Lattice Models Research Papers - Academia.edu (original) (raw)

An overview of the micromechanical theoretical and numerical models of wood is presented. Different methods of analysis of the effects of wood microstructures at different scale levels on the mechanical behaviour, deformation and strength of wood are discussed and compared. Micromechanical models of deformation and strength of wood are divided into three groups: cellular models (applied most often to the mesoscale or cell scale analysis of the wood deformation), continuum micromechanics and homogenization based methods, models which consider wood as a composite and are applied mainly to the analysis of wood at the microscale (cell wall scale) level and multiscale models. Lattice and composite models, which are used to analyze the damage and fracture of wood, are considered in a separate section. The areas of applicability and strong sides of each approach are discussed.

- by Vladimir Teif
- •
- DNA condensation, DNA-ligand binding, Cooperative Binding, Lattice Models

Combining a wide range of protein adsorption experiments (three globular proteins on eight well-defined homogeneous surfaces) with Monte Carlo simulations of lattice proteins at different concentrations and on surfaces of varying "polarity", we explore the extent and rheological behavior of adsorbed proteins as a function of substrate polarity, "on" rate constants (k a ) and steric parameters (|A 1 |) from the random sequential adsorption model, and demonstrate a folding to unfolding transition upon adsorption. We show that model globular proteins (hen egg lysozyme, ribonuclease A, and insulin dimer) behave similarly with respect to adsorption. Experimentally, above a substrate wettability cos θ > 0.4 (where θ is the sessile contact angle of water on a substrate in air), the adsorbed mass, rigidity, and k a of the proteins are diminished, while the steric factor |A 1 | is increased, suggesting a lower packing density. To analyze these results, we have invoked computer simulations. We show that changing surface polarity has two profound effects. First, the amount adsorbed increases as the surfaces become more apolar. Further, the proteins become less stable as their adsorbed amount increased because they gain a large number of interprotein and protein-surface interactions. Finally, apolar surfaces served to reduce the unfolding free energy barriers, further facilitating the reorganizing of proteins on these surfaces. Thus, increasing the nonpolar nature of the surfaces resulted in a more rigid adsorbed layer, in good agreement with the experiments.

- by Gaurav Anand
- •
- Protein adsorption, Protein Purification, Protein Folding, Protein Folding

We have developed a transfer matrix algorithm for the enumeration of compact self-avoiding walks on rectangular strips of the square lattice. The algorithm is easily adapted to other shapes or generalized to problems such as interacting... more

- by Iwan Jensen
- •
- Mathematical Sciences, Lattice Beam Model, Physical sciences, Lattice Models

In this paper, a previously developed meso-scale model for concrete, called the Confinement Shear Lattice (CSL) model, is extended in order to include the effect of loading rate on concrete strength and fracturing behavior. The rate dependence of concrete behavior is assumed to be caused by two different physical mechanisms. The first is a dependence of the fracture process on the rate of crack opening, and the second is the viscoelastic deformation of the intact (unfractured) cement paste. In this study, the first mechanism is described by the activation energy theory applied to the ruptures occurring along the crack surfaces, whereas the second mechanism is modeled by the MicroprestresseSolidification theory. The developed model is calibrated and validated on the basis of experimental data gathered from the literature.

- by Robert Helling
- •
- Mathematics, Thermodynamics, Protein Folding, Enumeration

A resistance network is a weighted graph (G,c) with intrinsic (resistance) metric R. We embed the resistance network into the Hilbert space H_ E of functions of finite energy. We use the resistance metric to study H_ E, and vice versa and show that the embedded images of the vertices {v_x} form a reproducing kernel for this Hilbert space. We also obtain a discrete version of the Gauss-Green formula for resistance networks and show that resistance networks which support nonconstant harmonic functions of finite energy have a certain type of boundary. We obtain an analytic boundary representation for the harmonic functions of finite energy in a sense analogous to the Poisson or Martin boundary representations, but with different hypotheses, and for a different class of functions. In the process, we construct a dense space of "smooth" functions of finite energy and obtain a Gel'fand triple for H_ E. This allows us to represent the resistance network as a system of Gaussian...

- by Palle Jorgensen
- •
- Mathematics, Mathematical Physics, Physics, Random Walk

Public reporting burden for the collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden, to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. 1. REPORT DATE The Lattice Discrete Particele Model (LDPM) formulated in the preceding Part I of this study is calibrated and validated in the present Part II. Calibration and validation is performed by comparing the results of numerical simulations with experimental data gathered from the literature. Simulated experiments include uniaxial and multiaxial compression, tensile fracture, shear strength, and cycling compression tests. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18. NUMBER OF PAGES 41 19a. NAME OF RESPONSIBLE PERSON a. REPORT unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Abstract: The Lattice Discrete Particele Model (LDPM) formulated in the preceding Part I of this study is calibrated and validated in the present Part II. Calibration and validation is performed by comparing the results of numerical simulations with experimental data gathered from the literature. Simulated experiments include uniaxial and multiaxial compression, tensile fracture, shear strength, and cycling compression tests.

- by gianluca cusatis
- •
- Civil Engineering, Fracture, Numerical Simulation, Lattice Beam Model

In this paper, we discuss the effect of the lattice model in dielectric or ferroelectric materials. The lattice model is used when we study the film configuration which includes the surface effec effective medium approach reflectivity of attenuated total reflection (ATR). Employing this formulation, we calculate numerically ATR reflection spectra by taking parameters appropriate for BaTiO lead to the existence of the disturbance in ATR spectra. The frequency frequency if the number of lattice is increased. The equivalent to bulk thickness. Keywords-Lattice model The Attenuated Total Reflection (ATR) is a non functional material. This method enables sample material to be analysed directly without doing specific preparation. This technique is able to examine both aqueous and solid samples. is successfully used in proof the emergence of magnon multiferroic system to get the magno reflection phenomena, therefo ensures total reflection in the bottom of prism if t elementary excitation of the material excitation of sample decrease. In ferroelectrics samples where the elementary excitation is phonon resulted from l electromagnetic waves will couple to the phonons around the phonon frequency of the sample. Hence, the ATR reflectance decreases near this frequency illustrating the generation of the phonon polaritons. represents surface modes while the shallow decrease illustrates bulk modes. reflectance for ferroelectric sample, homogeneous parameter. This is an open access article distributed under the terms of the Creative Commons Attribution License, Which Permits unrestricted use, distribution, and reproduction in any medium, provid and source are credited In this paper, we discuss the effect of the lattice model in dielectric or ferroelectric materials. The lattice model is used when we study the film configuration which includes the surface effec effective medium approach, the electric susceptibility is derived. Using this susceptibility, we derived the reflectivity of attenuated total reflection (ATR). Employing this formulation, we calculate numerically ATR by taking parameters appropriate for BaTiO lead to the existence of the disturbance in ATR spectra. The frequency frequency if the number of lattice is increased. The disturbance will disappear when the number of lattice is equivalent to bulk thickness.

- by Sumit Sharma
- •
- Water, Protein adsorption, Protein Purification, Protein Folding

We investigate the motion of pedestrians through obscure corridors where the lack of visibility (due to smoke, fog, darkness, etc.) hides the precise position of the exits. We focus our attention on a set of basic mechanisms, which we assume to be governing the dynamics at the individual level. Using a lattice model, we explore the effects of non-exclusion on the overall exit flux (evacuation rate). More precisely, we study the effect of the buddying threshold (of no-exclusion per site) on the dynamics of the crowd and investigate to which extent our model confirms the following pattern revealed by investigations on real emergencies: If the evacuees tend to cooperate and act altruistically, then their collective action tends to favor the occurrence of disasters. a(ℓ) := 1 Var 1 J J j=1 m(j)m(j + ℓ) − 1 J J j=1 m(j) 2 for ℓ = 0, . . . , J ′ with J ′ ≪ J, where Var is the variance of the sample defined as Var := 1 J J j=1

- by Emilio N M Cirillo
- •
- Mathematical Physics, Quantum Physics, Lattice Models

Integration and differentiation of non-integer orders for N-dimensional physical lattices with long-range particle interactions are suggested. The proposed lattice fractional derivatives and integrals are represented by kernels of lattice long-range interactions, such that their Fourier series transformations have a power-law form with respect to components of wave vector. Continuous limits for these lattice fractional derivatives and integrals give the continuum derivatives and integrals of non-integer orders with respect to coordinates. Lattice analogs of fractional differential equations that include suggested lattice differential and integral operators can serve as an important element of microscopic approach to nonlocal continuum models in mechanics and physics.

- by gianluca cusatis
- •
- Civil Engineering, Fracture, Numerical Simulation, Lattice Beam Model

We consider an " elastic " version of the statistical mechanical mo-nomer-dimer problem on the n-dimensional integer lattice. Our setting includes the classical " rigid " formulation as a special case and extends it by allowing each dimer to consist of particles at arbitrarily distant sites of the lattice, with the energy of interaction between the particles in a dimer depending on their relative position. We reduce the free energy of the elastic dimer-monomer (EDM) system per lattice site in the thermodynamic limit to the moment Lyapunov exponent (MLE) of a homogeneous Gaussian random field (GRF) whose mean value and covariance function are the Boltzmann factors associated with the monomer energy and dimer potential. In particular, the classical monomer-dimer problem becomes related to the MLE of a moving average GRF. We outline an approach to recursive computation of the partition function for " Manhattan " EDM systems where the dimer potential is a weighted 1-distance and the auxiliary GRF is a Markov random field of Pickard type which behaves in space like autoregressive processes do in time. For one-dimensional Manhattan EDM systems, we compute the MLE of the resulting Gaussian Markov chain as the largest eigenvalue of a compact transfer operator on a Hilbert space which is related to the annihilation and creation operators of the quantum harmonic oscillator and also recast it as the eigenvalue problem for a pantograph functional-differential equation.

A resistance network is a weighted graph (G,c)(G,c)(G,c) with intrinsic (resistance) metric RRR. We embed the resistance network into the Hilbert space mathcalHmathcalE{\mathcal H}_{\mathcal E}mathcalHmathcalE of functions of finite energy. We use the resistance metric to study mathcalHmathcalE{\mathcal H}_{\mathcal E}mathcalHmathcalE, and vice versa and show that the embedded images of the vertices vx\{v_x\}vx form a reproducing kernel for this Hilbert space. We also obtain a discrete version of the Gauss-Green formula for resistance networks and show that resistance networks which support nonconstant harmonic functions of finite energy have a certain type of \emph{boundary}. We obtain an analytic boundary representation for the harmonic functions of finite energy in a sense analogous to the Poisson or Martin boundary representations, but with different hypotheses, and for a different class of functions. In the process, we construct a dense space of "smooth" functions of finite energy and obtain a Gel'fand triple for ${\mathcal H}_{\mat...

- by Palle Jorgensen
- •
- Mathematics, Mathematical Physics, Physics, Spectral Theory

Calculations for maximum volume fraction (u m) for a monomodal and a bimodal dispersion are given. These are extended to express the volume fraction of dispersed phase (u < u m) for a bimodal distribution. By substituting the volume fraction, so obtained, various semiempirical laws relating relative viscosity to the volume fraction of the dispersed phase for monomodal dispersions can be extended to bimodal dispersions also. It was mathematically shown that the viscosity of a bimodal dispersion shows a minimum for a particular size ratio of small to large particles for a given relative number concentrations of small to large particles and the interspacing between the small and the large particles. Also, it was shown that an increase in the relative number concentrations of small to large particles, keeping the size ratio of small to large particles and the interspacing between the small and the large particles constant, always increases viscosity. These findings also have practical significance because they can be used to obtain high solid content dispersions with minimum viscosity. Candidate recipe and operating variables that can be varied to obtain either bimodal or very broad distributions through miniemulsion polymerization are finally identified.

- by Ashwini Sood
- •
- Engineering, Modeling, Emulsion polymerization, Lattice Beam Model

Dispersion of elastic waves Lattice models Long-range interactions Non-local elasticity Fractional calculus Fractional power law a b s t r a c t Aim of this paper is the study of waves propagation in a fractional, non-local 1D elastic continuum. The non-local effects are modeled introducing long-range central body interactions applied to the centroids of the infinitesimal volume elements of the continuum. These non-local interactions are proportional to a proper attenuation function and to the relative displacements between non-adjacent elements. It is shown that, assuming a power-law attenuation function, the governing equation of the elastic waves in the unbounded domain, is ruled by a Marchaud-type fractional differential equation. Wave propagation in bounded domain instead involves only the integral part of the Marchaud fractional derivative. The dispersion of elastic waves, as well as waves propagation in unbounded and bounded domains are discussed in detail.

We investigate a mutualistic metacommunity where the strength of the mutualistic interaction between species is measured by the extent to which the presence of one species on a patch either reduces the extinction rate of the others present on the same patch or increases their ability to colonize other patches. In both cases, a strong enough mutualism enables all species to persist at habitat densities where they would all be extinct in the absence of the interaction. However, a mutualistic interaction that enhances colonization enables the species to persist at lower habitat density than one that suppresses extinction. All species abruptly go extinct (catastrophe) when the habitat density is decreased infinitesimally below a critical value. A comparison of the mean field or spatially implicit case with unrestricted dispersal and colonization to all patches in the system with a spatially explicit case where dispersal is restricted to the immediate neighbours of the original patch leads to the intriguing conclusion that restricted dispersal can be favourable for species that have a beneficial effect on each other when habitat conditions are adverse. When the mutualistic interaction is strong enough, the extinction threshold or critical amount of habitat required for the persistence of all species is lower when the dispersal is locally restricted than when unrestricted ! The persistence advantage for all species created by the mutualistic interaction increases substantially with the number of species in the metacommunity, as does the advantage for restricted dispersal over global dispersal. r

- by Sona Prakash
- •
- Genetics, Ecology, Population Dynamics, Lattice Beam Model

- by Sona Prakash
- •
- Genetics, Ecology, Population Dynamics, Lattice Beam Model

A theoretical method for computer modeling of DNA condensation caused by ligand binding is developed. In the method, starting (s) and condensed (c) states are characterized by different free energies for ligand free DNA (F s and F c respectively), ligand binding constants (K s and K c ) and stoichiometry dependent parameters (c sm and c cm -maximum relative concentration of bound ligands (per base pair) for starting and condensed state respectively). The method allows computation of the dependence of the degree of condensation (the fraction of condensed DNA molecules) on ligand concentration. Calculations demonstrate that condensation transition occurs under an increase in ligand concentration if F s < F c (i.e.

- by Vladimir Teif
- •
- Mathematics, Biophysics, Thermodynamics, Molecular Biology

We study the conformations of polymer chains in a poor solvent, with and without bending rigidity, by means of a simple statistical mechanics model. This model can be exactly solved for chains of length up to N = 55 using exact enumeration techniques. We analyze in details the differences between the constant force and constant distance ensembles for large but finite N . At low temperatures, and in the constant force ensemble, the force-extension curve shows multiple plateaus (intermediate states), in contrast with the abrupt transition to an extended state prevailing in the N → ∞ limit. In the constant distance ensemble, the same curve provides a unified response to pulling and compressing forces, and agrees qualitatively with recent experimental results. We identify a cross-over length, proportional to N , below which the critical force of unfolding decreases with temperature, while above, it increases with temperature.

- by sanjay kumar
- •
- Statistical Mechanics, Behavior, Modeling, Ensemble
- by S. Granick
- •
- Engineering, Structure, Monte Carlo Simulation, Kinetics

Thermodynamics of water sorption in poly(-caprolactone) (PCL) has been interpreted by using three models based on compressible lattice fluid theories, addressing the issue of self-and cross-hydrogen bond interactions. The models, available in the literature, are of increasing complexity and consist of a compressible lattice fluid term which could account or not for non-randomness of contacts and, in the case of two of the models, of a hydrogen bonding contribution.

- by Ernesto Di Maio and +2
- •
- Chemical Engineering, Thermodynamics, Water, Classical Physics
- by Chor-Hoi Chan
- •
- Engineering, Physics, Materials Science, Monte Carlo Simulation

This paper deals with the formulation, calibration, and validation of the Lattice Discrete Particle Model (LDPM) suitable for the simulation of the failure behavior of concrete. LDPM simulates concrete at the meso-scale considered to be the length scale of coarse aggregate pieces. LDPM is formulated in the framework of discrete models for which the unknown displacement field is not continuous but only defined at a finite number of points representing the center of aggregate particles. Size and distribution of the particles are obtained according to the actual aggregate size distribution of concrete. Discrete compatibility and equilibrium equations are used to formulate the governing equations of the LDPM computational framework. Particle contact behavior represents the mechanical interaction among adjacent aggregate particles through the embedding mortar. Such interaction is governed by meso-scale constitutive equations simulating meso-scale tensile fracturing with strain-softening, cohesive and frictional shearing, and nonlinear compressive behavior with strain-hardening. The present, Part I, of this two-part study deals with model formulation leaving model calibration and validation to the subsequent Part II.

- by Andrea Mencarelli
- •
- Civil Engineering, Fracture, Numerical Simulation, Lattice Beam Model
- by Vladimir Teif
- •
- Bioinformatics, Biophysics, Thermodynamics, Molecular Biology

The types of phase equilibrium behavior for adsorbed binary mixtures that can be predicted by an equation of state (EOS) based on the lattice gas theory are investigated. The equilibrium conditions were obtained by solving the isofugacity equations between adsorbed phases. It is observed that the investigated EOS can predict complex behavior for adsorbed phases such as the existence of azeotropes, and retrograde and double retrograde phase transition phenomena, that are analogous to those found in bulk phase equilibrium. Furthermore, it was possible to find systems that presented phase equilibrium between two dense adsorbed phases, analogously to liquid-liquid equilibrium for bulk phases. Experimental data would be necessary to confirm the types of adsorbed phase behavior predicted by the calculations presented.

- by Frederico W Tavares
- •
- Chemical Engineering, Thermodynamics, Chemistry, Prediction

It has been noted that natural proteins adapt only a limited number of folds. The question why and how nature selected these small number of folds has intrigued several investigators. With the use of simple models of protein folding, we demonstrate systematically that there is a "designability principle" behind nature's selection of protein folds. The designability of a structure (fold) is measured by the number of sequences that can design the structure-- that is, sequences that possess the structure as their unique ground state. Structures differ drastically in terms of their designability. A small number of highly designable structures emerge with a number of associated sequences much larger than the average. These highly designable structures possess Present address: Max Planck Institut fur Gravitationsphysik, Albert-Einstein-Institut, Schlaatzweg 1, 14473 Potsdam, Germany y Present address: Department of Biochemistry and Biophysics, University of California at Sa...

- by Robert Helling
- •
- Mathematics, Thermodynamics, Protein Folding, Enumeration

The experimental phase diagrams (cloud point curves) of three series of epoxy/thermoplastic blends, namely, epoxy/polystyrene (PS), epoxy/poly(ether sulfone) (PES), and epoxy/poly(ether imide) (PEI) as a function of molar mass and composition have been analysed from a thermodynamic point of view. A model based on the Flory–Huggins lattice theory considering the concentration dependence of the interaction parameter as predicted by Koningsveld

- by Isidro-Salvador Monzo
- •
- Thermodynamics, Chemistry, Lattice Theory, Chemical thermodynamics

The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems-the profound effects of evolution. I will give an introduction to the problem, and then focus on some recent work concerning the so-called "designability principle". The designability of a structure is measured by the number of sequences that have that structure as their unique ground state. Structures differ drastically in terms of their designability; highly designable structures emerge with a number of associated sequences much larger than the average. These highly designable structures 1) possess "proteinlike" secondary structures and motifs, 2) are thermodynamically more stable, and 3) fold faster than other structures. These results suggest that protein structures are selected in nature because they are readily designed and stable against mutations, and that such selection simultaneously leads to thermodynamic stability and foldability. According to this picture, a key to the protein folding problem is to understand the emergence and the properties of the highly designable structures.

- by Chao Tang
- •
- Mathematical Physics, Quantum Physics, Statistical Mechanics, Thermodynamics

It has been noted that natural proteins adapt only a limited number of folds. Several researchers have investigated why and how nature has selected this small number of folds. Using simple models of protein folding, we demonstrate systematically that there is a "designability principle" behind nature's selection of protein folds. The designability of a structure (fold) is measured by the number of sequences that can design the structure-that is, sequences that possess the structure as their unique ground state. Structures differ drastically in terms of their designability. A small number of highly designable structures emerge with a number of associated sequences much larger than the average. These highly designable structures possess proteinlike secondary structures, motifs, and even tertiary symmetries. In addition, they are thermodynamically more stable and fold faster than other structures. These results suggest that protein structures are selected in nature because they are readily designed and stable against mutations, and that such a selection simultaneously leads to thermodynamic stability.

- by Chao Tang
- •
- Mathematics, Thermodynamics, Protein Folding, Enumeration

We analyze the collective behavior of a lattice model of pulse-coupled oscillators. By studying the intrinsic dynamics of each member of the population and their mutual interactions we observe the emergence of either spatio-temporal... more

- by Anna del Corral
- •
- Collective Behavior, Applied Mathematics, Coupled Oscillator, Lattice Beam Model

between low-energy states of the model) is a necessary and sufficient condition to ensure folding of a sequence to its lowest-energy 2 Center for Advanced conformation. Here, we show that this conclusion strongly depends on the Research in Biotechnology particular temperature scheme selected to govern the simulations. On the University of Maryland other hand, we show that there is a dominant factor determining if a Biotechnology Institute, 9600 sequence is foldable. That is, the strength of possible interactions between Gudelsky Drive, Rockville residues close in the sequence. We show that sequences with many MD 20850, USA possible strong local interactions (either favorable or, more surprisingly, a mixture of strong favorable and unfavorable ones) are easy to fold. Progressively increasing the strength of such local interactions makes sequences easier and easier to fold. These results support the idea that initial formation of local substructures is important to the foldability of real proteins.

- by Ron Unger
- •
- Molecular Biology, Protein Folding, Lattice Beam Model, Temperature

The Ziff-Gulari-Barshad (ZGB) model, a simplified description of the oxidation of carbon monoxide (CO) on a catalyst surface, is widely used to study properties of nonequilibrium phase transitions. In particular, it exhibits a nonequilibrium, discontinuous transition between a reactive and a CO poisoned phase. If one allows a nonzero rate of CO desorption (k), the line of phase transitions terminates at a critical point (k c). In this work, instead of restricting the CO and atomic oxygen (O) to react to form carbon dioxide (CO 2) only when they are adsorbed in close proximity, we consider a modified model that includes an adjustable probability for adsorbed CO and O atoms located far apart on the lattice to react. We employ large-scale Monte Carlo simulations for system sizes up to 240 × 240 lattice sites, using the crossing of fourth-order cumulants to study the critical properties of this system. We find that the nonequilibrium critical point changes from the two-dimensional Ising universality class to the mean-field universality class upon introducing even a weak long-range reactivity mechanism. This conclusion is supported by measurements of cumulant fixed-point values, cluster percolation probabilities, correlation-length finite-size scaling properties, and the critical exponent ratio β/ν. The observed behavior is consistent with that of the equilibrium Ising ferromagnet with additional weak long-range interactions [T. Nakada, P. A. Rikvold, T. Mori, M. Nishino, and S. Miyashita, Phys. Rev. B 84, 054433 (2011)]. The large system sizes and the use of fourth-order cumulants also enable determination with improved accuracy of the critical point of the original ZGB model with CO desorption.

- by Chor-Hoi Chan
- •
- Monte Carlo Simulation, Phase Transitions, Critical phenomena, Lattice Models

sulation are predicted by equating appropriate chemical po-The solubilization of solutes in surfactant aggregates (micelles ) tentials to each other. This approach is quite useful, but is studied using lattice-based Monte Carlo simulations. Various requires independent information on chemical potentials. properties such as the size and shape of the micelles, the critical Analytical results are also possible through a combination micelle concentration, the locus of solubilization, and the partition of lattice models and statistical thermodynamics under coefficient of the solute are obtained, and the implications of the sufficient simplifications ( 18, 19) . However, this route is results for the thermodynamics of solubilization are examined.

- by Raj Rajagopalan
- •
- Engineering, Thermodynamics, Monte Carlo Simulation, Monte Carlo

- by Iwan Jensen
- •
- Statistical Mechanics, Behavior, Modeling, Ensemble

Secondary structures of proteins were studied by recurrence quantification analysis (RQA). High-resolution, 3-dimensional coordinates of alpha-carbon atoms comprising a set of 68 proteins were downloaded from the Protein Data Bank. By fine-tuning four recurrence parameters (radius, line, residue, separation), it was possible to establish excellent agreement between percent contribution of alpha-helix and beta-sheet structures determined independently by RQA and that of the DSSP algorithm (Define Secondary Structure of Proteins). These results indicate that there is an equivalency between these two techniques, which are based upon totally different pattern recognition strategies. RQA enhances qualitative contact maps by quantifying the arrangements of recurrent points of alpha carbons close in 3-dimensional space. For example, the radius was systematically increased, moving the analysis beyond local alpha-carbon neighborhoods in order to capture super-secondary and tertiary structures. However, differences between proteins could only be detected within distances up to about 6 -11 Å, but not higher. This result underscores the complexity of alpha-carbon spacing when super-secondary structures appear at larger distances. Finally, RQA-defined secondary structures were found to be robust against random displacement of alpha carbons upwards of 1 Å. This finding has potential import for the dynamic functions of proteins in motion. Proteins 2001;44:292-303.

- by Alessandro Giuliani
- •
- Computational Biology, Vibration, Biological Sciences, Mathematical Sciences

- by Ernesto Di Maio and +2
- •
- Chemical Engineering, Thermodynamics, Water, Classical Physics
- by Vladimir Teif
- •
- Biophysics, Thermodynamics, Signal Transduction, Lattice Models

We examined the influence of dielectric stiffness, interface, and layer thickness on the hysteresis loops, including the remanent polarization and coercive field of a superlattice comprising alternate layers of ferroelectric and dielectric, using the Landau-Ginzburg theory. An interface energy term is introduced in the free energy functional to describe the formation of interface "dead" layers that are mutually coupled through polarization (or induced-polarization). Our studies reveal that the hysteresis loop is strongly dependent on the stiffness of the dielectric layer, the strength of the interface coupling and layer thickness. The intrinsic coupling at the interface between two neighboring layers reduces the coercive field, though the corresponding remanent polarization is significantly enhanced by a soft dielectric layer. (C) 2011 American Institute of Physics. [doi:10.1063/1.3630016]

- by khian-hooi chew
- •
- Phase Transitions, Thin Films, Lattice Models, Heterostructures