JCP: Biological Molecules, Biopolymers, and Biological Systems

Non-Hermitian exciton dynamics in a photosynthetic unit system

A. Thilagam
The non-Hermitian quantum dynamics of excitonic energy transfer in photosynthetic systems is investigated using a dissipative two-level dimer model. The approach is based on Green's function formalism which permits consideration of decoherence and intersite transfer processes on comparable terms. Th ... [J. Chem. Phys. 136, 065104 (2012)] published Mon Feb 13, 2012.

Kinetic pathways to peptide aggregation on surfaces: The effects of beta-sheet propensity and surface attraction

Alex Morriss-Andrews and Joan-Emma Shea
Mechanisms of peptide aggregation on hydrophobic surfaces are explored using molecular dynamics simulations with a coarse-grained peptide representation. Systems of peptides are studied with varying degrees of backbone rigidity (a measure of beta-sheet propensity) and degrees of attraction between t ... [J. Chem. Phys. 136, 065103 (2012)] published Fri Feb 10, 2012.

Folding of small origamis

Jean Michel Arbona, Jean-Pierre Aime, and Juan Elezgaray
A model that preserves the known thermodynamic properties of double stranded DNA is introduced to study the formation of more complex DNA constructions, such as small origamis or Holliday junctions. We show that the thermodynamic behaviour of these complex DNA constructions is not only given by thei ... [J. Chem. Phys. 136, 065102 (2012)] published Thu Feb 9, 2012.

The role of structure in the nonlinear mechanics of cross-linked semiflexible polymer networks

Nicholas Agung Kurniawan, Soren Enemark, and Raj Rajagopalan
The microstructural basis of the characteristic nonlinear mechanics of biopolymer networks remains unclear. We present a 3D network model of realistic, cross-linked semiflexible fibers to study strain-stiffening and the effect of fiber volume-occupancy. We identify two structural parameters, namely, ... [J. Chem. Phys. 136, 065101 (2012)] published Wed Feb 8, 2012.

Correlated intermolecular coupling fluctuations in photosynthetic complexes

Sebastiaan M. Vlaming and Robert J. Silbey
The functioning and efficiency of natural photosynthetic complexes is strongly influenced by their embedding in a noisy protein environment, which can even serve to enhance the transport efficiency. Interactions with the environment induce fluctuations of the transition energies and couplings betwee ... [J. Chem. Phys. 136, 055102 (2012)] published Mon Feb 6, 2012.

Combined depletion and electrostatic forces in polymer-induced membrane adhesion: A theoretical model

Antonio Raudino, Martina Pannuzzo, and Mikko Karttunen
We develop a semi-quantitative analytical theory to describe adhesion between two identical planar charged surfaces embedded in a polymer-containing electrolyte solution. Polymer chains are uncharged and differ from the solvent by their lower dielectric permittivity. The solution mimics physiologica ... [J. Chem. Phys. 136, 055101 (2012)] published Wed Feb 1, 2012.

Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA

David A. Sivak and Phillip L. Geissler
The wormlike chain model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for elasticity at the 110 basepair (bp) scale, which holds particular int ... [J. Chem. Phys. 136, 045102 (2012)] published Tue Jan 31, 2012.

Effects of static and temporally fluctuating tensions on semiflexible polymer looping

Jaeoh Shin and Wokyung Sung
Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene regulation, protein folding, etc. In cellular environments, biopolymers are often subject to tensions which are either static or temporally fluctuating far away from equilibrium. We study the dynamics of semiflexible ... [J. Chem. Phys. 136, 045101 (2012)] published Mon Jan 23, 2012.

Effective interactions in lysozyme aqueous solutions: A small-angle neutron scattering and computer simulation study

M. C. Abramo, C. Caccamo, D. Costa, G. Pellicane, R. Ruberto et al.
We report protein-protein structure factors of aqueous lysozyme solutions at different pH and ionic strengths, as determined by small-angle neutron scattering experiments. The observed upturn of the structure factor at small wavevectors, as the pH increases, marks a crossover between two different r ... [J. Chem. Phys. 136, 035103 (2012)] published Fri Jan 20, 2012.

Understanding the EF-hand closing pathway using non-biased interatomic potentials

L. Dupuis and Normand Mousseau
The EF-hand superfamily of proteins is characterized by the presence of calcium binding helix-loop-helix structures. Many of these proteins undergo considerable motion responsible for a wide range of properties upon binding but the exact mechanism at the root of this motion is not fully understood. ... [J. Chem. Phys. 136, 035101 (2012)] published Tue Jan 17, 2012.

Cross-linked biopolymer bundles: Cross-link reversibility leads to cooperative binding/unbinding phenomena

Richard L. C. Vink and Claus Heussinger
We consider a biopolymer bundle consisting of filaments that are cross-linked together. The cross-links are reversible: they can dynamically bind and unbind adjacent filament pairs as controlled by a binding enthalpy. The bundle is subjected to a bending deformation and the corresponding distributio ... [J. Chem. Phys. 136, 035102 (2012)] published Tue Jan 17, 2012.

Exploring the dynamics of dimer crossing over a Kramers type potential

Mesfin Asfaw and Yohannes Shiferaw
We explore the escape rate of a dimer crossing a potential barrier using both analytical and numerical approaches. We find that for small coupling strength k, the barrier hopping can be well approximated by a two step reaction scheme where one monomer hops over the barrier and is then followed by th ... [J. Chem. Phys. 136, 025101 (2012)] published Tue Jan 10, 2012.

On binding of DNA-bending proteins to DNA minicircles

Shlomi Medalion and Yitzhak Rabin
We present a theoretical study of binding of DNA-bending proteins to circular DNA, using computer simulations of the wormlike chain model of DNA. We find that the binding affinity is affected by the bending elasticity and the conformational entropy of the polymer and that while protein adsorption is ... [J. Chem. Phys. 136, 025102 (2012)] published Tue Jan 10, 2012.

Amino acid analogues bind to carbon nanotube via pi-pi interactions: Comparison of molecular mechanical and quantum mechanical calculations

Zaixing Yang, Zhigang Wang, Xingling Tian, Peng Xiu, and Ruhong Zhou
Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the pi-pi stacking interactions between protein's aromatic residues and CNTs might play a key role in their bindi ... [J. Chem. Phys. 136, 025103 (2012)] published Tue Jan 10, 2012.

Structure and dynamics of nano-sized raft-like domains on the plasma membrane

Fernando E. Herrera and Sergio Pantano
Cell membranes are constitutively composed of thousands of different lipidic species, whose specific organization leads to functional heterogeneities. In particular, sphingolipids, cholesterol and some proteins associate among them to form stable nanoscale domains involved in recognition, signaling, ... [J. Chem. Phys. 136, 015103 (2012)] published Thu Jan 5, 2012.

Effect of glycerol and dimethyl sulfoxide on the phase behavior of lysozyme: Theory and experiments

Christoph Gogelein, Dana Wagner, Frederic Cardinaux, Gerhard Nagele, and Stefan U. Egelhaaf
Salt, glycerol, and dimethyl sulfoxide (DMSO) are used to modify the properties of protein solutions. We experimentally determined the effect of these additives on the phase behavior of lysozyme solutions. Upon the addition of glycerol and DMSO, the fluidsolid transition and the gasliquid coexistenc ... [J. Chem. Phys. 136, 015102 (2012)] published Wed Jan 4, 2012.

Solid effect dynamic nuclear polarization and polarization pathways

Albert A. Smith, Bjorn Corzilius, Alexander B. Barnes, Thorsten Maly, and Robert G. Griffin
Using dynamic nuclear polarization (DNP)/nuclear magnetic resonance instrumentation that utilizes a microwave cavity and a balanced rf circuit, we observe a solid effect DNP enhancement of 94 at 5 T and 80 K using trityl radical as the polarizing agent. Because the buildup rate of the solid effect i ... [J. Chem. Phys. 136, 015101 (2012)] published Wed Jan 4, 2012.

Conformational fluctuations of a proteinDNA complex and the structure and ordering of water around it

Sudipta Kumar Sinha and Sanjoy Bandyopadhyay
ProteinDNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expe ... [J. Chem. Phys. 135, 245104 (2011)] published Fri Dec 23, 2011.

First passage time distribution of chaperone driven polymer translocation through a nanopore: Homopolymer and heteropolymer cases

Rouhollah Haji Abdolvahab, Ralf Metzler, and Mohammad Reza Ejtehadi
Combining the advection-diffusion equation approach with Monte Carlo simulations we study chaperone driven polymer translocation of a stiff polymer through a nanopore. We demonstrate that the probability density function of first passage times across the pore depends solely on the Peclet number, a d ... [J. Chem. Phys. 135, 245102 (2011)] published Fri Dec 23, 2011.

Preferential solvation of lysozyme in water/ethanol mixtures

Maria Grazia Ortore, Paolo Mariani, Flavio Carsughi, Stefania Cinelli, Giuseppe Onori et al.
We provide a quantitative description of the solvation properties of lysozyme in water/ethanol mixtures, which has been obtained by a simultaneous analysis of small-angle neutron scattering and differential scanning calorimetry experiments. All data sets were analyzed by an original method, which in ... [J. Chem. Phys. 135, 245103 (2011)] published Fri Dec 23, 2011.

Cotranscriptional folding kinetics of ribonucleic acid secondary structures

Peinan Zhao, Wenbing Zhang, and Shi-Jie Chen
We develop a systematic helix-based computational method to predict RNA folding kinetics during transcription. In our method, the transcription is modeled as stepwise process, where each step is the transcription of a nucleotide. For each step, the kinetics algorithm predicts the population kinetics ... [J. Chem. Phys. 135, 245101 (2011)] published Thu Dec 22, 2011.