2,222 research outputs found
Quantitative effect of the sun\u27s position on submarine light polarization
Over 1,000 measurements of the degree and plane of submarine light polarization have been made in littoral waters at depths of 3 to 41m. Using special polarimetric instruments, these parameters were visually measured mainly in horizontal lines of sight at times ranging from sunrise to sunset. Tests showed that observational errors were within ± 5° for the polarization plane, ± 5% for per cent polarization...
Genetic Correlations in Mutation Processes
We study the role of phylogenetic trees on correlations in mutation
processes. Generally, correlations decay exponentially with the generation
number. We find that two distinct regimes of behavior exist. For mutation rates
smaller than a critical rate, the underlying tree morphology is almost
irrelevant, while mutation rates higher than this critical rate lead to strong
tree-dependent correlations. We show analytically that identical critical
behavior underlies all multiple point correlations. This behavior generally
characterizes branching processes undergoing mutation.Comment: revtex, 8 pages, 2 fig
Nature of the glassy phase of RNA secondary structure
We characterize the low temperature phase of a simple model for RNA secondary
structures by determining the typical energy scale E(l) of excitations
involving l bases. At zero temperature, we find a scaling law E(l) \sim
l^\theta with \theta \approx 0.23, and this same scaling holds at low enough
temperatures. Above a critical temperature, there is a different phase
characterized by a relatively flat free energy landscape resembling that of a
homopolymer with a scaling exponent \theta=1. These results strengthen the
evidence in favour of the existence of a glass phase at low temperatures.Comment: 7 pages, 1 figur
Evolution Equation of Phenotype Distribution: General Formulation and Application to Error Catastrophe
An equation describing the evolution of phenotypic distribution is derived
using methods developed in statistical physics. The equation is solved by using
the singular perturbation method, and assuming that the number of bases in the
genetic sequence is large. Applying the equation to the mutation-selection
model by Eigen provides the critical mutation rate for the error catastrophe.
Phenotypic fluctuation of clones (individuals sharing the same gene) is
introduced into this evolution equation. With this formalism, it is found that
the critical mutation rate is sometimes increased by the phenotypic
fluctuations, i.e., noise can enhance robustness of a fitted state to mutation.
Our formalism is systematic and general, while approximations to derive more
tractable evolution equations are also discussed.Comment: 22 pages, 2 figure
Addition-Deletion Networks
We study structural properties of growing networks where both addition and
deletion of nodes are possible. Our model network evolves via two independent
processes. With rate r, a node is added to the system and this node links to a
randomly selected existing node. With rate 1, a randomly selected node is
deleted, and its parent node inherits the links of its immediate descendants.
We show that the in-component size distribution decays algebraically, c_k ~
k^{-beta}, as k-->infty. The exponent beta=2+1/(r-1) varies continuously with
the addition rate r. Structural properties of the network including the height
distribution, the diameter of the network, the average distance between two
nodes, and the fraction of dangling nodes are also obtained analytically.
Interestingly, the deletion process leads to a giant hub, a single node with a
macroscopic degree whereas all other nodes have a microscopic degree.Comment: 8 pages, 5 figure
Thermodynamics of protein folding: a random matrix formulation
The process of protein folding from an unfolded state to a biologically
active, folded conformation is governed by many parameters e.g the sequence of
amino acids, intermolecular interactions, the solvent, temperature and chaperon
molecules. Our study, based on random matrix modeling of the interactions,
shows however that the evolution of the statistical measures e.g Gibbs free
energy, heat capacity, entropy is single parametric. The information can
explain the selection of specific folding pathways from an infinite number of
possible ways as well as other folding characteristics observed in computer
simulation studies.Comment: 21 Pages, no figure
Rank Statistics in Biological Evolution
We present a statistical analysis of biological evolution processes.
Specifically, we study the stochastic replication-mutation-death model where
the population of a species may grow or shrink by birth or death, respectively,
and additionally, mutations lead to the creation of new species. We rank the
various species by the chronological order by which they originate. The average
population N_k of the kth species decays algebraically with rank, N_k ~ M^{mu}
k^{-mu}, where M is the average total population. The characteristic exponent
mu=(alpha-gamma)/(alpha+beta-gamma)$ depends on alpha, beta, and gamma, the
replication, mutation, and death rates. Furthermore, the average population P_k
of all descendants of the kth species has a universal algebraic behavior, P_k ~
M/k.Comment: 4 pages, 3 figure
Formation and Interaction of Membrane Tubes
We show that the formation of membrane tubes (or membrane tethers), which is
a crucial step in many biological processes, is highly non-trivial and involves
first order shape transitions. The force exerted by an emerging tube is a
non-monotonic function of its length. We point out that tubes attract each
other, which eventually leads to their coalescence. We also show that detached
tubes behave like semiflexible filaments with a rather short persistence
length. We suggest that these properties play an important role in the
formation and structure of tubular organelles.Comment: 4 pages, 3 figure
Membrane shape as a reporter for applied forces
Recent advances have enabled 3-dimensional reconstructions of biological structures in vivo, ranging in size and complexity from single proteins to multicellular structures. In particular, tomography and confocal microscopy have been exploited to capture detailed 3-dimensional conformations of membranes in cellular processes ranging from viral budding and organelle maintenance to phagocytosis. Despite the wealth of membrane structures available, there is as yet no generic, quantitative method for their interpretation. We propose that by modeling these observed biomembrane shapes as fluid lipid bilayers in mechanical equilibrium, the externally applied forces as well as the pressure, tension, and spontaneous curvature can be computed directly from the shape alone. To illustrate the potential power of this technique, we apply an axial force with optical tweezers to vesicles and explicitly demonstrate that the applied force is equal to the force computed from the membrane conformation
Modeling long-range memory with stationary Markovian processes
In this paper we give explicit examples of power-law correlated stationary
Markovian processes y(t) where the stationary pdf shows tails which are
gaussian or exponential. These processes are obtained by simply performing a
coordinate transformation of a specific power-law correlated additive process
x(t), already known in the literature, whose pdf shows power-law tails 1/x^a.
We give analytical and numerical evidence that although the new processes (i)
are Markovian and (ii) have gaussian or exponential tails their autocorrelation
function still shows a power-law decay =1/T^b where b grows with a
with a law which is compatible with b=a/2-c, where c is a numerical constant.
When a<2(1+c) the process y(t), although Markovian, is long-range correlated.
Our results help in clarifying that even in the context of Markovian processes
long-range dependencies are not necessarily associated to the occurrence of
extreme events. Moreover, our results can be relevant in the modeling of
complex systems with long memory. In fact, we provide simple processes
associated to Langevin equations thus showing that long-memory effects can be
modeled in the context of continuous time stationary Markovian processes.Comment: 5 figure
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