1,181 research outputs found
Imaging density disturbances in water with 41.3 attosecond time resolution
We show that the momentum flexibility of inelastic x-ray scattering may be
exploited to invert its loss function, alowing real time imaging of density
disturbances in a medium. We show the disturbance arising from a point source
in liquid water, with a resolution of 41.3 attoseconds (
sec) and 1.27 ( cm). This result is used to
determine the structure of the electron cloud around a photoexcited molecule in
solution, as well as the wake generated in water by a 9 MeV gold ion. We draw
an analogy with pump-probe techniques and suggest that energy-loss scattering
may be applied more generally to the study of attosecond phenomena.Comment: 4 pages, 4 color figure
Multi-site H-bridge breathers in a DNA--shaped double strand
We investigate the formation process of nonlinear vibrational modes
representing broad H-bridge multi--site breathers in a DNA--shaped double
strand.
Within a network model of the double helix we take individual motions of the
bases within the base pair plane into account. The resulting H-bridge
deformations may be asymmetric with respect to the helix axis. Furthermore the
covalent bonds may be deformed distinctly in the two backbone strands.
Unlike other authors that add different extra terms we limit the interaction
to the hydrogen bonds within each base pair and the covalent bonds along each
strand. In this way we intend to make apparent the effect of the characteristic
helicoidal structure of DNA. We study the energy exchange processes related
with the relaxation dynamics from a non-equilibrium conformation. It is
demonstrated that the twist-opening relaxation dynamics of a radially distorted
double helix attains an equilibrium regime characterized by a multi-site
H-bridge breather.Comment: 27 pages and 10 figure
Exact solution of a linear molecular motor model driven by two-step fluctuations and subject to protein friction
We investigate by analytical means the stochastic equations of motion of a
linear molecular motor model based on the concept of protein friction. Solving
the coupled Langevin equations originally proposed by Mogilner et al. (A.
Mogilner et al., Phys. Lett. {\bf 237}, 297 (1998)), and averaging over both
the two-step internal conformational fluctuations and the thermal noise, we
present explicit, analytical expressions for the average motion and the
velocity-force relationship. Our results allow for a direct interpretation of
details of this motor model which are not readily accessible from numerical
solutions. In particular, we find that the model is able to predict
physiologically reasonable values for the load-free motor velocity and the
motor mobility.Comment: 12 pages revtex, 6 eps-figure
Fluctuation-Facilitated Charge Migration along DNA
We propose a model Hamiltonian for charge transfer along the DNA double helix
with temperature driven fluctuations in the base pair positions acting as the
rate limiting factor for charge transfer between neighboring base pairs. We
compare the predictions of the model with the recent work of J.K. Barton and
A.H. Zewail (Proc.Natl.Acad.Sci.USA, {\bf 96}, 6014 (1999)) on the unusual
two-stage charge transfer of DNA.Comment: 4 pages, 2 figure
Stretching and relaxation dynamics in double stranded DNA
We study numerically the mechanical stability and elasticity properties of
duplex DNA molecules within the frame of a network model incorporating
microscopic degrees of freedom related with the arrangement of the base pairs.
We pay special attention to the opening-closing dynamics of double-stranded DNA
molecules which are forced into non-equilibrium conformations. Mechanical
stress imposed at one terminal end of the DNA molecule brings it into a
partially opened configuration. We examine the subsequent relaxation dynamics
connected with energy exchange processes between the various degrees of freedom
and structural rearrangements leading to complete recombination to the
double-stranded conformation. The similarities and differences between the
relaxation dynamics for a planar ladder-like DNA molecule and a twisted one are
discussed in detail. In this way we show that the attainment of a
quasi-equilibrium regime proceeds faster in the case of the twisted DNA form
than for its thus less flexible ladder counterpart. Furthermore we find that
the velocity of the complete recombination of the DNA molecule is lower than
the velocity imposed by the forcing unit which is in compliance with the
experimental observations for the opening-closing cycle of DNA molecules.Comment: 21 pages, 9 figure
Simple, Direct Routes to Polymer Brush Traps and Nanostructures for Studies of Diffusional Transport in Supported Lipid Bilayers
Patterned poly(oligo ethylene glycol) methyl ether methacrylate (POEGMEMA) brush structures may be formed by using a combination of atom-transfer radical polymerization (ATRP) and UV photopatterning. UV photolysis is used to selectively dechlorinate films of 4-(chloromethyl)phenyltrichlorosilane (CMPTS) adsorbed on silica surfaces, by exposure either through a mask or using a two-beam interferometer. Exposure through a mask yields patterns of carboxylic acid-terminated adsorbates. POEGMEMA may be grown from intact Cl initiators that were masked during exposure. Corrals, traps, and other structures formed in this way enable the patterning of proteins, vesicles, and, following vesicle rupture, supported lipid bilayers (SLBs). Bilayers adsorbed on the carboxylic acid-terminated surfaces formed by C–Cl bond photolysis in CMPTS exhibit high mobility. SLBs do not form on POEGMEMA. Using traps consisting of carboxylic acid-functionalized regions enclosed by POEGMEMA structures, electrophoresis may be observed in lipid bilayers containing a small amount of a fluorescent dye. Segregation of dye at one end of the traps was measured by fluorescence microscopy. The increase in the fluorescence intensity was found to be proportional to the trap length, while the time taken to reach the maximum value was inversely proportional to the trap length, indicating uniform, rapid diffusion in all of the traps. Nanostructured materials were formed using interferometric lithography. Channels were defined by exposure of CMPTS films to maxima in the interferogram, and POEGMEMA walls were formed by ATRP. As for the micrometer-scale patterns, bilayers did not form on the POEGMEMA structures, and high lipid mobilities were measured in the polymer-free regions of the channels
Stochastic Approach to Enantiomeric Excess Amplification and Chiral Symmetry Breaking
Stochastic aspects of chemical reaction models related to the Soai reactions
as well as to the homochirality in life are studied analytically and
numerically by the use of the master equation and random walk model. For
systems with a recycling process, a unique final probability distribution is
obtained by means of detailed balance conditions. With a nonlinear
autocatalysis the distribution has a double-peak structure, indicating the
chiral symmetry breaking. This problem is further analyzed by examining
eigenvalues and eigenfunctions of the master equation. In the case without
recycling process, final probability distributions depend on the initial
conditions. In the nonlinear autocatalytic case, time-evolution starting from a
complete achiral state leads to a final distribution which differs from that
deduced from the nonzero recycling result. This is due to the absence of the
detailed balance, and a directed random walk model is shown to give the correct
final profile. When the nonlinear autocatalysis is sufficiently strong and the
initial state is achiral, the final probability distribution has a double-peak
structure, related to the enantiomeric excess amplification. It is argued that
with autocatalyses and a very small but nonzero spontaneous production, a
single mother scenario could be a main mechanism to produce the homochirality.Comment: 25 pages, 6 figure
The statistical mechanics of complex signaling networks : nerve growth factor signaling
It is becoming increasingly appreciated that the signal transduction systems
used by eukaryotic cells to achieve a variety of essential responses represent
highly complex networks rather than simple linear pathways. While significant
effort is being made to experimentally measure the rate constants for
individual steps in these signaling networks, many of the parameters required
to describe the behavior of these systems remain unknown, or at best,
estimates. With these goals and caveats in mind, we use methods of statistical
mechanics to extract useful predictions for complex cellular signaling
networks. To establish the usefulness of our approach, we have applied our
methods towards modeling the nerve growth factor (NGF)-induced differentiation
of neuronal cells. Using our approach, we are able to extract predictions that
are highly specific and accurate, thereby enabling us to predict the influence
of specific signaling modules in determining the integrated cellular response
to the two growth factors. We show that extracting biologically relevant
predictions from complex signaling models appears to be possible even in the
absence of measurements of all the individual rate constants. Our methods also
raise some interesting insights into the design and possible evolution of
cellular systems, highlighting an inherent property of these systems wherein
particular ''soft'' combinations of parameters can be varied over wide ranges
without impacting the final output and demonstrating that a few ''stiff''
parameter combinations center around the paramount regulatory steps of the
network. We refer to this property -- which is distinct from robustness -- as
''sloppiness.''Comment: 24 pages, 10 EPS figures, 1 GIF (makes 5 multi-panel figs + caption
for GIF), IOP style; supp. info/figs. included as brown_supp.pd
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