1,381 research outputs found
Parsimonious evolutionary scenario for the origin of allostery and coevolution patterns in proteins
Proteins display generic properties that are challenging to explain by direct
selection, notably allostery, the capacity to be regulated through long-range
effects, and evolvability, the capacity to adapt to new selective pressures. An
evolutionary scenario is proposed where proteins acquire these two features
indirectly as a by-product of their selection for a more fundamental property,
exquisite discrimination, the capacity to bind discriminatively very similar
ligands. Achieving this task is shown to typically require proteins to undergo
a conformational change. We argue that physical and evolutionary constraints
impel this change to be controlled by a group of sites extending from the
binding site. Proteins can thus acquire a latent potential for allosteric
regulation and evolutionary adaptation because of long-range effects that
initially arise as evolutionary spandrels. This scenario accounts for the
groups of conserved and coevolving residues observed in multiple sequence
alignments. However, we propose that most pairs of coevolving and contacting
residues inferred from such alignments have a different origin, related to
thermal stability. A physical model is presented that illustrates this
evolutionary scenario and its implications. The scenario can be implemented in
experiments of protein evolution to directly test its predictions
Error Exponents of Low-Density Parity-Check Codes on the Binary Erasure Channel
We introduce a thermodynamic (large deviation) formalism for computing error
exponents in error-correcting codes. Within this framework, we apply the
heuristic cavity method from statistical mechanics to derive the average and
typical error exponents of low-density parity-check (LDPC) codes on the binary
erasure channel (BEC) under maximum-likelihood decoding.Comment: 5 pages, 4 figure
A Model for the Generation and Transmission of Variations in Evolution
The inheritance of characteristics induced by the environment has often been
opposed to the theory of evolution by natural selection. Yet, while evolution
by natural selection requires new heritable traits to be produced and
transmitted, it does not prescribe, per se, the mechanisms by which this is
operated. The mechanisms of inheritance are not, however, unconstrained, since
they are themselves subject to natural selection. We introduce a general,
analytically solvable mathematical model to compare the adaptive value of
different schemes of inheritance. Our model allows for variations to be
inherited, randomly produced, or environmentally induced, and, irrespectively,
to be either transmitted or not during reproduction. The adaptation of the
different schemes for processing variations is quantified for a range of
fluctuating environments, following an approach that links quantitative
genetics with stochastic control theory
Evolution of sparsity and modularity in a model of protein allostery
The sequence of a protein is not only constrained by its physical and
biochemical properties under current selection, but also by features of its
past evolutionary history. Understanding the extent and the form that these
evolutionary constraints may take is important to interpret the information in
protein sequences. To study this problem, we introduce a simple but physical
model of protein evolution where selection targets allostery, the functional
coupling of distal sites on protein surfaces. This model shows how the
geometrical organization of couplings between amino acids within a protein
structure can depend crucially on its evolutionary history. In particular, two
scenarios are found to generate a spatial concentration of functional
constraints: high mutation rates and fluctuating selective pressures. This
second scenario offers a plausible explanation for the high tolerance of
natural proteins to mutations and for the spatial organization of their least
tolerant amino acids, as revealed by sequence analyses and mutagenesis
experiments. It also implies a faculty to adapt to new selective pressures that
is consistent with observations. Besides, the model illustrates how several
independent functional modules may emerge within a same protein structure,
depending on the nature of past environmental fluctuations. Our model thus
relates the evolutionary history and evolutionary potential of proteins to the
geometry of their functional constraints, with implications for decoding and
engineering protein sequences
Gallium phosphide photonic crystal nanocavities in the visible
Photonic crystal nanocavities at visible wavelengths are fabricated in a high refractive index (n>3.2) gallium phosphide membrane. The cavities are probed via a cross-polarized reflectivity measurement and show resonances at wavelengths as low as 645 nm at room temperature, with quality factors between 500 and 1700 for modes with volumes 0.7(λ/n)^3. These structures could be employed for submicron scale optoelectronic devices in the visible, and for coupling to emitters with resonances in the visible such as nitrogen vacancy centers, and biomolecules and organic molecules
Cavity-enhanced second harmonic generation via nonlinear-overlap optimization
We describe an approach based on topology optimization that enables automatic
discovery of wavelength-scale photonic structures for achieving high-efficiency
second-harmonic generation (SHG). A key distinction from previous formulation
and designs that seek to maximize Purcell factors at individual frequencies is
that our method not only aims to achieve frequency matching (across an entire
octave) and large radiative lifetimes, but also optimizes the equally important
nonlinear--coupling figure of merit , involving a complicated
spatial overlap-integral between modes. We apply this method to the particular
problem of optimizing micropost and grating-slab cavities (one-dimensional
multilayered structures) and demonstrate that a variety of material platforms
can support modes with the requisite frequencies, large lifetimes ,
small modal volumes , and extremely large , leading to orders of magnitude enhancements in SHG efficiency
compared to state of the art photonic designs. Such giant
alleviate the need for ultra-narrow linewidths and thus pave the way for
wavelength-scale SHG devices with faster operating timescales and higher
tolerance to fabrication imperfections
Multiply resonant high quality photonic crystal nanocavities
We propose and experimentally demonstrate a photonic crystal nanocavity with
multiple resonances that can be tuned nearly independently. The design is
composed of two orthogonal intersecting nanobeam cavities. Experimentally, we
measure cavity quality factors of 6,600 and 1000 for resonances separated by
382 nm; we measure a maximum separation between resonances of 506 nm. These
structures are promising for enhancing efficiency in nonlinear optical
processes such as sum/difference frequency and stimulated Raman scattering.Comment: 3 figure
- …