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Lattice models intermediates

Computer simulation using lattice models and energy landscape theory using abstract models predict that the fastest folding of small proteins should occur without intermediates and by an extended nucleation process. Stable intermediates slow... [Pg.312]

An intermediate case (Bazin et al., 2002) between bulk and surface diffraction is reached for nanoparticles when the contribution from surface atoms becomes significant and diffraction analysis in the limit of infinite periodic lattice models inadequately describes the diffraction data. A case study with diamond nanoparticles (Palosz et al., 2002) describes elegantly the possibilities and limitations of diffraction analysis of such samples there is a focus on the nonperiodic structure such as strain and disorder induced by the dominant presence of a nonideal surface termination. [Pg.328]

Abkevich, V. I., Gutin, A. M., and Shakhnovich, E. I., Free energy landscape for protein folding kinetics Intermediates, traps, and multiple pathways in theory and lattice model simulations. J. Chem. Phys. 101, 6052 (1994). [Pg.76]

The single crystal method of (4.) can be repeated with other host crystals which are transparent in the visible or infrared. Since NaCl is isomorphous with AgBr and AgCl and has a lattice parameter intermediate between the two silver halides, it is a model host of choice for studies on the (100) face (22). It must, of course, be dyed out of nonaqueous media. Gypsum (CaSO t O) has also been... [Pg.10]

Figure 13. Orientational dynamics of the Lebwohl-Lasher lattice model (N = 1000) at temperatures near the isotropic-nematic transition, (a) Time evolution of the single-particle second-rank orientational time correlation function in a log-log plot at temperatures T = 1.213,1.176, 1.160,1.149,1.134. Temperature decreases from left to right, (b) Decay of the OKE signal in a log-log plot at short-to-intermediate time window at temperatures T = 1.176, and 1.149. Temperature decreases from top to bottom on the left side of the plot. The dashed lines are the simulation data and the continuous lines are the linear fits to the data. The system undergoes a transition from the isotropic to the nematic phase at T 1.14. (Reproduced from Ref. 115.)... Figure 13. Orientational dynamics of the Lebwohl-Lasher lattice model (N = 1000) at temperatures near the isotropic-nematic transition, (a) Time evolution of the single-particle second-rank orientational time correlation function in a log-log plot at temperatures T = 1.213,1.176, 1.160,1.149,1.134. Temperature decreases from left to right, (b) Decay of the OKE signal in a log-log plot at short-to-intermediate time window at temperatures T = 1.176, and 1.149. Temperature decreases from top to bottom on the left side of the plot. The dashed lines are the simulation data and the continuous lines are the linear fits to the data. The system undergoes a transition from the isotropic to the nematic phase at T 1.14. (Reproduced from Ref. 115.)...
The S-S theory is based on the lattice model, where a liquid is represented as a mixture of unoccupied, h = 1 - y, and occupied, y, sites. Eollowing the Significant Liquid Structures nomenclature [Eyring and Jhon, 1969], the model considers a liquid as being an intermediate between solid and gas. Eor liquid i , S-S used the following nomenclature ... [Pg.129]

In our studies, we consider several types of aggregated structures such as bispheres, linear chains, plane arrays on a plane rectangular lattice, compact and porous body-centered clusters embedded on the cubic lattice (bcc clusters, the porosity was simulated by random elimination of monomers), and random fractal aggregates (RF clusters). To generate RE clusters, a three-dimensional lattice model with Brownian or linear trajectories of both single particles and intermediate clusters was employed for computer simulations of aggregation process. At the initial time moment, = 50,000 particles are generated at... [Pg.272]

A three-dimensional lattice model (section 3.1.1) was used to simulate aggregation kinetics, in which single particles and intermediate clusters move on Brownian or linear trajectories. Initially, = 50,000 particles are placed randomly in a cubic lattice of size L = 215x 215x 215. A combined cluster is formed whenever a particle or a cluster moves to a lattice point adjacent to another particle or intermediate cluster. This model produces DLCA clusters [77] with fractal dimension around 1.8 (Brownian trajectories) and 2 (linear trajectories). A sequence of two integers is used to describe the... [Pg.290]

Kinetics of Protein Folding A Lattice Model Analysis of Multiple Pathways with Intermediates. [Pg.226]

A. R. Dinner and M. Karplus, The thermodynamics and kinetics of protein folding A lattice model analysis of multiple pathways with intermediates. J. Phys. Chem. B 103, 7976-7994 (1999). [Pg.33]

To clarify the relevance of non-native intermediates in the folding of proteins dictated by the formation of disulfide bonds Camacho and Thirumalai [45] used lattice models. While these models are merely caricatures of proteins, they contain the specific effects that can be studied in microscopic detail. We used a two-dimensional lattice sequence consisting of hydrophobic (H), polar (P), and Cys (C) residues. If two C beads are near neighbors on the lattice, they can form a S-S bond with an associated energy gain of —with > 0. Thus, topological specificity is required for native S-S bond formation in this model. We have studied the folding kinetics of this model, which is perhaps the simplest model that can probe the characteristics of native and non-native disulfide bonded intermediates. [Pg.58]

These measurements show that the (information changes of obin are 10 times as fest as th( of lysozyme and of trypsin. Only with a detailed lattice model and by teking into account the presence of the macaromolecular chain, can oik understand that su(ji a variation is indeed possible, by considering tte structure of the intermediates, as follows. It is to be concluded that in myc obin the chain is folded in such a way that the sequence (tf partly folded intermediates has a (in-siderably higher numb of hivorable contacts than in lysozyme or trypsin. These three proteins all have a rather (xjmpact native conforma-... [Pg.271]

In conclusion, the results on myoglobin analyzed here tk) not provide a test of the various aspects of the theory developed in Section VIII, mainly for lack of supplementary data. Certainly we do not note discrepanci between the behavior tlK model and experimental results, but our criteria as to what constitutes dkcrepancy are not very stringent Tlte theory presents a particular point of view, which in these cases does allow one to gain a re onable qualitative understanding of the experiments. The basic point in the theory k the instability of the intermediates in the folding process this is well reproduced by the lattice model, which allows one to calculate the kinetic behavior of a cooperative system with results which may, hopefully, be applied to other cooperative systems and in particular to protein molecules. Further experimental studies are needed to establish whether this is in fact the case. [Pg.274]

Methods treating a lipid as a particle are also applied in studies of the bending rigidity of membranes. These simplified methods constitute an intermediate bridging the gap between the simulation methods at the atomic level and the more simplified lattice model. In the lattice model it is assumed that atomic positions of lipids are restricted to discrete lattice points. Of course, this simplificatipn results in loss of realistic images for individual lipid mol ules, but it makes application of the formulae of the statistical mechanics more practical. Thus, the lattice model is important in the field of computational physics to calculate thermodynamic and physical properties. [Pg.139]


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