Now my main interest is the role of symmetries in life sciences: genetic code symmetry, Chargaff 2 versus quadrupole symmetry, tandem NBPF HORs an cognitive abilities, symmetries in evolution.
Proučavanje Newtonovih jednadžbi gibanja pomoću animacija u programskom jeziku Python u osnovnom i srednjoškolskom obrazovanju
Sažetak. Zadnjih godina programski jezik Python (https://www.python.org) je postao općeprihvaćen ... more Sažetak. Zadnjih godina programski jezik Python (https://www.python.org) je postao općeprihvaćen od velikog broja znanstvenika u svijetu. Njegovo korištenje ne zahtijeva kupnju licenci koje predstavljaju dodatne troškove školama. Prednost su i razne dodatne ugrađene biblioteke kao što su NumPy i SciPy (https://en.wikipedia.org/wiki/NumPy) te „Matplotlib“ (http://matplotlib.org/api/animation_api.html). Upravo zbog raširenosti ovog programskog jezika među znanstvenicima, njegovo uvođenje kao dodatnog alata za primjenu u nastavi fizike čini se kao razumno rješenje (pogotovo kada se tijekom razvoja novog kurikula govori i o uvođenju informatike kao obaveznog predmeta u osnovne škole). U ovom radu prikazana je njegova primjena s ciljem razvijanja učeničkog razumijevanja i sposobnosti računalnog rješavanja Newtonovih jednadžbi gibanja, pomoću Eulerove metode za zadane početne uvjete. Dajemo prijedlog za primjene u školama u okviru raznih nastavnih cjelina predmeta Fizike, uz razvijanje dodatnih aplikacija (skripti u Pythonu) unutar jednog paketa aplikacija. Taj paket bi se mogao upotrijebiti za istraživački tip nastave, za razvijanje i usvajanje fizikalnih koncepata te ispravljanje miskoncepcija, u kombinaciji s realnim pokusima ili kao samostalni istraživački alat, osobito u slučajevima gdje su realni pokusi složeni ili teško ostvarivi. Osobito korisna strana takvog pristupa je mogućnost da se računalno vođeni pokusi izvode i samostalno kod kuće, a ne samo na nastavi. Osim ujednačenosti razvijanja kritičkog razmišljanja u školama, prednost razvoja spomenutog paketa bila bi i usklađenost poučavanja fizike (i programiranja) od osnovne i srednje škole pa do fakulteta. Naime, uporabom simulacija učenici bi mogli objašnjavati prirodne pojave poput znanstvenika. Kao konkretan primjer prikazujemo metodički oblikovan pristup obradi jednolikog gibanja po kružnici uz pomoć Pythona.
Identification of the higher order repeats from T.castaneum to Human and Neanderthal genome using computational Global Repeat Map method
Higher order repeats (HORs) function in species genomes is still mainly unknown. HOR could be cla... more Higher order repeats (HORs) function in species genomes is still mainly unknown. HOR could be classified as regular (head-to-tail "tandem within tandem pattern") and complex, where for regular ones is known that they are a result of recent evolutionary processes in primates. We use our Global Repeat Map method (http://genom.hazu.hr/tools.html) for identification of tandem repeats and HORs. Main characteristic of this method is creation of global repeat map of the investigated DNA sequence by direct mapping of it into frequency domain using complete Kstring ensemble [1]. We identified in T.castaneum complex and, surprisingly, regular HORs, not identified previously in insects (only large tandem repeats and complex HOR with different size of primary repeat units were found). Moreover, in human and Neanderthal genome, we identified accelerated HOR structures [2] which are located in NBPF family gene. In addition, we confirm that there are no accelerated HOR structures in NBPF...
ABSTRACTModern synthetic biology depends on the manufacture of large DNA constructs from librarie... more ABSTRACTModern synthetic biology depends on the manufacture of large DNA constructs from libraries of genes, regulatory elements or other genetic parts. Type IIS restriction enzyme-dependent DNA assembly methods (e.g., Golden Gate) enable rapid one-pot, ordered, multi-fragment DNA assembly, facilitating the generation of high-complexity constructs. The order of assembly of genetic parts is determined by the ligation of flanking Watson-Crick base-paired overhangs. The ligation of mismatched overhangs leads to erroneous assembly, and the need to avoid such pairings has typically been accomplished by using small sets of empirically vetted junction pairs, limiting the number of parts that can be joined in a single reaction. Here, we report the use of a comprehensive method for profiling end-joining ligation fidelity and bias to predict highly accurate sets of connections for ligation-based DNA assembly methods. This data set allows quantification of sequence-dependent ligation efficienc...
Symmetries have not been completely determined and explained from the discovery of the DNA struct... more Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our discovery of the Supersymmetry Genetic Code table in the form of 2 × 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons, all built with the same physiochemical double mirror symmetry and Watson–Crick pairing. We also show that single-stranded RNA had the complete code of life in the form of the Supersymmetry Genetic Code table simultaneously with instructions of codons’ relationship as to how to develop the DNA molecule on the principle of Watson–Crick pairing. We show that the same symmetries between the genetic code and DNA quadruplet are highly conserved during the whole evolution even between phylogenetically distant organisms. In this way, decreasing disorder and entropy enabled the evolution of living beings up to sophisticated species with co...
IBFFM yrast states in odd-odd nuclei associated withO(6) andSU(3) limits
Zeitschrift f�r Physik A Atomic Nuclei, 1988
In the Interacting Boson-Fermion-Fermion Model (IBFFM) for odd-odd nuclei the yrast states are ca... more In the Interacting Boson-Fermion-Fermion Model (IBFFM) for odd-odd nuclei the yrast states are calculated fortilde j_pi = tilde h_{1 1/2} ,tilde j_v = tilde i_{1 3/2} , proton-neutron configurations coupled to the O(6) and SU(3) boson core. The results are discussed in terms of the strongly coupled/ decoupled band type criterion and in comparison to the peaceful and conflicting case of asymmetric rotor model.
Structure of 68As studied via the 12C(58Ni,pn) reaction
Nuclear Physics A, 1998
Excited states of 68As nucleus were populated through the 12C(58Ni,pn) reaction and investigated ... more Excited states of 68As nucleus were populated through the 12C(58Ni,pn) reaction and investigated by in-beam γ-spectroscopic methods. The NORDBALL detector array equipped with charged particle and neutron detectors was used to detect the evaporated particles and γ-rays. The level scheme of 68As was constructed on the basis of γγ-coincidence relations up to 6 MeV excitation energy and Jπ = (15+).
For linearly coupled double-well oscillators the regularity partial chaos regularity transition i... more For linearly coupled double-well oscillators the regularity partial chaos regularity transition is found. First, an incomplete KAM scenario develops with increasing energy, from integrable pattern comprising in-phase and out-of-phase small elliptic orbits towards a partial chaos, with a deformed regular island immersed in a chaotic sea. At a critical energy a new deformed island appears as a mirror image. Above
It is shown that the coefficients Ak of angles qk, corresponding to the minima of light intensity... more It is shown that the coefficients Ak of angles qk, corresponding to the minima of light intensity in the diffraction by a circular aperture, can successfully be described by a function which appears in the electrostatic interaction energy between two uniform surface-charged spheres. The coefficient Ak defines the angle qk by sinqk = Akl/d, k = 1,2,3, where l is the wavelength of light and d is the diameter of the aperture. These coefficients may be correlated with a dimensionless function fb/R, encountered in the relation of the interaction energy terms of two spheres of equal radii R, with uniformly-distributed surface charges q and q and at a mutual distance b. The total interaction energy, i.e. the Coulomb potential energy, is W = qq/(4pe0b), where e0 is the permitivity of vacuum. This energy contains two terms, a positive one W(+) = W fb/R and negative one W(-) = W (1-fb/R). The correlation between Ak and the function fb/R is given by Ak - k = u + v fb/R,k, where u and v are con...
We study local and global correlations between the naturally invariant measure of a chaotic one-d... more We study local and global correlations between the naturally invariant measure of a chaotic one-dimensional map f and the conditionally invariant measure of the transiently chaotic map f H. The two maps differ only within a narrow interval H, while the two measures significantly differ within the images f l (H), where l is smaller than some critical number l c. We point out two different types of correlations. Typically, the critical number l c is small. The 2 value, which characterizes the global discrepancy between the two measures, typically obeys a power-law dependence on the width ⑀ of the interval H, with the exponent identical to the information dimension. If H is centered on an image of the critical point, then l c increases indefinitely with the decrease of ⑀, and the 2 value obeys a modulated power-law dependence on ⑀.
Interacting-boson-fermion-fermion model description of La83140 and comparison with levels populated by beta decay and neutron capture
Physical Review C, 1990
Page 1. PHYSICAL REVIEW C VOLUME 41, NUMBER 3 MARCH 1990 Interacting-boson-fermion-fermion model ... more Page 1. PHYSICAL REVIEW C VOLUME 41, NUMBER 3 MARCH 1990 Interacting-boson-fermion-fermion model description of ' Las3 and comparison with levels populated by beta decay and neutron capture R. A. Meyer' Division ...
Alpha satellites are tandemly repeated sequences found in all human centromeres. In addition to t... more Alpha satellites are tandemly repeated sequences found in all human centromeres. In addition to the functional and structural role within centromere they are also a suitable model for evolutionary studies, because of being subject to concerted evolution. The Global Repeat Map (GRM) algorithm is a convenient computational tool to determine consensus repeat units and their exact size within a given genomic sequence, both of monomeric and higher-order (HOR) type. Using GRM, we identify in Build 37.2 assembly fifteen different alpha satellite HORs, three of them novel, not reported previously. In the next step we compute suprachromosomal family classification and CENP-B box / pJ distributions for these HORs. All human alpha satellite sequences originate from one pra-ancestral alpha satellite monomer. For the first time we perform GRM analysis and compare human and chimpanzee alpha satellite HORs for chromosomes 4 and give an evidence that the human and chimpanzee alpha satellites originate from a common ancestor that predated the human-chimpanzee separation. We also compare the codon-like trinucleotide (CLT) extensions of human and chimpanzee chromosome 4. Our results are consistent with the expectation that the alpha satellite HORs in human and chimpanzee have been created after the human-chimpanzee separation.
Proučavanje Newtonovih jednadžbi gibanja pomoću animacija u programskom jeziku Python u osnovnom i srednjoškolskom obrazovanju
Sažetak. Zadnjih godina programski jezik Python (https://www.python.org) je postao općeprihvaćen ... more Sažetak. Zadnjih godina programski jezik Python (https://www.python.org) je postao općeprihvaćen od velikog broja znanstvenika u svijetu. Njegovo korištenje ne zahtijeva kupnju licenci koje predstavljaju dodatne troškove školama. Prednost su i razne dodatne ugrađene biblioteke kao što su NumPy i SciPy (https://en.wikipedia.org/wiki/NumPy) te „Matplotlib“ (http://matplotlib.org/api/animation_api.html). Upravo zbog raširenosti ovog programskog jezika među znanstvenicima, njegovo uvođenje kao dodatnog alata za primjenu u nastavi fizike čini se kao razumno rješenje (pogotovo kada se tijekom razvoja novog kurikula govori i o uvođenju informatike kao obaveznog predmeta u osnovne škole). U ovom radu prikazana je njegova primjena s ciljem razvijanja učeničkog razumijevanja i sposobnosti računalnog rješavanja Newtonovih jednadžbi gibanja, pomoću Eulerove metode za zadane početne uvjete. Dajemo prijedlog za primjene u školama u okviru raznih nastavnih cjelina predmeta Fizike, uz razvijanje dodatnih aplikacija (skripti u Pythonu) unutar jednog paketa aplikacija. Taj paket bi se mogao upotrijebiti za istraživački tip nastave, za razvijanje i usvajanje fizikalnih koncepata te ispravljanje miskoncepcija, u kombinaciji s realnim pokusima ili kao samostalni istraživački alat, osobito u slučajevima gdje su realni pokusi složeni ili teško ostvarivi. Osobito korisna strana takvog pristupa je mogućnost da se računalno vođeni pokusi izvode i samostalno kod kuće, a ne samo na nastavi. Osim ujednačenosti razvijanja kritičkog razmišljanja u školama, prednost razvoja spomenutog paketa bila bi i usklađenost poučavanja fizike (i programiranja) od osnovne i srednje škole pa do fakulteta. Naime, uporabom simulacija učenici bi mogli objašnjavati prirodne pojave poput znanstvenika. Kao konkretan primjer prikazujemo metodički oblikovan pristup obradi jednolikog gibanja po kružnici uz pomoć Pythona.
Identification of the higher order repeats from T.castaneum to Human and Neanderthal genome using computational Global Repeat Map method
Higher order repeats (HORs) function in species genomes is still mainly unknown. HOR could be cla... more Higher order repeats (HORs) function in species genomes is still mainly unknown. HOR could be classified as regular (head-to-tail "tandem within tandem pattern") and complex, where for regular ones is known that they are a result of recent evolutionary processes in primates. We use our Global Repeat Map method (http://genom.hazu.hr/tools.html) for identification of tandem repeats and HORs. Main characteristic of this method is creation of global repeat map of the investigated DNA sequence by direct mapping of it into frequency domain using complete Kstring ensemble [1]. We identified in T.castaneum complex and, surprisingly, regular HORs, not identified previously in insects (only large tandem repeats and complex HOR with different size of primary repeat units were found). Moreover, in human and Neanderthal genome, we identified accelerated HOR structures [2] which are located in NBPF family gene. In addition, we confirm that there are no accelerated HOR structures in NBPF...
ABSTRACTModern synthetic biology depends on the manufacture of large DNA constructs from librarie... more ABSTRACTModern synthetic biology depends on the manufacture of large DNA constructs from libraries of genes, regulatory elements or other genetic parts. Type IIS restriction enzyme-dependent DNA assembly methods (e.g., Golden Gate) enable rapid one-pot, ordered, multi-fragment DNA assembly, facilitating the generation of high-complexity constructs. The order of assembly of genetic parts is determined by the ligation of flanking Watson-Crick base-paired overhangs. The ligation of mismatched overhangs leads to erroneous assembly, and the need to avoid such pairings has typically been accomplished by using small sets of empirically vetted junction pairs, limiting the number of parts that can be joined in a single reaction. Here, we report the use of a comprehensive method for profiling end-joining ligation fidelity and bias to predict highly accurate sets of connections for ligation-based DNA assembly methods. This data set allows quantification of sequence-dependent ligation efficienc...
Symmetries have not been completely determined and explained from the discovery of the DNA struct... more Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our discovery of the Supersymmetry Genetic Code table in the form of 2 × 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons, all built with the same physiochemical double mirror symmetry and Watson–Crick pairing. We also show that single-stranded RNA had the complete code of life in the form of the Supersymmetry Genetic Code table simultaneously with instructions of codons’ relationship as to how to develop the DNA molecule on the principle of Watson–Crick pairing. We show that the same symmetries between the genetic code and DNA quadruplet are highly conserved during the whole evolution even between phylogenetically distant organisms. In this way, decreasing disorder and entropy enabled the evolution of living beings up to sophisticated species with co...
IBFFM yrast states in odd-odd nuclei associated withO(6) andSU(3) limits
Zeitschrift f�r Physik A Atomic Nuclei, 1988
In the Interacting Boson-Fermion-Fermion Model (IBFFM) for odd-odd nuclei the yrast states are ca... more In the Interacting Boson-Fermion-Fermion Model (IBFFM) for odd-odd nuclei the yrast states are calculated fortilde j_pi = tilde h_{1 1/2} ,tilde j_v = tilde i_{1 3/2} , proton-neutron configurations coupled to the O(6) and SU(3) boson core. The results are discussed in terms of the strongly coupled/ decoupled band type criterion and in comparison to the peaceful and conflicting case of asymmetric rotor model.
Structure of 68As studied via the 12C(58Ni,pn) reaction
Nuclear Physics A, 1998
Excited states of 68As nucleus were populated through the 12C(58Ni,pn) reaction and investigated ... more Excited states of 68As nucleus were populated through the 12C(58Ni,pn) reaction and investigated by in-beam γ-spectroscopic methods. The NORDBALL detector array equipped with charged particle and neutron detectors was used to detect the evaporated particles and γ-rays. The level scheme of 68As was constructed on the basis of γγ-coincidence relations up to 6 MeV excitation energy and Jπ = (15+).
For linearly coupled double-well oscillators the regularity partial chaos regularity transition i... more For linearly coupled double-well oscillators the regularity partial chaos regularity transition is found. First, an incomplete KAM scenario develops with increasing energy, from integrable pattern comprising in-phase and out-of-phase small elliptic orbits towards a partial chaos, with a deformed regular island immersed in a chaotic sea. At a critical energy a new deformed island appears as a mirror image. Above
It is shown that the coefficients Ak of angles qk, corresponding to the minima of light intensity... more It is shown that the coefficients Ak of angles qk, corresponding to the minima of light intensity in the diffraction by a circular aperture, can successfully be described by a function which appears in the electrostatic interaction energy between two uniform surface-charged spheres. The coefficient Ak defines the angle qk by sinqk = Akl/d, k = 1,2,3, where l is the wavelength of light and d is the diameter of the aperture. These coefficients may be correlated with a dimensionless function fb/R, encountered in the relation of the interaction energy terms of two spheres of equal radii R, with uniformly-distributed surface charges q and q and at a mutual distance b. The total interaction energy, i.e. the Coulomb potential energy, is W = qq/(4pe0b), where e0 is the permitivity of vacuum. This energy contains two terms, a positive one W(+) = W fb/R and negative one W(-) = W (1-fb/R). The correlation between Ak and the function fb/R is given by Ak - k = u + v fb/R,k, where u and v are con...
We study local and global correlations between the naturally invariant measure of a chaotic one-d... more We study local and global correlations between the naturally invariant measure of a chaotic one-dimensional map f and the conditionally invariant measure of the transiently chaotic map f H. The two maps differ only within a narrow interval H, while the two measures significantly differ within the images f l (H), where l is smaller than some critical number l c. We point out two different types of correlations. Typically, the critical number l c is small. The 2 value, which characterizes the global discrepancy between the two measures, typically obeys a power-law dependence on the width ⑀ of the interval H, with the exponent identical to the information dimension. If H is centered on an image of the critical point, then l c increases indefinitely with the decrease of ⑀, and the 2 value obeys a modulated power-law dependence on ⑀.
Interacting-boson-fermion-fermion model description of La83140 and comparison with levels populated by beta decay and neutron capture
Physical Review C, 1990
Page 1. PHYSICAL REVIEW C VOLUME 41, NUMBER 3 MARCH 1990 Interacting-boson-fermion-fermion model ... more Page 1. PHYSICAL REVIEW C VOLUME 41, NUMBER 3 MARCH 1990 Interacting-boson-fermion-fermion model description of ' Las3 and comparison with levels populated by beta decay and neutron capture R. A. Meyer' Division ...
Alpha satellites are tandemly repeated sequences found in all human centromeres. In addition to t... more Alpha satellites are tandemly repeated sequences found in all human centromeres. In addition to the functional and structural role within centromere they are also a suitable model for evolutionary studies, because of being subject to concerted evolution. The Global Repeat Map (GRM) algorithm is a convenient computational tool to determine consensus repeat units and their exact size within a given genomic sequence, both of monomeric and higher-order (HOR) type. Using GRM, we identify in Build 37.2 assembly fifteen different alpha satellite HORs, three of them novel, not reported previously. In the next step we compute suprachromosomal family classification and CENP-B box / pJ distributions for these HORs. All human alpha satellite sequences originate from one pra-ancestral alpha satellite monomer. For the first time we perform GRM analysis and compare human and chimpanzee alpha satellite HORs for chromosomes 4 and give an evidence that the human and chimpanzee alpha satellites originate from a common ancestor that predated the human-chimpanzee separation. We also compare the codon-like trinucleotide (CLT) extensions of human and chimpanzee chromosome 4. Our results are consistent with the expectation that the alpha satellite HORs in human and chimpanzee have been created after the human-chimpanzee separation.
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Papers by Vladimir Paar