40 research outputs found
Model of a fluid at small and large length scales and the hydrophobic effect
We present a statistical field theory to describe large length scale effects
induced by solutes in a cold and otherwise placid liquid. The theory divides
space into a cubic grid of cells. The side length of each cell is of the order
of the bulk correlation length of the bulk liquid. Large length scale states of
the cells are specified with an Ising variable. Finer length scale effects are
described with a Gaussian field, with mean and variance affected by both the
large length scale field and by the constraints imposed by solutes. In the
absence of solutes and corresponding constraints, integration over the Gaussian
field yields an effective lattice gas Hamiltonian for the large length scale
field. In the presence of solutes, the integration adds additional terms to
this Hamiltonian. We identify these terms analytically. They can provoke large
length scale effects, such as the formation of interfaces and depletion layers.
We apply our theory to compute the reversible work to form a bubble in liquid
water, as a function of the bubble radius. Comparison with molecular simulation
results for the same function indicates that the theory is reasonably accurate.
Importantly, simulating the large length scale field involves binary arithmetic
only. It thus provides a computationally convenient scheme to incorporate
explicit solvent dynamics and structure in simulation studies of large
molecular assemblies
Onsager-Machlup theory and work fluctuation theorem for a harmonically driven Brownian particle
We extend Tooru-Cohen analysis for nonequilirium steady state(NSS) of a
Brownian particle to nonequilibrium oscillatory state (NOS) of Brownian
particle by considering time dependent external drive protocol. We consider an
unbounded charged Brownian particle in the presence of an oscillating electric
field and prove work fluctuation theorem, which is valid for any initial
distribution and at all times. For harmonically bounded and constantly dragged
Brownian particle considered by Tooru and Cohen, work fluctuation theorem is
valid for any initial condition(also NSS), but only in large time limit. We use
Onsager-Machlup Lagrangian with a constraint to obtain frequency dependent work
distribution function, and describe entropy production rate and properties of
dissipation functions for the present system using Onsager-Machlup functional.Comment: 6 pages, 1 figur
The Steady State Fluctuation Relation for the Dissipation Function
We give a proof of transient fluctuation relations for the entropy production
(dissipation function) in nonequilibrium systems, which is valid for most time
reversible dynamics. We then consider the conditions under which a transient
fluctuation relation yields a steady state fluctuation relation for driven
nonequilibrium systems whose transients relax, producing a unique
nonequilibrium steady state. Although the necessary and sufficient conditions
for the production of a unique nonequilibrium steady state are unknown, if such
a steady state exists, the generation of the steady state fluctuation relation
from the transient relation is shown to be very general. It is essentially a
consequence of time reversibility and of a form of decay of correlations in the
dissipation, which is needed also for, e.g., the existence of transport
coefficients. Because of this generality the resulting steady state fluctuation
relation has the same degree of robustness as do equilibrium thermodynamic
equalities. The steady state fluctuation relation for the dissipation stands in
contrast with the one for the phase space compression factor, whose convergence
is problematic, for systems close to equilibrium. We examine some model
dynamics that have been considered previously, and show how they are described
in the context of this work.Comment: 30 pages, 1 figur
Current Fluctuations of the One Dimensional Symmetric Simple Exclusion Process with Step Initial Condition
For the symmetric simple exclusion process on an infinite line, we calculate
exactly the fluctuations of the integrated current during time
through the origin when, in the initial condition, the sites are occupied with
density on the negative axis and with density on the positive
axis. All the cumulants of grow like . In the range where , the decay of the distribution of is
non-Gaussian. Our results are obtained using the Bethe ansatz and several
identities recently derived by Tracy and Widom for exclusion processes on the
infinite line.Comment: 2 figure
Heat release by controlled continuous-time Markov jump processes
We derive the equations governing the protocols minimizing the heat released
by a continuous-time Markov jump process on a one-dimensional countable state
space during a transition between assigned initial and final probability
distributions in a finite time horizon. In particular, we identify the
hypotheses on the transition rates under which the optimal control strategy and
the probability distribution of the Markov jump problem obey a system of
differential equations of Hamilton-Bellman-Jacobi-type. As the state-space mesh
tends to zero, these equations converge to those satisfied by the diffusion
process minimizing the heat released in the Langevin formulation of the same
problem. We also show that in full analogy with the continuum case, heat
minimization is equivalent to entropy production minimization. Thus, our
results may be interpreted as a refined version of the second law of
thermodynamics.Comment: final version, section 2.1 revised, 26 pages, 3 figure
Detection of paralytic shellfish toxins in mussels and oysters using the qualitative neogen lateral-flow immunoassay: an interlaboratory study
Paralytic shellfish toxins (PSTs) in bivalve molluscs represent a public health risk and are controlled via compliance with a regulatory limit of 0.8 mg saxitoxin (STX)center dot 2HCl equivalents per kilogram of shellfish meat (eq/kg). Shellfish industries would benefit from the use of rapid immunological screening tests for PSTs to be used for regulation, but to date none have been fully validated. An interlaboratory study involving 16 laboratories was performed to determine the suitability of the Neogen test to detect PSTs in mussels and oysters. Participants performed the standard protocol recommended by the manufacturer and a modified protocol with a conversion step to improve detection of gonyautoxin 1&4. The statistical analysis showed that the protocols had good homogeneity across all laboratories, with satisfactory repeatability, laboratory, and reproducibility variation near the regulatory level. The mean probability of detection (POD) at 0.8 mg STX center dot 2HCl eq/kg using the standard protocol in mussels and oysters was 0.966 and 0.997, respectively, and 0.968 and 0.966 using the modified protocol. The estimated LOD in mussels was 0.316 mg STX center dot 2HCl eq/kg with the standard and 0.682 mg STX center dot 2HCl eq/kg with the modified protocol, and 0.710 and 0.734 mg STX center dot 2HCl eq/kg for oysters, respectively. The Neogen test may be acceptable for regulatory purposes for oysters in accordance with European Commission directives in which the standard protocol provides, at the regulatory level, a probability of a negative response of 0.033 on 95% of occasions. Its use for mussels is less consistent at the regulatory level due to the wide prediction interval around the POD
Fragment edge and isolation affect the food web: effects on the strength of interactions among trophic guilds
Whole-genome sequencing reveals host factors underlying critical COVID-19
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease
Oral anticoagulation A community based review
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