arXiv subjects

David P. Landau

Publications and source records attributed to David P. Landau.

24 records · Page 2Linked to original sources

arXiv2013

Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins

The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are considered with different types of surfaces, each of which attract either all monomers, only hydrophobic (H) monomers, or only polar (P) monomers, respectively. The diversity of folding behavior in dependence of surface strength is discussed. Analyzing the combined patterns of various structural observables, such as, e.g., the derivatives of the numbers of surface contacts, together with the specific heat, we are able to identify generic categories of folding and transition hierarchies. We also infer a connection between these transition categories and the relative surface strengths, i.e., the ratio of the surface attractive strength to the interchain attraction among H monomers. The validity of our proposed classification scheme is reinforced by the analysis of additional benchmark sequences. We thus believe that the folding hierarchies and identification scheme are generic for HP proteins interacting with attractive surfaces, regardless of chain length, sequence, or surface attraction.

cond-mat.soft↗

arXiv2012

Optimized Wang-Landau sampling of lattice polymers: Ground state search and folding thermodynamics of HP model proteins

Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very demanding and the quest for efficient algorithms is as old as the models themselves. Expanding on our previous work [T. Wüst and D. P. Landau, Phys. Rev. Lett. 102, 178101 (2009)], we present a complete picture of a Monte Carlo method based on Wang-Landau sampling in combination with efficient trial moves (pull, bond-rebridging and pivot moves) which is particularly suited to the study of models such as the hydrophobic-polar (HP) lattice model of protein folding. With this generic and fully blind Monte Carlo procedure, all currently known putative ground states for the most difficult benchmark HP sequences could be found. For most sequences we could also determine the entire energy density of states and, together with suitably designed structural observables, explore the thermodynamics and intricate folding behavior in the virtually inaccessible low-temperature regime. We analyze the differences between random and protein-like heteropolymers for sequence lengths up to 500 residues. Our approach is powerful both in terms of robustness and speed, yet flexible and simple enough for the study of many related problems in protein folding.

cond-mat.soft↗

arXiv2012

Fictitious excitations in the classical Heisenberg antiferromagnet on the kagome lattice

Using an advanced Monte Carlo algorithm and high precision spin dynamics simulation, we investigated the dynamical behavior of the Heisenberg antiferromagnet on a kagome lattice at extremely low temperatures. We demonstrate that the detection and correct identification of propagating excitations depends crucially on the choice of coordinates and we show how modes are displaced in Fourier space if a single, global Cartesian coordinate system is chosen.

cond-mat.str-el↗

arXiv2011

Microcanonical entropy inflection points: Key to systematic understanding of transitions in finite systems

We introduce a systematic classification method for the analogs of phase transitions in finite systems. This completely general analysis, which is applicable to any physical system and extends towards the thermodynamic limit, is based on the microcanonical entropy and its energetic derivative, the inverse caloric temperature. Inflection points of this quantity signal cooperative activity and thus serve as distinct indicators of transitions. We demonstrate the power of this method through application to the long-standing problem of liquid-solid transitions in elastic, flexible homopolymers.

cond-mat.stat-mech↗

arXiv2011

Monte Carlo simulations of the HP model (the "Ising model" of protein folding)

Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse "transition" to a globule state followed by a second "transition" into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of "transitions". These transitions depend upon the relative interaction strengths and are largely inaccessible to "standard" Monte Carlo methods.

cond-mat.soft↗

arXiv2010

The Dynamic Scaling Study of Vapor Deposition Polymerization: A Monte Carlo Approach

The morphological scaling properties of linear polymer films grown by vapor deposition polymerization (VDP) are studied by 1+1D Monte Carlo simulations. The model implements the basic processes of random angle ballistic deposition ($F$), free-monomer diffusion ($D$) and monomer adsorption along with the dynamical processes of polymer chain initiation, extension, and merger. The ratio $G=D/F$ is found to have a strong influence on the polymer film morphology. Spatial and temporal behavior of kinetic roughening has been extensively studied using finite-length scaling and height-height correlations $H(r,t)$. The scaling analysis has been performed within the no-overhang approximation and the scaling behaviors at local and global length scales were found to be very different. The global and local scaling exponents for morphological evolution have been evaluated for varying free-monomer diffusion by growing the films at $G$ = $10$, $10^2$, $10^3$, and $10^4$ and fixing the deposition flux $F$. With an increase in $G$ from $10$ to $10^4$, the average growth exponent $β\approx 0.50$ was found to be invariant, where as the global roughness exponent $α_{g}$ decreased from $0.87(1)$ to $0.73(1)$ along with a corresponding decrease in the global dynamic exponent $z_g$ from $1.71(1)$ to $1.38(2)$. The global scaling exponents were observed to follow the dynamic scaling hypothesis, $z_g=α_{g}/β$. With a similar increase in $G$ however, the average local roughness exponent ${α_{l}}$ remained close to $0.46$ and the anomalous growth exponent $β_{\ast}$ decreased from 0.23(4) to 0.18(8). The interfaces display anomalous scaling and multiscaling in the relevant height-height correlations. The variation of $H(r,t)$ with deposition time $t$ indicates non-stationary growth.

physics.comp-ph↗