Scaling and self-organized criticality in proteins: Lysozyme c
J. C. Phillips
Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein functionality is often dominated by long-range hydro(phobic/philic) interactions, which both drive protein compaction and mediate ... [Phys. Rev. E 80, 051916 (2009)] published Fri Nov 20, 2009.
All-atom ab initio native structure prediction of a mixed fold (1FME): A comparison of structural and folding characteristics of various betabetaalpha miniproteins
Eunae Kim, Soonmin Jang, and Youngshang Pak
We performed an all-atom ab initio native structure prediction of 1FME, which is one of the computationally challenging mixed fold betabetaalpha miniproteins, by combining a novel conformational search algorithm (multiplexed Q-replica exchange molecular dynamics scheme) with a well-balanced all-atom ... [J. Chem. Phys. 131, 195102 (2009)] published Thu Nov 19, 2009.
Unpinning of a spiral wave anchored around a circular obstacle by an external wave train: Common aspects of a chemical reaction and cardiomyocyte tissue
Masanobu Tanaka, Akihiro Isomura, Marcel Horning, Hiroyuki Kitahata, Konstantin Agladze et al.
It is well known that spiral waves are often stabilized by anchoring to a local heterogeneity (pinning) and that such pinned waves are rather difficult to eliminate. In the present report, we show that pinned spiral waves can be eliminated through collision with a wave train arriving from the outer ... [Chaos 19, 043114 (2009)] published Thu Nov 19, 2009.
Hard x-ray phase contrast imaging of black lipid membranes
A. Beerlink, M. Mell, M. Tolkiehn, and T. Salditt
We report hard x-ray phase contrast imaging of black lipid membranes, freely suspended over a micromachined aperture in an aqueous solution. Biomolecular and organic substances can thus be probed in hydrated environments by parallel beam propagation imaging, using coherent multi-kilo-electronvolt x- ... [Appl. Phys. Lett. 95, 203703 (2009)] published Thu Nov 19, 2009.
The transition state transit time of WW domain folding is controlled by energy landscape roughness
Feng Liu, Marcelo Nakaema, and Martin Gruebele
Protein folding barriers can be so low that a substantial protein population diffusing in the transition state region can be detected. The very fast kinetic phase contributed by transition state transit is the molecular phase. We detect the molecular phase of the beta-sheet protein FiP35 from 60 to ... [J. Chem. Phys. 131, 195101 (2009)] published Mon Nov 16, 2009.
Detection of protein secondary structures via the discrete wavelet transform
Jesus Pando, Luke Sands, and Sean E. Shaheen
We subject the primary sequence of proteins gathered from the Structural Classification of Proteins (SCOP) database to a discrete wavelet transform (DWT) analysis to search for predictors of secondary structures. We use proteins with both alpha helices and beta sheets (the A/B, A+B databases from SC ... [Phys. Rev. E 80, 051909 (2009)] published Mon Nov 16, 2009.
From evidence to inference: probing the evolution of protein interaction networks
Oliver Ratmann, Carsten Wiuf, and John W. Pinney
The evolutionary mechanisms by which protein interaction networks grow and change are beginning to be appreciated as a major factor shaping their present-day structures and properties. Starting with a consideration of the biases and errors inherent in our current views of these networks, we discuss ... [HFSP J. 3, 290 (2009)] published Thu Nov 12, 2009.
Electrostatic correlations at the Stern layer: Physics or chemistry?
A. Travesset and S. Vangaveti
We introduce a minimal free energy describing the interaction of charged groups and counterions including both classical electrostatic and specific interactions. The predictions of the model are compared against the standard model for describing ions next to charged interfaces, consisting of Poisson ... [J. Chem. Phys. 131, 185102 (2009)] published Wed Nov 11, 2009.
Molecular dynamics simulations of glycine crystal-solution interface
Soumik Banerjee and Heiko Briesen
Glycine is an amino acid that has several applications in the pharmaceutical industry. Hence, growth of alpha-glycine crystals through solution crystallization is an important process. To gain a fundamental understanding of the seeded growth of alpha-glycine from aqueous solution, the (110) face of ... [J. Chem. Phys. 131, 184705 (2009)] published Tue Nov 10, 2009.
Non-Markovian quantum jumps in excitonic energy transfer
Patrick Rebentrost, Rupak Chakraborty, and Alan Aspuru-Guzik
We utilize the novel non-Markovian quantum jump (NMQJ) approach to stochastically simulate exciton dynamics derived from a time-convolutionless master equation. For relevant parameters and time scales, the time-dependent, oscillatory decoherence rates can have negative regions, a signature of non-Ma ... [J. Chem. Phys. 131, 184102 (2009)] published Mon Nov 9, 2009.
Model for amorphous aggregation processes
Samuel D. Stranks, Heath Ecroyd, Steven Van Sluyter, Elizabeth J. Waters, John A. Carver et al.
The amorphous aggregation of proteins is associated with many phenomena, ranging from the formation of protein wine haze to the development of cataract in the eye lens and the precipitation of recombinant proteins during their expression and purification. While much literature exists describing mode ... [Phys. Rev. E 80, 051907 (2009)] published Mon Nov 9, 2009.
Improving replica exchange using driven scaling
Alexis J. Lee and Steven W. Rick
Replica exchange is a powerful simulation method in which simulations are run at a series of temperatures, with the highest temperature chosen so phase space can be sampled efficiently. In order for swaps to be accepted, the energy distributions of adjacent replicas must have some overlap. This can ... [J. Chem. Phys. 131, 174113 (2009)] published Fri Nov 6, 2009.
Generalized Yvon-Born-Green Theory for Molecular Systems
J. W. Mullinax and W. G. Noid
We employ a basis set representation for classical force fields to derive an original system of exact integral equations relating each mode in the force field to an associated set of structural correlation functions. This generalized Yvon-Born-Green theory provides a framework for interpreting compl ... [Phys. Rev. Lett. 103, 198104 (2009)] published Fri Nov 6, 2009.
Effect of intrinsic curvature on semiflexible polymers
Surya K. Ghosh, Kulveer Singh, and Anirban Sain
Recently many important biopolymers have been found to possess intrinsic curvature. Tubulin protofilaments in animal cells, FtsZ filaments in bacteria and double stranded DNA are examples. We examine how intrinsic curvature influences the conformational statistics of such polymers. We give exact res ... [Phys. Rev. E 80, 051904 (2009)] published Thu Nov 5, 2009.
Charge transport in DNA molecules: Cooperative interplay between the disordered base-pair channel and the ordered backbone
Wei Zhang, Rong Yang, and Sergio E. Ulloa
Charge transport in DNA molecules has raised considerable interest because of its importance in biological processes and potential applications in nanoscale devices. A DNA molecule can be viewed as a quasi-one-dimensional system composed of stacked base pairs (AT, CG) together with backbones of suga ... [Phys. Rev. E 80, 051901 (2009)] published Wed Nov 4, 2009.
Monodisperse self-assembly in a model with protein-like interactions
Alex W. Wilber, Jonathan P. K. Doye, Ard A. Louis, and Anna C. F. Lewis
We study the self-assembly behavior of patchy particles with proteinlike interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the thermodynamics and dynamics of self-assembly as a function of the parame ... [J. Chem. Phys. 131, 175102 (2009)] published Mon Nov 2, 2009.
Thermodynamics of Intragenic Nucleosome Ordering
G. Chevereau, L. Palmeira, C. Thermes, A. Arneodo, and C. Vaillant
The nucleosome ordering observed in vivo along yeast genes is described by a thermodynamical model of nonuniform fluid of 1D hard rods confined by two excluding energy barriers at gene extremities. For interbarrier distances [script L]<~1.5 kbp, nucleosomes equilibrate into a crystal-like configura ... [Phys. Rev. Lett. 103, 188103 (2009)] published Fri Oct 30, 2009.
Inactivation of HN viruses exposed to acidic ozone water
Han S. Uhm, Kwang H. Lee, and Baik L. Seong
The inactivation of HN viruses upon exposure to acidic ozone water was investigated using chicken allantoic fluids of different dilutions, pH values, and initial ozone concentrations. The inactivation effect of the acidic ozone water was found to be stronger than the inactivation effect of the ozone ... [Appl. Phys. Lett. 95, 173704 (2009)] published Thu Oct 29, 2009.
Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations
Hongxing Lei, Zhi-Xiang Wang, Chun Wu, and Yong Duan
Successful ab initio folding of proteins with both alpha-helix and beta-sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any alpha/beta proteins to within experimental error has yet to be reported. Here we demonstra ... [J. Chem. Phys. 131, 165105 (2009)] published Thu Oct 29, 2009.
Mechanistic Study of Self-Assembling Peptide RADA16-I in Formation of Nanofibers and Hydrogels
Hangyu Zhang, Hanlin Luo, and Xiaojun Zhao
The biophysical and biochemical properties of RADA16-I, the representative of a class of self-assembling peptides, were studied to elucidate the molecular mechanism of nanofiber and hydrogel formations. We found that self-assembly occurs in the solution at low pH (pH 4), rather than the popular beli ... [J. Nanotechnol. Eng. Med. 1, 011007 (2009)] published Thu Oct 29, 2009.
Equilibrium Properties and Force-Driven Unfolding Pathways of RNA Molecules
A. Imparato, A. Pelizzola, and M. Zamparo
The mechanical unfolding of a simple RNA hairpin and of a 236-base portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising-like model. Phase diagrams and free energy landscapes are computed exactly and suggest a simple two-state behavior for the hairpin and the presence of in ... [Phys. Rev. Lett. 103, 188102 (2009)] published Thu Oct 29, 2009.