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Is anybody at the University of Manchester using SimCOAL or Bayesian Serial SimCOAL? I'm currently doing a lot of forward-time simulations of populations but could really benefit from someone giving me some pointers on how to translate these scenarios into SimCOAL scenarios Forward-time simulations allow one to specify starting conditions and demographic events but I would like to see if I can generate my starting populations by coalescent simulations taking the final populations as the baseline. This would allow me to check my results, but right now I'm having a hard time transposing the structure of my forward sims to a backward-sim format.

I am studying the solid-liquid interfaces. I created the solid-liquid coexistence system by combing solid part and liquid part with the same sectional areas together. Then the atoms in the solid were fixed, while the atoms in the liquid were allowed to move freely. The whole system reached equilibrium at a temperature above the melting point of the liquid. Then the system was slowly cooled down to a temperature below the melting point, which caused the liquid solidify. The problem was that the layers in the solidified structure as a whole move forward and backward in a plane parallel to the original solid-liquid interface. Why don't atoms in the solidified structure vibrate around their equilibrium sites? Why do they mainly move forward and backward along a particular direction?

Hello!

I am doing Erosion Simulation using a program called WEPP. I need to run more than 1000 scenarios in the Program. To make the work more efficient i need to learn Batch processing and Post processing of the results. And i want to learn this in R. I have used R for statistics and have begineer level knowledge about the problem but do not have programming background. I am willing to work hard but need someone to point me to the right direction about how i start and move forward.

Any help or Resources will be appreciated!

Thanks!

After completing of Protein-Protein docking in HEX programe how to go for MD simulations for the docking complex? How to calculate RMSD, RMSF plots in this programe?

I would like to pose a question that is relatively open. Computational simulation of fracture (crack initiation, crack growth and crack propagation including bifurcation and branching) is a very popular field in applied mechanics research. The complexities of the mechanics involved have prompted numerous approaches to modelling fracture such as eXtended FEM, Cohesive Zone Modelling etc., which have been applied to parallel simulations rather successfully.

For my part, I have been working on Continuum Mechanics based models, such as gradient modelling, phase field modelling, micromorphic modelling etc. The biggest advantage of using this type of approach is the possibility to develop a unified model that can simulate different mechanical processes as a material model (elasticity, plasticity, damage, heat transfer etc.), at various scales of the materials (nano-, micro-, meso- and macro-scale). Via my PhD work I am convinced that this approach to modelling is fairly robust in terms of handling coupled phenomena. Furthermore, it allows for a relatively easy implementation using standard FEM, with or without slightly modified elements (depending on the case).

The problem with these approaches lies in the parallelisation of the simulations. I am wondering if anyone in the RG community has had any experience, or has had any problems in attempting such parallelisation or has developed any algorithm to address this issue. If anyone has succeeded in parallel simulations, could you kindly indicate the numerical details of your simulations (if possible of course). For example, how many nodes, improvement in time observed, type of integration schemes used, elements used, global resolution algorithms used, time stepping techniques, error detection/correction, type of material tested etc. Looking forward to replies.

To be clear, by "parallelisation" I mean computing spread over different nodes on a cluster, which is not the same as "multi-threading", which is relatively straight forward to implement and is a completely different approach.

It would be great to hear from the community whether you have any experience (positive or negative) in applying gamification, simulations, and/or serious games in class.

Literature? Experience? Opinions? ... are most welcome ... Thank you!

Education 4.0 is a new educational paradigm designed to address the needs and opportunities of the fourth industrial revolution. Essentially, Education 4.0 is based on the concept of learning by doing, where students are encouraged to learn and discover different things in unique ways by experimenting [1]. In addition to the application of Industry 4.0 technologies, Education 4.0 relies on concepts such as gamification, simulations, and serious games [2].

Computer games that, in addition to their entertainment value, specifically promote the transfer of knowledge and skills or support behavioral changes are referred to as serious games. Serious games in education, especially at universities, have not yet been fully researched, although the pedagogical application of gamification, serious games, and computer simulations has long been known as an educational method and has demonstrably significant development potential [3, 4].

Recent studies, even before COVID-19, point to increasing numbers of users and an ever-greater integration of information and communication technology into existing educational processes [5, 6] in order to increase the attractiveness of teaching and learning [7-9]. Modern, well-designed learning games improve the user's problem-solving skills, enable effective learning, and can build bridges between theory and practical application by learning, retrieving, and assessing skills and knowledge in a positive, motivating, safe, simulated environment [10, 11]. In addition, game data can be analyzed relatively easily to provide useful information for measuring, assessing, and improving performance, but also for improving the learning environment [12].

Although interest in games in education has increased over the last decade, there is still much need for research on serious games and their effectiveness [13]. Moreover, theoretical and practical exploration requires interdisciplinary collaboration [14].

I am looking forward to your insights!

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the missing water molecules and save the updated PDB, PSF, and DCD files without having to rerun the simulation from scratch? Are there any methods to fill the uncovered protein areas with water molecules?

I have been using NAMD tool. I would be more than happy if you could suggest me and I am looking forward to hearing from you all.

#NAMD #VMD #water #trajectory #DCD #protein #membranr #CHARMMGUI

Dear Sir/ Ma'am,

The simulation I have run here is simple uniaxial tension test with Symmetric boundary contions in X,Y and Z on ABAQUS Explicit. This was done as a Test for a VUMAT code (Hyperelastic material with near incompressibility) that I had developed. The simulation starts with a loading phase, where the Stretch in X-direction is increased from 1 to 6, and a subsequent unloading phase coming back to the undeformed state. The analysis type is a Coupled Displacement + Temperature, with the C3D8RT (Reduced Integration) element type. The VUMAT code has been validated for a uniaxial tension 1-element simulation, but shows unrealisitic deformations during the unloading phase, when I use multiple elements (I have attached the pictures below).

What could be the causes for a change in solution after mesh refinement? Any help or inputs would be helpful, I look forward to your replies.

Different methods exist for simulating the dendrite formation in the solidifying metal, such as Level set, VOF, phase field and Cellular automata.

I want to know where do cellular automata method stands amongst these methods. What advantages and disadvantages it has as compared to other methods for dendrite simulations?

Looking forward to the discussion on this topic.

Hello all,

I am a Quantum espresso user and is aware of Boltztrap. But Boltztrap do not give us lattice thermal conductivity.!!! I found another code ShengBTE which gives this value but somehow didnot fully understood how to run it!!! anyone can help with this???