Spontaneous tunneling and near-infrared-induced interconversion between the amino-hydroxy conformers of cytosine
Igor Reva, Maciej J. Nowak, Leszek Lapinski, and Rui Fausto
Spontaneous and near-infrared/infrared (NIR/IR)-induced interconversions between two amino-hydroxy conformers of monomeric cytosine have been investigated for the compound isolated in a low-temperature argon matrix. Combined use of a laser source (which provides narrowband NIR radiation) and a broad ... [J. Chem. Phys. 136, 064511 (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.
Absorption by DNA single strands of adenine isolated in vacuo: The role of multiple chromophores
Lisbeth Munksgaard Nielsen, Sara Ovad Pedersen, Maj-Britt Suhr Kirketerp, and Steen Brondsted Nielsen
The degree of electronic coupling between DNA bases is a topic being up for much debate. Here we report on the intrinsic electronic properties of isolated DNA strands in vacuo free of solvent, which is a good starting point for high-level excited states calculations. Action spectra of DNA single str ... [J. Chem. Phys. 136, 064302 (2012)] published Fri Feb 10, 2012.
Dynamics and efficiency of a self-propelled, diffusiophoretic swimmer
Benedikt Sabass and Udo Seifert
Active diffusiophoresisswimming through interaction with a self-generated, neutral, solute gradientis a paradigm for autonomous motion at the micrometer scale. We study this propulsion mechanism within a linear response theory. First, we consider several aspects relating to the dynamics of the swimm ... [J. Chem. Phys. 136, 064508 (2012)] published Thu Feb 9, 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.
Stochastic mapping of the Michaelis-Menten mechanism
Eva Doka and Gabor Lente
The Michaelis-Menten mechanism is an extremely important tool for understanding enzyme-catalyzed transformation of substrates into final products. In this work, a computationally viable, full stochastic description of the Michaelis-Menten kinetic scheme is introduced based on a stochastic equivalent ... [J. Chem. Phys. 136, 054111 (2012)] published Mon Feb 6, 2012.
Enhanced bubble formation in looped short double-stranded DNA
O-chul Lee and Wokyung Sung
Recent experiments have shown the double-stranded (ds) DNAs readily bend and loop over the scale much shorter than their persistence length (50 nm). In an effort to unveil this seemingly surprising phenomenon, we study the emergence of bubbles in short ds DNA loops by simulating the breathing DNA mo ... [Phys. Rev. E 85, 021902 ] published .
Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol
Jane R. Allison, Sereina Riniker, and Wilfred F. van Gunsteren
The time- and length-scale accessible to molecular dynamics simulations of biomolecular systems using atomic-level (AL) models is most limited by the calculation of the solvent-solvent interactions, which comprise the majority of the interactions and yet are seldom of specific interest. Coarse-grain ... [J. Chem. Phys. 136, 054505 (2012)] published Fri Feb 3, 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.
Solution-phase photochemistry of a [FeFe]hydrogenase model compound: Evidence of photoinduced isomerisation
Rafal Kania, Pim W. J. M. Frederix, Joseph A. Wright, Rein V. Ulijn, Christopher J. Pickett et al.
The solution-phase photochemistry of the [FeFe] hydrogenase subsite model ([mu]-S(CH)S)Fe(CO)(PMe) has been studied using ultrafast time-resolved infrared spectroscopy supported by density functional theory calculations. In three different solvents, n-heptane, methanol, and acetonitrile, relaxation ... [J. Chem. Phys. 136, 044521 (2012)] published Tue Jan 31, 2012.
Optimal Placement of Origins for DNA Replication
Jens Karschau, J. Julian Blow, and Alessandro P. S. de Moura
DNA replication is an essential process in biology and its timing must be robust so that cells can divide properly. Random fluctuations in the formation of replication starting points, called origins, and the subsequent activation of proteins lead to variations in the replication time. We analyze th ... [Phys. Rev. Lett. 108, 058101 ] published .
DNA Transport and Delivery in Thermal Gradients near Optofluidic Resonators
Xavier Serey, Sudeep Mandal, Yih-Fan Chen, and David Erickson
Heat generation and its impact on DNA transport in the vicinity of an optofluidic silicon photonic crystal resonator are studied theoretically and experimentally. The temperature rise is measured to be as high as 57 K for 10 mW of input power. The resulting optical trapping and biomolecular sensing ... [Phys. Rev. Lett. 108, 048102 ] published .
Signal transduction across cellular membranes can be mediated by coupling of the clustering of anchored proteins in both leaflets
Tongtao Yue and Xianren Zhang
One key question in signal transduction is how the signal is relayed from the outer leaflet of a cellular membrane to the inner leaflet. Using a simulation model, a mechanism for the mediation of signal transduction is proposed here in which the coupling between membrane proteins in different leafle ... [Phys. Rev. E 85, 011917 ] published .
Compact-envelope bright solitary wave in a DNA double strand
P. B. Ndjoko, J. M. Bilbault, S. Binczak, and T. C. Kofane
We study the nonlinear dynamics of a homogeneous DNA chain that is based on site-dependent finite stacking and pairing enthalpies. We introduce an extended nonlinear Schrodinger equation describing the dynamics of modulated wave in DNA model. We obtain envelope bright solitary waves with compact sup ... [Phys. Rev. E 85, 011916 ] published .
Potential of mean force between hydrophobic solutes in the Jagla model of water and implications for cold denaturation of proteins
Moumita Maiti, Saul Weiner, Sergey V. Buldyrev, H. Eugene Stanley, and Srikanth Sastry
Using the Jagla model potential we calculate the potential of mean force (PMF) between hard sphere solutes immersed in a liquid displaying water-like properties. Consistent estimates of the PMF are obtained by (a) umbrella sampling, (b) calculating the work done by the mean force acting on the hard ... [J. Chem. Phys. 136, 044512 (2012)] published Wed Jan 25, 2012.
Chiral Quasicrystalline Order and Dodecahedral Geometry in Exceptional Families of Viruses
O. V. Konevtsova, S. B. Rochal, and V. L. Lorman
On the example of exceptional families of viruses we (i) show the existence of a completely new type of matter organization in nanoparticles, in which the regions with a chiral pentagonal quasicrystalline order of protein positions are arranged in a structure commensurate with the spherical topology ... [Phys. Rev. Lett. 108, 038102 ] published .
Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA
John F. Marko and Sebastien Neukirch
Recent single-molecule experiments have observed that formation of a plectonemically supercoiled region in a stretched, twisted DNA proceeds via abrupt formation of a small plectonemic bubble. A detailed mesoscopic model is presented for the formation of plectonemic domains, including their position ... [Phys. Rev. E 85, 011908 ] published .
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.
Size and shape effects on receptor-mediated endocytosis of nanoparticles
Xinlei Li
We present a thermodynamic approach to elucidate the effects of the size and shape of nanoparticles (NPs) on endocytosis. It is found that endocytosis needs to surmount a thermodynamic energy barrier and has a minimum radius of NPs for endocytosis. Through referring to the concept of diffusion lengt ... [J. Appl. Phys. 111, 024702 (2012)] published Wed Jan 18, 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.
Homochiral oligopeptides by chiral amplification: Interpretation of experimental data with a copolymerization model. (arXiv:1202.2268v1 [q-bio.QM])
ePrint arXiv http://arXiv.org/
Entropic Tension in Crowded Membranes. (arXiv:1103.5796v2 [physics.bio-ph] UPDATED)
ePrint arXiv http://arXiv.org/