Dynamic simulation studies of structural formation and transition in electro-magneto-rheological fluids

The computer simulation method has been used to study the structural formation and transition of electro-magneto-rheological (EMR) fluids under compatible electric and magnetic fields. When the fields are applied simultaneously and perpendicularly to each other, the particles rapidly arrange into two-dimensional close-packed layer structures parallel to both fields. The layers then combine together to form thicker sheet-like structures, which finally relax into three-dimensional close-packed structures with the help of the thermal fluctuations. On the other hand, if the electric field is applied firstly to induce the body-centered tetragonal (BCT) columns in the system, and then the magnetic field is applied in the perpendicular direction. the BCT to face-centered cubic (FCC) structure transition is observed in very short time. Following that. the structure keeps on evolving due to the demagnetization effect and finally form the three-dimensional close-packed structures.

Simulation of field-induced structural formation and transition in electromagnetorheological suspensions

A computer simulation method has been used to study the three-dimensional structural formation and transition of eleetromagnetorheological (EMR) suspensions under compatible electric and magnetic fields. When the fields are applied simultaneously and perpendicularly to each other, the particles rapidly arrange into single layer structures parallel to both fields. In each layer, there is a two-dimensional hexagonal lattice. The single layers then combine together to form thicker sheetlike structures. With the help of the thermal fluctuations, the thicker structures relax into three-dimensional close-packed structures, which may be face-centered cubic (fcc), hexagonal close-packed (hup) lattices, or, more probably, the mixture of them, depending on the initial configurations and the thermal fluctuations. On the other hand, if the electric field is applied first to induce the body-centered tetragonal (bct) columns in the system, and then the magnetic field is applied in the perpendicular direction, the bet to fee structure transition is observed in a very short time. Following that, the structure keeps on evolving due to the demagnetization effect and finally forms close-packed structures with fee and hcp lattice character. The simulation results are in agreement with the theoretical and experimental results.

Noise and ultraviolet divergences in the dynamics of the chiral condensate in QCD

The time evolution of the matter produced in high energy heavy-ion collisions seems to be well described by relativistic viscous hydrodynamics. In addition to the hydrodynamic degrees of freedom related to energy-momentum conservation, degrees of freedom associated with order parameters of broken continuous symmetries must be considered because they are all coupled to each other. of particular interest is the coupling of degrees of freedom associated with the chiral symmetry of QCD. Quantum and thermal fluctuations of the chiral fields act as noise sources in the classical equations of motion, turning them into stochastic differential equations in the form of Ginzburg-Landau-Langevin (GLL) equations. Analytic solutions of GLL equations are attainable only in very special circumstances and extensive numerical simulations are necessary, usually by discretizing the equations on a spatial lattice. However, a not much appreciated issue in the numerical simulations of GLL equations is that ultraviolet divergences in the form of lattice-spacing dependence plague the solutions. The divergences are related to the well-known Rayleigh-Jeans catastrophe in classical field theory. In the present communication we present a systematic lattice renormalization method to control the catastrophe. We discuss the implementation of the method for a GLL equation derived in the context of a model for the QCD chiral phase transition and consider the nonequilibrium evolution of the chiral condensate during the hydrodynamic flow of the quark-gluon plasma.

Influence from the free volume on the photoinduced birefringence in azocompound-containing polymers

The photoinduced birefringence is analyzed in a guest-host azobenzene-containing polymer in the temperature range from 20 to 330 K. An anomalous behavior arises in the low-temperature range, suggesting strong influence from the free volume for the chromophores in the polymer. This influence is so strong that quenched samples have a photoinduced signal ca. 5 times greater than the annealed ones at room temperature. An extended free volume model is presented based on two assumptions about thermal fluctuations in the cavities and their size distribution. This model, which is an extension of the model by Mita et al., can explain the main features of the photoinduced birefringence as a function of time, temperature, and initial free volume state. To account for the influence of free volume on the photoorientation, the detailed reorientation model by Sekkat's was used. We show that Sekkat's model leads to an exponential behavior at small orientation regimes, which simplifies the mathematical treatment and allows the mean free volume to be obtained from the data fitting.

Investigação da dinâmica sequêncial Monte Carlo/Mecânica Quântica para sitemas moleculares orgânicos

O principal objetivo deste trabalho é investigar teóricamente as propriedades eletrônicas e óticas de compostos orgânicos em ambiente líquido. A compreensão das interações em sistemas líquidos é muito importante para a descrição de fenômenos em muitas partes da ciência, como Física, Química, Biologia e Materiais, bem como no desenvolvimento de materiais óticos. As flutuações térmicas fazem que inumaram das configurações para os líquidos possam ser gerados. Esta é a razão do comportamento estatístico observado em sistemas líquidos. Considerando estas dificuldades, o tratamento sequencial Monte Carlo / Mecânica Quântica (SMC/QM) é usado neste trabalho. Neste procedimento, a estrutura líquida é gerada primeiramente por simulações clássicas de MC e mais tarde, somente a parte mais importante do sistema é tratada com mecânica quântica. Usando o procedimento acima, os propriedades do quantum o pirazine dimethyl do thiene Methyl da laranja (MO) e do O 2,3-dimetil tieno[3,4-b] pirazina (DTP) foram investigados. O MO é um conhecido indicador de pH e pode ser encontrado sob circunstâncias básicas e acidas. Suas geometrias de mínima energia foram obtidas mediante a Teoria do Funcional da Densidade pelo funcional B3LYP, sendo o sistema descrito pelas bases de Pople com uma função de polarização (6-31G*). Para obter as propriedades médias dos observaveis, cálculos de química quântica foram executados dentro da aproximação semi-empírica de INDO/S-CI. Com respeito ao espectro de absorção, os dados experimentais existentes na literatura científica reportam a existência de uma larga banda localizada na região de baixas energias, mais precisamente entre 400 e 600 nm. Nossos resultados teóricos para a forma alcalina mostram uma transição intensa transição π → π* aproximadamente à 432.4 ± 0.03 nm e, sob condições ácidas, esta transição aparece aproximadamente à 507.4 ± 0.12, 496.4 ± 0.28 ou 545.3 ± 0.10 nm, dependendo da estrutura, mostrando bom acordo com resultados experimentais. O DTP é um sistema particular usado na produção de polímeros de baixo gap. Suas propriedades elétricas e óticas foram obtidas através de um novo procedimento conhecido por Configuração Eletrostática Média do Solvent (ASEC). O procedimento ASEC inclui moléculas do solvente como cargas pontuais e permite o obtenção das quantidades quânticas executando somente poucos cálculos de mecânica quântica. Para o DTP, usando a teoria das perturbações de segunda ordem Mφller-Plesset (MP2) e o conjunto de bases aug-cc-pVDZ, a convergência do momento de dipolo foi alcançada com apenas quatro cálculos de mecânica quântica à 1.16 D, apresentando um aumento de 42% quando comparado ao dipolo isolado. O polarizabilidade corresponde à outra característica elétrica que pôde ser medida. Considerando o mesmo nível empregado ao cálculo do dipolo, o valor médio 132.7 a30 foi observado. A região de mais baixas da energias do espectro de absorption foi investigada também atravé de procedimento de ASEC usando ambos as aproximações, semi-empírico e DFT. Esta região de absorção é motivo de conclusões contraditórias com relação à natureza das transições n → π* e π → π*. Nossos resultados mostram que realmente que essas excitações são realmente observadas simultanemente podendo sobrepôr-se. Como exemplo, nossos resultados para DFT, encontrados usando o funcional B3LYP nos mostra que estas transições aparecem aproximadamente à 360.6 e 351.1 nm.

Molecular and Electronic Structure of the Peptide Subunit of Geobacter sulfurreducens Conductive Phi from First Principles

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved a-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pain was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's alpha-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

Dynamic symmetry loss of high-frequency hysteresis loops in single-domain particles with uniaxial anisotropy

Understanding how magnetic materials respond to rapidly varying magnetic fields, as in dynamic hysteresis loops, constitutes a complex and physically interesting problem. But in order to accomplish a thorough investigation, one must necessarily consider the effects of thermal fluctuations. Albeit being present in all real systems, these are seldom included in numerical studies. The notable exceptions are the Ising systems, which have been extensively studied in the past, but describe only one of the many mechanisms of magnetization reversal known to occur. In this paper we employ the Stochastic Landau-Lifshitz formalism to study high-frequency hysteresis loops of single-domain particles with uniaxial anisotropy at an arbitrary temperature. We show that in certain conditions the magnetic response may become predominantly out-of-phase and the loops may undergo a dynamic symmetry loss. This is found to be a direct consequence of the competing responses due to the thermal fluctuations and the gyroscopic motion of the magnetization. We have also found the magnetic behavior to be exceedingly sensitive to temperature variations, not only within the superparamagnetic-ferromagnetic transition range usually considered, but specially at even lower temperatures, where the bulk of interesting phenomena is seen to take place. (C) 2011 Elsevier B.V. All rights reserved.

Mechanics and dynamics of liposomes and cells studied by QCM and ECIS

The present thesis introduces a novel sensitive technique based on TSM resonators that provides quantitative information about the dynamic properties of biological cells and artificial lipid systems. In order to support and complement results obtained by this method supplementary measurements based on ECIS technique were carried out. The first part (chapters 3 and 4) deals with artificial lipid systems. In chapter 3 ECIS measurements were used to monitor the adsorption of giant unilamellar vesicles as well as their thermal fluctuations. From dynamic Monte Carlo Simulations the rate constant of vesicle adsorption was determined. Furthermore, analysis of fluctuation measurements reveals Brownian motion reflecting membrane undulations of the adherent liposomes. In chapter 4 QCM-based fluctuation measurements were applied to quantify nanoscopically small deformations of giant unilamellar vesicles with an external electrical field applied simultaneously. The response of liposomes to an external voltage with shape changes was monitored as a function of cholesterol content and adhesion force. In the second part (chapters 5 - 8) attention was given to cell motility. It was shown for the first time, that QCM can be applied to monitor the dynamics of living adherent cells in real time. QCM turned out to be a highly sensitive tool to detect the vertical motility of adherent cells with a time resolution in the millisecond regime. The response of cells to environmental changes such as temperature or osmotic stress could be quantified. Furthermore, the impact of cytochalasin D (inhibits actin polymerization) and taxol (facilitate polymerization of microtubules) as well as nocodazole (depolymerizes microtubules) on the dynamic properties of cells was scrutinized. Each drug provoked a significant reduction of the monitored cell shape fluctuations as expected from their biochemical potential. However, not only the abolition of fluctuations was observed but also an increase of motility due to integrin-induced transmembrane signals. These signals were activated by peptides containing the RGD sequence, which is known to be an integrin recognition motif. Ultimately, two pancreatic carcinoma cell lines, derived from the same original tumor, but known to possess different metastatic potential were studied. Different dynamic behavior of the two cell lines was observed which was attributed to cell-cell as well as cell-substrate interactions rather than motility. Thus one may envision that it might be possible to characterize the motility of different cell types as a function of many variables by this new highly sensitive technique based on TSM resonators. Finally the origin of the broad cell resonance was investigated. Improvement of the time resolution reveals the "real" frequency of cell shape fluctuations. Several broad resonances around 3-5 Hz, 15-17 Hz and 25-29 Hz were observed and that could unequivocally be assigned to biological activity of living cells. However, the kind of biological process that provokes this synchronized collective and periodic behavior of the cells remains to be elucidated.

The coupling between electron transfer and Protein/Solvent Dynamics in Photosynthetic Reaction Centers: Spectroscopic Studies in Amorphous Matrices

We investigated at the molecular level protein/solvent interactions and their relevance in protein function through the use of amorphous matrices at room temperature. As a model protein, we used the bacterial photosynthetic reaction center (RC) of Rhodobacter sphaeroides, a pigment protein complex which catalyzes the light-induced charge separation initiating the conversion of solar into chemical energy. The thermal fluctuations of the RC and its dielectric conformational relaxation following photoexcitation have been probed by analyzing the recombination kinetics of the primary charge-separated (P+QA-) state, using time resolved optical and EPR spectroscopies. We have shown that the RC dynamics coupled to this electron transfer process can be progressively inhibited at room temperature by decreasing the water content of RC films or of RC-trehalose glassy matrices. Extensive dehydration of the amorphous matrices inhibits RC relaxation and interconversion among conformational substates to an extent comparable to that attained at cryogenic temperatures in water-glycerol samples. An isopiestic method has been developed to finely tune the hydration level of the system. We have combined FTIR spectral analysis of the combination and association bands of residual water with differential light-minus-dark FTIR and high-field EPR spectroscopy to gain information on thermodynamics of water sorption, and on structure/dynamics of the residual water molecules, of protein residues and of RC cofactors. The following main conclusions were reached: (i) the RC dynamics is slaved to that of the hydration shell; (ii) in dehydrated trehalose glasses inhibition of protein dynamics is most likely mediated by residual water molecules simultaneously bound to protein residues and sugar molecules at the protein-matrix interface; (iii) the local environment of cofactors is not involved in the conformational dynamics which stabilizes the P+QA-; (iv) this conformational relaxation appears to be rather delocalized over several aminoacidic residues as well as water molecules weakly hydrogen-bonded to the RC.

Quantum and classical criticality in a dimerized quantum antiferromagnet

A quantum critical point (QCP) is a singularity in the phase diagram arising because of quantum mechanical fluctuations. The exotic properties of some of the most enigmatic physical systems, including unconventional metals and superconductors, quantum magnets and ultracold atomic condensates, have been related to the importance of critical quantum and thermal fluctuations near such a point. However, direct and continuous control of these fluctuations has been difficult to realize, and complete thermodynamic and spectroscopic information is required to disentangle the effects of quantum and classical physics around a QCP. Here we achieve this control in a high-pressure, high-resolution neutron scattering experiment on the quantum dimer material TlCuCl3. By measuring the magnetic excitation spectrum across the entire quantum critical phase diagram, we illustrate the similarities between quantum and thermal melting of magnetic order. We prove the critical nature of the unconventional longitudinal (Higgs) mode of the ordered phase by damping it thermally. We demonstrate the development of two types of criticality, quantum and classical, and use their static and dynamic scaling properties to conclude that quantum and thermal fluctuations can behave largely independently near a QCP.

Ice and snow measurements during Nathaniel B. Palmer cruise NBP0709 (SIMBA experiment)

The Sea Ice Mass Balance in the Antarctic (SIMBA) experiment was conducted from the RVIB N.B. Palmer in September and October 2007 in the Bellingshausen Sea in an area recently experiencing considerable changes in both climate and sea ice cover. Snow and ice properties were observed at 3 short-term stations and a 27-day drift station (Ice Station Belgica, ISB) during the winter-spring transition. Repeat measurements were performed on sea ice and snow cover at 5 ISB sites, each having different physical characteristics, with mean ice (snow) thicknesses varying from 0.6 m (0.1 m) to 2.3 m (0.7 m). Ice cores retrieved every five days from 2 sites and measured for physical, biological, and chemical properties. Three ice mass-balance buoys (IMBs) provided continuous records of snow and ice thickness and temperature. Meteorological conditions changed from warm fronts with high winds and precipitation followed by cold and calm periods through four cycles during ISB. The snow cover regulated temperature flux and controlled the physical regime in which sea ice morphology changed. Level thin ice areas had little snow accumulation and experienced greater thermal fluctuations resulting in brine salinity and volume changes, and winter maximum thermodynamic growth of ~0.6 m in this region. Flooding and snow-ice formation occurred during cold spells in ice and snow of intermediate thickness. In contrast, little snow-ice formed in flooded areas with thicker ice and snow cover, instead nearly isothermal, highly permeable ice persisted. In spring, short-lived cold air episodes did not effectively penetrate the sea ice nor overcome the effect of ocean heat flux, thus favoring net ice thinning from bottom melt over ice thickening from snow-ice growth, in all cases. These warm ice conditions were consistent with regional remote sensing observations of earlier ice breakup and a shorter sea ice season, more recently observed in the Bellingshausen Sea.

Monte Carlo simulation of circular grain growth

Monte Carlo simulations have been carried out to study the effect of temperature on the growth kinetics of a circular grain. This work demonstrates the importance of roughening fluctuations on the growth dynamics. Since the effect of thermal fluctuations is stronger in d =2 than in d =3, as predicted by d =3 theories of domain kinetics, the circular domain shrinks linearly with time as A (t)=A(0)-αt, where A (0) and A(t) are the initial and instantaneous areas, respectively. However, in contrast to d =3, the slope α is strongly temperature dependent for T≥0.6TC. An analytical theory which considers the thermal fluctuations agrees with the T dependence of the Monte Carlo data in this regime, and this model show that these fluctuations are responsible for the strong temperature dependence of the growth rate for d =2. Our results are particularly relevant to the problem of domain growth in surface science

Underground dwellings in the Tajuña valley, Madrid, Spain and their bioclimatic adaptation

Underground dwellings are the maximum example of the vernacular architecture adaptation to the climatic conditions in areas with high annual and daily thermal fluctuations. This paper summarizes the systematic research about the energy performance of this popular architecture and their adaptation to the outdoor conditions in the case of the low area of the River Tajuña and its surroundings. Some considerations on their maintenance and renovation arise from the research.

Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure

Single chicken erythrocyte chromatin fibers were stretched and released at room temperature with force-measuring laser tweezers. In low ionic strength, the stretch-release curves reveal a process of continuous deformation with little or no internucleosomal attraction. A persistence length of 30 nm and a stretch modulus of ≈5 pN is determined for the fibers. At forces of 20 pN and higher, the fibers are modified irreversibly, probably through the mechanical removal of the histone cores from native chromatin. In 40–150 mM NaCl, a distinctive condensation-decondensation transition appears between 5 and 6 pN, corresponding to an internucleosomal attraction energy of ≈2.0 kcal/mol per nucleosome. Thus, in physiological ionic strength the fibers possess a dynamic structure in which the fiber locally interconverting between “open” and “closed” states because of thermal fluctuations.

Interaction of the histone (H3-H4)2 tetramer of the nucleosome with positively supercoiled DNA minicircles: Potential flipping of the protein from a left- to a right-handed superhelical form.

We have studied the ability of the histone (H3-H4)2 tetramer, the central part of the nucleosome of eukaryotic chromatin, to form particles on DNA minicircles of negative and positive superhelicities, and the effect of relaxing these particles with topoisomerase I. The results show that even modest positive torsional stress from the DNA, and in particular that generated by DNA thermal fluctuations, can trigger a major, reversible change in the conformation of the particle. Neither a large excess of naked DNA, nor a crosslink between the two H3s prevented the transition from one form to the other. This suggested that during the transition, the histones neither dissociated from the DNA nor were even significantly reshuffled. Moreover, the particles reconstituted on negatively and positively supercoiled minicircles look similar under electron microscopy. These data agree best with a transition involving a switch of the wrapped DNA from a left- to a right-handed superhelix. It is further proposed, based on the left-handed overall superhelical conformation of the tetramer within the octamer [Arents, G., Burlingame, R. W., Wang, B. C., Love, W. E. & Moudrianakis, E. N. (1991) Proc. Natl.Acad. Sci. USA 88, 10148-10152] that this change in DNA topology is mediated by a similar change in the topology of the tetramer itself, which may occur through a rotation (or a localized deformation) of the two H3-H4 dimers about their H3-H3 interface. Potential implications of this model for nucleosome dynamics in vivo are discussed.