Mihaela Păun

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Papers by Mihaela Păun

Networks of splicing processors: simulations between topologies

Journal of Membrane Computing

Networks of splicing processors are one of the theoretical computational models that take inspira... more Networks of splicing processors are one of the theoretical computational models that take inspiration from nature to efficiently solve problems that our current computational knowledge is not able to. One of the issues restricting/hindering is practical implementation is the arbitrariness of the underlying graph, since our computational systems usually conform to a predefined topology. We propose simulations of networks of splicing processors having arbitrary underlying graphs by networks whose underlying graphs are of a predefined topology: complete, star, and grid graphs. We show that all of these simulations are time efficient in the meaning that they preserve the time complexity of the original network: each computational step in that network is simulated by a fixed number of computational steps in the new topologic networks. Moreover, these simulations do not modify the order of magnitude of the network size.

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How accurate is the remote sensing based estimate of water physico-chemical parameters in the Danube Delta (Romania)?

Annals of Forest Research

The current paper estimated the physico-chemical properties of water in the Danube Delta (Romania... more The current paper estimated the physico-chemical properties of water in the Danube Delta (Romania), based on Sentinel 2 remote sensing data. Eleven sites from the Danube Delta were sampled in spring and autumn for three years (2018-2020) and 21 water physico-chemical parameters were measured in laboratory. Several families of machine learning algorithms, translated into hundreds of models with different parameterizations for each machine learning algorithm, based on remote sensing data input from Sentinel 2 spectral bands, were employed to find the best models that predicted the values measured in laboratory. This was a novel approach, reflected in the types of selected models that minimised the values of performance metrics for the tested parameters. For alkalinity, calcium, chloride, carbon dioxide, hardness, potassium, sodium, ammonium, dissolved oxygen, sulphates, and suspended matter the results were promising, with an overall percentage bias of the estimates of +/- 10% from th...

Simulations between Three Types of Networks of Splicing Processors

Mathematics, 2021

Networks of splicing processors (NSP for short) embody a subcategory among the new computational ... more Networks of splicing processors (NSP for short) embody a subcategory among the new computational models inspired by natural phenomena with theoretical potential to handle unsolvable problems efficiently. Current literature considers three variants in the context of networks managed by random-context filters. Despite the divergences on system complexity and control degree over the filters, the three variants were proved to hold the same computational power through the simulations of two computationally complete systems: Turing machines and 2-tag systems. However, the conversion between the three models by means of a Turing machine is unattainable because of the huge computational costs incurred. This research paper addresses this issue with the proposal of direct and efficient simulations between the aforementioned paradigms. The information about the nodes and edges (i.e., splicing rules, random-context filters, and connections between nodes) composing any network of splicing proces...

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PACHETUL DE LUCRU # 3 STRUCTURA SI MANAGEMENTUL CENTRULUI DANUBIUS-RI Autori: GEOECOMAR INSB FM Management Consultancy SRL GEA Strategy & Consulting SA

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Phytoremediation research-how Romania is placed worldwide

In the last few decades, due to the global industrialization and population expansion the level o... more In the last few decades, due to the global industrialization and population expansion the level of pollutants has largely increased, being one of the main environmental problems faced worldwide. Consequently, phytoremediation research had been gathering more and more interest. A study of data selected from Scopus is presented by the authors, identifying trends in publication number, collaboration and impact. The trends are identified at the global level followed by a discussion of how Romania performs with respect to the identified trends. When evaluating the research produced by the Romanian institutions, two characteristics are considered: phytoremediation potential of the plants in the Danube Delta and the coastal region and the phytoremediation research temporal evolution and international impact. The paper presents a quantitative analysis without adding variable weights to citations and publications based on the publications ranks offering an overview of the national research s...

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PACHET DE LUCRU # 4 STRUCTURAREA PROPUNERII DE PROIECT ESFRI Autori: GEOECOMAR INSB FM Management Consultancy SRL GEA Strategy & Consulting SA

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DNA-Guided Assembly for Fibril Proteins

Mathematics, 2021

Current advances in computational modelling and simulation have led to the inclusion of computer ... more Current advances in computational modelling and simulation have led to the inclusion of computer scientists as partners in the process of engineering of new nanomaterials and nanodevices. This trend is now, more than ever, visible in the field of deoxyribonucleic acid (DNA)-based nanotechnology, as DNA’s intrinsic principle of self-assembly has been proven to be highly algorithmic and programmable. As a raw material, DNA is a rather unremarkable fabric. However, as a way to achieve patterns, dynamic behavior, or nano-shape reconstruction, DNA has been proven to be one of the most functional nanomaterials. It would thus be of great potential to pair up DNA’s highly functional assembly characteristics with the mechanic properties of other well-known bio-nanomaterials, such as graphene, cellulos, or fibroin. In the current study, we perform projections regarding the structural properties of a fibril mesh (or filter) for which assembly would be guided by the controlled aggregation of DN...

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Efficient synthetic generation of ecological data with preset spatial association of individuals

Canadian Journal of Forest Research, 2021

Many experiments cannot feasibly be conducted as factorials. Simulations using synthetically gene... more Many experiments cannot feasibly be conducted as factorials. Simulations using synthetically generated data are viable alternatives to such factorial experiments. The main objective of the present research is to develop a methodology and platform to synthetically generate spatially explicit forest ecosystems represented by points with a predefined spatial pattern. Using algorithms with polynomial complexity and parameters that control the number of clusters, the degree of clusterization, and the proportion of nonrandom trees, we show that spatially explicit forest ecosystems can be generated time efficiently, which enables large factorial simulations. The proposed method was tested on 1200 synthetically generated forest stands, each of 25 ha, using 10 spatial indices: Clark–Evans aggregation index; Ripley’s K; Besag’s L; Morisita’s dispersion index; Greig–Smith index; the size dominance index of Hui; index of nonrandomness of Pielou; directional index and mean directional index of C...

DNA-Guided Assembly of Nanocellulose Meshes

Nanoengineered materials are a product of joint collaboration of theoreticians and experimentalis... more Nanoengineered materials are a product of joint collaboration of theoreticians and experimentalists, of physicists, (bio-)chemists, and recently, of computer scientists. In the field of Nanotechnology and Nanoengineering, DNA (algorithmic) self-assembly has an acknowledged leading position. As a fabric, DNA is a rather inferior material; as a medium for shape, pattern, and dynamic behavior reconstruction, it is one of the most versatile nanomaterials. This is why the prospect of combining the physical properties of known high performance nanomaterials, such as cellulose, graphene, or fibroin, with the assembly functionality of DNA scaffolds is a very promising prospect. In this work we analyze the dynamical and structural properties of a would-be DNA-guided assembly of nanocellulose meshes. The aim is to generate pre-experimental insights on possible ways of manipulating structural properties of such meshes. The mechanistic principles of these systems, implemented through the DNA as...

{Networks of Uniform Splicing Processors

ArXiv, 2019

In this note we consider a new variant of network of splicing processors which simplifies the gen... more In this note we consider a new variant of network of splicing processors which simplifies the general model such that filters remain associated with nodes but the input and output filters of every node coincide. This variant is called {\it network of uniform splicing processors}. Although the communication in the new variant seems less powerful, being based on simpler filters, the new variant is sufficiently powerful to be computationally complete. The main result is that nondeterministic Turing machines can be simulated by networks of uniform splicing processors. Furthermore, the simulation is time efficient.

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DNA origami design and implementation

Since its introduction in the early 2000s, DNA origami had a big impact on the development of nan... more Since its introduction in the early 2000s, DNA origami had a big impact on the development of nanotechnology by gathering numerous applications. During this time, many tools were designed and used to generate arbitrary shapes capable of self-assembly which make this technique more approachable. In this paper, we have created the map of Romania at nanoscale dimensions by using a new open-source software-PERDIX. For this purpose, we used a scaffold strand with a length of 6959 nucleotides and 162 staple strands with a variable length ranging between 20 and 63 nucleotides. All the computational tools that were used in this experiment are open-source and user-friendly.

One Dimensional DNA Tiles Self Assembly Model Simulation

Int. J. Unconv. Comput., 2018

– 255 3 D DNA Origami Map Structure Simulation

This paper presents the latest trends and approaches used for constructing nanoscale structures o... more This paper presents the latest trends and approaches used for constructing nanoscale structures of 2D objects through DNA folding based on the DNA origami technology developed by Rothemund. The Rothemund method has been used in the construction of various shapes, such as the development of the nanoscale structure for the United States map. Following the steps of Rothemund’s technique, we simulate the construction of the Romanian map nanoscale 2D structure, embedding the number 100 into it. Key-words: DNA; origami; self-assembly; nanostructure; Romanian map

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Resuscitating Old Forest Models to Meet Present Environmental Reporting Needs

Resuscitating old forest models to meet present environmental reporting needs A plethora of fores... more Resuscitating old forest models to meet present environmental reporting needs A plethora of forest models were developed by transforming dependent variable, which introduces bias in estimation if appropriate correction are not applied when back-transforming to the original units. The need for accurate reporting of environmental statistics to national and international agencies lead to improvement of existing models or development of new ones. However, in many instances, not only that no original models were established, but original data sets are no longer available, which recommends ad-hoc bias corrections of existing models. The present research presents a procedure for bias correction based on information extracted from summary statistics, specifically coefficient of determination and standard error. The transformations considered in this study are trigonometric (i.e. sine, cosine, tangent, arcsine, and arctangent), hyperbolic (i.e., sine, secant, and tangent), power, and logarithm. The method was applied to site index equations of Douglas Fir and Ponderosa Pine [Hann and Scrivani, 1987], and tree volume of 27 species from Romania [Giurgiu, 1974]. Using only the information describing the models, such as variance or range, the proposed method corrected the bias, and proved that estimates can change from 1% (the site index equations of Hann and Scrivani) to 40% (the tree volumes of Giurgiu).

Two Decades of Research Collaboration: A Keyword Scopus Evaluation

The Romanian Statistical Review, 2016

One issue that has become more important over the years is to evaluate the capability for worldwi... more One issue that has become more important over the years is to evaluate the capability for worldwide research networks on different areas of research, especially in the areas that are identified as being worldwide significant. The study investigated the research output, citations impact and collaborations on publications listed in Scopus authored by researchers all over the world, research published between 1999-2014, selected by a group of keywords identified by authors. The results of the analysis identified an increasing trend in scientific publications starting with 2006, especially on three of the analyzed keywords. We also found differences in the citations patterns for the Black Sea and Danube Delta keywords in the contributing countries. The results of this study revealed a steady increase of the collaboration output and an increasing trend in the collaboration behavior, both at the European and national level. Additionally, at the national level the study identified the coll...

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Nonlinear parsimonious forest modeling assuming normal distribution of residuals

European Journal of Forest Research, 2021

To avoid the transformation of the dependent variable, which introduces bias when back-transforme... more To avoid the transformation of the dependent variable, which introduces bias when back-transformed, complex nonlinear forest models have the parameters estimated with heuristic techniques, which can supply erroneous values. The solution for accurate nonlinear models provided by Strimbu et al. (Ecosphere 8:e01945, 2017) for 11 functions (i.e., power, trigonometric, and hyperbolic) is not based on heuristics but could contain a Taylor series expansion. Therefore, the objectives of the present study are to present the unbiased estimates for variance following the transformation of the predicted variable and to identify an expansion of the Taylor series that does not induce numerical bias for mean and variance. We proved that the Taylor series expansion present in the unbiased expectation of mean and variance depends on the variance. We illustrated the new modeling approach on two problems, one at the ecosystem level, namely site productivity, and one at individual tree level, namely st...

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Impact of Algorithm Selection on Modeling Ozone Pollution: A Perspective on Box and Tiao (1975)

Forests, 2020

Estimation using a suboptimal method can lead to imprecise models, with cascading effects in comp... more Estimation using a suboptimal method can lead to imprecise models, with cascading effects in complex models, such as climate change or pollution. The goal of this study is to compare the solutions supplied by different algorithms used to model ozone pollution. Using Box and Tiao (1975) study, we have predicted ozone concentration in Los Angeles with an ARIMA and an autoregressive process. We have solved the ARIMA process with three algorithms (i.e., maximum likelihood, like Box and Tiao, conditional least square and unconditional least square) and the autoregressive process with four algorithms (i.e., Yule–Walker, iterative Yule–Walker, maximum likelihood, and unconditional least square). Our study shows that Box and Tiao chose the appropriate algorithm according to the AIC but not according to the mean square error. Furthermore, Yule–Walker, which is the default algorithm in many software, has the least reliable results, suggesting that the method of solving complex models could al...

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Development of Nonlinear Parsimonious Forest Models Using Efficient Expansion of the Taylor Series: Applications to Site Productivity and Taper

Forests, 2020

The parameters of nonlinear forest models are commonly estimated with heuristic techniques, which... more The parameters of nonlinear forest models are commonly estimated with heuristic techniques, which can supply erroneous values. The use of heuristic algorithms is partially rooted in the avoidance of transformation of the dependent variable, which introduces bias when back-transformed to original units. Efforts were placed in computing the unbiased estimates for some of the power, trigonometric, and hyperbolic functions since only few transformations of the predicted variable have the corrections for bias estimated. The approach that supplies unbiased results when the dependent variable is transformed without heuristic algorithms, but based on a Taylor series expansion requires implementation details. Therefore, the objective of our study is to investigate the efficient expansion of the Taylor series that should be included in applications, such that numerical bias is not present. We found that five functions require more than five terms, whereas the arcsine, arccosine, and arctangen...

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Hairpin completions and reductions: semilinearity properties

Natural Computing, 2020

This paper is part of the investigation of some operations on words and languages with motivation... more This paper is part of the investigation of some operations on words and languages with motivations coming from DNA biochemistry, namely three variants of hairpin completion and three variants of hairpin reduction. Since not all the hairpin completions or reductions of semilinear languages remain semilinear, we study sufficient conditions for semilinear languages to preserve their semilinearity property after applying the non-iterated hairpin completion or hairpin reduction. A similar approach is then applied to the iterated variants of these operations. Along these lines, we define the hairpin reduction root of a language and show that the hairpin reduction root of a semilinear language is not necessarily semilinear except the universal language. A few open problems are finally discussed.

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A parsimonious approach for modeling uncertainty within complex nonlinear relationships

Ecosphere, 2017

Advancements in information technology led environmental scientists to the illusion that efforts ... more Advancements in information technology led environmental scientists to the illusion that efforts should be mainly focused on developing models that reduce uncertainty rather than on models adjusted to the existing uncertainty. As a result, environmental relationships are represented by non‐parsimonious and suboptimal models, which in many instances could be even wrong. The objective of this research was to provide scientists focused on modeling ecosystem processes with a procedure that supplies parsimonious correct results. The procedure transforms the response variable to achieve a linear model and the normality of the residuals. After the parameters of the transformed model are estimated, the bias induced by back‐transforming is corrected. We have computed the bias corrections for 11 of the most popular functions from the power, trigonometric, and hyperbolic families by considering the truncated normal distribution, when necessary. Using generated data, we have shown that the prop...

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