407 research outputs found
Heat conductivity of DNA double helix
Thermal conductivity of isolated single molecule DNA fragments is of
importance for nanotechnology, but has not yet been measured experimentally.
Theoretical estimates based on simplified (1D) models predict anomalously high
thermal conductivity. To investigate thermal properties of single molecule DNA
we have developed a 3D coarse-grained (CG) model that retains the realism of
the full all-atom description, but is significantly more efficient. Within the
proposed model each nucleotide is represented by 6 particles or grains; the
grains interact via effective potentials inferred from classical molecular
dynamics (MD) trajectories based on a well-established all-atom potential
function. Comparisons of 10 ns long MD trajectories between the CG and the
corresponding all-atom model show similar root-mean-square deviations from the
canonical B-form DNA, and similar structural fluctuations. At the same time,
the CG model is 10 to 100 times faster depending on the length of the DNA
fragment in the simulation. Analysis of dispersion curves derived from the CG
model yields longitudinal sound velocity and torsional stiffness in close
agreement with existing experiments. The computational efficiency of the CG
model makes it possible to calculate thermal conductivity of a single DNA
molecule not yet available experimentally. For a uniform (polyG-polyC) DNA, the
estimated conductivity coefficient is 0.3 W/mK which is half the value of
thermal conductivity for water. This result is in stark contrast with estimates
of thermal conductivity for simplified, effectively 1D chains ("beads on a
spring") that predict anomalous (infinite) thermal conductivity. Thus, full 3D
character of DNA double-helix retained in the proposed model appears to be
essential for describing its thermal properties at a single molecule level.Comment: 16 pages, 12 figure
Phase diagram and symmetry breaking of SU(4) spin-orbital chain in a generalized external field
The ground state phases of a one-dimensional SU(4) spin-orbital Hamiltonian
in a generalized external field are studied on the basis of Bethe-ansatz
solution. Introducing three Land\'e factors for spin, orbital and their
products in the SU(4) Zeeman term, we discuss systematically the various
symmetry breaking. The magnetization versus external field are obtained by
solving Bethe-ansatz equations numerically. The phase diagrams corresponding to
distinct residual symmetries are given by means of both numerical and
analytical methods.Comment: Revtex4, 16 pages, 7 figure
Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics
An extension of the constant pH method originally implemented by Mongan et al. (J. Comput. Chem.2004, 25, 2038−2048) is proposed in this study. This adapted version of the method couples the constant pH methodology with the enhanced sampling technique of accelerated molecular dynamics, in an attempt to overcome the sampling issues encountered with current standard constant pH molecular dynamics methods. Although good results were reported by Mongan et al. on application of the standard method to the hen egg-white lysozyme (HEWL) system, residues which possess strong interactions with neighboring groups tend to converge slowly, resulting in the reported inconsistencies for predicted pKa values, as highlighted by the authors. The application of the coupled method described in this study to the HEWL system displays improvements over the standard version of the method, with the improved sampling leading to faster convergence and producing pKa values in closer agreement to those obtained experimentally for the more slowly converging residues
Room Temperature Kondo effect in atom-surface scattering: dynamical 1/N approach
The Kondo effect may be observable in some atom-surface scattering
experiments, in particular, those involving alkaline-earth atoms. By combining
Keldysh techniques with the NCA approximation to solve the time-dependent
Newns-Anderson Hamiltonian in the infinite-U limit, Shao, Nordlander and
Langreth found an anomalously strong surface-temperature dependence of the
outgoing charge state fractions. Here we employ the dynamical 1/N expansion
with finite Coulomb interaction U to provide a more realistic description of
the scattering process. We test the accuracy of the 1/N expansion in the
spinless N = 1 case against the exact independent-particle solution. We then
compare results obtained in the infinite-U limit with the NCA approximation and
recover qualitative features found previously. Finally, we analyze the
realistic situation of Ca atoms with U = 5.8 eV scattered off Cu(001) surfaces.
Although the presence of the doubly-ionized Ca species can change the absolute
scattered positive Ca yields, the temperature dependence is qualitatively the
same as that found in the infinite-U limit. One of the main difficulties that
experimentalists face in attempting to detect this effect is that the atomic
velocity must be kept small enough to reduce possible kinematic smearing of the
metal's Fermi surface.Comment: 15 pages, 10 Postscript figures; references and typos correcte
Dominant Folding Pathways of a WW Domain
We investigate the folding mechanism of the WW domain Fip35 using a realistic
atomistic force field by applying the Dominant Reaction Pathways (DRP)
approach. We find evidence for the existence of two folding pathways, which
differ by the order of formation of the two hairpins. This result is consistent
with the analysis of the experimental data on the folding kinetics of WW
domains and with the results obtained from large-scale molecular dynamics (MD)
simulations of this system. Free-energy calculations performed in two
coarse-grained models support the robustness of our results and suggest that
the qualitative structure of the dominant paths are mostly shaped by the native
interactions. Computing a folding trajectory in atomistic detail only required
about one hour on 48 CPU's. The gain in computational efficiency opens the door
to a systematic investigation of the folding pathways of a large number of
globular proteins
Dynamical 1/N approach to time-dependent currents through quantum dots
A systematic truncation of the many-body Hilbert space is implemented to
study how electrons in a quantum dot attached to conducting leads respond to
time-dependent biases. The method, which we call the dynamical 1/N approach, is
first tested in the most unfavorable case, the case of spinless fermions (N=1).
We recover the expected behavior, including transient ringing of the current in
response to an abrupt change of bias. We then apply the approach to the
physical case of spinning electrons, N=2, in the Kondo regime for the case of
infinite intradot Coulomb repulsion. In agreement with previous calculations
based on the non-crossing approximation (NCA), we find current oscillations
associated with transitions between Kondo resonances situated at the Fermi
levels of each lead. We show that this behavior persists for a more realistic
model of semiconducting quantum dots in which the Coulomb repulsion is finite.Comment: 18 pages, 7 eps figures, discussion extended for spinless electrons
and typo
Integrity of H1 helix in prion protein revealed by molecular dynamic simulations to be especially vulnerable to changes in the relative orientation of H1 and its S1 flank
In the template-assistance model, normal prion protein (PrPC), the pathogenic
cause of prion diseases such as Creutzfeldt-Jakob (CJD) in human, Bovine
Spongiform Encephalopathy (BSE) in cow, and scrapie in sheep, converts to
infectious prion (PrPSc) through an autocatalytic process triggered by a
transient interaction between PrPC and PrPSc. Conventional studies suggest the
S1-H1-S2 region in PrPC to be the template of S1-S2 -sheet in PrPSc, and
the conformational conversion of PrPC into PrPSc may involve an unfolding of H1
in PrPC and its refolding into the -sheet in PrPSc. Here we conduct a
series of simulation experiments to test the idea of transient interaction of
the template-assistance model. We find that the integrity of H1 in PrPC is
vulnerable to a transient interaction that alters the native dihedral angles at
residue Asn, which connects the S1 flank to H1, but not to interactions
that alter the internal structure of the S1 flank, nor to those that alter the
relative orientation between H1 and the S2 flank.Comment: A major revision on statistical analysis method has been made. The
paper now has 23 pages, 11 figures. This work was presented at 2006 APS March
meeting session K29.0004 at Baltimore, MD, USA 3/13-17, 2006. This paper has
been accepted for pubcliation in European Biophysical Journal on Feb 2, 200
Ground State and Excitations of Spin Chain with Orbital Degeneracy
The one dimensional Heisenberg model in the presence of orbital degeneracy is
studied at the SU(4) symmetric viewpoint by means of Bethe ansatz. Following
Sutherland's previous work on an equivalent model, we discuss the ground state
and the low-lying excitations more extensively in connection to the spin
systems with orbital degeneracy. We show explicitly that the ground state is a
SU(4) singlet. We study the degeneracies of the elementary excitations and the
spectra of the generalized magnons consisting of these excitations. We also
discuss the complex 2-strings in the context of the Bethe ansatz solutions.Comment: Revtex, 9 pages, 3 figures; typos correcte
Four small puzzles that Rosetta doesn't solve
A complete macromolecule modeling package must be able to solve the simplest
structure prediction problems. Despite recent successes in high resolution
structure modeling and design, the Rosetta software suite fares poorly on
deceptively small protein and RNA puzzles, some as small as four residues. To
illustrate these problems, this manuscript presents extensive Rosetta results
for four well-defined test cases: the 20-residue mini-protein Trp cage, an even
smaller disulfide-stabilized conotoxin, the reactive loop of a serine protease
inhibitor, and a UUCG RNA tetraloop. In contrast to previous Rosetta studies,
several lines of evidence indicate that conformational sampling is not the
major bottleneck in modeling these small systems. Instead, approximations and
omissions in the Rosetta all-atom energy function currently preclude
discriminating experimentally observed conformations from de novo models at
atomic resolution. These molecular "puzzles" should serve as useful model
systems for developers wishing to make foundational improvements to this
powerful modeling suite.Comment: Published in PLoS One as a manuscript for the RosettaCon 2010 Special
Collectio
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