7,177 research outputs found

### J-factors of short DNA molecules

The propensity of short DNA sequences to convert to the circular form is
studied by a mesoscopic Hamiltonian method which incorporates both the bending
of the molecule axis and the intrinsic twist of the DNA strands. The base pair
fluctuations with respect to the helix diameter are treated as path
trajectories in the imaginary time path integral formalism. The partition
function for the sub-ensemble of closed molecules is computed by imposing chain
ends boundary conditions both on the radial fluctuations and on the angular
degrees of freedom. The cyclization probability, the J-factor, proves to be
highly sensitive to the stacking potential, mostly to its nonlinear parameters.
We find that the J-factor generally decreases by reducing the sequence length (
N ) and, more significantly, below N = 100 base pairs. However, even for very
small molecules, the J-factors remain sizeable in line with recent experimental
indications. Large bending angles between adjacent base pairs and anharmonic
stacking appear as the causes of the helix flexibility at short length scales.Comment: The Journal of Chemical Physics - May 2016 ; 9 page

### Comment on ``Consistency, amplitudes and probabilities in quantum theory'' by A. Caticha

A carefully written paper by A. Caticha [Phys. Rev. A57, 1572 (1998)] applies
consistency arguments to derive the quantum mechanical rules for compounding
probability amplitudes in much the same way as earlier work by the present
author [J. Math. Phys. 29, 398 (1988) and Int. J. Theor. Phys. 27, 543 (1998)].
These works are examined together to find the minimal assumptions needed to
obtain the most general results

### Quantum initial condition sampling for linearized density matrix dynamics: Vibrational pure dephasing of iodine in krypton matrices

This paper reviews the linearized path integral approach for computing time
dependent properties of systems that can be approximated using a mixed
quantum-classical description. This approach is applied to studying vibrational
pure dephasing of ground state molecular iodine in a rare gas matrix. The
Feynman-Kleinert optimized harmonic approximation for the full system density
operator is used to sample initial conditions for the bath degrees of freedom.
This extremely efficient approach is compared with alternative initial
condition sampling techniques at low temperatures where classical initial
condition sampling yields dephasing rates that are nearly an order of magnitude
too slow compared with quantum initial condition sampling and experimental
results.Comment: 20 pages and 8 figure

### Bose Fluids Above Tc: Incompressible Vortex Fluids and "Supersolidity"

This paper emphasizes that non-linear rotational or diamagnetic
susceptibility is characteristic of Bose fluids above their superfluid Tcs, and
for sufficiently slow rotation or weak B-fields amounts to an incompressible
response to vorticity. The cause is a missing term in the conventionally
accepted model Hamiltonian for quantized vortices in the Bose fluid. The
resulting susceptibility can account for recent observations of Chan et al on
solid He, and Ong et al on cuprate superconductors

### Fermat's principle of least time in the presence of uniformly moving boundaries and media

The refraction of a light ray by a homogeneous, isotropic and non-dispersive
transparent material half-space in uniform rectilinear motion is investigated
theoretically. The approach is an amalgamation of the original Fermat's
principle and the fact that an isotropic optical medium at rest becomes
optically anisotropic in a frame where the medium is moving at a constant
velocity. Two cases of motion are considered: a) the material half-space is
moving parallel to the interface; b) the material half-space is moving
perpendicular to the interface. In each case, a detailed analysis of the
obtained refraction formula is provided, and in the latter case, an intriguing
backward refraction of light is noticed and thoroughly discussed. The results
confirm the validity of Fermat's principle when the optical media and the
boundaries between them are moving at relativistic speeds.Comment: 11 pages, 6 figures, RevTeX 4, comments welcome; V2: revised, Fig. 7
added; V3: several typos corrected, accepted for publication in European
Journal of Physics (online at: http://stacks.iop.org/EJP/28/933

### High order Chin actions in path integral Monte Carlo

High order actions proposed by Chin have been used for the first time in path
integral Monte Carlo simulations. Contrarily to the Takahashi-Imada action,
which is accurate to fourth order only for the trace, the Chin action is fully
fourth order, with the additional advantage that the leading fourth and sixth
order error coefficients are finely tunable. By optimizing two free parameters
entering in the new action we show that the time step error dependence achieved
is best fitted with a sixth order law. The computational effort per bead is
increased but the total number of beads is greatly reduced, and the efficiency
improvement with respect to the primitive approximation is approximately a
factor of ten. The Chin action is tested in a one-dimensional harmonic
oscillator, a H$_2$ drop, and bulk liquid $^4$He. In all cases a sixth-order
law is obtained with values of the number of beads that compare well with the
pair action approximation in the stringent test of superfluid $^4$He.Comment: 19 pages, 8 figure

### Dynamic shear suppression in quantum phase space

Â© 2019 American Physical Society. All rights reserved.Classical phase space flow is inviscid. Here we show that in quantum phase space Wigner's probability current J can be effectively viscous. This results in shear suppression in quantum phase space dynamics which enforces Zurek's limit for the minimum size scale of spotty structures that develop dynamically. Quantum shear suppression is given by gradients of the quantum terms of J's vorticity. Used as a new measure of quantum dynamics applied to several evolving closed conservative 1D bound state systems, we find that shear suppression explains the saturation at Zurek's scale limit and additionally singles out special quantum states.Peer reviewe

### Impact Parameter Space Interpretation for Generalized Parton Distributions

The Fourier transform of generalized parton distribution functions at xi=0
describes the distribution of partons in the transverse plane. The physical
significance of these impact parameter dependent parton distribution functions
is discussed. In particular, it is shown that they satisfy positivity
constraints which justify their physical interpretation as a probability
density. The generalized parton distribution H is related to the impact
parameter distribution of unpolarized quarks for an unpolarized nucleon,
H-tilde is related to the distribution of longitudinally polarized quarks in a
longitudinally polarized nucleon, and $E$ is related to the distortion of the
unpolarized quark distribution in the transverse plane when the nucleon has
transverse polarization.Comment: addtl. corrections, 34 page

### The Boltzmann Equation in Classical and Quantum Field Theory

Improving upon the previous treatment by Mueller and Son, we derive the
Boltzmann equation that results from a classical scalar field theory. This is
obtained by starting from the corresponding quantum field theory and taking the
classical limit with particular emphasis on the path integral and perturbation
theory. A previously overlooked Van-Vleck determinant is shown to control the
tadpole type of self-energy that can still appear in the classical perturbation
theory. Further comments on the validity of the approximations and possible
applications are also given.Comment: 22 pages, 3 eps figures. Version to appear in Physical Review

### The Boltzmann factor, DNA melting, and Brownian ratchets: Topics in an introductory physics sequence for biology and premedical students

Three, interrelated biologically-relevant examples of biased random walks are
presented: (1) A model for DNA melting, modelled as DNA unzipping, which
provides a way to illustrate the role of the Boltzmann factor in a venue
well-known to biology and pre-medical students; (2) the activity of helicase
motor proteins in unzipping double-stranded DNA, for example, at the
replication fork, which is an example of a Brownian ratchet; (3) force
generation by actin polymerization, which is another Brownian ratchet, and for
which the force and actin-concentration dependence of the velocity of actin
polymerization is determined

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