2,855 research outputs found
Precision shooting: Sampling long transition pathways
The kinetics of collective rearrangements in solution, such as protein
folding and nanocrystal phase transitions, often involve free energy barriers
that are both long and rough. Applying methods of transition path sampling to
harvest simulated trajectories that exemplify such processes is typically made
difficult by a very low acceptance rate for newly generated trajectories. We
address this problem by introducing a new generation algorithm based on the
linear short-time behavior of small disturbances in phase space. Using this
``precision shooting'' technique, arbitrarily small disturbances can be
propagated in time, and any desired acceptance ratio of shooting moves can be
obtained. We demonstrate the method for a simple but computationally
problematic isomerization process in a dense liquid of soft spheres. We also
discuss its applicability to barrier crossing events involving metastable
intermediate states.Comment: 9 pages, 12 figures, submitted to J. Chem. Phy
Rough interfaces, accurate predictions: The necessity of capillary modes in a minimal model of nanoscale hydrophobic solvation
Modern theories of the hydrophobic effect highlight its dependence on length
scale, emphasizing in particular the importance of interfaces that emerge in
the vicinity of sizable hydrophobes. We recently showed that a faithful
treatment of such nanoscale interfaces requires careful attention to the
statistics of capillary waves, with significant quantitative implications for
the calculation of solvation thermodynamics. Here we show that a coarse-grained
lattice model in the spirit of those pioneered by Chandler and coworkers, when
informed by this understanding, can capture a broad range of hydrophobic
behaviors with striking accuracy. Specifically, we calculate probability
distributions for microscopic density fluctuations that agree very well with
results of atomistic simulations, even many standard deviations from the mean,
and even for probe volumes in highly heterogeneous environments. This accuracy
is achieved without adjustment of free parameters, as the model is fully
specified by well-known properties of liquid water. As illustrative examples of
its utility, we characterize the free energy profile for a solute crossing the
air-water interface, and compute the thermodynamic cost of evacuating the space
between extended nanoscale surfaces. Together, these calculations suggest that
a highly reduced model for aqueous solvation can serve as the basis for
efficient multiscale modeling of spatial organization driven by hydrophobic and
interfacial forces.Comment: 14 pages, 7 figure
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Comparative composition, diversity, and abundance of oligosaccharides in early lactation milk from commercial dairy and beef cows.
Prebiotics are nondigestible dietary ingredients, usually oligosaccharides (OS), that provide a health benefit to the host by directly modulating the gut microbiota. Although there is some information describing OS content in dairy-source milk, no information is available to describe the OS content of beef-source milk. Given the different trait emphasis between dairy and beef for milk production and calf survivability, it is plausible that OS composition, diversity, and abundance differ between production types. The goal of this study was to compare OS in milk from commercial dairy and beef cows in early lactation. Early-lactation multiparous cows (5-12 d in milk) from 5 commercial Holstein dairy herds and 5 Angus or Angus hybrid beef herds were sampled once. Milk was obtained from each enrolled cow and frozen on the farm. Subsequently, each milk sample was assessed for total solids, pH, and OS content and relative abundance. Oligosaccharide diversity and abundance within and between samples was transformed through principal component analysis to reduce data complexity. Factors from principal component analysis were used to create similarity clusters, which were subsequently used in a multivariate logistic regression. In total, 30 OS were identified in early-lactation cow milk, including 21 distinct OS and 9 isomers with unique retention times. The majority of OS detected in the milk samples were present in all individual samples regardless of production type. Two clusters described distribution patterns of OS for the study sample; when median OS abundance was compared between the 2 clusters, we found that overall OS relative abundance was consistently greater in the cluster dominated by beef cows. For several of the structures, including those with known prebiotic effect, the difference in abundance was 2- to 4-fold greater in the beef-dominated cluster. Assuming that beef OS content in milk is the gold standard for cattle, it is likely that preweaning dairy calves are deprived of dietary-source OS. Although supplementing rations with OS is an approach to rectify this deficiency, understanding the health and productivity effects of improving OS abundance being fed to preweaning calves is a necessary next step before recommending supplementation. These studies should account for the observation that OS products are variable for both OS diversity and structural complexity, and some products may not be suitable as prebiotics
Synchronization of unidirectional time delay chaotic networks and the greatest common divisor
We present the interplay between synchronization of unidirectional coupled
chaotic nodes with heterogeneous delays and the greatest common divisor (GCD)
of loops composing the oriented graph. In the weak chaos region and for GCD=1
the network is in chaotic zero-lag synchronization, whereas for GCD=m>1
synchronization of m-sublattices emerges. Complete synchronization can be
achieved when all chaotic nodes are influenced by an identical set of delays
and in particular for the limiting case of homogeneous delays. Results are
supported by simulations of chaotic systems, self-consistent and mixing
arguments, as well as analytical solutions of Bernoulli maps.Comment: 7 pages, 5 figure
Efficiency and Large Deviations in Time-Asymmetric Stochastic Heat Engines
In a stochastic heat engine driven by a cyclic non-equilibrium protocol,
fluctuations in work and heat give rise to a fluctuating efficiency. Using
computer simulations and tools from large deviation theory, we have examined
these fluctuations in detail for a model two-state engine. We find in general
that the form of efficiency probability distributions is similar to those
described by Verley et al. [2014 Nat Comm, 5 4721], in particular featuring a
local minimum in the long-time limit. In contrast to the time-symmetric engine
protocols studied previously, however, this minimum need not occur at the value
characteristic of a reversible Carnot engine. Furthermore, while the local
minimum may reside at the global minimum of a large deviation rate function, it
does not generally correspond to the least likely efficiency measured over
finite time. We introduce a general approximation for the finite-time
efficiency distribution, , based on large deviation statistics of work
and heat, that remains very accurate even when deviates significantly
from its large deviation form.Comment: 10 pages, 3 figure
Near-optimal protocols in complex nonequilibrium transformations
The development of sophisticated experimental means to control nanoscale
systems has motivated efforts to design driving protocols which minimize the
energy dissipated to the environment. Computational models are a crucial tool
in this practical challenge. We describe a general method for sampling an
ensemble of finite-time, nonequilibrium protocols biased towards a low average
dissipation. We show that this scheme can be carried out very efficiently in
several limiting cases. As an application, we sample the ensemble of
low-dissipation protocols that invert the magnetization of a 2D Ising model and
explore how the diversity of the protocols varies in response to constraints on
the average dissipation. In this example, we find that there is a large set of
protocols with average dissipation close to the optimal value, which we argue
is a general phenomenon.Comment: 6 pages and 3 figures plus 4 pages and 5 figures of supplemental
materia
Force-induced unfolding of a homopolymer on fractal lattice: exact results vs. mean field predictions
We study the force-induced unfolding of a homopolymer on the three
dimensional Sierpinski gasket. The polymer is subject to a contact energy
between nearest neighbour sites not consecutive along the chain and to a
stretching force. The hierarchical nature of the lattice we consider allows for
an exact treatment which yields the phase diagram and the critical behaviour.
We show that for this model mean field predictions are not correct, in
particular in the exact phase diagram there is {\em not} a low temperature
reentrance and we find that the force induced unfolding transition below the
theta temperature is second order.Comment: 15 pages, 5 eps figure
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Catastrophic stress corrosion failure of Zr-base bulk metallic glass through hydrogen embrittlement
Zr-base bulk metallic glasses (BMG) are prone to pitting corrosion in halide containing solutions and also stress corrosion cracking (SCC) is often interpreted in this context. This work presents in situ SCC experiments on notched Zr52.5Cu17.9Ni14.6Al10Ti5 (at.%) BMG bars under 3-point bending in dilute NaCl solution. They show that pitting corrosion is only the initiating process. The pitted areas have a lower local corrosion potential and the reaction of Zr4+ to zirconyl ions in solution produces H+ that can be reduced and absorbed in the local acidic environment. So, hydrogen embrittlement causes the observed catastrophic failure and peculiar fracture surface characteristics. © 2019 The Author
Equilibrium free energies from fast-switching trajectories with large time steps
Jarzynski's identity for the free energy difference between two equilibrium
states can be viewed as a special case of a more general procedure based on
phase space mappings. Solving a system's equation of motion by approximate
means generates a mapping that is perfectly valid for this purpose, regardless
of how closely the solution mimics true time evolution. We exploit this fact,
using crudely dynamical trajectories to compute free energy differences that
are in principle exact. Numerical simulations show that Newton's equation can
be discretized to low order over very large time steps (limited only by the
computer's ability to represent resulting values of dynamical variables)
without sacrificing thermodynamic accuracy. For computing the reversible work
required to move a particle through a dense liquid, these calculations are more
efficient than conventional fast switching simulations by more than an order of
magnitude. We also explore consequences of the phase space mapping perspective
for systems at equilibrium, deriving an exact expression for the statistics of
energy fluctuations in simulated conservative systems
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