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The study investigated the phenomenon of the fast aggregation of single-domain magnetic iron oxide nanoparticles in stable aqueous colloidal suspensions due to the presence of a radio-frequency (RF) magnetic field. Single-domain nanoparticles have specific magnetic properties, especially the unique property of absorbing the energy of such a field and releasing it in the form of heat. The localized heating causes the colloid to become unstable, leading to faster agglomeration of nanoparticles and, consequently, to rapid sedimentation. It has been shown that the destabilization of a stable magnetic nanoparticle colloid by the RF magnetic field can be used for the controlled filtration of larger agglomerates of the colloid solution. Two particular cases of stable colloidal suspensions were considered: a suspension of the bare nanoparticles in an alkaline solution and the silica-stabilized nanoparticles in a neutral solution. The obtained results are important primarily for biomedical applications and wastewater treatment.

In this work, we use computer simulations (Molecular Dynamics) to analyse the behaviour of a specific auxetic hierarchical mechanical metamaterial composed of square-like elements. We show that, depending on the design of hinges connecting structural elements, the system can exhibit a controllable behaviour where different hierarchical levels can deform to the desired extent. We also show that the use of different hinges within the same structure can enhance the control over its deformation and mechanical properties, whose results can be applied to other mechanical metamaterials. In addition, we analyse the effect of the size of the system as well as the variation in the stiffness of its hinges on the range of the exhibited auxetic behaviour (negative Poisson’s ratio). Finally, it is discussed that the concept presented in this work can be used amongst others in the design of highly efficient protective devices capable of adjusting their response to a specific application.

Metallic surfaces, exposed to a proton flux, start to degradate by molecular hydrogen blisters. These are created by recombination of protons with metal electrons. Continued irradiation progresses blistering, which is undesired for many technical applications. In this work, the effect of the proton flux magnitude onto the degradation of native metal oxide layers and its consequences for blister formation has been examined. To study this phenomenon, we performed proton irradiation experiments of aluminium surfaces. The proton kinetic energy was chosen so that all recombined hydrogen is trapped within the metal structure. As a result, we discovered that intense proton irradiation increases the permeability of aluminium oxide layers for hydrogen atoms, thereby counteracting blister formation. These findings may improve the understanding of the hydrogen blistering process, are valid for all metals kept under terrestrial ambient conditions, and important for the design of proton irradiation tests.

Through the use of the Monte Carlo simulations utilising the mean-field approach, we show that a dense assembly of separated ultra-small magnetic nanoparticles embedded into a non-magnetic deformable matrix can be characterized by a large isothermal magnetic entropy change even upon applying a weak magnetic field with values much smaller than one Tesla. We also show that such entropy change may be very significant in the vicinity of the room temperature which effect normally requires an application of a strong external magnetic field. The deformable matrix chosen in this work as a host for magnetic nanoparticles adopts a thin film form with a large surface area to volume ratio. This in turn in combination with a strong magneto-volume coupling exhibited by this material allows us to show its suitability to be used in the case of a variety of applications utilising local cooling/heating such as future magnetic refrigerants.

H2O ice is known to exist as a number of different polymorphs. One such polymorph is ice X, a symmetrical phase of ice which is known to be stable at high pressures and low temperatures. In this work, the mechanical properties of ice X have been studied through DFT simulations, and it has been shown that ice X has the potential to exhibit auxetic behaviour (negative Poisson's ratio) at 45° off-axis in the (100), (010) and (001) planes. Studying the deformation of two orthogonally interconnected rhombi has shown that this predicted negative Poisson's ratio can be attributed to the interplay between distortion and hinging of these rhombi. Moreover, it has been shown that the auxetic potential of ice X increases with an increase in hydrostatic pressure, which behaviour is explained by the rhombi approaching quasi-perfect behaviour resulting in a decrease in the distortion of the rhombi and an increase in hinging mechanism.

Distribution of the isoelectric point (pI) was calculated for the hypervariable regions of Fab fragments of the antibody molecules, which structure is annotated in the structural antibody database SabDab. The distribution is consistent with the universal for all organisms dividing the proteome into two sets of acidic and basic proteins. It shows the additional fine structure in a form of the narrow-sized peaks of pI values. This is an explanation why a small change of the environmental pH can have a strong effect on the antibody-antigen affinity. To show this, a typical enzyme-linked immunospecific assay experiment for testing the reaction of goat anti-human IgA antibodies with human IgA immunoglobulins of saliva as antigens was modified in such a way that Fe3O4 magnetic nanoparticles were added to PBS buffer. The magnetic nanoparticles were remotely heated by the radio frequency magnetic field providing the local change of temperature and pH. It was observed that short times of the heating were significantly increasing the antibody-antigen binding strength while it was not the case for a longer time. The finding discussed in the study can be useful for biopharmaceuticals using antibodies, the immunoassay techniques as well as for control over the use of hyperthermia.

This paper presents a description of an experiment in which the survival rate of the probiotic bacteria Lactobacillus acidophilus PCM2499 was increased only due to the presence of Fe3O4 magnetic nanoparticles. The survival rate increased from 1.3 to 10 times compare to the control. It has been shown that the minimum concentration of NPs with a positive effect equals 8 mg/ml and the maximum concentration of the NPs equals 24 mg/ml.

The potential of several classes of mechanical metamaterials to induce their own overall rotational motion through the individual rotation of their subunits is examined. Using a theoretical approach, we confirm that for various rotating rigid unit systems, if by design the sum of angular momentum of subunits rotating in different directions is made to be unequal, then the system will experience an overall rotation, the extent of which may be controlled through careful choice of the geometric parameters defining these systems. This phenomenon of self-induced rotation is also confirmed experimentally. Furthermore, we discuss how these systems can be designed in a special way so as to permit extended rotations which allows them to overcome geometric lockage and the relevance of this concept in applications ranging from satellites to spacecraft and telescopes employed in space.

In this work, we investigate the possibility of using magnetic nanoparticles embedded into the silica to locally heat up the silica-water interface where the increase in temperature of nanoparticles is induced by an external radio-frequency magnetic field. Through the use of the theoretical model, it is shown that such the process leads to an increase in the total negative charge of the silica surface due to the deprotonation of silanol groups. It is also shown that the efficiency of such an electric charging process depends on the size of nanoparticles. Moreover, the optimal size of nanoparticles allowing for a maximum charging efficiency is determined. This observation may prove to be very important from the point of view of potential applications as it may allow to fine-tune chemical reactions on the silica surface. Some aspects of this work related to the magnetically heated nanoparticles were verified by the experiment.

C. Zerafa and R. Cauchi acknowledge the support of the Strategic Educational Pathways Scholarship Scheme (Malta). These STEPS scholarships are part-financed by the European Union European Social Fund. B. Zapotoczny thanks for the PhD grant under Sub-Action 8.2.2 Regional Innovation Strategies, Activity 8.2 Know-How Transfer, Priority VIII Regional Business Personnel of the Human Capital Operational Programme, co-funded from the EU resources within the European Social Fund as well as the state budget and the Lubuskie Voivodship., It is shown that the self-consistency condition which is the basic equation for calculating the mean-field order parameter of any mean-field model Hamiltonian can be replaced by the standard Metropolis Monte Carlo scheme. The advantage of this method is its ease of implementation for both the homogeneous mean-field order parameter and the heterogeneous one. To be specific, the mean-field version of the Ising model spin system is discussed in detail and the resulting magnetization is the same as in the case of solving the respective mean-field self-consistency equation. In addition, it is shown that if a high temperature phase of such system is quenched below critical temperature then the mean field experienced by spins develops into a network of domains in analogous way as it happens with the spins in the case of the exact many-body Hamiltonian system and the coarsening processes start to take place. To show that the introduced Metropolis Monte Carlo method works also in case of the continuous variables the order parameter for the Maier-Saupe model for nematic liquid crystals has been calculated., peer-reviewed

In the present study, the buffering effect of magnetite nanoparticles (Fe 3 O 4 ) dispersed in an aqueous solution on the local p H value is investigated. It manifests itself in the fact that when some amount of acid or base is added to the solution then the solution near the nanoparticles surface becomes, respectively, less acidic and less alkaline than it is expected. It is the result of both the local electrostatic field, which represents the electric double layer at the surface of magnetic nanoparticles and the magnetic field around the nanoparticles. The magnetite nanoparticles exhibit very low toxicity and they are becoming increasingly important for new biomedical applications related to their effects on chemical reactions in body tissues and cells. The question arises, how strong are these effects at the nanoscale? The strength of the buffering property of magnetite nanoparticles is investigated both theoretically and experimentally by the direct measurement of the local p H value of a magnetic nanoparticles suspension. The theoretical model is based on stochastic equations describing the ions diffusing in the neighborhood of the electric double layer of the magnetic material. The electric double layer is modeled with the help of the Poisson–Boltzmann model. It is directly shown that both the electrostatic field and the magnetic field are responsible for the observed local changes of the p H value with respect to the bulk p H value.

In this work, we investigate the deformation mechanism of auxetic hierarchical rotating square systems through a dynamics approach. We show how their deformation behaviour, hence their mechanical properties and final configuration for a given applied load, can be manipulated solely by altering the resistance to rotational motion of the hinges within the system. This provides enhanced tunability without necessarily changing the geometry of the system, a phenomenon which is not typically observed in other non-hierarchical unimode auxetic systems. This gives this hierarchical system increased versatility and tunability thus making it more amenable to be employed in practical application which may range from smart filtration to smart dressings.

In this work, we propose the concept that a device based on mechanical metamaterials can be used to induce and control its own rotational motion as a result of internal deformations due to the conversion of translational degrees of freedom into rotational ones. The application of a linear force on the structural units of the system may be fine-tuned in order to obtain a desired type of rotation. In particular, we show, how it is possible to maximise the extent of rotation of the system through the alteration of the geometry of the system. We also show how a device based on this concept can be connected to an external body in order to rotate it which result may potentially prove to be very important in the case of applications such as telescopes employed in space., peer-reviewed

Nanocrystalline 0.95MnO/0.05ZnO sample has been prepared by coprecipitation and calcination processes. X-ray diffraction showed the presence of Mn 3 O 4 nanocrystallites with an average size of 43 nm. Magnetic properties of the 0.95MnO/0.05ZnO sample have been investigated by dc magnetization and magnetic resonances (electron paramagnetic resonance (EPR), ferromagnetic resonance (FMR)) methods. The magnetization study has shown the presence of dominating Mn 3 O 4 paramagnetic and ferrimagnetic (below 46 K) phases. The blocking temperature determined from magnetization measurements was 41 K. An FMR study has shown the evidence of the spread of nanoparticles sizes. An EPR signal from paramagnetic phase of Mn 3 O 4 was observed at temperatures above 45 K and from defects/spurious phases in the low temperature range ( T

Modified titanate nanotubes (TNT) were tested for their adsorption of methylene blue (MB) from water solutions. They were obtained from the TiO2 nanopowder using a standard alkaline hydrothermal method but in the stage of acid washing, when the titanate flakes begin to roll into nanotubes, magnetite nanoparticles were added. The Fe3O4 magnetic nanoparticles with diameter of around 2[Formula: see text]nm and 12[Formula: see text]nm were used in the tests. Significantly stronger adsorption of MB was observed when smaller nanoparticles were used compared to using larger nanoparticles and compared to the case of unmodified nanotubes. It was shown that the increased adsorption of MB is associated with a more negative value of [Formula: see text]-potential for titanates modified by the ultra-small nanoparticles. In the adsorption experiment, pH 7 was selected. These results may prove to be of great importance in the case of potential applications corresponding to the use of such material for wastewater purification.

The magnetic properties of the viscoelastic materials filled with magnetic nanoparticles strongly depend on the viscosity of these materials. The time–temperature changes of the viscosity can affect the orientation ordering of the anisotropy axes of the magnetic nanoparticles after an external magnetic field is applied. In consequence, the absorption lines obtained in the ferromagnetic resonance experiment (FMR) will possess an additional temperature dependence through the viscosity of the materials under consideration. The particular case of the temperature dependence of the FMR signal detected from the γ-Fe2O3 (maghemite) magnetic nanoparticles dispersed at low concentration (0.1 wt.%) in a poly(ether-ester) multiblock copolymer (PEN-block-PTMO)) matrix has been investigated. A strong increase of the resonance line amplitude is observed with increasing temperature. We note also two qualitatively different temperature dependences of the magnetic resonance field at low and high temperatures. A simplified theoretical model of a single cluster consisting of N magnetic nanoparticles in an elastic polymer matrix is introduced to explain these temperature dependences of the absorption lines. The model is based on the stochastic version of the Lifshitz–Landau equation for nanoparticle magnetization.

This work discusses the concept of allowing the control of the stiffness of a particular class of re-entrant auxetic magneto-mechanical metamaterials through the introduction of magnets to the system. It is shown, through experimental testing backed up by a theoretical model, that the appropriate insertion of magnets in such a system will alter its stiffness, possibly even making it exhibit ‘negative stiffness’. This leads to a completely different behaviour of the structure in terms of stability. It is also reported that the investigated mechanical metamaterials may exhibit both negative stiffness and negative Poisson's ratio at the same time. Moreover, it is shown that the effect which magnets have on the stiffness of the system may be fine-tuned upon replacing magnets with electromagnets. Such systems have the potential to be used in a wide range of practical applications such as vibration damping devices where achieving a negative stiffness is of fundamental importance.

Mechanical properties of a thin magnetic film subjected to an external, rotating magnetic field have been studied by computer simulations. The film is modeled by a two-dimensional bead-spring model of a non-magnetic polymer matrix with inclusions of magnetic nanoparticles (nanograins) of uniaxial anisotropy. The isotropic polymer matrix is represented as a hexagonal structure with sites decorated with small hexagonal particles containing magnetic nanograins. The beads correspond to polymer segments and the springs between them imitate chemical bonds, approximated by harmonic interactions. The beads also interact by the Lennard–Jones potential whose role is to mimic the core of non-bonded polymer segments. The Poisson ratio of the constructed polymer matrix is negative, i.e. the system expands laterally under longitudinal stretching force. It is shown that the magneto-elastic coupling can be used to control the expansion and contraction of the polymer matrix. Depending on the applied magnetic field, the Poisson ratio of the magnetic film may assume positive or negative values.

A ferromagnetic resonance (FMR) spectrum of carbon coated magnetic nanoparticles in a non-magnetic elastic matrix has been investigated. The experimental absorption data have been compared with analogous data obtained with the help of the stochastic Landau–Lifshitz equation for the magnetic moment of a ferromagnetic single-domain nanoparticle and stochastic equations describing rotational oscillations of the polymer region containing a magnetic nanoparticle. We have shown that if polymer matrix anisotropies are blocking the rotational freedom of the easy axes direction of the magnetic nanoparticles, additional resonance peaks can appear in the FMR spectrum which are satellite peaks accompanying the main resonance peak. This is another mechanism for the appearance of additional peaks in the FMR spectra besides the spin-waves exchange mode in nanoparticles or inter-particle dipolar interactions. The compound Poisson process has been used to model this effect of additional correlations introduced on the motion of the particle’s magnetic moment.

We have presented some practical consequences on the molecular-dynamics simulations arising from the numerical algorithm published recently in paper Int. J. Mod. Phys. C 16, 413 (2005). The algorithm is not a finite-difference method and therefore it could be complementary to the traditional numerical integrating of the motion equations. It consists of two steps. First, an analytic form of polynomials in some formal parameter $\lambda$ (we put $\lambda=1$ after all) is derived, which approximate the solution of the system of differential equations under consideration. Next, the numerical values of the derived polynomials in the interval, in which the difference between them and their truncated part of smaller degree does not exceed a given accuracy $\epsilon$, become the numerical solution. The particular examples, which we have considered, represent the forced linear and nonlinear oscillator and the 2D Lennard-Jones fluid. In the latter case we have restricted to the polynomials of the first degree in formal parameter $\lambda$. The computer simulations play very important role in modeling materials with unusual properties being contradictictory to our intuition. The particular example could be the auxetic materials. In this case, the accuracy of the applied numerical algorithms as well as various side-effects, which might change the physical reality, could become important for the properties of the simulated material., Comment: 11 pages

There are three main elements deciding about the effect of mutations on the protein coding sequences-the type of the substitution of nucleotide, the selection for the function of the gene product and the nature of the genetic code itself. Selection used to be considered as the only directional process among the evolutionary mechanisms. In fact the mutational pressure is also ''directional'' which means that the rates of particular nucleotide substitutions tend to produce a DNA molecule with a specific nucleotide composition. Using Monte Carlo simulations we have shown that the genetic code plays the central role in buffering the effect of mutations and that all three elements are optimised in the generation of the genetic diversity in such a way that deleterious effects of mutations are substantially reduced.

Directional mutation pressure associated with replication processes is the main cause of the asymmetry between the leading and lagging DNA strands in bacterial genomes. On the other hand, the asymmetry between sense and antisense strands of protein coding sequences is a result of both mutation and selection pressures. Thus, there are two different ways of superposition of the sense strand, on the leading or lagging strand. Besides many other implications of these two possible situations, one seems to be very important - because of the asymmetric replication-associated mutation pressure, the mutation rate of genes depends on their location. Using Monte Carlo methods, we have simulated, under experimentally determined directional mutation pressure, the divergence rate and the elimination rate of genes depending on their location in respect to the leading/lagging DNA strands in the asymmetric prokaryotic genome. We have found that the best survival strategy for the majority of genes is to sometimes switch between DNA strands. Paradoxically, this strategy results in higher substitution rates but remains in agreement with observations in bacterial genomes that such inversions are very frequent and divergence rate between homologs lying on different DNA strands is very high.

We present an algorithm for the Cauchy problem for the ordinary differential equations which is based on symbolic programming. It is complementary to numerical methods, which use the finite differences. The algorithm consists of two steps. First, it yields a set of polynomials of a given degree n in some formal parameter λ. They represent an analytic form of the truncated solution of the system of differential equations under consideration and the larger value of n the larger interval in which this approximation satisfies the chosen accuracy criterion. We put λ = 1 afterall. The second step is purely numerical. Namely, the numerical values of the polynomials in the interval, in which the difference between them and the polynomials of the smaller degree n - j (for certain j) does not exceed a given accuracy ε, become the numerical solution. In the point, where this accuracy criterion fails the new initial values are defined, just at this "disagreement point", and the whole procedure is repeated.

Three methods, based on DNA asymmetry, the distribution of DnaA boxes and dnaA gene location, were applied to identify the putative replication origins in 120 chromosomes. The chromosomes were classified according to the agreement of these methods and the applicability of these methods was evaluated. DNA asymmetry is the most universal method of putative oriC identification in bacterial chromosomes, but it should be applied together with other methods to achieve better prediction. The three methods identify the same region as a putative origin in all Bacilli and Clostridia, many Actinobacteria and gamma Proteobacteria. The organization of clusters of DnaA boxes was analysed in detail. For 76 chromosomes, a DNA fragment containing multiple DnaA boxes was identified as a putative origin region. Most bacterial chromosomes exhibit an overrepresentation of DnaA boxes; many of them contain at least two clusters of DnaA boxes in the vicinity of the oriC region. The additional clusters of DnaA boxes are probably involved in controlling replication initiation. Surprisingly, the characteristic features of the initiation of replication, i.e. a cluster of DnaA boxes, a dnaA gene and a switch in asymmetry, were not found in some of the analysed chromosomes, particularly those of obligatory intracellular parasites or endosymbionts. This is presumably connected with many mechanisms disturbing DNA asymmetry, translocation or disappearance of the dnaA gene and decay of the Escherichia coli perfect DnaA box pattern.

Surprisingly, still very little is known about the mathematical modeling of peaks in the binding affinities distribution function. In general, it is believed that the peaks represent antibodies directed towards single epitopes. In this paper, we refer to fluorescence flow cytometry experiments and show that even monoclonal antibodies can display multi-modal histograms of affinity distribution. This result take place when some obstacles appear in the paratope–epitope reaction such that the process of reaching the specific epitope ceases to be a point Poisson process. A typical example is the large area of cell surface, which could be unreachable by antibodies leading to the heterogeneity of the cell surface repletion. In this case the affinity of cells to bind the antibodies should be described by a more complex process than the pure-Poisson point process. We suggested to use a doubly stochastic Poisson process, where the points are replaced by a binomial point process resulting in the Neyman distribution. The distribution can have a strongly multinomial character, and with the number of modes depending on the concentration of antibodies and epitopes. All this means that there is a possibility to go beyond the simplified theory, one response towards one epitope. As a consequence, our description provides perspectives for describing antigen–antibody reactions, both qualitatively and quantitavely, even in the case when some peaks result from more than one binding mechanism.

The two main mechanisms generating the genetic diversity, mutation and recombination, have random character but they are biased which has an e1ect on the generation ofasymmetry in the bacterial chromosome structure and in the protein coding sequences. Thus, like in a case oftwo chiral molecules—the two possible orientations ofa gene in relation to the topology ofa chromosome are not equivalent. Assuming that the sequence ofa gene may oscillate only between certain limits ofits structural composition means that the gene could be f orced out ofthese limits by the directional mutation pressure, in the course ofevolution. The probability ofthe event depends on the time the gene stays under the same mutation pressure. Inversion ofthe gene changes the directional mutational pressure to the reciprocal one and hence it changes the distance ofthe gene to its lower and upper bound ofthe structural tolerance. Using Monte Carlo methods we were able to simulate the evolution ofgenes under experimentally found mutational pressure, assuming simple mechanisms of selection. We found that the mutation and recombination should work in accordance to lower their negative e1ects on the f unction ofthe products ofcoding sequences. c

The widespread use of metallic structures in space technology brings risk of degradation which occurs under space conditions. New types of materials dedicated for space applications, that have been developed in the last decade, are in majority not well tested for different space mission scenarios. Very little is known how material degradation may affect the stability and functionality of space vehicles and devices during long term space missions. Our aim is to predict how the solar wind and electromagnetic radiation degrade metallic structures. Therefore both experimental and theoretical studies of material degradation under space conditions have been performed. The studies are accomplished at German Aerospace Center (DLR) in Bremen (Germany) and University of Zielona Gora (Poland). The paper presents the results of the theoretical part of those studies. It is proposed that metal bubbles filled with Hydrogen molecular gas, resulting from recombination of the metal free electrons and the solar protons, are formed on the irradiated surfaces. A thermodynamic model of bubble formation has been developed. We study the creation process of H 2 -bubbles as function of, inter alia, the metal temperature, proton dose and energy. Our model has been verified by irradiation experiments completed at the DLR facility in Bremen. Consequences of the bubble formation are changes of the physical and thermo-optical properties of such degraded metals. We show that a high surface density of bubbles (up to 10 8 cm - 2 ) with a typical bubble diameter of ∼ 0.4 μm will cause a significant increase of the metallic surface roughness. This may have serious consequences to any space mission. Changes in the thermo-optical properties of metallic foils are especially important for the solar sail propulsion technology because its efficiency depends on the effective momentum transfer from the solar photons onto the sail structure. This transfer is proportional to the reflectivity of a sail. Therefore, the propulsion abilities of sail material will be affected by the growing population of the molecular Hydrogen bubbles on metallic foil surfaces.

There are many biological mechanisms which introduce long-range correlations into the DNA molecule. One of the most important is replication of chromosomes, its mechanisms andtopology. Replication associatedmutational pressure, d e3nedas speci3c preferences in nucleotid e substitutions during replication, generates asymmetry in the genome. On the other hand, substitution rates, which determine the evolutionary turnover time of a nucleotide, are highly correlated with the fraction of that nucleotide in the genome. Assuming the Azbel hypothesis that the number of mutations per genome per generation is invariant anduniversal, a general rule for mutational pressure can be formulated: the half-time of a nucleotide turnover in the genome is linearly dependent on the number of this nucleotide in the genome. c

In this work, we investigate the evolution of magnetic domains with time in magnetic auxetic systems using the Ising model. We show that the mechanical deformation of the structure affects the way how domains evolve and that their rate of growth does not follow a well-known power law associated with the Ising model for systems corresponding to a specific distance between Ising spins. We also show that the variation in the rate of deformation of the system leads to completely different results in terms of the change in size of magnetic domains and domain energy. This means that upon changing the speed used to deform the system, it is possible to control the growth of magnetic domains and hence control the magnetic properties of the whole system. This may prove to be very important in the case of potential applications such as magnetic freezers where the magnetocaloric effect resulting with a change in temperature could be affected by the rate of deformation of the discussed auxetic structure.

We have elaborated a method which has allowed us to estimate the direction of translocation of orthologs which have changed, during the phylogeny, their positions on chromosome in respect to the leading or lagging role of DNA strands. We have shown that the relative number of translocations which have switched positions of genes from the leading to the lagging DNA strand is lower than the number of translocations which have transferred genes from the lagging strand to the leading strand of prokaryotic genomes. This paradox could be explained by assuming that the stronger mutation pressure and selection after inversion preferentially eliminate genes transferred from the leading to the lagging DNA strand.

We discuss the Lotka–Volterra dynamics of two populations, preys and predators, in the case when the predators posses a genetic information. The genetic information is inherited according to the rules of the Penna model of genetic evolution. Each individual of the predator population is uniquely determined by sex, genotype and phenotype. In our case, the genes are represented by 8-bit integers and the phenotypes are defined with the help of the 8-state Potts model Hamiltonian. We showed that during time evolution, the population of the predators can experience a series of dynamical phase transitions which are connected with the different types of the dominant phenotypes present in the population.

We have analyzed the inuence of constant mutational pressure and selection on the nucleotide composition of DNA sequences of various size, which were represented by the genes of the Borrelia burgdorferi genome. With the help of MC simulations we have found that longer DNA sequences accumulate much less base substitutions per sequence length than short sequences. This leads us to the conclusion that the accuracy of replication may determine the size of genome. c 1999 Elsevier Science B.V. All rights reserved. PACS: 87.14.G; 87.23.Kg

We have performed detrended DNA walks on whole prokaryotic genomes, on noncoding sequences and, separately, on each position in codons of coding sequences. Our method enables us to distinguish between the mutational pressure associated with replication and the mutational pressure associated with transcription and other mechanisms that introduce asymmetry into prokaryotic chromosomes. In many prokaryotic genomes, each component of mutational pressure affects coding sequences not only in silent positions but also in positions in which changes cause amino acid substitutions in coded proteins. Asymmetry in the silent positions of codons differentiates the rate of translation of mRNA produced from leading and lagging strands. Asymmetry in the amino acid composition of proteins resulting from replication-associated mutational pressure also corresponds to leading and lagging roles of DNA strands, whereas asymmetry connected with transcription and coding function corresponds to the distance of genes from the origin or terminus of chromosome replication.

We have analyzed third position in codons and have observed strong long-range correlations along DNA sequence. We have shown that the correlations are caused mostly by asymmetric replication. In the analysis, we have used a DNA walk (spider analysis Cebrat et al., Microbial Comparative Genomics 2(4) (1997) 259–268) in two-dimensional space [A–T,G–C]. The particular case of the E.coli sequence has been studied in detail.

We have performed several kinds of DNA walks which often are the first steps for further analysis of DNA structure and long range correlations. The DNA walks analysing frequency of G+C versus A+T cannot indicate the coding strand while purine versus pyrimidine DNA walks or two-dimensional (A-T,G-C) DNA walks in some instances can indicate the coding strand but cannot resolve the coding frame. The modified two-dimensional (A-T,G-C) DNA walks respecting the three-nucleotide codon structure show very high correlation in nucleotide composition of DNA coding sequences. They can distinguish between coding and non-coding sequences and indicate the strand and the phase in which DNA is coding.

We have studied the Q +1 state Potts model to describe the late stage sintering process in metal powders. Potts spins with the values q =1,..., Q were associated with the metal grain orientations, whereas the value q = Q +1 was associated with vacancies. With the help of Monte Carlo simulations, we showed that the kinetics of growing metal grains with small porosity is consistent with the classic t 1/2 domain growth law for non-conserved systems.

The genetic code has a very interesting property--it generates an open reading frame (ORF) inside a coding sequence, in a specific phase of the antisense strand with much higher probability than in the random DNA sequences. Furthermore, these antisense ORFs (A-ORFs) possess the same features as real genes--the asymmetry in the nucleotide composition at the first and second positions in codons. About two thirds of the 2997 overlapping ORFs in the yeast genome possess this feature. Thus, the question arises: has this feature of the genetic code been exploited in the evolution of genes? We have searched the FASTA data bases for homologies with the antisense translation products of a specific class of genes and we have found some sequences with relatively high homology. Many of them have scores which could be randomly found in the searched data bases with a probability lower than 10(-6). We conclude that some genes could arise by positioning a copy of the original gene under a promoter in the opposite direction in such a way that both, the original gene and its copy initially use the same nucleotides in the third, degenerated positions in codons.

We have examined a lattice model of strip spreading in the presence of surface potential and repulsive interactions between adatoms. In particular, we have analyzed adsorbate island evolution during the transition to a more stable configuration of adatoms. We present a concentration profile evolution, corresponding diffraction pattern changes, diffusion coefficients obtained from Boltzmann-Matano analysis, and a dynamic structure factor S ( k , t ).

We have used the asymmetry between the coding and noncoding strands in different codon positions of coding sequences of DNA as a parameter to evaluate the coding probability for open reading frames (ORFs). The method enables an approximation of the total number of coding ORFs in the set of analyzed sequences as well as an estimation of the coding probability for the ORFs. The asymmetry observed in the nucleotide composition of codons in coding sequences has been used successfully for analysis of the genomes completed at the time of this analysis.

We consider, using Monte Carlo simulations, diffusion of particles on a square lattice. The particles do not interact among themselves, except that at the same lattice site there cannot be more than particles. Since the interactions in our model are a milder version of the well known hard-core (HC) lattice gas, for which , we decided to call our model the soft-core (SC) lattice gas. We find the dependence of the correlation factor on the concentration of completely filled sites and show that the correlations decrease with increasing . We calculate analytically and via the Monte Carlo simulations the distribution function of the average number of sites occupied by a given number of particles. The curves show that for our model the `particle - hole' symmetry, typical for the HC lattice gas, disappears. In addition, we have found in 1D two regimes of diffusion for . For shorter times the diffusion is anomalous, while for longer times it becomes normal.

An algorithm determining the most likely trajectories on a percolation cluster of a random walker subject to a constant field has been constructed. The resulting trajectories are represented by self-avoiding walks for which the average time spent at a percolation incipient cluster obeys finite-size scaling behavior.

Magnetic nanopowders placed in the nonmagnetic polymer matrices become a new type of smart materials which combine mechanical properties of temperature responsive polymer matrix and magnetic response of nanoparticles. These properties are used in some biotechnological and medical applications like hyperthermia treatment, nanocolloids, magnetic nanocapsules for drug targeting, magnetic resonance imaging (MRI), intracellular manipulation etc. (e.g. (Gao & Xu, 2009; Liu et al., 2009)), in the processes of mechanical and electrical micropower generation, in nanoelectromechanical systems as MEMS/NEMS devices (e.g. (Zahn, 2001)), electromagnetic interference suppression (Wilson et al., 2004). Recently, the unusual polymer/magnetic nanoparticles systems with a negative Poisson’s ratio (e.g. ferrogels Dudek & Wojciechowski (2008); Wood & Camp (2011)) have begun to be studied. They belong to the so-called auxetic materials Evans et al. (1991); Lakes (1987); Smith & Wojciechowski (2008).

The results of research on new magnetic materials for biomedical applications are discussed. These materials are porous silicate glasses with magnetic fillers. To ensure the smallest number of components for subsequent removal from the body, the magnetic fillers are bare magnetite nanoparticles (Fe3O4). The magnetic properties of these materials have been investigated using the ferromagnetic resonance method (FMR). The FMR analysis has been complemented by scanning electron microscope (SEM) measurements. In order to examine the effect of time degradation on filling the porous glass with bare magnetite nanoparticles the FMR measurement was repeated five months later. For the samples with high degree of pore filling, in contrast to the samples with low degree of pore filling, the FMR signal was still strong. The influence of different pH values of magnetite nanoparticles aqueous suspension on the degree of filling the pores of glasses is also discussed. The experimental results are supported by computer simulations of FMR experiment for a cluster ofNmagnetic nanoparticles locked in a porous medium based on a stochastic version of the Landau-Lifshitz equation for nanoparticle magnetization.

We describe analytically the relaxation process of Brownian motion of rotators subjected to external field E, which is suddenly switched on at time t=0. The field E is constant, E=E0, or time dependent, E=E0 sin ωt. We make detailed calculations, respectively, for one dipole in the field E and two interacting dipoles in the field E. However, the method involving any finite number of rotators is described. In particular, we derive analytical formulas for the first dipole moment and compare the numerical results with the computer experiment.