.K.C.).  ...  Thus, HIV infection is characterized by complex dynamics of host-virus interaction, which remain poorly understood.  ...  To this end, we report fully stochastic computer simulations of the CTL response to natural infection using simplified but realistic models of the fitness landscape of HIV.  ... 
doi:10.1073/pnas.1206940109 pmid:23112156 pmcid:PMC3511713 fatcat:jy7vlfuwtnaqvd7tkirets77se

Continuous Models of Epidemic Spreading in Heterogeneous Dynamically Changing Random Networks [article]

S. V. Ivanov, A. V. Boukhanovsky, P. M. A. Sloot
2012 arXiv   pre-print
Despite many results in the area of network modeling the selection of the best computational representation of the model dynamics remains a challenge.  ...  We successfully apply this approach to predict the dynamics of HIV-AIDS spreading in sexual networks, and compare it to historical data.  ...  PS also acknowledges support from the NTU complexity program.  ... 
arXiv:1211.4422v1 fatcat:r7wk4ybz3bbxvi6cskiabwwldq

Mathematical Modeling and Dynamic Analysis of Complex Biological Systems

Alain Vande Wouwer, Philippe Bogaerts, Jan Van Impe, Alejandro Vargas
2019 Complexity  
In their paper titled "Analytical Reduction of Nonlinear Metabolic Networks Accounting for Dynamics in Enzymatic Reactions," C. L.  ...  and a better understanding of the interplay between complex phenomena.  ...  In "Dynamical Analysis of Approximate Solutions of HIV-1 Model with an Arbitrary Order," Asma et al. generalize an AIDS/HIV model to a fractional order system.  ... 
doi:10.1155/2019/4858423 fatcat:apktcezpfrdybgy77dvbcrkvpu

Insights into the Dynamics of HIV-1 Protease: A Kinetic Network Model Constructed from Atomistic Simulations

Nan-jie Deng, Weihua Zheng, Emillio Gallicchio, Ronald M. Levy
2011 Journal of the American Chemical Society  
We develop a kinetic network model, constructed from detailed atomistic simulations, to determine the kinetic mechanisms of the conformational transitions in HIV-1 PR.  ...  The conformational dynamics in the flaps of HIV-1 protease plays a crucial role in the mechanism of substrate binding.  ...  Acknowledgments We thank Kristina Paris for providing the results of clustering experimental structures of HIV-1 PR.  ... 
doi:10.1021/ja2008032 pmid:21561098 pmcid:PMC3116037 fatcat:7ihqszs7ivenpaf7ea5tlg2geq

Surface Display of a Unique Enzyme as a New Reporter in Synthetic Biology

Felicia Y. Scott, Warren C. Ruder
2015 Biophysical Journal  
of population heterogeneity.  ...  To address this issue, we have developed a stochastic model for the intracellular genetic circuit controlling HIV latency and transactivation, and computed directly the steady state and time evolving probability  ...  of population heterogeneity.  ... 
doi:10.1016/j.bpj.2014.11.2536 fatcat:yexn5emf6ncttfjll5z3w6jwim
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