22,286 research outputs found
Extending fragment-based free energy calculations with library Monte Carlo simulation: Annealing in interaction space
Pre-calculated libraries of molecular fragment configurations have previously
been used as a basis for both equilibrium sampling (via "library-based Monte
Carlo") and for obtaining absolute free energies using a polymer-growth
formalism. Here, we combine the two approaches to extend the size of systems
for which free energies can be calculated. We study a series of all-atom
poly-alanine systems in a simple dielectric "solvent" and find that precise
free energies can be obtained rapidly. For instance, for 12 residues, less than
an hour of single-processor is required. The combined approach is formally
equivalent to the "annealed importance sampling" algorithm; instead of
annealing by decreasing temperature, however, interactions among fragments are
gradually added as the molecule is "grown." We discuss implications for future
binding affinity calculations in which a ligand is grown into a binding site
Hairpins in the conformations of a confined polymer
If a semiflexible polymer confined to a narrow channel bends around by 180
degrees, the polymer is said to exhibit a hairpin. The equilibrium extension
statistics of the confined polymer are well understood when hairpins are
vanishingly rare or when they are plentiful. Here we analyze the extension
statistics in the intermediate situation via experiments with DNA coated by the
protein RecA, which enhances the stiffness of the DNA molecule by approximately
one order of magnitude. We find that the extension distribution is highly
non-Gaussian, in good agreement with Monte Carlo simulations of confined
discrete wormlike chains. We develop a simple model that qualitatively explains
the form of the extension distribution. The model shows that the tail of the
distribution at short extensions is determined by conformations with one
hairpin.Comment: Revised version. 22 pages, 7 figures, 2 tables, supplementary
materia
Stochastic dynamics of macromolecular-assembly networks
The formation and regulation of macromolecular complexes provides the
backbone of most cellular processes, including gene regulation and signal
transduction. The inherent complexity of assembling macromolecular structures
makes current computational methods strongly limited for understanding how the
physical interactions between cellular components give rise to systemic
properties of cells. Here we present a stochastic approach to study the
dynamics of networks formed by macromolecular complexes in terms of the
molecular interactions of their components. Exploiting key thermodynamic
concepts, this approach makes it possible to both estimate reaction rates and
incorporate the resulting assembly dynamics into the stochastic kinetics of
cellular networks. As prototype systems, we consider the lac operon and phage
lambda induction switches, which rely on the formation of DNA loops by proteins
and on the integration of these protein-DNA complexes into intracellular
networks. This cross-scale approach offers an effective starting point to move
forward from network diagrams, such as those of protein-protein and DNA-protein
interaction networks, to the actual dynamics of cellular processes.Comment: Open Access article available at
http://www.nature.com/msb/journal/v2/n1/full/msb4100061.htm
Pause Point Spectra in DNA Constant-Force Unzipping
Under constant applied force, the separation of double-stranded DNA into two
single strands is known to proceed through a series of pauses and jumps. Given
experimental traces of constant-force unzipping, we present a method whereby
the locations of pause points can be extracted in the form of a pause point
spectrum. A simple theoretical model of DNA constant-force unzipping is
demonstrated to produce good agreement with the experimental pause point
spectrum of lambda phage DNA. The locations of peaks in the experimental and
theoretical pause point spectra are found to be nearly coincident below 6000
bp. The model only requires the sequence, temperature and a set of empirical
base pair binding and stacking energy parameters, and the good agreement with
experiment suggests that pause points are primarily determined by the DNA
sequence. The model is also used to predict pause point spectra for the
BacterioPhage PhiX174 genome. The algorithm for extracting the pause point
spectrum might also be useful for studying related systems which exhibit
pausing behavior such as molecular motors.Comment: 15 pages, 12 figure
Piecewise Parabolic Method on a Local Stencil for Magnetized Supersonic Turbulence Simulation
Stable, accurate, divergence-free simulation of magnetized supersonic
turbulence is a severe test of numerical MHD schemes and has been surprisingly
difficult to achieve due to the range of flow conditions present. Here we
present a new, higher order-accurate, low dissipation numerical method which
requires no additional dissipation or local "fixes" for stable execution. We
describe PPML, a local stencil variant of the popular PPM algorithm for solving
the equations of compressible ideal magnetohydrodynamics. The principal
difference between PPML and PPM is that cell interface states are evolved
rather that reconstructed at every timestep, resulting in a compact stencil.
Interface states are evolved using Riemann invariants containing all transverse
derivative information. The conservation laws are updated in an unsplit
fashion, making the scheme fully multidimensional. Divergence-free evolution of
the magnetic field is maintained using the higher order-accurate constrained
transport technique of Gardiner and Stone. The accuracy and stability of the
scheme is documented against a bank of standard test problems drawn from the
literature. The method is applied to numerical simulation of supersonic MHD
turbulence, which is important for many problems in astrophysics, including
star formation in dark molecular clouds. PPML accurately reproduces in
three-dimensions a transition to turbulence in highly compressible isothermal
gas in a molecular cloud model. The low dissipation and wide spectral bandwidth
of this method make it an ideal candidate for direct turbulence simulations.Comment: 28 pages, 18 figure
Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments
In many biochemical processes, proteins bound to DNA at distant sites are
brought into close proximity by loops in the underlying DNA. For example, the
function of some gene-regulatory proteins depends on such DNA looping
interactions. We present a new technique for characterizing the kinetics of
loop formation in vitro, as observed using the tethered particle method, and
apply it to experimental data on looping induced by lambda repressor. Our
method uses a modified (diffusive) hidden Markov analysis that directly
incorporates the Brownian motion of the observed tethered bead. We compare
looping lifetimes found with our method (which we find are consistent over a
range of sampling frequencies) to those obtained via the traditional
threshold-crossing analysis (which can vary depending on how the raw data are
filtered in the time domain). Our method does not involve any time filtering
and can detect sudden changes in looping behavior. For example, we show how our
method can identify transitions between long-lived, kinetically distinct states
that would otherwise be difficult to discern
Resolution requirements for numerical simulations of transition
The resolution requirements for direct numerical simulations of transition to turbulence are investigated. A reliable resolution criterion is determined from the results of several detailed simulations of channel and boundary-layer transition
- …