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How does generative AI technology help in scientific research, developing research projects, conducting scientific research, collecting research data, processing data collected from scientific research and developing the results of research work?
From many data, situations, examples, etc., it is clear that generative artificial intelligence (AI) technology significantly supports scientific research at every stage of its implementation, from concept design to the development of results. In the preparation phase of research projects, generative AI can help analyze scientific literature quickly and comprehensively. Natural language processing algorithms make it possible to search for relevant publications, identify key trends in the literature and pinpoint research gaps. This allows researchers to create more precise research questions and legitimate hypotheses, which is crucial to the quality and value of research. But does generative artificial intelligence technology help research mainly in terms of processing large data sets in a relatively short period of time, or is it also helpful in many other issues of ongoing scientific research? And how about the ethics and objectivity of conducting scientific research? Does generative artificial intelligence technology help with these issues as well?
I described the key issues of opportunities and threats to the development of artificial intelligence technology in my article below:
OPPORTUNITIES AND THREATS TO THE DEVELOPMENT OF ARTIFICIAL INTELLIGENCE APPLICATIONS AND THE NEED FOR NORMATIVE REGULATION OF THIS DEVELOPMENT
Please write what you think in this issue? Do you see rather threats or opportunities associated with the development of artificial intelligence technology?
And what is your opinion on this topic?
What is your opinion on this issue?
Please answer,
I invite everyone to join the discussion,
Thank you very much,
Warm regards,
I would like to invite you to join me in scientific cooperation,
Dariusz Prokopowicz
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New Challenges in Scientific Publications: Referencing, Artificial Intelligence and ChatGPT
"The COVID-19 pandemic has led to a surge in scientific publications, some of which have bypassed the usual peer-review processes, leading to an increase in unsupported claims being referenced. Therefore, the need for references in scientific articles is increasingly being questioned. The practice of relying solely on quantitative measures, such as impact factor, is also considered inadequate by many experts. This can lead to researchers choosing research ideas that are likely to generate favourable metrics instead of interesting and important topics. Evaluating the quality and scientific value of articles requires a rethinking of current approaches, with a move away from purely quantitative methods. Artificial intelligence (AI)-based tools are making scientific writing easier and less time-consuming, which is likely to further increase the number of scientific publications, potentially leading to higher quality articles. AI tools for searching, analysing, synthesizing, evaluating and writing scientific literature are increasingly being developed. These tools deeply analyse the content of articles, consider their scientific impact, and prioritize the retrieved literature based on this information, presenting it in simple visual graphs. They also help authors to quickly and easily analyse and synthesize knowledge from the literature, prepare summaries of key information, aid in organizing references, and improve manuscript language. The language model ChatGPT has already greatly changed the way people communicate with computers, bringing it closer to human communication. However, while AI tools are helpful, they must be u​s​ed carefully and ethically. In summary, AI has already changed the way we write articles, and its use in scientific publishing will continue to enhance and streamline the process."
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Hello fellow researchers and devs. First of all, I would like to thank you for taking the time to participate in this discussion.
Based on your experience of programming with Python, which IDE do you currently prefer for programming with Python?
In my case and after testing other IDE's for Python like VScode, right now I am using a lot of the Spyder IDE for Python 3, mostly for its quick feedback at the time of experimentation and amazing collaborative github community.
So I would like to know your preferred Python IDE.
Regards.
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I recommend Visual Studio Code. Its the best
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In your opinion, what is the greatest role, function, importance, etc. of the development of international scientific cooperation?
International scientific cooperation plays an important role in the development of science and scientific research. In recent years, the development of online knowledge bases, online indexing databases of scientific publications, online science portals facilitates the development of international scientific cooperation. During the Covid-19 pandemic, the scale of remote communication conducted via the Internet increased significantly. The scale of realization of scientific conferences and symposia remotely through online video conferencing platforms has increased. With online science portals enabling discussions, the development of scientific cooperation on an international scale has been facilitated. Thanks to the aforementioned online science portals, i.e. this Research Gate portal, it is possible to set up and operate international research teams, where researchers and scientists operating in different countries can conduct collaborative scientific research, exchange experiences from their research, jointly publish the results of their research work in scientific articles and monographs. I hereby inform you that I am open to scientific cooperation, including scientific cooperation carried out internationally. I invite you to publish the results of the conducted scientific research in a scientific journal:
"International Journal of Legal Studies" (ISSN 2543-7097):
Legal sciences, normative aspects of various issues, various issue described in normative terms:
Publisher: International Institute of Innovation "Science - Education - Development" in Warsaw
"International Journal of Legal Studies" is a scientific journal published semi-annually (semiannual). After the publication of each issue of the journal, all articles are posted in a number of databases for indexing of scientific publications in the formula of open access. This significantly increases the visibility of articles on the Internet and translates into higher citability.
I invite you to join me in scientific cooperation.
I invite you to contact me by email: darprokop111@gmail.com
In view of the above, I address the following question to the esteemed community of scientists and researchers:
In your opinion, what is the greatest role, function, importance, etc. of the development of international scientific cooperation?
In your opinion, what is the greatest role of international scientific organizations?
What do you think about this topic?
Please answer,
I invite everyone to join the discussion,
Thank you very much,
Warm regards,
Dariusz Prokopowicz
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Interesting question.
If I had to answer in one sentence - their role is to reduce the costs of cooperation.
Best regards,
Kamil.
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By now, we've all realised how well GPT AI is able to find and replicate patterns in language and in 2D images. Its ability to find and interact with data patterns sometimes allows it to answer questions better than some students.
I expect that right now there will be teams training GPT installations with molecular structure and physical characteristics data to try to find candidates for new materials for high-temperature superconductors, or to find organic lattice structures with high hydrogen affinity to replace palladium for hydrogen storage cells. The financial and social rewards for success in these areas make it difficult to justify NOT trying out GPT AI.
But what about fundamental physics theory? Could AI find a solution to the current mismatch between Einstein's general relativity and quantum mechanics? Could it start to solve hard problems that have defeated mainstream academia for decades? If so, what happens to the instiutions?
Further reading:
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AI might have trouble giving us a new theory of physics directly, because (as you say) it'll be encoded with all the mistaken assumptions that are already preventing humans from finding a new theory.
But what AI should be able to do is to find the mistakes (or, a least, find "mistake-candidates"). If we tell it that a theory has a mistake, it'll dutifully report back what it thinks the mistake might be.
Suppose that we train an AI to find inconsistencies and paradoxes and contradictions, or missing logical steps in a block of text representing a "story". This "story" could be a novel, or a history of World War One, or a physics theory. The AI may go through the text and identify a huge list of provisional entities (perhaps hundreds of thousands of them), then tentatively associate entities with each other with a confidence rating ("Simon" in chapter one is probably the same "Simon" that appears in Chapter Two). It can then use its understanding of language to create a web of interrelationships between those entities.
The AI could be trained on simple stories that have obvious contradictions. Different types of contradictions may show up in a network as distinctive topological features: a Moebius-strip-like structure in the network may represent the ability of the story to generate one logical output if we go around the network one way, but to assign a different logical status to the same node if we traverse the network another way. The AI could then look for these possible topological network features and rank them according to the confidence rankings of the connections reponsible for the features.
One could feed in all known accounts of World War One, and identify where different sources appear to give conflicting information.
A whole web of spurious "lightweight" possible inconsistencies might be due to "frivolous" or "bad faith" misconnections and misidentifications between entities, created by software that is looking for problems. With these resolved, we may have a set of more heavy-duty apparent inconsistencies due to resolvable ambiguities in the text. With these eliminated, there might be some ambiguities that cannot be resolved, in which case the ambiguities are hiding structural conflicts in the theory. And there may also be some real, explicit structural conflicts that are not caused by ambiguity, but have been missed because they only appear as global features.
So once you've trained an AI to hunt down logical inconsistencies, and you give it a set of texts on general relativity, it might report:
  1. " MTW and a range of other high-confidence sources say that if inertial physics is correctly described by SR, a forcibly-accelerated body MUST NOT be associated with intrinsic curvature. "
  2. " Einstein is another high-confidence source. His 1921 Princeton lecture says that according to GR principles, and the GR equations, a forcibly-accelerated body MUST be associated with intrinsic curvature. "
  3. " Einstein's writings defining the structure of GR say that it must both conform to the general principle (giving outcome #2), but must also conform to special relativity (giving outcome #1) "
  4. " Since outcomes #1 and #2 represent two contradictory connection states of the same two nodes, either the two nodes can support multiple connection states, or one of the authoritative sources is wrong, or the entire theory is pathologically misconstructed. "
So an AI ought to be able to highlight the fact that, logically, either Einstein didn't understand the correct behaviour for his theory and got it wrong, or GR textbooks don't understand the correct behviour of SR and get it wrong, or Einstein was wrong about SR being able to be a component of GR.
AI can force us to accept that the existing system doesn't work (a fact that seems to have eluded academic human brains for over a century), and once we've accepted that, humans can examine the nature of the breakdown and use what they learn from it to construct a better theory.
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Can Big Data Analytics technology be helpful in forecasting complex multi-faceted climate, natural, social, economic, pandemic, etc. processes?
Industry 4.0 technologies, including Big Data Analytics technology, are used in multi-criteria processing, analyzing large data sets. The technological advances taking place in the field of ICT information technology make it possible to apply analytics carried out on large sets of data on various aspects of the activities of companies, enterprises and institutions operating in different sectors and branches of the economy.
Before the development of ICT information technologies, IT tools, personal computers, etc. in the second half of the 20th century as part of the 3rd technological revolution, computerized, partially automated processing of large data sets was very difficult or impossible. As a result, building multi-criteria, multi-article, big data and information models of complex structures, simulation models, forecasting models was limited or impossible. However, the technological advances made in the current fourth technological revolution and the development of Industry 4.0 technology have changed a lot in this regard. More and more companies and enterprises are building computerized systems that allow the creation of multi-criteria simulation models within the framework of so-called digital twins, which can present, for example, computerized models that present the operation of economic processes, production processes, which are counterparts of the real processes taking place in the enterprise. An additional advantage of this type of solution is the ability to create simulations and study the changes of processes fictitiously realized in the model after the application of certain impact factors and/or activation, materialization of certain categories of risks. When large sets of historical quantitative data presenting changes in specific factors over time are added to the built multi-criteria simulation models within the framework of digital twins, it is possible to create complex multi-criteria forecasting models presenting potential scenarios for the development of specific processes in the future. Complex multi-criteria processes for which such forecasting models based on computerized digital twins can be built include climatic, natural, social, economic, pandemic, etc. processes, which can be analyzed as the environment of operating specific companies, enterprises and institutions.
In view of the above, I address the following question to the esteemed community of researchers and scientists:
In forecasting complex multi-faceted climate, natural, social, economic, pandemic, etc. processes, can Big Data Analytics technology be helpful?
What is your opinion on this issue?
Please answer,
I invite everyone to join the discussion,
Thank you very much,
Best wishes,
Dariusz Prokopowicz
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Dear Dariusz
The simple answer is YES!
The problem, however, is that the analytics are imperfect...
It is necessary to understand how human intuition (expert intuition) works... I am convinced that understanding the mechanisms of intuition holds great potential for improving analytics and forecasting...
My own research shows that nature has found genius ways to deal with radical uncertainty with limited resources...
Yurii
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Dear Colleagues and Friends from RG,
What are the main problems in the development of science?
What are the key problems of research development?
What are the limitations for research work?
What do you think are the main problems with publishing research results?
Are these financial constraints or other problems?
How can these problems be solved?
What do you think about it?
What's your opinion on this topic?
Please reply,
I invite everyone to the discussion,
Thank you very much,
Best regards,
Dariusz Prokopowicz
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Dear Gioacchino,
Yes, that is correct. When debates are conducted in the popular meanstream, politicised media, scientific data are rarely taken into account, scientific findings are rarely used reliably and objectively as arguments to support specific theses.
Thank you very much,
Greetings,
Dariusz
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Hello everyone,
I am looking for links of Mexican datasets that can be used in classification tasks in machine learning. Preferably the datasets have been exposed in scientific journals.
Thank you for your attention and valuable support.
Regards,
Cecilia-Irene Loeza-Mejía
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Can you translate Vietnamese to Mexican datasets? https://www.researchgate.net/post/Can_you_show_me_Vietnamese_datasets
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There is probably no other science portal that would offer all the same functions for researchers as the Research Gate portal.
Do you agree with me on the above matter?
In the context of the above issues, I am asking you the following question:
Does the Research Gate research portal offer the most information services for researchers that researchers and scientists need?
Please reply
I invite you to the discussion
Thank you very much
Best wishes
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A bit too much of the results is presented on Researchgate with the lack of the backyard and preparation process for research. It could be good to see also the kitchen of the dinner of the researchers.
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Dear Friends and Colleagues from RG,
I wish You all the best in the New Year. I wish you a successful continuation and successes in scientific work, achieving interesting results of scientific research in the New Year 2019 and I also wish you good luck in your personal life, all the best.
In the New Year, I wish You success in personal and professional life, fulfillment of plans and dreams, including successes in scientific work, All Good.
In the ending year, we often ask ourselves:
Have we successfully implemented our research plans in the ending year? We usually answer this question that a lot has been achieved, that some of the plans a year ago have been realized, but not all goals have been achieved.
I wish You that the Next Year would be much better than the previous ones, that each of us would also achieve at least some of the planned most important goals to be achieved in personal, professional and scientific life.
I wish You dreams come true regarding the implementation of interesting research, I wish You fantastic results of research and effective development of scientific cooperation.
I wish You effective development of scientific cooperation, including international scientific cooperation, implementation of interesting research projects within international research teams and that the results of scientific research are appreciated, I wish You awards and prizes for achievements in scientific work.
I wish You many successes in scientific work, in didactic work and in other areas of your activity in the New Year, and I also wish you health, peace, problem solving, prosperity in your personal life, all the best.
Thank you very much.
Best wishes.
I wish you the best in New Year 2019.
Happy New Year 2020.
Dariusz Prokopowicz
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Dear Colleagues and Friends from RG,
Hello Dear Everyone,
In the New Year of 2021, I wish all researchers, scientists and users of the Research Gate portal fulfill their plans and dreams, success in their professional work and personal life, success in the field of research and publication of their results, all the best. I wish all my colleagues and friends from the Research Gate portal that the New Year 2021 will be better than the previous years, that the SARS-CoV-2 (Covid-19) coronavirus pandemic ends as soon as possible, that there is a quick return to "normal", to the pre-pandemic state . The year 2021 begins a new decade of many new challenges related to solving key problems of the development of civilization, solving problems resulting from the pandemic crisis, economic, social and climate crises, etc. Let us hope that the development of science, further scientific research, new technologies, the current fourth technological revolution will enable the solution of key problems of civilization development.
Happy New Year 2021
Best regards, Stay healthy!
Dariusz Prokopowicz
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I need to multiply the inverse of a matrix A to another matrix B. If B were to be a vector, I would simply solve a linear system Ax = B to get the product x=inv(A)B. With B being a matrix, I don't know the most efficient way|method to compute inv(A)B.
Kindly share your experience.
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As your system matrix most probably is sparse, you might be better off with numerical linear algebra routines especially designed for large, sparse matrices. I did stuff on that in the late 80s, through the Cray-2 machine, but there must be more streamlined ways to do it nowadays. (In those days one had to "cut" the lengths of the vectors in order to match the smartest size of sub-vectors for the linear algebra routines, but nowadays that will most surely be automatic, to a degree, nowadays.) Talk with numerical linear algebra experts, and they will help you.
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I couldn't see any options to show complete axes of 3D plot in MATLAB software ?
There is option to tick Box. But it doesn't covers top axes in
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the best answer is set(gca,'box','on') but in this situation the you add axis. if you want to change the thickness of axis, therefore
set(gca,'linewidth', 2) 2 can be change to an arbitrary thickness
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In which areas of science are adequate research carried out by research teams, and in which areas, scientific disciplines are research conducted by researchers more often? Do you know fields, disciplines in which research is usually conducted by research teams? Do team research projects have specific attributes that generate additional added value or do they have an advantage over research conducted individually by scientists?
Do you agree with me on the above matter?
What is your opinion on this topic?
Please reply.
I invite you to discussion and scientific cooperation.
Thank you very much.
Best wishes.
Dariusz Prokopowicz
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Dear Colleagues and Friends from RG,
In the context of the above discussion, I propose to add to our considerations the following important issue:
The impact of scientific conferences on the development of science.
Scientific conferences make it possible to make friends with other scientists and researchers. During the conference there are opportunities to conduct discussions and debates on interesting topics. Thanks to this, it is possible to undertake scientific cooperation and create international research teams and projects.
Do you agree with me on the above matter?
- What do you think about this topic?
- What is your opinion on this topic?
Please reply.
I invite you to discussion and scientific cooperation.
Thank you very much.
Best wishes.
Dariusz Prokopowicz
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Could there be nonlinear ODEs that could not even be solved numerically?
I am working on a third-order nonlinear problem which is giving accurate results for a given set of initial conditions (ICs) but for other ICs the matlab ODE solver (checked 4-5 algorithms) do not converge.
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If your equation/system of equations is prone to stiffness or strongly nonlinear the ode 45 solver may not be adapted for some ICs because it uses a fully explicit numerical scheme. This page can help you to chose better adapted solvers: https://www.mathworks.com/help/matlab/math/choose-an-ode-solver.html
If none of these solvers works then you may need to write yourself a numerical scheme adapted to your case, probably an implicit or semi-implicit scheme (more stable than explicit schemes) since matlab solvers don't work.
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How can we define “infinite” and “finite” if we agree with the idea and the operations in Cantor's proofs that many infinite sets in mathematics actually can be proved (turned into) finite set-------the elements in real number set are never-be-finished, endless, limitless and they are really infinite while those in natural number set are sure-be-finished, ended, limited and they are actually finite?
This conundrum has disclosed two infinite related fundamental defects in present infinite set theory and mathematical analysis:
(1)the theoretical and practical confusions of “finite--infinite” caused by the theoratical and practical confusions of “potential infinite, actual infinite”;
(2)the absence of systematic “scientific carrier theory” and the absence of systematic “infinite related number spectrum and set spectrum”.
Because of the absence of systematic “scientific carrier theory”, in present infinite theory system (The First Generation of Infinite Theory System) basing on “potential infinite, actual infinite”, people have had to use the unscientific “potential infinite, actual infinite” theory for the quantitative cognitions of those “finite--infinite” related mathematical things since antiquity. And, because all the “infinite related concepts and contents” for quantitative cognizing in our mathematics have been being unscientifically defined as “non—infinite infinite, finite infinite, infinite finite, both finite and infinite, number of non-number, ...” in present infinite theory system, no one is able to know clearly when and where they should be “finite or infinite, number or non-number, ...” and why. This situation is not only unable us to cognize scientifically two concepts of “finite, infinite” and the relationship between them, but also unable us to cognize scientifically three contents of “finite mathematical things, potential infinite mathematical things, actual infinite mathematical things” and the relationship among them in present infinite related mathematical fields------very free and arbitrary when dealing with any “infinite related mathematical things”. So, many suspended infinite related paradox families have been produced inevitably. It is because of such fatal fundamental defects that results in the frequently performings of the mathematical version of Andersen's THE EMPEROR'S NEW CLOTHES Fairy Tale in all infinite related mathematical fields ever since “potential infinite, actual infinite” came into our science and mathematics, the only thing most people are able to do is just echoing in earnest to what the authorities said.
In new infinite theory system basing on the new concepts of "abstract infinite law and carriers of abstract infinite law " (The Second Generation of Infinite Theory System), the concepts of “finite, infinite, finite scientific carrier, infinite scientific carrier” have been clearlly and scientifically defined. “Infinite” is a kind of “invisible and intangible abstract scientific law”, it is a scientific (mathematical) content for qualitative but not quantitative studies and cognizings; while the “abstract scientific infinite law carriers" is a kind of “visible and tangible scientific concrete manifestation (entity) of abstract scientific law”, it is a scientific (mathematical) content specially fot quantitative studies and cognizings. In our science, we can only conduct the quantitative studying and cognizing on the “abstract scientific law carriers" but not on the “abstract scientific law". Basing on new infinite theory system, now we are perfectly justifiable to construct a systematic and scientific “theory of infinite related mathematical carriers" and able to conduct quantitative studying and cognizing on all kinds of “infinite related mathematical carriers" scientifically (such as their computations as well as the comparetions among them). The quantitative related systematic and scientific “theory of carriers" decides that we must have quantitative studies and cognizings on “different infinite law carriers, big (small) infinite law carriers, bigger (smaller) infinite law carriers, more bigger (more smaller) infinite law carriers, ..." but not on “different infinite laws, big (small) infinite laws, bigger (smaller) infinite laws, more bigger (more smaller) infinite laws, ..." or even arbitrarily on the “finite—infinite mixing up things” as what have been done in presentmathematical analysis and set theory (such as taking them as finite things first then as infinite things later or taking them as infinite things first then as finite things later or the elements belonging to an infinite set but being impossible to exist in this very infinite set, ...). So, in the Second Generation of Set Theory, it is impossible at all to have such contents as “the infinite of more infinite, more more infinite, more more more infinite, ... super infinite, super super infinite, super super super infinite, super super super super infinite, ...”; All the mathematical contents of “X--->0, Y--->📷, ...” for quantitative cognizing in our new infinite related mathematical analysis and set theory are the “scientific carriers" with clear and scientific quantitative natures and definitions in new systematic and scientific “infinite related number spectrum (number system) and set spectrum (set system)”. The replacement of “potential infinite, actual infinite” concepts by new "abstract infinite law and carriers of abstract infinite law" concepts in present infinite theory system and the development of systematic “theory of scientific carriers” inevitably result in great theoretical and operational reformations (a revolution) in the quantitative--quantitative studies and cognizings in our infinite related science areas and, eliminate scientifically and thoroughly the suspended conundrums of “’potential infinite, actual infinite’ confusing" and “’finit--infinite’ confusing" since antiquity.
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Gang, I think that problem is ( partially) with the use of a language. To get clear understanding what a particular language expression mean you need a higher ( the second) level f language ,or meta language to describe the first level language . This in turn will call for a meta meta language and so on. Those are difficult problems and I have not enough expertise in that field to comment any further.
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We are currently building a medical prediction platform (Evidencio) for researchers and physicians to facilitate translation of scientific articles to medical practice (www.evidencio.com). Evidencio is a platform created for and by scientists/physicians that allows for easy external validation of prediction models as well as conversion to easy-to-use online calculators for everyday practice. 
Which (type of) prediction models would be most usefull for you to add to the platform? And, as a researcher/physician, would you be interested in adding your own prediction model to the platform?  
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The IOTA simple and advance rules for predicting ovarian cancer. Although there already is an app for that from the IOTA collaboration study group, so you might have a copyright issue. Still, having everything in one place increases visiability and the more people who use the, the better for patients
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With the continuing funding cuts in some countries, if your work is primarily computational or theoretical in nature could you successfully be an independent scientist? Are there limitations in trying to get your work published in this situation? Will science become more like journalism and are we looking at the prospect of freelance scientists?
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No, you can be based in industry. As long as you write up and publish your research, you can achieve standing. Same thing as to being an independent scientist. The biggest issue is the access to resources.
In regards to your last question. Prior to the last 100-150 years, almost all scientists were "freelance". It is only recently that universities and industry have monopolized the scientific field. You should read "Big Science, Little Science" by Derek Price on this topic.
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I have written codes for generating series of patterns using matlab. I want to save the images generated in each loop indexed with the looping variable. I tried concatenation of strings but it shows error.
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you can use these samples for saving your images:
%% saving images in an avi video file
clear;
clc;
for i=1:50
A(:,:,:,i)=uint8(255*rand(500,500,3));
imshow(A(:,:,:,i))
F(i)=getframe;
end
movie2avi(F,'test.avi')
%% saving images in n mat file
clear;
clc;
for i=1:10
B=uint8(255*rand(500,500,3));
save(strcat('A',num2str(i),'.mat'),'B');
end
%% saving images in n image file
clear;
clc;
for i=1:10
A(:,:,:,i)=uint8(255*rand(500,500,3));
imwrite(A(:,:,:,i),strcat('A',num2str(i),'.jpg'),'jpg')
end
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We would like to connect such oscillator circuits together to excite or inhibit other threshold oscillator circuits.
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A You Tube video of the world's simplest single transistor oscillator circuit:
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Some works in the literature (Goldberg/Bridges, for instance) have demonstrated that standard Genetic Algorithms (GAs) usually cause the building blocks disruption of the solutions. On the other hand, some current papers have shown that the use of a GA special implementation may be a viable alternative in order to overcome this issue. In this sense, I would like to know what you think about that. Please, try answering my question in a short clear response if possible.
Thank you very much in advance!
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Dear Lauro Cássio:
The building blocks problem depends on the nature of the concrete task you are solving. But there are a variety of algorithms that makes evolve solutions codes populations (one or more) helped by a diversity of operators, GA could be included in this variety. Some of these algorithms could be more effective for a diversity of tasks.
 The first article I wrotte devoted to this method "The Integration of Variables method". an additional information you can find in other works that you can download in my researchgate page, like Analysis and Synthesis of Engineering Systems.
Excepting the GA, the rest of the algorithms included in the method doesn't present the building blocks problem.
Best wishes,
José Arzola
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Hi All, I have difficulty in writing a mix of string and string arrays  by FORTRAN, for example (the following two lines):
write (cout,1052) (cd(ii),ii=1+1,9),(cy(ib),ib=10,(inmt*2))
1052 format ('c=[c1',8(';c',a1),79(';c',a2),'];')
this piece of code is working, where cd(ii) and cy(ib) are string arrays. 
I need to write variable number of the string arrays cells (cy(ib)) followed by a bracket, so I need to replace "79" in the format line with "(inmt*2)-9", because each case has a different number of cells to be written, when I do that, it is not anymore working.
Any ideas please?
Thanks,
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It looks like you are coming from a C++ background (or at least the first implementers of your code have). The 'cout' is giving you away. Most of the time you can just use
write(*,*) 'Some text.'
Furthermore, in modern Fortran you would rather provide the format string directly instead of using labels:
write(*,'(I)') 1
You can also provide the format string as a string variable. In this case you can also first compose the format string:
write(format_string,'(A,I,A)') '(A,', 3, 'E)'  ! format string to print some text and 3 reals
write(*,format_string) 'x=', x(1:3)
I see that you have now used a version without formatting. But, if you ever want to introduce formatting again, this might be an easy option.
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The development of correlations for computing the critical velocity required for avoiding sedimentation in two phase liquid-solids in pipes under pressure was subject of many studies since several decades ago. However, the simultaneous effects of particles size and its distribution, concentration and density of solid particles, liquid viscosity, diameter and slope of upward pipes in turbulent flows look globally a complex issue. What are the possible approaches for these phenomena? New approaches, pertinent references and particularly any pertinent summary about the state of art in this field will be appreciated.
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Hi Krishnan, thanks for the very instructive paper on flushing and driplines/pipelines. I sullfy agree that there are the four regimes you mentioned.Actually they represent four different regimes of the same physical system, if you may you can call them different phases. A major point in the present discussion is in my view to describe the general phase transitions between the four regimes. This seams to be possible only if there is a sufficiently general system of eqns covering mean flow, turbulence, particle properties like form, stickiness, density. Real challenge ...
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It has been shown that WENO-Z is less dissipative than WENO-JS.
Are the conclusion and numerical results hold in the attached article if one replaces the baseline 
WENO-JS scheme with WENO-Z scheme and that Compact Reconstructed WENO scheme is stiill substantially faster and more accurate than the pure WENO-Z scheme?  How about for a higher order scheme, say 9th order WENO schemes?
Note, please take the sensitivity parameter epsilon = O(dx^3) and power parameter p=2 in the definition of WENO-Z nonlinear weights.
For reference, see my list of publications on WENO-Z scheme.
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I am currently working on a complex network in MATLAB2010b because we have the license in the college for it only but it only allows execution on 8 cores. I am a little familiar with Scilab but on one of the page (http://julialang.org/) comparing octave, matlab, julia,python etc.(except Scilab), octave was significantly slower than matlab. But what is the execution speed of running a program in scilab. Can anyone suggest me, some sample parallelised code in Scilab as its website lacks comprehensive information on its usage?
Also, can anyone suggest how to read about julia with example codes as its very fast among others?
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Rohan, I have not worked with Scilab yet, but I suggest you to use Matlab. It is and have been a very helpful tool in many areas of study. Matlab may be considered as a complete tool. If you have a NVIDIA's graphics card, you can parallelize some portion of your code just using the Matlab built-in function. You do not have to worry about parallelism details, the Parallel Computing Toolbox makes everything implicit for you. Try it and you'll see.
Best regards!
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Execution time is between one or two months using i7 processor with four cores for a Gaussian 09 job that contains more than 50 heavy atoms. Is there any way to reduce this time? And how much the reduction can be? What is the alternative without sacrificing accuracy (method and basis vectors)?
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Mr. Abdulsattar,
Deffinitively in all chases the application of DFT approachers is highly recommendable. They provided a very balanced strategy between the comoputational-cost and accuracy. For large (bio)macromolecules the molecular mechanics/dynamics (MM/MD) calculations are recommendably.
A. For pure organic molecules suitable methods are described in the paper 1:
Paper 1. International Journal of Biological Macromolecules, 64, 2014, 383–391, Macromolecular ensembles of cyclodextrin crystallohydrates and clathrates – experimental and theoretical gas – and condense phase study, Bojidarka Ivanova, Michael Spiteller
The utilization of Truhlar' functionals such as M05, M06, M06-2X provide highly accurate information about the structure an dproperties. Details of the theoretical background is given in papers 2 and 3, where are compared also the data with other ab initio and DFT methods:
Paper 2:Theoretical Chemistry Accounts, 2008, 120, 215-241,The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals, Yan Zhao, Donald G. Truhlar
Paper 3: Theoretical Chemistry Accounts, 2011, 129, 219-227, Coupled cluster, B2PLYP and M06-2X investigation of the thermochemistry of five-membered nitrogen containing heterocycles, furan, and thiophene, Pablo A. Denis
Towards the besis sets very accurate information is achieved utilizing the Dunning's correlation consisted basis sets such as cc-pVDZ, cc-pVTZ, cc-pVQZ, cc-pV5Z, aug-cc-pVDZ, are related. But their utilization is relatively time consuming. So that some of the Pople's basis sets such as 6-31+G*, 6-31G(3df, 3pd), 6-311G or related with suitable polarization and diffusion function also provide very accurate data at a relatively balansing computational costs.
B. For inorganic or metal organic compounds suitable theoretical levels are shown in the paper 4.
Paper 4: Adsorption of uranium composites onto saltrock oxides – experimental and theoretical study, Journal of Environmental Radioactivity, 135, 2014, 75-83, Bojidarka Ivanova, Michael Spiteller
The utilization of quasirelativistic effective core pseudopotentials
from Stuttgart-Dresden (SDD) provide highly meaningful information at relatively significantly reduced computational time (resp. costs).
C. For large (bio)macromolecules, theoretical levels are described in paper 5:
Paper 5: International Journal of Biological Macromolecules, 65, 2014, 314–324, Evodiamine and rutaecarpine alkaloids as highly selective transient receptor potential vanilloid 1 agonists, Bojidarka Ivanova, Michael Spiteller
 
 
 
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I have lots of experience using Java, C and FORTRAN for scientific programming. In Java I make heavy use of abstract classes, interfaces and generics to make my code as re-usable as possible. This has really cut down my development overhead without having too much impact on runtime. I have yet to experiment with hardware acceleration such as that offered by Cuda, which other use to good advantage, in my scientific programming (quantum dynamics of open/stochastic systems). Working mainly on Mac's the emergence of Swift and Metal provide new opportunities for scientific programming in a modern environment with fast execution.
I have started to play with Swift and it seems promising - with the playground looking like a potentially good teaching too for my students.
Especially from those who have experience using hardware acceleration and have benchmarked some relevant simple Swift+Metal code (e.g. matrix multiplication). I would be grateful for information of your experience or opinions on the future potential of Swift+Metal for high performance scientific simulation.
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I don't have any experience with either Swift or Metal, but I already had a quick look at Swift as a programming language. My first impression is that Swift will be fast enough for scientific computing. In the keynote presentation they already showed that in some cases it can be faster than Objective-C. That is due to new language features that are more high-level, but because of this allow for better compiler optimizations. The underlying Objective-C runtime is already highly optimized and very fast. The only disadvantage I see is the lack of compatible scientific libraries written directly for Swift. It is possible to interface with C and C++, but programming can only be efficient in Swift if you have an interface optimized for the language. That means that you need to write your own wrapper classes for existing libraries.
I also had a quick look at the link you provided on Metal compute shaders. It looks all straight forward. Since Apple conceived OpenCL I guess they know what they are doing here. Though Apple has the best OpenCL wrappers around. It seems that similar wrappers are still missing for Metal. What I don't like about the compute shader kernels is that their syntax is closer to graphics shader programming than to regular function calls like in CUDA or OpenCL. If you already know OpenGL and GLSL this approach is easy to understand, but for the regular scientific programmer this concept is harder to grasp. You need to know a little bit about graphics hardware to understand the concepts. I don't expect Metal to be faster than OpenCL. Therefore, I suggest trying to use Swift with OpenCL in the hope that Apple's OpenCL wrappers can also be used with Swift.
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I am currently fitting an ITC curve that fits to the two sites model. I curious why the N1 number is always bigger than the N2. What I've got at the moment is that the N1 is 0.999 while the N2 is 0.768. I suppose those numbers should be 1. What does this means
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You may follow Alberto's suggestion, but...
Allosteric effects would be reflected in binding cooperativity. And this cooperativity will be the result of direct ligand-ligand interaction when bound to the protein, or long range ligand-ligand interaction through a conformational change in the protein.
Your data do not seem to correspond to positive cooperativity, but to negative cooperativity.
In a homodimeric protein like yours there are two possibilities: 1) identical and independent binding sites; 2) identical and cooperative binding sites (with positive or negative cooperativity). Because of symmetry, the binding sites in your protein cannot be non-identical and independent.
You are analysing the experimental data with a model considering two non-identical and independent binding sites. Despite this is not right (as mentioned before) it is not a big problem, because that model is mathematically identical to the one considering two identical binding sites with negative cooperativity. If the non-identical and independent bidning sites model fits a given experiment, the identical binding sites with negative cooperativity model will also fit that experiment. Besides, once you get the interaction parameters using one model, you can calculate the interaction parameters for the other model. For a thorough description of ligand binding to a protein with two binding sites studied by ITC you may take a look to this article:
Therefore, because of all these facts and after taking a look to the ITC experiment, I have some doubts for any improvement in the stoichiometry by using the negative cooperativity model.
Having said all this, I must say that the ITC experiment looks very nice, and that a stoichimetry of 1.0 and 0.8 does not seem to be a "big" problem. In the literature you may find experimental systems where the stoichiometries are not just plain integer numbers or match perfectly.
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Has anybody experienced small scale scientific HPC using Amazon EC2?
I currently lack decent HPC support at my work, and for that, I am considering to use Amazon's EC2 services, possibly spot instance services.
For the work in my lab, I occasionally (perhaps a number of times a month) need to compute *typically independent) tasks on up to max. 100 nodes that run for a couple of days, typically using torque grid system/c++/matlab etc. I am wondering how costs / ease of use compare to buying and running a couple of 4/8core blades in the closet around the corner...
(And yes, I am aware of Amazon's budget calculator; however, I didn't find its answers very useful.)
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Spot instances would not work for us, so we calculated using the \
on-demand price, and it was cheaper to run our own.
If the tasks are at least nearly independent, you really only
need a compute farm, and can forgo an expensive Infiniband switch.
Are you running 100 nodes, or 100 cores? If nodes, how much memory
and cores per node.
We have 4 SMP SuperMicro machines each with 64 cores (Opteron Interlagos
processors) and 256GB of RAM. They allow us to use lots of compute
cycles and run the occasional large shared memory problem.
You could also share time and costs with another group, to allow you to
get more equipment, since Torque would allow you to set fair usage policies.
That is essentially what the cloud is doing for you, sharing costs and compute time.
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I have a FORTRAN source code consisting of many different .F and .h files. How to create a makefile to compile these files?
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It depends on the code. Whether (and where) there are INCLUDE statements are used or not.
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I have a program that calculates temperatures using finite elemento methods, but I haven't considering using sparse matrix, all my calculations considers matrix as dense. Does anyone know some good sources that I can use to implement a sparse matrix?
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