Science topics: Mathematical SciencesComputational Modeling

Science topic

# Computational Modeling - Science topic

Explore the latest questions and answers in Computational Modeling, and find Computational Modeling experts.

Questions related to Computational Modeling

**Most pharmacy students rated the use of complex molecular modelling or computational tools as useful for improving engagement and learning outcomes. Further, it significantly improves students' understanding of pharmacological concepts necessary for competency in medication management, based on significant improvements in post-test scores.**

**My concern is that if all the above mentioned/stated positive outcomes generated through the use of these pedagogical tools in some ways or other help to reduce the cognitive load or not? Do we have reasons to believe this? I am trying to establish the link between how 2D or 3D visualisation technologies and their relation to cognitive load management.**I want to do computational modelling of microstructure followed by property prediction. However, I don't know where to start and which methods to learn as primary level.

- I was wondering which model is the best fit to dopamine neuron? introducing some references also is very appreciated!

Does anyone know any simple and inexpensive proof that with the help of a spectrophotometer allows me to evaluate the biological activity of several components of an essential oil on the same enzyme?I am trying to correlate computational models (docking)(see attached document) and biological activity of compounds of essential oils

I would like to study the apo form (lipid-free) of a protein that only has been crystallized with lipids. I want to explore if it is possible to generate with a molecular dynamic a reasonable structure, making subtraction of lipids in several steps until obtaining the apo form. Likewise, I don't know if, during the molecular dynamic trajectory, it is possible to disappear lipids. I am thinking of using programs like GROMACS, AMBER, etc.

I want to start some chemical reaction calculations, but I need some basic reference to get started. Thank you in advance. Sincerely.

Hi,

I have three separate pdb (protein databank) files that each represent a different segment of my protein (ex. pdb1 has residues 1-20, pdb2 has residues 20-80 and pdb3 has residues 80-100) and I want to connect these to form one pdb file (pdb4 to have residues 1-100). Also note that I want to keep the secondary structure defined in my "middle" pdb file (pdb2). Can Pymol "attatch" my 3 pdb files? If so, how can I do this? I'm new to Pymol so any help would be greatly appreciated.

Thanks,

Thomas

Computational modelling

Machine learning-Artificial neural networks ,Support vector machine etc

I am working on a synthetic biology project in which I am redesigning the pathways in photosynthesis of

*Synechococcus elongatus*to become more efficient, evaluated by increase in biomass. We want to computationally model this in R but we are struggling to find packages that can help us with this. I've looked at deSolve::aquaphy which models C and N assimilation but photosynthesis rate is an input and we want to model this also.Hi, I've been an experimentalist throughout my career and I want to add to my knowledge and expertise in Materials Science by delving into computation, modeling and simulation. However, I'm very confused about where to begin as it appears that field of modeling and simulation is quite vast and expansive. If I had to choose a starting material type, I'd say composites and modeling of failure modes of composites. Can anyone guide me on where to begin? I'm a complete novice when it comes to anything computational. Where do I begin, if I'm starting from scratch.

Greetings all,

I am investigating the topic of emotional contagion. While there are numerous papers that refer to it as having the potential to spread similarly to an infectious disease, I have not yet been able to find any computation models that try to predict the contagion rate.

Essentially what I'm looking for is "are there any computational models that can predict the potential viral impact of a negative mood".

Thanks in advance for any assistance.

What has changed since this Pezzulo et al Paper?

All,

I am trying to equilibrate an Ice 1h crystalline structure to 250K in LAMMPS. When I tried to do this at 250K directly, the structure lost it's crystalline shape and became disordered post equilibration.

Based on the advise given by previous researchers who have worked with ice structures in LAMMPS, this should be done in small incremental steps from 10, 100, 150, 200, to finally 250K using a 0.5fs timestep. A minimum of 60ps relaxation is recommended at each temp.

Can anyone kindly help me understand what a script for this part of the simulation will look like? Below I post, the first few steps of the equilibration using fix npt (chosen after careful consideration of other ensembles and trials with fix nvt) as per my understanding. Please let me know if this looks correct. Any insight is appreciated.

**#First step equilibration at 50K***timestep 0.5*

*velocity all create 50 34455 dist gaussian mom yes rot yes*

*fix 1 all shake 1e-6 10 1000 b 1 a 1*

*fix 2 all npt temp 50 50 $(100.0*dt) iso 0 0 $(1000.0*dt)*

*thermo_style custom step temp pe ke etotal press vol density*

*thermo 1000*

*run 120000*

*unfix 2*

**#Second step equilibration to 100K***fix 2 all npt temp 50 100 $(100.0*dt) iso 0 0 $(1000.0*dt)*

*thermo_style custom step temp pe ke etotal press vol density*

*thermo 1000*

*run 5000*

*unfix 2*

**#Third step equilibration at 100K***fix 2 all npt temp 100 100 $(100.0*dt) iso 0 0 $(1000.0*dt)*

*thermo_style custom step temp pe ke etotal press vol density*

*thermo 1000*

*run 120000*

*unfix 2*

I am looking for a research paper about the mathematical or computational modelling of protein oxidation (caused by reactive oxygen species).. I would really appreciate that if someone helps me with this.

Hi, I am trying to create a computation model of acoustic plane wave propagation through multiple layers of fluid. What should be the appropriate boundary conditions in my fluid-fluid interface? Thank you.

We have used DOT to dock DNA to proteins but increasingly need to examine computational models for RNA docking onto proteins. Would appreciate advice and examples where this has proven successful.

I have been working on a project that requires the use of a protein-protein docking structure to generate a computational model of a protein interaction. I used pyDockWEB and have been trying to find some literature to help me understand their scoring method, but one question I have is that when I add restrictions to the model, the total binding energy is around -115, compared to just submitting the PDB files for a global search, the best model has a total binding energy of closer to -20, which seems crazy considering the amount of orientations they evaluate and can't create a model with any lower energy. Can anyone tell me why such a discrepancy exists?

I am starting a new lab this fall at Florida International University (FIU). Our lab will focus on

**understanding the neurocognitive processes that allow for the emergence of cognitive control**(how the human brain/mind monitors and adapts itself overtime to achieve task goals). Moreover, we will seek to understand how this system develops across adolescence, and relations to social behavior and social anxiety. Towards this end, methods that I currently employ, include: (single-trial) ERP analyses, time-frequency analyses of EEG (power and phase relations), source-localization of EEG, traditional fMRI approaches (GLM-based), and basic computational modeling (drift-diffusion models). Our lab is currently purchasing a high-density EEG system and FIU houses an fMRI scanner.I am

**seeking collaborators**that may or may not currently work in the fields of psychology or neuroscience, but that have at least some**expertise in one or more of the following domains: data science, advanced signal processing, machine learning, computational modeling, graph-theoretic/network analysis.***I am most interested in finding collaborators that can help generate the best science; location, status, affiliation, or degrees earned are not important.*I also intend to take on at least one PhD student this fall and welcome responses from prospective students.The scientific goal of this collaboration will be to combine skillsets in order to test novel hypotheses regarding the human cognitive control system, its developmental trajectory across adolescence, and relations to social behavior and social anxiety. At a practical level, we would seek to produce high-impact publications and to generate pilot data for pursuing collaborative grant proposals.

**Depending on the situation, initial funding may be available for potential collaborators, consultants, or contractors.**For examples of recent studies that will inform the work in our lab, please refer to the following publications:

I am starting a new lab this fall at Florida International University (FIU). Our lab will focus on

**understanding the neurocognitive processes that allow for the emergence of cognitive control**(how the human brain/mind monitors and adapts itself overtime to achieve task goals). Moreover, we will seek to understand how this system develops across adolescence, and relations to social behavior and social anxiety. Towards this end, methods that I currently employ, include: (single-trial) ERP analyses, time-frequency analyses of EEG (power and phase relations), source-localization of EEG, traditional fMRI approaches (GLM-based), and basic computational modeling (drift-diffusion models). Our lab is currently purchasing a high-density EEG system and FIU houses an fMRI scanner.I am

**seeking collaborators**that may or may not currently work in the fields of psychology or neuroscience, but that have at least some**expertise in one or more of the following domains: data science, advanced signal processing, machine learning, computational modeling, graph-theoretic/network analysis.***I am most interested in finding collaborators that can help generate the best science; location, status, affiliation, or degrees earned are not important.*I also intend to take on at least one PhD student this fall and welcome responses from prospective students.The scientific goal of this collaboration will be to combine skillsets in order to test novel hypotheses regarding the human cognitive control system, its developmental trajectory across adolescence, and relations to social behavior and social anxiety. At a practical level, we would seek to produce high-impact publications and to generate pilot data for pursuing collaborative grant proposals.

**Depending on the situation, initial funding may be available for potential collaborators, consultants, or contractors.**For examples of recent studies that will inform the work in our lab, please refer to the following publications:

Hello,

How to quantify the molecule induction effect? What parameters obtained by quantum chemical analysis of a molecule will help evaluate the molecule induction effect?

Say I am interested in examining individual differences in cognition and behavior and am interested in how specific survey scores and parameters predict/covary with performance on a task. How would I analyze this data based on the literature?

Are there conventional methods for analyzing differences in psychological phenomenon across individuals? Is that exactly what uni/multivariate statistics is for? Or are there alternative methods? Are there where advanced statistics comes in?

Is it more compelling and/or informative to analyze individual differences in a single subject design, an aggregate model/submodel (GLM), or as a dynamical system?

What does the basic and current literature say? What papers or books explicitly discuss this?

Thanks,

JD

Dear Colleaugues,

There was a proposal of a researcher who asked me to write down a paper which will more or less extend the poster (link bellow) published at ICCB 2016 in Prague. This all happened by an accident. I did not like to come at a conference without some presentation. Hence, I did quickly put the ideas that are resonating in my head for years on that poster to allow other researchers to benefit from it. Surprisingly, this poster is getting a great deal of attention. Therefore, I am thinking about to write down a review (prescription) how to design sel-organizing and emergennt systems with a rich example aparatus. If you like the idea then wisit the poster and let there a comment about it (bellow the poster).

The whole project is meant as a service to the community of biological and medical researchers who would like to know more but have no time to study mathematics and programming in depth.

All the best at your research,

Jiri

Knowing the best computational modeling for simulation of Masonry ARCH with BACK-FILL using Discrete Element Method (DEM)

I would like to ask whether there exists a computational model that explains the complex interactions between Brainstem structures and Limbic system?

I am new to hyper-elastic modelling.I have performed curve-fitting for Neo-Hookean and Mooney-Rivlin model using experimental data obtained from shear test. Now I am required to approximate the material parameters of Holzapfel-Gassar-Ogden model.From this literature, https://pdfs.semanticscholar.org/d166/eab636ec656cec025a28671285f0909c17bc.pdf I could find the equation 3.27 but have few questions,

In equation 3.27, how to find the value of (B + m ⊗ m), I4 and I1 ?

My material is an incompressible biological tissue.

How can we find the material parameters of HGO model ?

Hello

I decided to work on computational model of motivation for my project. I have problem to find a proper dataset, would you help me how can I find this?

Best Regards

Fateme Saberi

Hello all,

I am working on computational modeling of bone internal microstructure. I was wondering if any sample micro-CT data sets available/shared

Thanks,

I want to model the interaction between

**different oxidation states of iron**and a ligand for optimization and calculation of energy, and wonder how I can define these states with Spartan, Gaussview,....All what I can do is defining whether the complex is tetrahedral or octahedral, but not the oxidation state. Any ideas?

Hi,

I am R.Thiruchelvi currently working red algae on my research.My research is to characterisation of sulphated polysaccharides from red algae and to study antitumor activity both invitro and invivo.

I have come across the computational modelling in algae research. May i know in deep where i have yo start? What concepts involve in modelling of algae research?

Can u explain so that it will be very useful for me to update in this field.....

I am performing a sequence of modeling steps using Spartan which takes a long time, and wonder if I can pause the calculations, and run again from the end point.

I could only export stress at nodal/integration points. But, I want to find the volume average of the stress over the element. I was wondering can elemental stress be obtained directly from ABAQUS?

We believe that in the future Data Science Methods will be considered as a powerful tool, which supports an interchange between experiment, computer simulation, and engineering calculation. We invite those who are interested in the creation of Multifactor Computational Models of the Energetic Materials Combustion and Detonation to joint research.

This is needed for a computational model (multi-agent) of behaviour of smokers in NSW Australia.

In order to model how energy distributions on nerve endings become percepts about surfaces and objects, there is a hard 'binding problem'. There are no computational models of binding that I know of. Will this project attempt one?

Dear all,

Please provide some good help / reference documents or texts to understand the Finite Element Analysis using getDP tool .It would be great if anyone can provide the detailed step-by-step procedure to work on the getDP tool as I am a beginner in the field of Finite Element Analysis.

Thanks,

Raghu

Greetings,

Can you recommend any modern article on interactions and

**steric**forces between two or multiple**magnetic**nanoparticles with brushes in a**nonpolar**solvents? preferably computational model and more mathematical/physical.Thank you,

Factors

· Formalization

· Structure

· A first attempt

· A simple transducer

· The ultimate computing model

· transition function

· auxiliary Memory

I'd like to analyse asymptotic data using the nlme package in R but cannot figure out how to specify two crossed random effects (instead of nested random effects).

The data comes from a computational modelling study. The dependent variable is test accuracy as predicted by time (iteration) and the random intercepts should be network and trial. I'm using the following code for the base model:

base_model <- nlme(accuracy ~ SSlogis(iter, Asym, xmid, scal),

data = test,

fixed = list(Asym ~ 1, xmid ~ 1, scal ~ 1),

random = Asym + xmid + scal ~ 1 | network,

start = initialParams)

I know that it's easier to specify nested random effects in nlme so I tried to create a dummy variable (with the same value for all observations) to then specify two random effects, which are both nested in the dummy variable. However, I couldn't really figure out the syntax for that either.

I'd be happy to hear any thoughts on that. Or if you have an idea on how to analyse the data without using nlme, please let me know.

Thanks a lot in advance.

I want to know what according to you is one among the best methods or concept in complex mathematics which you use or used to exploit or simplify problems or use to build computational models.

Dear researcher,

In regard to disease modeling methods,

A. Is there a precise taxonomy of disease modeling methods? If not, what are your suggestions?

B. How do expand these methods with details in a hierarchical structure?

For example:

1- in vivo model

1-1 animal model

1-1-1 rat model

1-1-2 mice model

2- in vitro model

3- in silico model

3-1 mechanistic model

3-1-1 integrative model

3-1-2 causal model

3-2 quantitative model

3-2-1 statistic model

.....

Best regards

We developed an application for

**Mathematical and Computational Modelling of the Tumor Growth Based on Evolutionary Aspects of Hypoxia and Acidosis on the Microenvironment of Cancer Cells**.This application has the potential to be used in the study the growth pattern of the different cancer phenotypes, the clonal evolution of tumor, the tumor heterogenicity, Multi Drug Resistance and interactions of cancer cells and their microenvironment.You can find more details about the project in the link below.

I would like to ask, how we can label and define each cell is this kind of models to understand to know the origin of each cell, lifetime, and similar cells which create clones and generally how we can define clones in the mathematical models?

We applied a great idea to this question but I didn't find any similar approaches. Therefore, I will thankful if there is anyone who can help us to get more info.

I would like to model each concentrations of the same inhibitor. I've not really seen any article where this is done through molecular modelling software. Though, I'm thinking this might be possible through changing the solvent dielectric constant, I'm not sure. I need guidance please. Thanks.

Hello. If you know some references about heterogeneous-agent stochastic OLG model with idiosyncratic risk and incomplete markets, tell me please. (Other than Huggett 1996 JME)

A computational model is even better but an analytical one is also good.

When is DMA( Dynamic Mechanical Analysis) Experimental data, not a good choice in predicting exact Visco elastic behavior(Relaxation and Creep) of short fiber reinforced thermoplastics?

I was trying to model the behavior of concrete for its possible crack propogation, i was planning to use smeared crack and cohesive zone models in ABAQUS. Do i need the experimental data to input the required parameters? If not do suggest suitable way to get the input data.

While modeling amorphous materials computationally, I have seen papers using periodic boundary conditions. But glasses/amorphous materials doesn't have any periodic nature. Is it some kind of approximation? Or do we have some other way to model aperiodic materials?

Lets assume the data were pulled from an assumed normal distribution although due to not enough data points the distribution is more or less skewed.

Is it unwise to combine raw data with averaged data to train models and why?

Hi everyone!

I'm working with a dataset with imagery movement and I want extracted the features using ERS/ERD. It is possible?

I'm trying to compute these features following the paper of Bernhard and Graimman, (see attach file), but I don't understand how it could be used like features. Also, how can i plot the ERS/ERD. ?

Attach a piece of code that computes the ERS/ERD for alpha band. (I'm using EEGLAB)

Thanks !

I am trying to create a threshold where the difference between the feature vectors of two different images of same person should be below that threshold while two different people must cross that threshold. What measure of comparison should i use to to find this threshold. As of now i subtract the two feature vectors and calculate the resultant's magnitude which turns out to be a very big number for same people and that there is no pattern in it. Sometimes for different people it will be a smaller number. What mathematical function can i use for this? I would be thankful if you could provide me some help on this.

Regards

I am using a tool Brian Hears of a program called Brian (it runs on Python ) to create a computational model of the ear and part of afferent fibers to the inner hair cells . At the end of the simulation I export a .dat file that contains the numbers of neurons that generated the spike and the time at which they were generated . Unfortunately, the time in which the spikes are generated is indicated in ms or in sec . Is it possible to start to export the spike timing with a uniform measurement units , it means all the spike timing in ms or seconds ?

Logistic growth describes somes phenomena (for example, population growth, bubble markets, tumor growth, etc) but the current models don't consider an abrupt fall ("crash"). Tsoularis et al (1997) suggested the "Generalized Logistic Growh" with four or five parameters but none of the linked equations (Blumberg, Bertalanffy, etc) simulate this situations.

Individuals are often taken as agents, with its specific characteristics and criterion. Butm is it posssible to consider groups as individuals, and their agragated characterisitcs as a sigle unit?

Neural network output should be in the form of equation? Or number? In Response Surface Methodology (RSM) either a single order or second order equation can be used as fitness function for PSO. But ANN output for PSO?

are there differences between math model and regression equation, and are math model build on theory while regression equation build on experimental result?

i am working on a method for synthesis of functions to using of Majority and NOT gates. i see papers that are in field reversible circuits and QCA. in this papers for evaluation of functions synthesized to Majority and NOT gates , the numbers of constant inputs is computed then is used from LANDAUER formula. but in qca is allowed to use from fanout. so, to use of fanout, the numbers of constant inputs are two, 0 and 1. why must all constant inputs is computed?

My pharmacophore modeling experiment in Accelrys Discovery Studio constitute 36 actives and 43 inactives as validation set towards one pharmacophore hypothesis (2 HBA, 1HBD and 1 hydrophobe). I got predictions in 2 models:

Model 1: True Positives=34 True Negatives=11 False Positives=32 False negatives=2 Sensitivity=0.94 Specificity=0.25

Model 2: True Positives=36 True Negatives=2 False Positives=41 False negatives=0 Sensitivity=1.0 Specificity=0.04

Which one Pharmacophore model you will recommend to select me for further analysis? Specificity is more important than sensitivity or vice versa. Please give valuable suggestions.

For instance, FLAME, MAMID, EMA, GRACE are computational models of emotions. What are the different parameters on basis of which, output of these models can be compared.?

What are the different ways to validate such model?

In finite Element Modelling, what material model is best for modelling steel frame and RC frame?

is there any comprehensive computational, or formal model (and/or visual representation) for Generalized Anxiety Disorder or any other mental disorder or disease?

Suppose I have the dispersal kernel (frequency distribution of individuals across space after a dispersal event i.e. x-axis: distances from a common origin (binned) and y-axis: frequency of individuals present at the corresponding distance-bin) for two populations of one species. How can these two kernels be compared quantitatively and inferred whether they are statistically same or different?

Dear all,

there are different studies supporting the hypothesis that the vertebrate motor system produces movements by combining a set of building blocks named motor primitives or motor synergies.

One year ago, Levine and colleagues identified classes of interneurons in the mouse spinal cord that could support motor primitives in mammals (http://www.nature.com/neuro/journal/v17/n4/full/nn.3675.html).

I'm developing a computational model of the spinal cord and i would like to take into account these kind of networks but it seems that at the moment none know how to implement the motor primitives by a neurobiological point of view.

In particular, i want to investigate the role of this kind of spinal circuitry in the execution of reaching movements. D'avella and colleagues have shown (just for example here https://www.researchgate.net/publication/5818579_Combining_modules_for_movement) how a reaching movement can be decomposed in a linear combination of muscle synergies but it's a mathematical model.

Can you suggest me any papers that can help me to model a motor primitive circuitry?

Thank you for your support,

Antonio

Article Combining modules for movement

Is there any good books or resources on Agent-Based Modeling?

Evaluation of a surface equation of state generally involves an evaluation of its ability to represent raw experimental data, or information derived from such data. The parameters of the equation have been adjusted to

optimize this representation, they are followed by an evaluation of the physical reasonableness of the optimizing parameters

in terms of the physical model on which the equation of state is based.

I have a complex geometry and there is no node connectivity as for transferring lodes I think it is necessary. There are more the 400 instance in it so partition and meshing every is very tedious I have tried both dependent as well as Independent meshing but unable to merge. Is there any method in which it can be merged easily.

Thanks in advance

CATIA has wireframe and surface design workbench and generative shape design workbench.

Let me describe my task in short.

I've created the electronic map of forestry, which includes a set of objects (polygons) of different nature, such as forest plants, roads, lakes etc. Each object is homogeneous. I have to write a program for mapping the dynamic of fire contour on the map. I’m going to use Rothermel’s model, because I have all input data for this model. But this model is good for homogeneous terrain, but my terrain is heterogeneous. I’m looking for the information, how Rothermel’s model can be adjusted to solve my task. Can anyone help me with the information on this question? Maybe there are other models, appropriate for programming... I would be grateful for any help.

Tools especially for trust evaluation based on the log details and feedbacks.

Can anybody help me to find out birefringence value of Paclitaxel (Toxol), ordinary and extraordinary refractive index values, for computational modelling in COMSOL?

Thanks,

Mahendar.

I am looking for a way to connect the order parameter to the changes in the mass.

I am modeling a steel bridge by OpenSees. I have to model it with ndm 3 and ndf 6 and using ForceBeamColumn elements because have to model frames. But I want to release the end moments of other members (bracings) to behave as truss elements.

I tried assigning a ZeroLength element for one member and it gives following error in eigenvalue analysis-

"

**FullGenEigenSolver::solve() - the eigenvalue 83 is complex with magnitude 81246.8****ProfileSPDLinDirectSolver::solve() - aii < minDiagTol (i, aii): (81, -3.37889e-027)**

**WARNING NewtonRaphson::solveCurrentStep() -the LinearSysOfEqn failed in solve()**

**DirectIntegrationAnalysis::analyze() - the Algorithm failed at time 0.0001**

**OpenSees > analyze failed, returned: -3 error flag**"

My question is how to release end moments with Zerolength elements. Though it can be done, also it is difficult to assign ZeroLength elements because there are large number of members in a bridge. Are there any other methods to release ends.

Please advise me.

I am working on invariant object recognition problem. Now, i required to compare my model with CNNs. I am looking for an open source code for CNNs. Please let me know if there is open code for CNNs.