JCP: BioChemical Physics

Understanding two-pulse phase-modulated decoupling in solid-state NMR

Ingo Scholz, Paul Hodgkinson, Beat H. Meier, and Matthias Ernst
A theoretical description of the two-pulse phase-modulated (TPPM) decoupling sequence in magic-angle spinning NMR is presented using a triple-mode Floquet approach. The description is formulated in the radio-frequency interaction-frame representation and is valid over the entire range of possible pa ... [J. Chem. Phys. 130, 114510 (2009)] published Fri Mar 20, 2009.

Structural properties of polymeric DNA from molecular dynamics simulations

Sudipta Samanta, Supti Mukherjee, Jaydeb Chakrabarti, and Dhananjay Bhattacharyya
Most of the reported DNA structural studies are based on oligonucleotide structures, which have artifacts due to unstable terminal base pairs (bps). We have carried out molecular dynamics simulation of DNA oligonucleotides in such a manner that gives rise to properties of polymeric DNA of infinite l ... [J. Chem. Phys. 130, 115103 (2009)] published Fri Mar 20, 2009.

Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization

Li L. Duan, Ye Mei, Qing G. Zhang, and John Z. H. Zhang
Molecular dynamics (MD) simulation has been carried out to study dynamical stability of intra-protein hydrogen bonds based on two set of atomic charges, the standard AMBER charge and the polarized protein-specific charge (PPC). The latter is derived from quantum mechanical calculation for protein in ... [J. Chem. Phys. 130, 115102 (2009)] published Thu Mar 19, 2009.

Topology-based potentials and the study of the competition between protein folding and aggregation

Lidia Prieto and Antonio Rey
Topology-based or Go-type potentials have been shown to be very useful in the understanding of the relations between the structure of the native state of a protein and some of its folding characteristics. A different question is whether they can also make such a contribution when the aggregation pro ... [J. Chem. Phys. 130, 115101 (2009)] published Thu Mar 19, 2009.

Fragmentation of adenine under energy control

Richard Bredy, Jerome Bernard, Li Chen, Guillaume Montagne, Bin Li et al.
We present results on the fragmentation of adenine dication as a function of the excitation energy. The adenine molecule is charged and excited in a single collision with Cl ion at 3 keV and the excitation energy distribution is obtained for each fragmentation channel by measuring the kinetic energy ... [J. Chem. Phys. 130, 114305 (2009)] published Thu Mar 19, 2009.

Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach

Jeremy Curuksu and Martin Zacharias
Although molecular dynamics (MD) simulations have been applied frequently to study flexible molecules, the sampling of conformational states separated by barriers is limited due to currently possible simulation time scales. Replica-exchange (Rex)MD simulations that allow for exchanges between simula ... [J. Chem. Phys. 130, 104110 (2009)] published Fri Mar 13, 2009.

Response to Comment on `On the Crooks fluctuation theorem and the Jaraynski equality' and `Nonequilibrium fluctuation dissipation theorem of Brownian dynamics' [J. Chem. Phys. 130, 107101 (2009)]

L. Y. Chen
Contrary to what Crooks asserts, the self-consistency requirement put forward in J. Chem. Phys.129, 091101 (2008) is necessary for the Jarzynski equality (JE) and the Crooks fluctuation theorem (CFT) to be valid regardless which definition of work one uses, the force-displacement definition or the t ... [J. Chem. Phys. 130, 107102 (2009)] published Wed Mar 11, 2009.

Comment regarding On the Crooks fluctuation theorem and the Jarzynski equality [J. Chem. Phys. 129, 091101 (2008)] and Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics [J. Chem. Phys. 129, 144113 (2008)]

G. E. Crooks
The incongruous unexpected inapplicability of the Crook's fluctuation theorem is due to an inexplicable, inappropriate use of inconsistent expressions. The girding is secure. ... [J. Chem. Phys. 130, 107101 (2009)] published Wed Mar 11, 2009.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation

Jaydeep P. Bardhan, Matthew G. Knepley, and Mihai Anitescu
The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with s ... [J. Chem. Phys. 130, 104108 (2009)] published Wed Mar 11, 2009.

Molecular biosensor based on a coordinated iron complex

Karim Salazar-Salinas, Luis A. Jauregui, Carlos Kubli-Garfias, and Jorge M. Seminario
A sensor model based on the porphyrin nucleus of the soluble guanylate cyclase enzyme is modeled and tested with nitric oxide and carbon monoxide. Molecular oxygen is tested as a possible interferer. Geometries and electronic structures of the model are assessed by density functional theory. Vibrati ... [J. Chem. Phys. 130, 105101 (2009)] published Mon Mar 9, 2009.

Statistical thermodynamics of residue fluctuations in native proteins

Osman N. Yogurtcu, Mert Gur, and Burak Erman
Statistical thermodynamics of residue fluctuations of native proteins in a temperature, pressure, and force reservoir is formulated. The general theory is discussed in terms of harmonic and anharmonic fluctuations of residues. The two elastic network models based on the harmonic approximation, the a ... [J. Chem. Phys. 130, 095103 (2009)] published Fri Mar 6, 2009.

Diffusion-influenced reactions involving a reactant with two active sites

Aeri Kang, Ji-Hyun Kim, Sangyoub Lee, and Hwangseo Park
We consider the kinetics of diffusion-influenced reactions which involve a reactant species that can be modeled as a sphere with two reactive patches located on its surface at an arbitrary angular distance. An approximate analytic expression for the rate coefficient is derived based on the WilemskiF ... [J. Chem. Phys. 130, 094507 (2009)] published Fri Mar 6, 2009.

Vibrational solvatochromism and electrochromism: Coarse-grained models and their relationships

Minhaeng Cho
A theoretical description of vibrational solvatochromism and electrochromism is presented by using a coarse-grained model based on a distributed charge and multipole interaction theory. Solvatochromic frequency shift has been described by considering the interaction between distributed charges of a ... [J. Chem. Phys. 130, 094505 (2009)] published Thu Mar 5, 2009.

One-dimensional counterion gas between charged surfaces: Exact results compared with weak- and strong-coupling analyses

David S. Dean, Ron R. Horgan, Ali Naji, and Rudolf Podgornik
We evaluate exactly the statistical integral for an inhomogeneous one-dimensional (1D) counterion-only Coulomb gas between two charged boundaries and from this compute the effective interaction, or disjoining pressure, between the bounding surfaces. Our exact results are compared to the limiting cas ... [J. Chem. Phys. 130, 094504 (2009)] published Thu Mar 5, 2009.

Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. II. The nu and nu modes of iron-protoporphyrin IX and iron porphine

Yong Zhang and John E. Straub
The mode-specific vibrational energy relaxation (VER) of the iron-protoporphyrin IX (the heme) was studied using a non-Markovian time-dependent perturbation theory at the UB3LYP/6-31G(d) level. The derived VER time constants of the excited nu and nu modes, 1.20.1 and 2.10.1 ps, respectively, agree ... [J. Chem. Phys. 130, 095102 (2009)] published Thu Mar 5, 2009.

Brownian dynamics simulations of single-stranded DNA hairpins

Martin Kenward and Kevin D. Dorfman
We present a Brownian dynamics model which we use to study the kinetics and thermodynamics of single-stranded DNA hairpins, gaining insights into the role of stem mismatches and the kinetics rates underlying the melting transition. The model is a base-backbone type in which the DNA bases and sugar-p ... [J. Chem. Phys. 130, 095101 (2009)] published Tue Mar 3, 2009.

Water-mediated interactions between hydrophobic and ionic species in cylindrical nanopores

S. Vaitheeswaran, G. Reddy, and D. Thirumalai
We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled pores. Confinement strongly alters the interactions between the nonpolar solutes and completely eliminates the solvent ... [J. Chem. Phys. 130, 094502 (2009)] published Tue Mar 3, 2009.

Molecular simulation of protein dynamics in nanopores. II. Diffusion

Leili Javidpour, M. Reza Rahimi Tabar, and Muhammad Sahimi
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with th ... [J. Chem. Phys. 130, 085105 (2009)] published Fri Feb 27, 2009.

Fast acquisition of high-resolution NMR spectra in inhomogeneous fields via intermolecular double-quantum coherences

Zhong Chen, Shuhui Cai, Zhiwei Chen, and Jianhui Zhong
A pulse sequence, IDEAL-II, is proposed based on the concept of intermolecular dipolar-interaction enhanced all lines [Z. Chen et al., J. Am. Chem. Soc. 126, 446 (2004)] for obtaining one-dimensional (1D) high-resolution liquid NMR spectra in inhomogeneous fields via two-dimensional acquisitions. Wi ... [J. Chem. Phys. 130, 084504 (2009)] published Fri Feb 27, 2009.

Protein displacements under external forces: An atomistic Langevin dynamics approach

David Gnandt, Nadine Utz, Alexander Blumen, and Thorsten Koslowski
We present a fully atomistic Langevin dynamics approach as a method to simulate biopolymers under external forces. In the harmonic regime, this approach permits the computation of the long-term dynamics using only the eigenvalues and eigenvectors of the Hessian matrix of second derivatives. We apply ... [J. Chem. Phys. 130, 085104 (2009)] published Thu Feb 26, 2009.