383 research outputs found
Reversible stretching of homopolymers and random heteropolymers
We have analyzed the equilibrium response of chain molecules to stretching.
For a homogeneous sequence of monomers, the induced transition from compact
globule to extended coil below the -temperature is predicted to be
sharp. For random sequences, however, the transition may be smoothed by a
prevalence of necklace-like structures, in which globular regions and coil
regions coexist in a single chain. As we show in the context of a random
copolymer, preferential solvation of one monomer type lends stability to such
structures. The range of stretching forces over which necklaces are stable is
sensitive to chain length as well as sequence statistics.Comment: 14 pages, 4 figure
Mechanical response of random heteropolymers
We present an analytical theory for heteropolymer deformation, as exemplified
experimentally by stretching of single protein molecules. Using a mean-field
replica theory, we determine phase diagrams for stress-induced unfolding of
typical random sequences. This transition is sharp in the limit of infinitely
long chain molecules. But for chain lengths relevant to biological
macromolecules, partially unfolded conformations prevail over an intermediate
range of stress. These necklace-like structures, comprised of alternating
compact and extended subunits, are stabilized by quenched variations in the
composition of finite chain segments. The most stable arrangements of these
subunits are largely determined by preferential extension of segments rich in
solvophilic monomers. This predicted significance of necklace structures
explains recent observations in protein stretching experiments. We examine the
statistical features of select sequences that give rise to mechanical strength
and may thus have guided the evolution of proteins that carry out mechanical
functions in living cells.Comment: 10 pages, 6 figure
Free induction signal from biexcitons and bound excitons
A theory of the free induction signal from biexcitons and bound excitons is
presented. The simultaneous existence of the exciton continuum and a bound
state is shown to result in a new type of time dependence of the free
induction. The optically detected signal increases in time and oscillates with
increasing amplitude until damped by radiative or dephasing processes.
Radiative decay is anomalously fast and can result in strong picosecond pulses.
The expanding area of a coherent exciton polarization (inflating antenna),
produced by the exciting pulse, is the underlying physical mechanism. The
developed formalism can be applied to different biexciton transients.Comment: RevTeX, 20 p. + 2 ps fig. To appear in Phys. Rev. B1
Theory of mechanical unfolding of homopolymer globule: all-or-none transition in force-clamp mode vs phase coexistence in position-clamp mode
Equilibrium mechanical unfolding of a globule formed by long flexible
homopolymer chain collapsed in a poor solvent and subjected to an extensional
force f (force-clamp mode) or extensional deformation D (position-clamp mode)
is studied theoretically. Our analysis, like all previous analysis of this
problem, shows that the globule behaves essentially differently in two modes of
extension. In the force-clamp mode, mechanical unfolding of the globule with
increasing applied force occurs without intramolecular microphase segregation,
and at certain threshold value of the pulling force the globule unfolds as a
whole ("all-or-none" transition). The value of the threshold force and the
corresponding jump in the distance between the chain ends increase with a
deterioration of the solvent quality and/or with an increase in the degree of
polymerization. In the position-clamp mode, the globule unfolding occurs via
intramolecular microphase coexistence of globular and extended microphases
followed by an abrupt unraveling transition. Reaction force in the microphase
segregation regime demonstrates an "anomalous" decrease with increasing
extension. Comparison of deformation curves in force and position-clamp modes
demonstrates that at weak and strong extensions the curves for two modes
coincide, differences are observed in the intermediate extension range. Another
unfolding scenario is typical for short globules: in both modes of extension
they unfold continuously, without jumps or intramolecular microphase
coexistence, by passing a sequence of uniformly elongated configurations.Comment: 19 pages, 13 figures, 1 tabl
Single Molecule Statistics and the Polynucleotide Unzipping Transition
We present an extensive theoretical investigation of the mechanical unzipping
of double-stranded DNA under the influence of an applied force. In the limit of
long polymers, there is a thermodynamic unzipping transition at a critical
force value of order 10 pN, with different critical behavior for homopolymers
and for random heteropolymers. We extend results on the disorder-averaged
behavior of DNA's with random sequences to the more experimentally accessible
problem of unzipping a single DNA molecule. As the applied force approaches the
critical value, the double-stranded DNA unravels in a series of discrete,
sequence-dependent steps that allow it to reach successively deeper energy
minima. Plots of extension versus force thus take the striking form of a series
of plateaus separated by sharp jumps. Similar qualitative features should
reappear in micromanipulation experiments on proteins and on folded RNA
molecules. Despite their unusual form, the extension versus force curves for
single molecules still reveal remnants of the disorder-averaged critical
behavior. Above the transition, the dynamics of the unzipping fork is related
to that of a particle diffusing in a random force field; anomalous,
disorder-dominated behavior is expected until the applied force exceeds the
critical value for unzipping by roughly 5 pN.Comment: 40 pages, 18 figure
Spatio-temporal dynamics of quantum-well excitons
We investigate the lateral transport of excitons in ZnSe quantum wells by
using time-resolved micro-photoluminescence enhanced by the introduction of a
solid immersion lens. The spatial and temporal resolutions are 200 nm and 5 ps,
respectively. Strong deviation from classical diffusion is observed up to 400
ps. This feature is attributed to the hot-exciton effects, consistent with
previous experiments under cw excitation. The coupled transport-relaxation
process of hot excitons is modelled by Monte Carlo simulation. We prove that
two basic assumptions typically accepted in photoluminescence investigations on
excitonic transport, namely (i) the classical diffusion model as well as (ii)
the equivalence between the temporal and spatial evolution of the exciton
population and of the measured photoluminescence, are not valid for
low-temperature experiments.Comment: 8 pages, 6 figure
Development of the fully Geant4 compatible package for the simulation of Dark Matter in fixed target experiments
The search for new comparably light (well below the electroweak scale) feebly
interacting particles is an exciting possibility to explain some mysterious
phenomena in physics, among them the origin of Dark Matter. The sensitivity
study through detailed simulation of projected experiments is a key point in
estimating their potential for discovery.
Several years ago we created the DMG4 package for the simulation of DM (Dark
Matter) particles in fixed target experiments. The natural approach is to
integrate this simulation into the same program that performs the full
simulation of particles in the experiment setup. The Geant4 toolkit framework
was chosen as the most popular and versatile solution nowadays.
The simulation of DM particles production by this package accommodates
several possible scenarios, employing electron, muon or photon beams and
involving various mediators, such as vector, axial vector, scalar,
pseudoscalar, or spin 2 particles. The bremsstrahlung, annihilation or
Primakoff processes can be simulated.
The package DMG4 contains a subpackage DarkMatter with cross section methods
weakly connected to Geant4. It can be used in different frameworks.
In this paper, we present the latest developments of the package, such as
extending the list of possible mediator particle types, refining formulas for
the simulation and extending the mediator mass range. The user interface is
also made more flexible and convenient.
In this work, we also demonstrate the usage of the package, the improvements
in the simulation accuracy and some cross check validations.Comment: 17 pages, 11 figures, 1 tabl
The Integrated Monarch Monitoring Program: From Design to Implementation
Steep declines in North American monarch butterfly (Danaus plexippus) populations have prompted continent-wide conservation efforts. While monarch monitoring efforts have existed for years, we lack a comprehensive approach to monitoring population vital rates integrated with habitat quality to inform adaptive management and effective conservation strategies. Building a geographically and ecologically representative dataset of monarchs and their habitat will improve these efforts. These data will help track long-term changes in the distribution and abundance of monarchs and their habitats, refine population and habitat models, and illuminate how conservation activities affect monarchs and their habitats. The Monarch Conservation Science Partnership developed the Integrated Monarch Monitoring Program (IMMP) to profile breeding habitats and their use by monarchs in North America. A spatially balanced random sampling framework guides site selection, while also allowing opportunistic inclusion of sites chosen by participants, such as conservation areas. The IMMP weaves new protocols together with those from existing monitoring programs to improve data compatibility for assessing milkweed (Asclepias spp.) density, nectar resources, monarch reproduction and survival, and adult monarch habitat use. Participants may select a protocol subset according to interests or local monitoring objectives, thereby maximizing contributions. Conservation partners, including public and private land managers, academic researchers, and citizen scientists contribute data to a national dataset available for analyses at multiple scales. We describe the program and its development, implementation elements that make the program robust and feasible, participation to date, and how IMMP data can advance research and conservation for monarchs, pollinators, and their habitats
Single-molecule experiments in biological physics: methods and applications
I review single-molecule experiments (SME) in biological physics. Recent
technological developments have provided the tools to design and build
scientific instruments of high enough sensitivity and precision to manipulate
and visualize individual molecules and measure microscopic forces. Using SME it
is possible to: manipulate molecules one at a time and measure distributions
describing molecular properties; characterize the kinetics of biomolecular
reactions and; detect molecular intermediates. SME provide the additional
information about thermodynamics and kinetics of biomolecular processes. This
complements information obtained in traditional bulk assays. In SME it is also
possible to measure small energies and detect large Brownian deviations in
biomolecular reactions, thereby offering new methods and systems to scrutinize
the basic foundations of statistical mechanics. This review is written at a
very introductory level emphasizing the importance of SME to scientists
interested in knowing the common playground of ideas and the interdisciplinary
topics accessible by these techniques. The review discusses SME from an
experimental perspective, first exposing the most common experimental
methodologies and later presenting various molecular systems where such
techniques have been applied. I briefly discuss experimental techniques such as
atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers
(MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I
then present several applications of SME to the study of nucleic acids (DNA,
RNA and DNA condensation), proteins (protein-protein interactions, protein
folding and molecular motors). Finally, I discuss applications of SME to the
study of the nonequilibrium thermodynamics of small systems and the
experimental verification of fluctuation theorems. I conclude with a discussion
of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond.
Matt
Insect threats and conservation through the lens of global experts
While several recent studies have focused on global insect population trends, all are limited in either space or taxonomic scope. As global monitoring programs for insects are currently not implemented, inherent biases exist within most data. Expert opinion, which is often widely available, proves to be a valuable tool where hard data are limited. Our aim is to use global expert opinion to provide insights on the root causes of potential insect declines worldwide, as well as on effective conservation strategies that could mitigate insect biodiversity loss. We obtained 753 responses from 413 respondents with a wide variety of spatial and taxonomic expertise. The most relevant threats identified through the survey were agriculture and climate change, followed by pollution, while land management and land protection were recognized as the most significant conservation measures. Nevertheless, there were differences across regions and insect groups, reflecting the variability within the most diverse class of eukaryotic organisms on our planet. Lack of answers for certain biogeographic regions or taxa also reflects the need for research in less investigated settings. Our results provide a novel step toward understanding global threats and conservation measures for insects.Peer reviewe
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